Realizing visionary goals for the International Year of Millet (IYoM): accelerating interventions through advances in molecular breeding and multiomics resources.

Tilak Chandra, Sarika Jaiswal, Rukam Singh Tomar, Mir Asif Iquebal, Dinesh Kumar
Author Information
  1. Tilak Chandra: Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
  2. Sarika Jaiswal: Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
  3. Rukam Singh Tomar: Department of Biotechnology, Junagadh Agricultural University, Junagadh, Gujarat, 110012, India.
  4. Mir Asif Iquebal: Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India. ma.iquebal@icar.gov.in. ORCID
  5. Dinesh Kumar: Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.

Abstract

MAIN CONCLUSION: Leveraging advanced breeding and multi-omics resources is vital to position millet as an essential "nutricereal resource," aligning with IYoM goals, alleviating strain on global cereal production, boosting resilience to climate change, and advancing sustainable crop improvement and biodiversity. The global challenges of food security, nutrition, climate change, and agrarian sustainability demand the adoption of climate-resilient, nutrient-rich crops to support a growing population amidst shifting environmental conditions. Millets, also referred to as "Shree Anna," emerge as a promising solution to address these issues by bolstering food production, improving nutrient security, and fostering biodiversity conservation. Their resilience to harsh environments, nutritional density, cultural significance, and potential to enhance dietary quality index made them valuable assets in global agriculture. Recognizing their pivotal role, the United Nations designated 2023 as the "International Year of Millets (IYoM 2023)," emphasizing their contribution to climate-resilient agriculture and nutritional enhancement. Scientific progress has invigorated efforts to enhance millet production through genetic and genomic interventions, yielding a wealth of advanced molecular breeding technologies and multi-omics resources. These advancements offer opportunities to tackle prevailing challenges in millet, such as anti-nutritional factors, sensory acceptability issues, toxin contamination, and ancillary crop improvements. This review provides a comprehensive overview of molecular breeding and multi-omics resources for nine major millet species, focusing on their potential impact within the framework of IYoM. These resources include whole and pan-genome, elucidating adaptive responses to abiotic stressors, organelle-based studies revealing evolutionary resilience, markers linked to desirable traits for efficient breeding, QTL analysis facilitating trait selection, functional gene discovery for biotechnological interventions, regulatory ncRNAs for trait modulation, web-based platforms for stakeholder communication, tissue culture techniques for genetic modification, and integrated omics approaches enabled by precise application of CRISPR/Cas9 technology. Aligning these resources with the seven thematic areas outlined by IYoM catalyzes transformative changes in millet production and utilization, thereby contributing to global food security, sustainable agriculture, and enhanced nutritional consequences.

Keywords

References

  1. Abdullah SN, Mayes S, Moradpour M (2021) Target gene identification and sgRNA design for waterlogging tolerance in foxtail millet via CRISPR-based transcriptional activation. Curr Chin Sci 1(5):523���533
  2. Agarwal P, Agarwal PK, Joshi AJ, Sopory SK, Reddy MK (2010) Overexpression of PgDREB2A transcription factor enhances abiotic stress tolerance and activates downstream stress-responsive genes. Mol Biol Rep 37:1125���1135 [PMID: 19826914]
  3. Agrama H, Widle G, Reese J, Campbell L, Tuinstra M (2002) Genetic mapping of QTLs associated with greenbug resistance and tolerance in Sorghum bicolor. Theor Appl Genet 104:1373���1378 [PMID: 12582593]
  4. Ahn E, Prom LK, Hu Z, Odvody G, Magill C (2021) Genome-wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose. Plant Genome 14(2):e20097 [PMID: 33900689]
  5. Ajeesh Krishna TP, Maharajan T, Ceasar SA (2022) Improvement of millets in the post-genomic era. Physiol Mol Biol Plants 28(3):669���685 [PMID: 35465206]
  6. Akosambo-Ayoo LM, Bader M, Loerz H, Becker D (2011) Transgenic sorghum (Sorghum bicolor L. Moench) developed by transformation with chitinase and chitosanase genes from Trichoderma harzianum expresses tolerance to anthracnose. Afr J Biotech 10(19):3659���3670
  7. Alagarasan G, Dubey M, Aswathy KS, Chandel G (2017) Genome wide identification of orthologous ZIP genes associated with zinc and iron translocation in Setaria italica. Front Plant Sci 8:775 [PMID: 28555148]
  8. Ambawat S, Senthilvel S, Hash CT, Nepolean T, Rajaram V, Eshwar K, Sharma R, Thakur RP, Rao VP, Yadav RC, Srivastava RK (2016) QTL mapping of pearl millet rust resistance using an integrated DArT-and SSR-based linkage map. Euphytica 209:461���476
  9. Ananda G, Norton S, Blomstedt C, Furtado A, M��ller B, Gleadow R, Henry R (2021) Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes. Plant Genome 14(3):e20123 [PMID: 34323394]
  10. Anjaneyulu E, Reddy PS, Sunita MS, Kishor PB, Meriga B (2014) Salt tolerance and activity of antioxidative enzymes of transgenic finger millet overexpressing a vacuolar H-pyrophosphatase gene (SbVPPase) from Sorghum bicolor. J Plant Physiol 171(10):789���798 [PMID: 24877670]
  11. Antony Ceasar S, Ignacimuthu S (2011) Agrobacterium-mediated transformation of finger millet (Eleusine coracana (L.) Gaertn.) using shoot apex explants. Plant Cell Rep 30:1759���1770 [PMID: 21584677]
  12. Antony Ceasar S, Maharajan T (2022) The role of millets in attaining United Nation���s sustainable developmental goals. Plants People Planet 4(4):345���349
  13. Antony Ceasar S, Maharajan T, Ajeesh Krishna TP, Ramakrishnan M, Victor Roch G, Satish L, Ignacimuthu S (2018) Finger millet [Eleusine coracana (L.) Gaertn.] improvement: current status and future interventions of whole genome sequence. Front Plant Sci 23(9):1054
  14. Aregawi K, Shen J, Pierroz G, Sharma MK, Dahlberg J, Owiti J, Lemaux PG (2022) Morphogene-assisted transformation of Sorghum bicolor allows more efficient genome editing. Plant Biotechnol J 20(4):748���760 [PMID: 34837319]
  15. Awan SA, Khan I, Rizwan M, Irshad MA, Xiaosan W, Zhang X, Huang L (2023) Reduction in the cadmium (Cd) accumulation and toxicity in pearl millet (Pennisetum glaucum L.) by regulating physio-biochemical and antioxidant defense system via soil and foliar application of melatonin. Environ Pollut 328:121658 [PMID: 37075919]
  16. Awika HO, Hays DB, Mullet JE, Rooney WL, Weers BD (2017) QTL mapping and loci dissection for leaf epicuticular wax load and canopy temperature depression and their association with QTL for staygreen in Sorghum bicolor under stress. Euphytica 213:207
  17. Babu RN, Jyothi MN, Sharadamma N, Sahu S, Rai DV, Devaraj VR (2013) Computational identification of conserved micro RNAs from kodo millet (Paspalum scrobiculatum). Afr Crop Sci J 21(1):75���83
  18. Baek YS, Goodrich LV, Brown PJ, James BT, Moose SP, Lambert KN, Riechers DE (2019) Transcriptome profiling and genome-wide association studies reveal GSTs and other defense genes involved in multiple signaling pathways induced by herbicide safener in grain sorghum. Front Plant Sci 10:192 [PMID: 30906302]
  19. Bai C, Wang C, Wang P, Zhu Z, Cong L, Li D, Liu Y, Zheng W, Lu X (2017) QTL mapping of agronomically important traits in sorghum (Sorghum bicolor L.). Euphytica 213:285
  20. Baillo EH, Hanif MS, Guo Y, Zhang Z, Xu P, Algam SA (2020) Genome-wide identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench). PLoS ONE 15(8):e0236651 [PMID: 32804948]
  21. Bandyopadhyay T, Swarbreck SM, Jaiswal V, Maurya J, Gupta R, Bentley AR, Griffiths H, Prasad M (2022) GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C4 model Setaria italica (L.). J Adv Res 42:249���261 [PMID: 36513416]
  22. Banshidhar PS, Singh A, Jaiswal P, Singh MK, Meena KR, Singh SK (2023) The potentialities of omics resources for millet improvement. Funct Integr Genomics 23(3):210 [PMID: 37355501]
  23. Basso MF, Duarte KE, Santiago TR, de Souza WR, de Oliveira GB, da Cunha BD, Kobayashi AK, Molinari HB (2021) Efficient genome editing and gene knockout in Setaria viridis with CRISPR/Cas9 directed gene editing by the non-homologous end-joining pathway. Plant Biotechnology 38(2):227���238 [PMID: 34393601]
  24. Bayer GY, Yemets AI, Blume YB (2014) Obtaining the transgenic lines of finger millet Eleusine coracana (L.). with dinitroaniline resistance. Cytol Genet 48:139���144
  25. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30:555���561 [PMID: 22580951]
  26. Bernardino KC, Pastina MM, Menezes CB, de Sousa SM, Maciel LS, Carvalho G Jr, Guimar��es CT, Barros BA, da Costa E Silva L, Carneiro PC, Schaffert RE (2019) The genetic architecture of phosphorus efficiency in sorghum involves pleiotropic QTL for root morphology and grain yield under low phosphorus availability in the soil. BMC Plant Biol 19(1):87 [PMID: 30819116]
  27. Bhatt D, Fairos M, Mazumdar A (2022) Millets: nutritional composition, production and significance: a review. J Pharm Innov 11:1577���1582
  28. Bian YL, Yazaki S, Inoue M, Cai HW (2006) QTLs for sugar content of stalk in sweet sorghum (Sorghum bicolor L. Moench). Agric Sci China 5(10):736���744
  29. Bidinger FR, Nepolean T, Hash CT, Yadav RS, Howarth CJ (2007) Quantitative trait loci for grain yield in pearl millet under variable postflowering moisture conditions. Crop Sci 47(3):969���980
  30. Bonthala VS, Muthamilarasan M, Roy R, Prasad M (2014) FmTFDb: a foxtail millet transcription factors database for expediting functional genomics in millets. Mol Biol Rep 41:6343���6348 [PMID: 25005261]
  31. Boretti A, Rosa L (2019) Reassessing the projections of the world water development report. Npj Clean Water 2(1):15
  32. Boukail S, Macharia M, Miculan M, Masoni A, Calamai A, Palchetti E, Dell���Acqua M (2021) Genome wide association study of agronomic and seed traits in a world collection of proso millet (Panicum miliaceum L.). BMC Plant Biol 21(1):330 [PMID: 34243721]
  33. Boyles RE, Cooper EA, Myers MT, Brenton Z, Rauh BL, Morris GP, Kresovich S (2016) Genome���wide association studies of grain yield components in diverse sorghum germplasm. Plant Genome 9(2):plantgenome2015-09
  34. Brant EJ, Baloglu MC, Parikh A, Altpeter F (2021) CRISPR/Cas9 mediated targeted mutagenesis of LIGULELESS-1 in sorghum provides a rapidly scorable phenotype by altering leaf inclination angle. Biotechnol J 16(11):2100237
  35. Burow G, Burke JJ, Xin Z, Franks CD (2011) Genetic dissection of early-season cold tolerance in sorghum (Sorghum bicolor (L.) Moench). Mol Breeding 28:391���402
  36. Cao X, Wang J, Wang H, Liu S, Chen L, Tian X, Qin H, Wang L, Na X, Qiao Z (2017) The complete chloroplast genome of Panicum miliaceum. Mitochondrial DNA B Resour 2(1):43���45 [PMID: 33473711]
  37. Cao X, Hu L, Chen X, Zhang R, Cheng D, Li H, Xu Z, Li L, Zhou Y, Liu A, Song J (2019) Genome-wide analysis and identification of the low potassium stress responsive gene SiMYB3 in foxtail millet (Setaria italica L.). BMC Genomics 20(1):136 [PMID: 30767761]
  38. Casas AM, Kononowicz AK, Zehr UB, Tomes DT, Axtell JD, Butler LG, Bressan RA, Hasegawa PM (1993) Transgenic sorghum plants via microprojectile bombardment. Proc Natl Acad Sci 90(23):11212���11216 [PMID: 8248230]
  39. Ceasar A (2022) Genome-editing in millets: current knowledge and future perspectives. Mol Biol Rep 49(1):773���781 [PMID: 34825322]
  40. Ceasar SA, Hodge A, Baker A, Baldwin SA (2014) Phosphate concentration and arbuscular mycorrhizal colonisation influence the growth, yield and expression of twelve PHT1 family phosphate transporters in foxtail millet (Setaria italica). PLoS ONE 9(9):e108459 [PMID: 25251671]
  41. Ceasar SA, Baker A, Ignacimuthu S (2017) Functional characterization of the PHT1 family transporters of foxtail millet with development of a novel Agrobacterium-mediated transformation procedure. Sci Rep 7(1):14064 [PMID: 29070807]
  42. Ceasar SA, Prabhu S, Ebeed HT (2024) Protein research in millets: current status and way forward. Planta 260(2):43 [PMID: 38958760]
  43. Chai W, Si W, Ji W, Qin Q, Zhao M, Jiang H (2018) Genome-wide investigation and expression profiling of HD-zip transcription factors in foxtail millet (Setaria italica L.). Biomed Res Int 2018:8457614 [PMID: 29862293]
  44. Chakraborty A, Viswanath A, Malipatil R, Rathore A, Thirunavukkarasu N (2020) Structural and functional characteristics of miRNAs in five strategic millet species and their utility in drought tolerance. Front Genet 11:608421 [PMID: 33363575]
  45. Chandel G, Dubey M, Gupta S, Patil AH, Rao AR (2017) Identification and characterization of a grain micronutrient-related OsFRO2 rice gene ortholog from micronutrient-rich little millet (Panicum sumatrense). 3 Biotech 7(1):80 [PMID: 28500402]
  46. Chanwala J, Satpati S, Dixit A, Parida A, Giri MK, Dey N (2020) Genome-wide identification and expression analysis of WRKY transcription factors in pearl millet (Pennisetum glaucum) under dehydration and salinity stress. BMC Genomics 21(1):231 [PMID: 32171257]
  47. Chanwala J, Jha DK, Giri MK, Dey N (2024) PgWRKY44, a pearl millet WRKY transcription factor-Calmodulin module, enhances salt and drought stress resilience in transgenic plants. Environ Exp Bot 219:105629
  48. Char SN, Wei J, Mu Q, Li X, Zhang ZJ, Yu J, Yang B (2020) An Agrobacterium-delivered CRISPR/Cas9 system for targeted mutagenesis in sorghum. Plant Biotechnol J 18(2):319���321 [PMID: 31374142]
  49. Chase CD, Pring DR (1985) Circular plasmid DNAs from mitochondria of Sorghum bicolor. Plant Mol Biol 5:303���311 [PMID: 24306922]
  50. Chase CD, Pring DR (1986) Properties of the linear N1 and N2 plasmid-like DNAs from mitochondria of cytoplasmic male-sterile Sorghum bicolor. Plant Mol Biol 6:53���64 [PMID: 24307154]
  51. Che P, Anand A, Wu E, Sander JD, Simon MK, Zhu W, Sigmund AL, Zastrow-Hayes G, Miller M, Liu D, Lawit SJ (2018) Developing a flexible, high-efficiency Agrobacterium-mediated sorghum transformation system with broad application. Plant Biotechnol J 16(7):1388���1395 [PMID: 29327444]
  52. Che P, Wu E, Simon MK, Anand A, Lowe K, Gao H, Sigmund AL, Yang M, Albertsen MC, Gordon-Kamm W, Jones TJ (2022) Wuschel2 enables highly efficient CRISPR/Cas-targeted genome editing during rapid de novo shoot regeneration in sorghum. Commun Biol 5(1):344 [PMID: 35410430]
  53. Chelpuri D, Sharma R, Durga KK, Katiyar P, Mahendrakar MD, Singh RB, Yadav RS, Gupta R, Srivastava RK (2019) Mapping quantitative trait loci (QTLs) associated with resistance to major pathotype-isolates of pearl millet downy mildew pathogen. Eur J Plant Pathol 154:983���994
  54. Chen H, Ge W (2022) Identification, molecular characteristics, and evolution of GRF gene family in foxtail millet (Setaria italica L.). Front Genet 12:2776
  55. Chen BR, Wang CY, Ping W, Zhu ZX, Ning XU, Shi GS, Miao Y, Nai W, Li JH, Hou JM, Li SJ (2019) Genome-wide association study for starch content and constitution in sorghum (Sorghum bicolor (L.) Moench). J Integr Agric 18(11):2446���2456
  56. Chen H, Qin L, Tian J, Wang X (2022) Identification and evolutionary analysis of the GOLDEN 2-LIKE gene family in foxtail millet. Trop Plant Biol 15:301���318
  57. Cheng Z, Sun Y, Yang S, Zhi H, Yin T, Ma X, Zhang H, Diao X, Guo Y, Li X, Wu C (2021) Establishing in planta haploid inducer line by edited SiMTL in foxtail millet (Setaria italica). Plant Biotechnol J 19(6):1089 [PMID: 33749085]
  58. Chinchole M, Pathak RK, Singh UM, Kumar A (2017) Molecular characterization of EcCIPK 24 gene of finger millet (Eleusine coracana) for investigating its regulatory role in calcium transport. 3 Biotech 7(4):267 [PMID: 28794922]
  59. Chopperla R, Singh S, Mohanty S, Reddy N, Padaria JC, Solanke AU (2017) Isolation and expression analysis of EcbZIP17 from different finger millet genotypes shows conserved nature of the gene. 3 Biotech 7(5):342 [PMID: 28955639]
  60. Chou J, Huang J, Huang Y (2020) Simple and efficient genetic transformation of sorghum using immature inflorescences. Acta Physiol Plant 42:41
  61. Choudhary P, Shukla P, Muthamilarasan M (2023) Genetic enhancement of climate-resilient traits in small millets: a review. Heliyon 9(4):e14502 [PMID: 37064482]
  62. Cruet-Burgos C, Cox S, Ioerger BP, Perumal R, Hu Z, Herald TJ, Bean SR, Rhodes DH (2020) Advancing provitamin A biofortification in sorghum: genome-wide association studies of grain carotenoids in global germplasm. Plant Genome 13(1):e20013 [PMID: 33016639]
  63. Das RR, Pradhan S, Parida A (2020) De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense. Sci Rep 10(1):21251 [PMID: 33277539]
  64. Deng Y, Zhang H, Wang H, Xing G, Lei B, Kuang Z, Zhao Y, Li C, Dai S, Yang X, Wei J (2022) The construction and exploration of a comprehensive microRNA centered regulatory network in foxtail millet (Setaria italica L.). Front Plant Sci 13:848474 [PMID: 35599893]
  65. Desai MK, Mishra RN, Verma D, Nair S, Sopory SK, Reddy MK (2006) Structural and functional analysis of a salt stress inducible gene encoding voltage dependent anion channel (VDAC) from pearl millet (Pennisetum glaucum). Plant Physiol Biochem 44:483���493 [PMID: 17023166]
  66. Desai H, Hamid R, Ghorbanzadeh Z, Bhut N, Padhiyar SM, Kheni J, Tomar RS (2021) Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing. Sci Rep 11(1):20620 [PMID: 34663808]
  67. Devi PB, Sticklen MB (2003) In vitro culture and genetic transformation of sorghum by microprojectile bombardment. Plant Biosyst 137(3):249���254
  68. Devos KM, Qi P, Bahri BA, Gimode DM, Jenike K, Manthi SJ, Lule D, Lux T, Martinez-Bello L, Pendergast TH IV, Plott C (2023) Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat Commun 14(1):3694 [PMID: 37344528]
  69. Dhivya AB, Subashini S, Chandrababu R, Ramalingam J (2015) Establishment of MilletDB: TNAU released millet varieties with their morphological traits. International Journal of Computer Applications 111(14):24���26
  70. Dudhate A, Shinde H, Yu P, Tsugama D, Gupta SK, Liu S, Takano T (2021) Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum). BMC Genomics 22(1):70 [PMID: 33478383]
  71. Fakurdin B, Kavil SP, Girma Y, Arun SS, Dadakhalandar D, Gurusiddesh BH, Patil A, Thudi M, Bhairappanavar SB, Narayana YD, Krishnaraj PU (2013) Molecular mapping of genomic regions harbouring QTLs for root and yield traits in sorghum (Sorghum bicolor L. Moench). Physiol Mol Biol Plants 1���1
  72. Fan Y, Lai D, Yang H, Xue G, He A, Chen L, Feng L, Ruan J, Xiang D, Yan J, Cheng J (2021a) Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.). BMC Genomics 22(1):778 [PMID: 34717536]
  73. Fan Y, Wei X, Lai D, Yang H, Feng L, Li L, Niu K, Chen L, Xiang D, Ruan J, Yan J (2021b) Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.). BMC Plant Biol 21(1):508 [PMID: 34732123]
  74. Fan Y, Yan J, Lai D, Yang H, Xue G, He A, Guo T, Chen L, Cheng XB, Xiang DB, Ruan J (2021c) Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. BMC Genomics 22:1���21
  75. Fang X, Dong K, Wang X, Liu T, He J, Ren R, Zhang L, Liu R, Liu X, Li M, Huang M (2016) A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genomics 17(1):336 [PMID: 27146360]
  76. Feng LY, Gao LZ (2021) Characterization of chloroplast genome of Eleusine coracana, a highly adaptable cereal crop with high nutritional reputation. Mitochondrial DNA B Resour 6(10):2816���2818 [PMID: 34514138]
  77. Feng ZJ, He GH, Zheng WJ, Lu PP, Chen M, Gong YM, Ma YZ, Xu ZS (2015) Foxtail millet NF-Y families: genome-wide survey and evolution analyses identified two functional genes important in abiotic stresses. Front Plant Sci 6:1142 [PMID: 26734043]
  78. Feng ZJ, Xu ZS, Sun J, Li LC, Chen M, Yang GX, He GY, Ma YZ (2016) Investigation of the ASR family in foxtail millet and the role of ASR1 in drought/oxidative stress tolerance. Plant Cell Rep 35:115���128 [PMID: 26441057]
  79. Ferguson JN, Fernandes SB, Monier B, Miller ND, Allen D, Dmitrieva A, Schmuker P, Lozano R, Valluru R, Buckler ES, Gore MA (2021) Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. Plant Physiol 187(3):1481���1500 [PMID: 34618065]
  80. Fu F, Girma G, Mengiste T (2020) Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum. BMC Genomics 21(1):760 [PMID: 33143636]
  81. Gaur VS, Kumar L, Gupta S, Jaiswal JP, Pandey D, Kumar A (2018) Identification and characterization of finger millet OPAQUE2 transcription factor gene under different nitrogen inputs for understanding their role during accumulation of prolamin seed storage protein. 3 Biotech 8(3):163 [PMID: 29527450]
  82. Ge L, Dou Y, Li M, Qu P, He Z, Liu Y, Xu Z, Chen J, Chen M, Ma Y (2019) SiMYB3 in foxtail millet (Setaria italica) confers tolerance to low-nitrogen stress by regulating root growth in transgenic plants. Int J Mol Sci 20(22):5741 [PMID: 31731735]
  83. Ge W, Chen H, Zhang Y, Feng S, Wang S, Shang Q, Wu M, Li Z, Zhang L, Guo H, Jin Y (2022) Integrative genomics analysis of the ever-shrinking pectin methylesterase (PME) gene family in foxtail millet (Setaria italica). Funct Plant Biol 49(10):874���886 [PMID: 35781367]
  84. Gelli M, Mitchell SE, Liu K, Clemente TE, Weeks DP, Zhang C, Holding DR, Dweikat IM (2016) Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. BMC Plant Biol 16:16 [PMID: 26759170]
  85. Gelli M, Konda AR, Liu K, Zhang C, Clemente TE, Holding DR, Dweikat IM (2017) Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum. BMC Plant Biol 17(1):123 [PMID: 28697783]
  86. Geng Z, Liu J, Li D, Zhao G, Liu X, Dou H, Lv L, Zhang H, Wang Y (2021) A conserved miR394-targeted F-box gene positively regulates drought resistance in foxtail millet. Journal of Plant Biology 64:243���252
  87. Girgi M, O���Kennedy MM, Morgenstern A, Mayer G, L��rz H, Oldach KH (2002) Transgenic and herbicide resistant pearl millet (Pennisetum glaucum L.) R. Br. via microprojectile bombardment of scutellar tissue. Mol Breeding 10:243���252
  88. Girgi M, Breese WA, L��rz H, Oldach KH (2006) Rust and downy mildew resistance in pearl millet (Pennisetum glaucum) mediated by heterologous expression of the afp gene from Aspergillus giganteus. Transgenic Res 15:313���324 [PMID: 16779647]
  89. Girijashankar V, Sharma HC, Sharma KK, Swathisree V, Prasad LS, Bhat BV, Royer M, Secundo BS, Narasu ML, Altosaar I, Seetharama N (2005) Development of transgenic sorghum for insect resistance against the spotted stem borer (Chilo partellus). Plant Cell Rep 24:513���522 [PMID: 16172896]
  90. Gladman N, Olson A, Wei S, Chougule K, Lu Z, Tello-Ruiz M, Meijs I, Van Buren P, Jiao Y, Wang B, Kumar V (2022) SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta 255(2):35 [PMID: 35015132]
  91. Goldman JJ, Hanna WW, Fleming G, Ozias-Akins P (2003) Fertile transgenic pearl millet [Pennisetum glaucum (L.) R. Br.] plants recovered through microprojectile bombardment and phosphinothricin selection of apical meristem-, inflorescence-, and immature embryo-derived embryogenic tissues. Plant Cell Rep 21:999���1009 [PMID: 12835911]
  92. Guan YA, Wang HL, Qin L, Zhang HW, Yang YB, Gao FJ, Li RY, Wang HG (2011) QTL mapping of bio-energy related traits in Sorghum. Euphytica 182:431���440
  93. Guo L, Qiu J, Ye C, Jin G, Mao L, Zhang H, Yang X, Peng Q, Wang Y, Jia L, Lin Z (2017) Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Nat Commun 8(1):1031 [PMID: 29044108]
  94. Gupta P, Raghuvanshi S, Tyagi AK (2001) Assessment of the efficiency of various gene promoters via biolistics in leaf and regenerating seed callus of millets, Eleusine coracana and Echinochloa crusgalli. Plant Biotechnology 18(4):275���282
  95. Gupta AK, Gaur VS, Gupta S, Kumar A (2013) Nitrate signals determine the sensing of nitrogen through differential expression of genes involved in nitrogen uptake and assimilation in finger millet. Funct Integr Genomics 13:179���190 [PMID: 23435937]
  96. Gupta S, Gupta SM, Gupta AK, Gaur VS, Kumar A (2014) Fluctuation of Dof1/Dof2 expression ratio under the influence of varying nitrogen and light conditions: involvement in differential regulation of nitrogen metabolism in two genotypes of finger millet (Eleusine coracana L.). Gene 546(2):327���335 [PMID: 24875415]
  97. Hall ND, Zhang H, Mower JP, McElroy JS, Goertzen LR (2020) The mitochondrial genome of Eleusine indica and characterization of gene content within Poaceae. Genome Biol Evol 12(1):3684���3697 [PMID: 31665327]
  98. Han J, Xie H, Sun Q, Wang J, Lu M, Wang W, Guo E, Pan J (2014) Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setaria italica). Gene 546(2):367���377 [PMID: 24862217]
  99. Han L, Chen J, Mace ES, Liu Y, Zhu M, Yuyama N, Jordan DR, Cai H (2015) Fine mapping of qGW1, a major QTL for grain weight in sorghum. Theor Appl Genet 128:1813���1825 [PMID: 26071275]
  100. Hart GE, Schertz KF, Peng Y, Syed NH (2001) Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters. Theor Appl Genet 103:1232���1242
  101. Hatakeyama M, Aluri S, Balachadran MT, Sivarajan SR, Patrignani A, Gr��ter S, Poveda L, Shimizu-Inatsugi R, Baeten J, Francoijs KJ, Nataraja KN (2018) Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Res 25:39���47 [PMID: 28985356]
  102. Haussmann B, Mahalakshmi V, Reddy B, Seetharama N, Hash C, Geiger H (2002) QTL mapping of stay-green in two sorghum recombinant inbred populations. Theor Appl Genet 106:133���142 [PMID: 12582881]
  103. He Q, Zhi H, Tang S, Xing L, Wang S, Wang H, Zhang A, Li Y, Gao M, Zhang H, Chen G (2021) QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map. Theor Appl Genet 134:557���572 [PMID: 33128073]
  104. Hema R, Vemanna RS, Sreeramulu S, Reddy CP, Senthil-Kumar M, Udayakumar M (2014) Stable expression of mtlD gene imparts multiple stress tolerance in finger millet. PLoS ONE 9(6):e99110 [PMID: 24922513]
  105. Hittalmani S, Mahesh HB, Shirke MD, Biradar H, Uday G, Aruna YR, Lohithaswa HC, Mohanrao A (2017) Genome and transcriptome sequence of finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties. BMC Genomics 18:465 [PMID: 28619070]
  106. Hostetler AN, Govindarajulu R, Hawkins JS (2021) QTL mapping in an interspecific sorghum population uncovers candidate regulators of salinity tolerance. Plant Stress 2:100024
  107. Howe A, Sato S, Dweikat I, Fromm M, Clemente T (2006) Rapid and reproducible Agrobacterium-mediated transformation of sorghum. Plant Cell Rep 25:784���791 [PMID: 16528567]
  108. Huang S, Hu L, Xu D, Li W, Xu Z, Li L, Zhou Y, Diao X, Jia G, Ma Y, Chen M (2016) Transcription factor SiNF-YA5 from foxtail millet (Setaria italica) conferred tolerance to high-salt stress through ABA-independent pathway in transgenic Arabidopsis. Acta Agron Sin 42(12):1787���1797
  109. Huang YW, Chang CY, Hsu YH (2020) Virus-induced gene silencing in Poaceae using a Foxtail mosaic virus vector. Methods Mol Biol 2172:15���25 [PMID: 32557358]
  110. Huang B, Yan H, Sun M, Jin Y (2023) Novel discovery in roles of structural variations and RWP-RK transcription factors in heat tolerance for pearl millet. Stress Biol 3(1):12 [PMID: 37676357]
  111. Ignacimuthu S, Ceasar SA (2012) Development of transgenic finger millet (Eleusine coracana (L.) Gaertn.) resistant to leaf blast disease. J Biosci 37:135���147 [PMID: 22357211]
  112. Ishikawa G, Seimiya Y, Saito M, Nakamura T, Hoshino T (2013) Molecular characterization of spontaneous and induced mutations in the three homoeologous waxy genes of Japanese barnyard millet [Echinochloa esculenta (A. Braun) H. Scholz]. Mol Breeding 31:69���78
  113. Jadhav Y, Thakur NR, Ingle KP, Ceasar SA (2024) The role of phenomics and genomics in delineating the genetic basis of complex traits in millets. Physiol Plant 176(3):e14349 [PMID: 38783512]
  114. Jagadeesh Selvam HR, Senthil N, Manikanda Boopathi N, Raveendran M (2015) Computational identification of salinity responsive microRNAs in contrasting genotypes of Finger millet (Eleusine coracana L.). Res J Biotechnol 10(9):52���64
  115. Jagga-Chugh S, Kachhwaha S, Sharma M, Kothari-Chajer A, Kothari SL (2012) Optimization of factors influencing microprojectile bombardment-mediated genetic transformation of seed-derived callus and regeneration of transgenic plants in Eleusine coracana (L.) Gaertn. Plant Cell Tissue Organ Cult 109:401���410
  116. Jaiswal S, Antala TJ, Mandavia MK, Chopra M, Jasrotia RS, Tomar RS, Kheni J, Angadi UB, Iquebal MA, Golakia BA, Rai A (2018) Transcriptomic signature of drought response in pearl millet Pennisetum glaucum (L.) and development of web-genomic resources. Sci Rep 8(1):3382 [PMID: 29467369]
  117. Jaiswal V, Gupta S, Gahlaut V, Muthamilarasan M, Bandyopadhyay T, Ramchiary N, Prasad M (2019a) Genome-wide association study of major agronomic traits in foxtail millet (Setaria italica L.) using ddRAD sequencing. Sci Rep 9(1):5020 [PMID: 30903013]
  118. Jaiswal V, Bandyopadhyay T, Gahlaut V, Gupta S, Dhaka A, Ramchiary N, Prasad M (2019b) Genome-wide association study (GWAS) delineates genomic loci for ten nutritional elements in foxtail millet (Setaria italica L.). J Cereal Sci 85:48���55
  119. Jayakodi M, Madheswaran M, Adhimoolam K, Perumal S, Manickam D, Kandasamy T, Yang TJ, Natesan S (2019) Transcriptomes of Indian barnyard millet and barnyardgrass reveal putative genes involved in drought adaptation and micronutrient accumulation. Acta Physiol Plant 41:66
  120. Jayasudha BG, Sushma AM, Hanjagi PS, Sashidhar VR (2014) An efficient in-vitro Agrobacterium-mediated transformation protocol for raising salinity tolerant transgenic plants in finger millet [Eleusine coracana (L.) Gaertn.]. Plant Arch 14(2):823���829
  121. Jha P, Shashi RA, Agnihotri PK, Kulkarni VM, Bhat V (2011) Efficient Agrobacterium-mediated transformation of Pennisetum glaucum (L.) R. Br. using shoot apices as explant source. Plant Cell Tissue Organ Cult 107:501���512
  122. Jha DK, Chanwala J, Sandeep IS, Dey N (2021) Comprehensive identification and expression analysis of GRAS gene family under abiotic stress and phytohormone treatments in Pearl millet. Funct Plant Biol 48(10):1039���1052 [PMID: 34266539]
  123. Jiang Y, Dong L, Li H, Liu Y, Wang X, Liu G (2024) Genetic linkage map construction and QTL analysis for plant height in proso millet (Panicum miliaceum L.). Theor Appl Genet 137(4):78 [PMID: 38466414]
  124. Jie GU, Zhou XT, Dai KL, Yuan XY, Guo PY, Shi WP, Zhou MX (2022) Comprehensive analysis of YABBY gene family in foxtail millet (Setaria italica) and functional characterization of SiDL. J Integr Agric 21(10):2876���2887
  125. Jin P, Wang L, Zhao W, Zheng J, Wang YH, Liu Y, Meng R, Dai J, Zhou L, Li J (2021) Construction of high density genetic map and QTL mapping in sorghum�� sudangrass. Euphytica 217:162
  126. Kadri SU, Mulla SI, Suchithra B, Bilal M, Ameen F, Bharagava RN, Saratale GD, Ferreira LF, Am��rico-Pinheiro JH (2022) Transcriptome-wide identification and computational insights into protein modeling and docking of CAMTA transcription factors in Eleusine coracana L. (finger millet). Int J Biol Macromol 206:768���776 [PMID: 35306013]
  127. Kajiya-Kanegae H, Takanashi H, Fujimoto M, Ishimori M, Ohnishi N, Wacera WF, Omollo EA, Kobayashi M, Yano K, Nakano M, Kozuka T (2020) RAD-seq-based high-density linkage map construction and QTL mapping of biomass-related traits in sorghum using the Japanese landrace Takakibi NOG. Plant Cell Physiol 61(7):1262���1272 [PMID: 32353144]
  128. Kante M, Rattunde HF, N��bi�� B, Weltzien E, Haussmann BI, Leiser WL (2018) QTL mapping and validation of fertility restoration in West African sorghum A 1 cytoplasm and identification of a potential causative mutation for Rf 2. Theor Appl Genet 131:2397���2412 [PMID: 30132022]
  129. Kaur P, Gaikwad K (2017) From genomes to GENE-omes: exome sequencing concept and applications in crop improvement. Front Plant Sci 8:2164 [PMID: 29312405]
  130. Kavuluko J, Kibe M, Sugut I, Kibet W, Masanga J, Mutinda S, Wamalwa M, Magomere T, Odeny D, Runo S (2021) GWAS provides biological insights into mechanisms of the parasitic plant (Striga) resistance in sorghum. BMC Plant Biol 21(1):392 [PMID: 34418971]
  131. Kebede H, Subudhi PK, Rosenow DT, Nguyen HT (2001) Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench). Theor Appl Genet 103:266���276
  132. Khan Y, Yadav A, Bonthala VS, Muthamilarasan M, Yadav CB, Prasad M (2014) Comprehensive genome-wide identification and expression profiling of foxtail millet [Setaria italica (L.)] miRNAs in response to abiotic stress and development of miRNA database. Plant Cell Tissue Organ Cult 118:279���292
  133. Khan I, Awan SA, Rizwan M, Akram MA, Zia-ur-Rehman M, Wang X, Zhang X, Huang L (2023) Physiological and transcriptome analyses demonstrate the silver nanoparticles mediated alleviation of salt stress in pearl millet (Pennisetum glaucum L). Environ Pollut 318:120863 [PMID: 36526056]
  134. Kiranmayee KU, Hash CT, Sivasubramani S, Ramu P, Amindala BP, Rathore A, Kishor PK, Gupta R, Deshpande SP (2020) Fine-mapping of sorghum stay-green QTL on chromosome10 revealed genes associated with delayed senescence. Genes 11(9):1026 [PMID: 32883037]
  135. Knoll J, Gunaratna N, Ejeta G (2008) QTL analysis of early-season cold tolerance in sorghum. Theor Appl Genet 116:577���587 [PMID: 18097644]
  136. Kudapa H, Barmukh R, Vemuri H, Gorthy S, Pinnamaneni R, Vetriventhan M, Srivastava RK, Joshi P, Habyarimana E, Gupta SK, Govindaraj M (2023) Genetic and genomic interventions in crop biofortification: examples in millets. Front Plant Sci 14:1123655 [PMID: 36950360]
  137. Kumar S, Hash CT, Thirunavukkarasu N, Singh G, Rajaram V, Rathore A, Senapathy S, Mahendrakar MD, Yadav RS, Srivastava RK (2016) Mapping quantitative trait loci controlling high iron and zinc content in self and open pollinated grains of pearl millet [Pennisetum glaucum (L.) R. Br.]. Front Plant Sci 7:1636 [PMID: 27933068]
  138. Kumar S, Hash CT, Nepolean T, Satyavathi CT, Singh G, Mahendrakar MD, Yadav RS, Srivastava RK (2017) Mapping QTLs controlling flowering time and important agronomic traits in pearl millet. Front Plant Sci 8:1731 [PMID: 29326729]
  139. Kumar A, Kumar S, Fougat RS, Zala HN (2018a) In-silico identification and validation of miRNAs in pearl millet [Pennisetum glaucum L.]. Curr Plant Biol 14:41���49
  140. Kumar S, Hash CT, Nepolean T, Mahendrakar MD, Satyavathi CT, Singh G, Rathore A, Yadav RS, Gupta R, Srivastava RK (2018b) Mapping grain iron and zinc content quantitative trait loci in an iniadi-derived immortal population of pearl millet. Genes 9(5):248 [PMID: 29751669]
  141. Kumar S, Hash CT, Singh G, Nepolean T, Srivastava RK (2021) Mapping QTLs for important agronomic traits in an Iniadi-derived immortal population of pearl millet. Biotechnol Not 2:26���32
  142. Kumar B, Kumar A, Jaiswal S, Iquebal MA, Angadi UB, Tomar RS, Rai A, Kumar D (2022) Genome-wide identification of long non-coding rnas in pearl millet (Pennisetum glaucum (L.)) genotype subjected to drought stress. Agronomy 12(8):1976
  143. Lai D, Fan Y, Xue G, He A, Yang H, He C, Li Y, Ruan J, Yan J, Cheng J (2022a) Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica). BMC Genomics 23(1):389 [PMID: 35596144]
  144. Lai D, Yan J, He A, Xue G, Yang H, Feng L, Wei X, Li L, Xiang D, Ruan J, Fan Y (2022b) Genome-wide identification, phylogenetic and expression pattern analysis of MADS-box family genes in foxtail millet (Setaria italica). Sci Rep 12(1):4979 [PMID: 35322041]
  145. Lai D, Yao X, Yan J, Gao A, Yang H, Xiang D, Ruan J, Fan Y, Cheng J (2022c) Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in foxtail millet (Setaria italica). BMC Genomics 23(1):549 [PMID: 35918632]
  146. Lambe P, Dinant M, Matagne R (1995) Differential long-term expression and methylation of the hygromycin phosphotransferase (hph) and ��-glucuronidase (GUS) genes in transgenic pearl millet (Pennisetum glaucum) callus. Plant Sci 108(1):51���62
  147. Lata C, Bhutty S, Bahadur RP, Majee M, Prasad M (2011) Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]. J Exp Bot 62(10):3387���3401 [PMID: 21414959]
  148. Latha AM, Rao KV, Reddy VD (2005) Production of transgenic plants resistant to leaf blast disease in finger millet (Eleusine coracana (L.) Gaertn.). Plant Sci 169(4):657���667
  149. Latha AM, Rao KV, Reddy TP, Reddy VD (2006) Development of transgenic pearl millet (Pennisetum glaucum (L.) R. Br.) plants resistant to downy mildew. Plant Cell Rep 25:927���935 [PMID: 16607531]
  150. Li HZ (2022) Genome-wide identification and analysis of PLATZ transcription factor gene family in foxtail millet. Chin Bull Bot 58(4):584
  151. Li LB, Zhang YR, Liu KC, Ni ZF, Fang ZJ, Sun QX, Gao JW (2010) Identification and bioinformatics analysis of SnRK2 and CIPK family genes in sorghum. Agric Sci China 9(1):19���30
  152. Li C, Yue J, Wu X, Xu C, Yu J (2014) An ABA-responsive DRE-binding protein gene from Setaria italica, SiARDP, the target gene of SiAREB, plays a critical role under drought stress. J Exp Bot 65(18):5415���5427 [PMID: 25071221]
  153. Li WW, Chen M, Zhong L, Liu JM, Xu ZS, Li LC, Zhou YB, Guo CH, Ma YZ (2015) Overexpression of the autophagy-related gene SiATG8a from foxtail millet (Setaria italica L.) confers tolerance to both nitrogen starvation and drought stress in Arabidopsis. Biochem Biophys Res Commun 468(4):800���806 [PMID: 26577407]
  154. Li W, Chen M, Wang E, Hu L, Hawkesford MJ, Zhong L, Chen Z, Xu Z, Li L, Zhou Y, Guo C (2016a) Genome-wide analysis of autophagy-associated genes in foxtail millet (Setaria italica L.) and characterization of the function of SiATG8a in conferring tolerance to nitrogen starvation in rice. BMC Genomics 17(1):797 [PMID: 27733118]
  155. Li W, Tang S, Zhang S, Shan J, Tang C, Chen Q, Jia G, Han Y, Zhi H, Diao X (2016b) Gene mapping and functional analysis of the novel leaf color gene SiYGL1 in foxtail millet [Setaria italica (L.) P. Beauv]. Physiol Plant 157(1):24���37 [PMID: 26559175]
  156. Li J, Dong Y, Li C, Pan Y, Yu J (2017) SiASR4, the target gene of SiARDP from Setaria italica, improves abiotic stress adaption in plants. Front Plant Sci 7:2053 [PMID: 28127300]
  157. Li A, Jia S, Yobi A, Ge Z, Sato SJ, Zhang C, Angelovici R, Clemente TE, Holding DR (2018a) Editing of an alpha-kafirin gene family increases, digestibility and protein quality in sorghum. Plant Physiol 177(4):1425���1438 [PMID: 29925584]
  158. Li J, Tang W, Zhang YW, Chen KN, Wang C, Liu Y, Zhan Q, Wang C, Wang SB, Xie SQ, Wang L (2018b) Genome-wide association studies for five forage quality-related traits in sorghum (Sorghum bicolor L.). Front Plant Sci 9:1146 [PMID: 30186292]
  159. Li C, Wang G, Li H, Wang G, Ma J, Zhao X, Huo L, Zhang L, Jiang Y, Zhang J, Liu G (2021a) High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet. Theor Appl Genet 134:1303���1317 [PMID: 33566123]
  160. Li W, Zhang L, Faheeda S, Guo P, Yuan X, Wang Y (2021b) Foxtail millet stress associated protein gene SiSAP4 enhances drought stress tolerance in transgenic Arabidopsis. Int J Agric Biol 25(2):441���449
  161. Li ZJ, Jia GQ, Li XY, Li YC, Hui ZH, Sha TA, Zhang S, Li YD, Shang ZL, Diao XM (2021c) Identification of blast-resistance loci through genome-wide association analysis in foxtail millet (Setaria italica (L.) Beauv.). J Integr Agric 20(8):2056���2064
  162. Li Y, Yu S, Zhang Q, Wang Z, Liu M, Zhang A, Dong X, Fan J, Zhu Y, Ruan Y, Li C (2022) Genome-wide identification and characterization of the CCT gene family in foxtail millet (Setaria italica) response to diurnal rhythm and abiotic stress. Genes 13(10):1829 [PMID: 36292714]
  163. Li K, Wei Y, Wang Y, Tan B, Chen S, Li H (2023a) Genome-wide identification of LBD genes in foxtail millet (Setaria italica) and functional characterization of SiLBD21. Int J Mol Sci 24(8):7110 [PMID: 37108274]
  164. Li X, Hou S, Feng M, Xia R, Li J, Tang S, Han Y, Gao J, Wang X (2023b) MDSi: multi-omics database for Setaria italica. BMC Plant Biol 23(1):223 [PMID: 37101150]
  165. Li X, Wang L, Li W, Zhang X, Zhang Y, Dong S, Song XE, Zhao J, Chen M, Yuan X (2023c) Genome-wide identification and expression profiling of cytochrome P450 monooxygenase superfamily in foxtail millet. Int J Mol Sci 24(13):11053 [PMID: 37446233]
  166. Liang Y, Han Y (2024) Pan-genome brings opportunities to revitalize the ancient crop foxtail millet. Plant Commun 5(1):100735 [PMID: 37864332]
  167. Liang Z, Wu Y, Ma L, Guo Y, Ran Y (2022) Efficient genome editing in Setaria italica using CRISPR/Cas9 and base editors. Front Plant Sci 12:3349
  168. Liang H, He Q, Zhang H, Zhi H, Tang S, Wang H, Meng Q, Jia G, Chang J, Diao X (2023a) Identification and haplotype analysis of SiCHLI: a gene for yellow���green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding. Theor Appl Genet 136(1):24 [PMID: 36739566]
  169. Liang Z, Wei S, Guo Y, Wu Y (2023b) Genome-wide identification of MPK and MKK gene families and their responses to phytohormone treatment and abiotic stress in foxtail millet. Plant Growth Regul 99(1):85���99
  170. Lijavetzky D, Carolina Mart��nez M, Carrari F, Esteban Hopp H (2000) QTL analysis and mapping of pre-harvest sprouting resistance in sorghum. Euphytica 112:125���135
  171. Lin CS, Hsu CT, Yang LH, Lee LY, Fu JY, Cheng QW, Wu FH, Hsiao HC, Zhang Y, Zhang R, Chang WJ (2018) Application of protoplast technology to CRISPR/Cas9 mutagenesis: from single-cell mutation detection to mutant plant regeneration. Plant Biotechnol J 16(7):1295���1310 [PMID: 29230929]
  172. Lin M, Dong Z, Zhou H, Wu G, Xu L, Ying S, Chen M (2023) Genome-wide identification and transcriptional analysis of the myb gene family in pearl millet (Pennisetum glaucum). Int J Mol Sci 24(3):2484 [PMID: 36768807]
  173. Liu G, Godwin ID (2012) Highly efficient sorghum transformation. Plant Cell Rep 31:999���1007 [PMID: 22234443]
  174. Liu Y, Feng X, Xu Y, Yu J, Ao G, Peng Z, Zhao Q (2009) Overexpression of millet ZIP-like gene (SiPf40) affects lateral bud outgrowth in tobacco and millet. Plant Physiol Biochem 47(11���12):1051���1060 [PMID: 19766013]
  175. Liu G, Gilding EK, Godwin ID (2015) A robust tissue culture system for sorghum [Sorghum bicolor (L.) Moench]. S Afr J Bot 98:157���160
  176. Liu JM, Xu ZS, Lu PP, Li WW, Chen M, Guo CH, Ma YZ (2016a) Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet. BMC Genomics 17(1):840 [PMID: 27793078]
  177. Liu X, Tang S, Jia G, Schnable JC, Su H, Tang C, Zhi H, Diao X (2016b) The C-terminal motif of SiAGO1b is required for the regulation of growth, development and stress responses in foxtail millet (Setaria italica (L.) P. Beauv.). J Exp Bot 67(11):3237���3249 [PMID: 27045099]
  178. Liu N, Xie K, Jia Q, Zhao J, Chen T, Li H, Wei X, Diao X, Hong Y, Liu Y (2016c) Foxtail mosaic virus-induced gene silencing in monocot plants. Plant Physiol 171(3):1801���1807 [PMID: 27225900]
  179. Liu G, Li J, Godwin ID (2019) Genome editing by CRISPR/Cas9 in sorghum through biolistic bombardment. Methods Mol Biol 1931:169���183 [PMID: 30652290]
  180. Liu T, He J, Dong K, Wang X, Wang W, Yang P, Ren R, Zhang L, Zhang Z, Yang T (2020) QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica). BMC Genomics 21(1):141 [PMID: 32041544]
  181. Liu D, Cui Y, Zhao Z, Li S, Liang D, Wang C, Feng G, Wang J, Liu Z (2021a) Genome-wide identification and characterization of the BES/BZR gene family in wheat and foxtail millet. BMC Genomics 22(1):682 [PMID: 34548036]
  182. Liu Y, Wang Z, Wu X, Zhu J, Luo H, Tian D, Li C, Luo J, Zhao W, Hao H, Jing HC (2021b) SorGSD: updating and expanding the sorghum genome science database with new contents and tools. Biotechnol Biofuels 14(1):165 [PMID: 34344425]
  183. Liu X, Zhang N, Sun Y, Fu Z, Han Y, Yang Y, Jia J, Hou S, Zhang B (2024) QTL mapping of downy mildew resistance in foxtail millet by SLAF-seq and BSR-seq analysis. Theor Appl Genet 137(7):168 [PMID: 38909331]
  184. Lou Y, Chen Y, Liu Z, Sun M, Han F, Wang T, Wang H, Zhuge Y, Chen L (2019) Genome-wide association mapping for agronomic and quality traits in foxtail millet. preprint.
  185. Lu L, Wu X, Yin X, Morrand J, Chen X, Folk WR, Zhang ZJ (2009) Development of marker-free transgenic sorghum [Sorghum bicolor (L.) Moench] using standard binary vectors with bar as a selectable marker. Plant Cell Tissue Organ Cult 99:97���108
  186. Lu M, Wang Z, Fu S, Yang G, Shi M, Lu Y, Wang X, Xia J (2017) Functional characterization of the SbNrat1 gene in sorghum. Plant Sci 262:18���23 [PMID: 28716414]
  187. Lule D, de Villiers S, Fetene M, Odeny DA, Rathore A, Das RR, Tesfaye K (2018) Genetic diversity and association mapping of Ethiopian and exotic finger millet accessions. Crop Pasture Sci 69(9):879���891
  188. Luo H, Zhao W, Wang Y, Xia Y, Wu X, Zhang L, Tang B, Zhu J, Fang L, Du Z, Bekele WA (2016) SorGSD: a sorghum genome SNP database. Biotechnol Biofuels 9(1):6 [PMID: 26744602]
  189. Ma Q, Wang J, Cheng L, Li Y, Zhang Q, Li H, Han Y, Zhen X, Zhang B (2022) The potential function of SiLOX4 on millet discoloration during storage in foxtail millet. Agriculture 12(8):1283
  190. Ma X, Dai S, Qin N, Zhu C, Qin J, Li J (2023) Genome-wide identification and expression analysis of the SAUR gene family in foxtail millet (Setaria italica L.). BMC Plant Biol 23(1):31 [PMID: 36639742]
  191. Mace ES, Singh V, Van Oosterom EJ, Hammer GL, Hunt CH, Jordan DR (2012) QTL for nodal root angle in sorghum (Sorghum bicolor L. Moench) co-locate with QTL for traits associated with drought adaptation. Theor Appl Genet 124:97���109 [PMID: 21938475]
  192. Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X, Cruickshank A (2013) Whole-genome sequencing reveals untapped genetic potential in Africa���s indigenous cereal crop sorghum. Nat Commun 4(1):2320 [PMID: 23982223]
  193. Mahalakshmi S, Christopher GS, Reddy TP, Rao KV, Reddy VD (2006) Isolation of a cDNA clone (PcSrp) encoding serine-rich-protein from Porteresia coarctata T. and its expression in yeast and finger millet (Eleusine coracana L.) affording salt tolerance. Planta 224:347���359 [PMID: 16450172]
  194. Maharajan T, Ceasar SA, Krishna TP, Ignacimuthu S (2019) Phosphate supply influenced the growth, yield and expression of PHT1 family phosphate transporters in seven millets. Planta 250:1433���1448 [PMID: 31300887]
  195. Maharajan T, Ceasar SA, Krishna TP, Ignacimuthu S (2022) Mining genes and markers across minor millets using comparative genomics approaches. Omics of climate resilient small millets. Springer, Singapore, pp 185���203
  196. Maharajan T, Ajeesh Krishna TP, Rakkammal K, Ramakrishnan M, Ceasar SA, Ramesh M, Ignacimuthu S (2023) Identification of QTL associated with agro-morphological and phosphorus content traits in finger millet under differential phosphorus supply via linkage mapping. Agriculture 13:262
  197. Maharajan T, Ceasar SA, Ajeesh Krishna TP (2024a) Harnessing the transcriptomic resources of millets to decipher climate resilience and nutrient enrichment traits. Crit Rev Plant Sci 43(5):348���375
  198. Maharajan T, Krishna TP, Krishnakumar NM, Vetriventhan M, Kudapa H, Ceasar SA (2024b) Role of genome sequences of major and minor millets in strengthening food and nutritional security for future generations. Agriculture 14(5):670
  199. Mahendrakar MD, Parveda M, Kishor PK, Srivastava RK (2020) Discovery and validation of candidate genes for grain iron and zinc metabolism in pearl millet [Pennisetum glaucum (L.) R. Br.]. Sci Rep 10(1):16562 [PMID: 33024155]
  200. Maina F, Harou A, Hamidou F, Morris GP (2022) Genome-wide association studies identify putative pleiotropic locus mediating drought tolerance in sorghum. Plant Direct 6(6):e413 [PMID: 35774626]
  201. Makita Y, Shimada S, Kawashima M, Kondou-Kuriyama T, Toyoda T, Matsui M (2015) MOROKOSHI: transcriptome database in Sorghum bicolor. Plant Cell Physiol 56(1):e6 [PMID: 25505007]
  202. Mallu TS, Irafasha G, Mutinda S, Owuor E, Githiri SM, Odeny DA, Runo S (2022) Mechanisms of pre-attachment Striga resistance in sorghum through genome-wide association studies. Mol Genet Genomics 297(3):751���762 [PMID: 35305146]
  203. Mamidi S, Healey A, Huang P, Grimwood J, Jenkins J, Barry K, Sreedasyam A, Shu S, Lovell JT, Feldman M, Wu J (2020) A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nat Biotechnol 38(10):1203���1210 [PMID: 33020633]
  204. Masumoto H, Takagi H, Mukainari Y, Terauchi R, Fukunaga K (2016) Genetic analysis of NEKODE1 gene involved in panicle branching of foxtail millet, Setaria italica (L.) P. Beauv., and mapping by using QTL-seq. Mol Breeding 36:59
  205. Mochida K, Shinozaki K (2010) Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol 51(4):497���523 [PMID: 20208064]
  206. Mohanty IC, Gangasagar PS, Rath SN (2013) Amplification and molecular characterization of DREB1A transcription factor fragment from finger millet [Eleusine coracana (L.) Gaertn]. J Agric Sci 5(8):37���49
  207. Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J (2013) Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci 110(2):453���458 [PMID: 23267105]
  208. Mullet JE, Klein RR, Klein PE (2002) Sorghum bicolor���an important species for comparative grass genomics and a source of beneficial genes for agriculture. Curr Opin Plant Biol 5(2):118���121 [PMID: 11856606]
  209. Muthamilarasan M, Misra G, Prasad M (2013) FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research. PLoS ONE 8(8):e71418 [PMID: 23951158]
  210. Muthamilarasan M, Khandelwal R, Yadav CB, Bonthala VS, Khan Y, Prasad M (2014) Identification and molecular characterization of MYB transcription factor superfamily in C4 model plant foxtail millet (Setaria italica L.). PLoS ONE 9(10):e109920 [PMID: 25279462]
  211. Nadeem F, Ahmad Z, Wang R, Han J, Shen Q, Chang F, Diao X, Zhang F, Li X (2018) Foxtail millet [Setaria italica (L.) Beauv.] grown under low nitrogen shows a smaller root system, enhanced biomass accumulation, and nitrate transporter expression. Front Plant Sci 9:205 [PMID: 29520286]
  212. Nagaraja Reddy R, Madhusudhana R, Murali Mohan S, Chakravarthi DV, Mehtre SP, Seetharama N, Patil JV (2013) Mapping QTL for grain yield and other agronomic traits in post-rainy sorghum [Sorghum bicolor (L.) Moench]. Theor Appl Genet 126(8):1921���1939 [PMID: 23649648]
  213. Nagarjuna KN, Parvathi MS, Sajeevan RS, Pruthvi V, Mamrutha HM, Nataraja KN (2016) Full-length cloning and characterization of abiotic stress responsive CIPK31-like gene from finger millet, a drought-tolerant crop. Curr Sci 10:890���894
  214. Nageshbabu R, Jyothi MN, Sharadamma N, Rai DV, Devaraj VR (2013) Expression of miRNAs confers enhanced tolerance to drought and salt stress in Finger millet (Eleusine coracona). J Stress Physiol Biochem 9(3):220���231
  215. Narayanrao DR, Tomar RS, Padhiyar SM, Jasminkumar K, Ashish G, Chauhan NM, Singh SC, Upadhye V, Kuddus M, Kamble L, Hajare ST (2023) De novo transcriptome sequencing of drought tolerance-associated genes in little millet (Panicum sumatrense L.). Funct Integr Genomics 23(4):303 [PMID: 37723408]
  216. Nguyen TV, Thanh Thu T, Claeys M, Angenon G (2007) Agrobacterium-mediated transformation of sorghum (Sorghum bicolor (L.) Moench) using an improved in vitro regeneration system. Plant Cell, Tissue Organ Cult 91:155���164
  217. Ni X, Xia Q, Zhang H, Cheng S, Li H, Fan G, Guo T, Huang P, Xiang H, Chen Q, Li N (2017) Updated foxtail millet genome assembly and gene mapping of nine key agronomic traits by resequencing a RIL population. GigaScience 6(2):giw005
  218. Nie X, Zhao X, Wang S, Zhang T, Li C, Liu H, Tong W, Guo Y (2018) Complete chloroplast genome sequence of broomcorn millet (Panicum miliaceum L.) and comparative analysis with other Panicoideae species. Agronomy 8(9):159
  219. O���Kennedy MM, Burger JT, Botha FC (2004) Pearl millet transformation system using the positive selectable marker gene phosphomannose isomerase. Plant Cell Rep 22:684���690 [PMID: 14727053]
  220. Odonkor S, Choi S, Chakraborty D, Martinez-Bello L, Wang X, Bahri BA, Tenaillon MI, Panaud O, Devos KM (2018) QTL mapping combined with comparative analyses identified candidate genes for reduced shattering in Setaria italica. Front Plant Sci 9:918 [PMID: 30073004]
  221. Palakolanu SR, Gupta S, Yeshvekar RK, Chakravartty N, Kaliamoorthy S, Shankhapal AR, Vempati AS, Kuriakose B, Lekkala SP, Philip M, Perumal RC (2022) Genome-wide miRNAs profiles of pearl millet under contrasting high vapor pressure deficit reveal their functional roles in drought stress adaptations. Physiol Plant 174(1):e13521 [PMID: 34392545]
  222. Pan Y, Ma X, Liang H, Zhao Q, Zhu D, Yu J (2015) Spatial and temporal activity of the foxtail millet (Setaria italica) seed-specific promoter pF128. Planta 241:57���67 [PMID: 25204632]
  223. Pan Y, Li J, Jiao L, Li C, Zhu D, Yu J (2016) A non-specific Setaria italica lipid transfer protein gene plays a critical role under abiotic stress. Front Plant Sci 24(7):1752
  224. Pandey AK, Bhat BV, Balakrishna D, Seetharama N (2010) Genetic transformation of sorghum (Sorghum bicolor (L.) Moench.). Int J Biotechnol Biochem 6(1):45���53
  225. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D, Prasad M (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20(2):197���207 [PMID: 23382459]
  226. Parh DK, Jordan DR, Aitken EA, Mace ES, Jun-Ai P, McIntyre CL, Godwin ID (2008) QTL analysis of ergot resistance in sorghum. Theor Appl Genet 117:369���382 [PMID: 18481043]
  227. Parvathi MS, Nataraja KN (2017) Discovery of stress responsive TATA-box binding protein associated Factor6 (TAF6) from finger millet (Eleusine coracana (L.) Gaertn). Journal of Plant Biology 60:335���342
  228. Parvathi MS, Nataraja KN, Yashoda BK, Ramegowda HV, Mamrutha HM, Rama N (2013) Expression analysis of stress responsive pathway genes linked to drought hardiness in an adapted crop, finger millet (Eleusine coracana). J Plant Biochem Biotechnol 22:193���201
  229. Parvathi MS, Nataraja KN, Reddy YN, Naika MB, Gowda MC (2019) Transcriptome analysis of finger millet (Eleusine coracana (L.) Gaertn.) reveals unique drought responsive genes. J Genet 98(2):46 [PMID: 31204698]
  230. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551���556 [PMID: 19189423]
  231. Pegler JL, Nguyen DQ, Grof CP, Eamens AL (2020) Profiling of the salt stress responsive microRNA landscape of C4 genetic model species Setaria viridis (L.) Beauv. Agronomy 10(6):837
  232. Pendergast TH IV, Qi P, Odeny DA, Dida MM, Devos KM (2022) A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits. Plant Genome 15(1):e20175 [PMID: 34904374]
  233. Peng Y, Zhang J, Cao G, Xie Y, Liu X, Lu M, Wang G (2010) Overexpression of a PLD��1 gene from Setaria italica enhances the sensitivity of Arabidopsis to abscisic acid and improves its drought tolerance. Plant Cell Rep 29:793���802 [PMID: 20490504]
  234. Perumal S, Jayakodi M, Kim DS, Yang TJ, Natesan S (2016) The complete chloroplast genome sequence of Indian barnyard millet, Echinochloa frumentacea (Poaceae). Mitochondrial DNA Part B 1(1):79���80 [PMID: 33644328]
  235. Prom LK, Ahn E, Isakeit T, Magill C (2019) GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola. Theor Appl Genet 132:1389���1396 [PMID: 30688991]
  236. Prusty A, Panchal A, Singh RK, Prasad M (2024) Major transcription factor families at the nexus of regulating abiotic stress response in millets: a comprehensive review. Planta 259(5):118 [PMID: 38592589]
  237. Pudake RN, Mehta CM, Mohanta TK, Sharma S, Varma A, Sharma AK (2017) Expression of four phosphate transporter genes from finger millet (Eleusine coracana L.) in response to mycorrhizal colonization and Pi stress. 3 Biotech. 7(1):17 [PMID: 28391483]
  238. Pujar M, Gangaprasad S, Govindaraj M, Gangurde SS, Kanatti A, Kudapa H (2020) Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet. Sci Rep 10(1):19473 [PMID: 33173120]
  239. Punnuri S, Huang Y, Steets J, Wu Y (2013) Developing new markers and QTL mapping for greenbug resistance in sorghum [Sorghum bicolor (L.) Moench]. Euphytica 191:191���203
  240. Puranik S, Bahadur RP, Srivastava PS, Prasad M (2011) Molecular cloning and characterization of a membrane associated NAC family gene, SiNAC from foxtail millet [Setaria italica (L.) P. Beauv.]. Mol Biotechnol 49:138���150 [PMID: 21312005]
  241. Puranik S, Sahu PP, Mandal SN, Parida SK, Prasad M (2013) Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PLoS ONE 8(5):e64594 [PMID: 23691254]
  242. Puranik S, Sahu PP, Beynon S, Srivastava RK, Sehgal D, Ojulong H, Yadav R (2020) Genome-wide association mapping and comparative genomics identifies genomic regions governing grain nutritional traits in finger millet (Eleusine coracana L. Gaertn.). Plants People Planet 2(6):649���662
  243. Qi X, Xie S, Liu Y, Yi F, Yu J (2013) Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. Plant Mol Biol 83:459���473 [PMID: 23860794]
  244. Qin FF, Zhao Q, Ao GM, Yu JJ (2008) Co-suppression of Si401, a maize pollen specific Zm401 homologous gene, results in aberrant anther development in foxtail millet. Euphytica 163:103���111
  245. Qin L, Chen E, Li F, Yu X, Liu Z, Yang Y, Wang R, Zhang H, Wang H, Liu B, Guan YA (2020) Genome-wide gene expression profiles analysis reveal novel insights into drought stress in foxtail millet (Setaria italica L.). Int J Mol Sci 21(22):8520 [PMID: 33198267]
  246. Raghuwanshi A, Birch RG (2010) Genetic transformation of sweet sorghum. Plant Cell Rep 29:997���1005 [PMID: 20535472]
  247. Rahman H, Ramanathan V, Nallathambi J, Duraialagaraja S, Muthurajan R (2016) Over-expression of a NAC 67 transcription factor from finger millet (Eleusine coracana L.) confers tolerance against salinity and drought stress in rice. BMC Biotechnol 16:35 [PMID: 27213684]
  248. Rajasekaran R, Francis N (2021) Genetic and genomic resources for improving proso millet (Panicum miliaceum L.): a potential crop for food and nutritional security. Nucleus 64(1):21���32
  249. Rajput SG, Santra DK, Schnable J (2016) Mapping QTLs for morpho-agronomic traits in proso millet (Panicum miliaceum L.). Mol Breeding 36:37
  250. Ramadevi R, Rao KV, Reddy VD (2014) Agrobacterium tumefaciens-mediated genetic transformation and production of stable transgenic pearl millet (Pennisetum glaucum [L.] R. Br.). In Vitro Cell Dev Biol Plant 50:392���400
  251. Ramakrishna C, Singh S, Raghavendrarao S, Padaria JC, Mohanty S, Sharma TR, Solanke AU (2018) The membrane tethered transcription factor EcbZIP17 from finger millet promotes plant growth and enhances tolerance to abiotic stresses. Sci Rep 8(1):2148 [PMID: 29391403]
  252. Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, Vinod KK, Kalpana K, Al-Dhabi NA, Ignacimuthu S (2016) Tracing QTLs for leaf blast resistance and agronomic performance of finger millet (Eleusine coracana (L.) Gaertn.) genotypes through association mapping and in silico comparative genomics analyses. PLoS ONE 11(7):e0159264 [PMID: 27415007]
  253. Ramakrishnan M, Ceasar SA, Vinod KK, Duraipandiyan V, Ajeesh Krishna TP, Upadhyaya HD, Al-Dhabi NA, Ignacimuthu S (2017) Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis. PLoS ONE 12(8):e0183261 [PMID: 28820887]
  254. Ramegowda V, Senthil-Kumar M, Nataraja KN, Reddy MK, Mysore KS, Udayakumar M (2012) Expression of a finger millet transcription factor, EcNAC1, in tobacco confers abiotic stress-tolerance. PLoS ONE 7(7):e40397 [PMID: 22808152]
  255. Ramegowda Y, Venkategowda R, Jagadish P, Govind G, Hanumanthareddy RR, Makarla U, Guligowda SA (2013) Expression of a rice Zn transporter, OsZIP1, increases Zn concentration in tobacco and finger millet transgenic plants. Plant Biotechnol Rep 7:309���319
  256. Ramegowda V, Gill US, Sivalingam PN, Gupta A, Gupta C, Govind G, Nataraja KN, Pereira A, Udayakumar M, Mysore KS, Senthil-Kumar M (2017) GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana. Sci Rep 7(1):9148 [PMID: 28831141]
  257. Raveendar S, Lee GA, Lee KJ, Shin MJ, Lee JR, Lee SY, Cho GT, Ma KH, Chung JW (2019) The complete chloroplast genome of pearl millet (Pennisetum glaucum (L.) R. Br.) and comparative analysis within the family Poaceae. Cereal Res Commun 47(1):1���10
  258. Rayaprolu L, Selvanayagam S, Rao DM, Gupta R, Das RR, Rathore A, Gandham P, Kiranmayee KN, Deshpande SP, Are AK (2021) Genome-wide association study for major biofuel traits in sorghum using minicore collection. Protein Pept Lett 28(8):909���928 [PMID: 33588716]
  259. Reddy PS, Mallikarjuna G, Kaul T, Chakradhar T, Mishra RN, Sopory SK, Reddy MK (2010) Molecular cloning and characterization of gene encoding for cytoplasmic Hsc70 from Pennisetum glaucum may play a protective role against abiotic stresses. Mol Genet Genomics 283:243���254 [PMID: 20127116]
  260. Reddy PS, Reddy GM, Pandey P, Chandrasekhar K, Reddy MK (2012) Cloning and molecular characterization of a gene encoding late embryogenesis abundant protein from Pennisetum glaucum: protection against abiotic stresses. Mol Biol Rep 39:7163���7174 [PMID: 22311039]
  261. Reddy PS, Dhaware MG, Sivasakthi K, Divya K, Nagaraju M, Sri Cindhuri K, Kavi Kishor PB, Bhatnagar-Mathur P, Vadez V, Sharma KK (2022) Pearl millet aquaporin gene PgPIP2;6 improves abiotic stress tolerance in transgenic tobacco. Front Plant Sci 13:133
  262. Renganathan VG, Renuka R, Vanniarajan C, Raveendran M, Elangovan A (2023) Selection and validation of reliable reference genes for quantitative real-time PCR in Barnyard millet (Echinochloa spp.) under varied abiotic stress conditions. Sci Rep 13(1):15573 [PMID: 37731036]
  263. Rhodes DH, Hoffmann L Jr, Rooney WL, Ramu P, Morris GP, Kresovich S (2014) Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) Moench] germplasm. J Agric Food Chem 62(45):10916���10927 [PMID: 25272193]
  264. Ritter KB, Jordan DR, Chapman SC, Godwin ID, Mace ES, Lynne McIntyre C (2008) Identification of QTL for sugar-related traits in a sweet�� grain sorghum (Sorghum bicolor L. Moench) recombinant inbred population. Mol Breeding 22:367���384
  265. Ruperao P, Thirunavukkarasu N, Gandham P, Selvanayagam S, Govindaraj M, Nebie B, Manyasa E, Gupta R, Das RR, Odeny DA, Gandhi H (2021) Sorghum pan-genome explores the functional utility for genomic-assisted breeding to accelerate the genetic gain. Front Plant Sci 12:666342 [PMID: 34140962]
  266. Saidou AA, Mariac C, Luong V, Pham JL, Bezan��on G, Vigouroux Y (2009) Association studies identify natural variation at PHYC linked to flowering time and morphological variation in pearl millet. Genetics 182(3):899���910 [PMID: 19433627]
  267. Satish K, Srinivas G, Madhusudhana R, Padmaja PG, Nagaraja Reddy R, Murali Mohan S, Seetharama N (2009) Identification of quantitative trait loci for resistance to shoot fly in sorghum [Sorghum bicolor (L.) Moench]. Theor Appl Genet 119:1425���1439 [PMID: 19763534]
  268. Satish L, Ceasar SA, Ramesh M (2017) Improved Agrobacterium-mediated transformation and direct plant regeneration in four cultivars of finger millet (Eleusine coracana (L.) Gaertn.). Plant Cell Tissue Organ Cult 131:547���565
  269. Schoeman I (2011) Evaluation of two viral vectors for virus-induced gene silencing in pearl millet. University of Pretoria, South Africa
  270. Sebastin R, Lee GA, Lee KJ, Shin MJ, Cho GT, Lee JR, Ma KH, Chung JW (2018) The complete chloroplast genome sequences of little millet (Panicum sumatrense Roth ex Roem. and Schult.) (Poaceae). Mitochondrial DNA B Resour 3(2):719���720 [PMID: 33474296]
  271. Sebastin R, Lee KJ, Cho GT, Lee JR, Shin MJ, Kim SH, Lee GA, Chung JW, Hyun DY (2019) The complete chloroplast genome sequence of Japanese Millet Echinochloa esculenta (A. braun) H. scholz (Poaceae). Mitochondrial DNA B Resour 4(1):1392���1393
  272. Sharma M, Kothari-Chajer A, Jagga-Chugh S, Kothari SL (2011) Factors influencing Agrobacterium tumefaciens-mediated genetic transformation of Eleusine coracana (L.) Gaertn. Plant Cell Tissue Organ Cult 105:93���104
  273. Sharma D, Tiwari A, Sood S, Jamra G, Singh NK, Meher PK, Kumar A (2018) Genome wide association mapping of agro-morphological traits among a diverse collection of finger millet (Eleusine coracana L.) genotypes using SNP markers. PLoS ONE 13(8):e0199444 [PMID: 30092057]
  274. Sharma D, Tiwari A, Sood S, Meher PK, Kumar A (2022) Identification and validation of candidate genes for high calcium content in finger millet [Eleusine coracana (L.) Gaertn.] through genome-wide association study. J Cereal Sci 107:103517
  275. Shehzad T, Okuno K (2015) QTL mapping for yield and yield-contributing traits in sorghum (Sorghum bicolor (L.) Moench) with genome-based SSR markers. Euphytica 203:17���31
  276. Shehzad T, Iwata H, Okuno K (2009) Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breed Sci 59(3):217���227
  277. Shekhar S, Prasad AS, Banjare K, Kaushik A, Mannade AK, Dubey M, Patil A, Premi V, Vishwakarma AK, Sao A, Saxena RR (2023) LMT: a comprehensive transcriptome database for climate-resilient, nutritionally rich little millet (Panicum sumatrense). Front Plant Sci 14:1106104 [PMID: 36993866]
  278. Shields L, Gang Y, Jordan K, Sapkota S, Boatwright L, Jiang X, Kresovich S, Boyles R (2021) Genome-wide association studies of antimicrobial activity in global sorghum. Crop Sci 61:1301���1316
  279. Shiringani AL, Friedt W (2011) QTL for fibre-related traits in grain�� sweet sorghum as a tool for the enhancement of sorghum as a biomass crop. Theor Appl Genet 123:999���1011 [PMID: 21739141]
  280. Shiringani AL, Frisch M, Friedt W (2010) Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench Theor Appl Genet 121:323���336 [PMID: 20229249]
  281. Singh UM, Chandra M, Shankhdhar SC, Kumar A (2014) Transcriptome wide identification and validation of calcium sensor gene family in the developing spikes of finger millet genotypes for elucidating its role in grain calcium accumulation. PLoS ONE 9(8):e103963 [PMID: 25157851]
  282. Singh RK, Singh VK, Raghavendrarao S, Phanindra ML, Venkat Raman K, Solanke AU, Kumar PA, Sharma TR (2015) Expression of finger millet EcDehydrin7 in transgenic tobacco confers tolerance to drought stress. Appl Biochem Biotechnol 177:207���216 [PMID: 26160315]
  283. Singh RK, Jaishankar J, Muthamilarasan M, Shweta S, Dangi A, Prasad M (2016) Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress. Sci Rep 6(1):32641 [PMID: 27586959]
  284. Singh RK, Shweta S, Muthamilarasan M, Rani R, Prasad M (2019) Study on aquaporins of Setaria italica suggests the involvement of SiPIP3;1 and SiSIP1;1 in abiotic stress response. Funct Integr Genomics 19:587���596 [PMID: 30759293]
  285. Singh S, Chopperla R, Shingote P, Chhapekar SS, Deshmukh R, Khan S, Padaria JC, Sharma TR, Solanke AU (2021) Overexpression of EcDREB2A transcription factor from finger millet in tobacco enhances tolerance to heat stress through ROS scavenging. J Biotechnol 336:10���24 [PMID: 34116128]
  286. Singh J, Varshney V, Tak N, Jha S (2023) Genome-wide identification and expression analysis of glycogen synthase kinase encoding genes in foxtail millet (Setaria italica L.) under salinity, dehydration, and oxidative stress. Plant Stress 8:100165
  287. Smith RL, Chowdhury MK (1991) Characterization of pearl millet mitochondrial DNA fragments rearranged by reversion from cytoplasmic male sterility to fertility. Theor Appl Genet 81:793���799 [PMID: 24221443]
  288. Sood S, Joshi DC, Rajashekara H, Tiwari A, Bhinda MS, Kumar A, Kant L, Pattanayak A (2023) Deciphering the genomic regions governing major agronomic traits and blast resistance using genome wide association mapping in finger millet. Gene 854:147115 [PMID: 36526121]
  289. Sreeja R, Balaji S, Arul L, Nirmala Kumari A, Kannan Bapu JR, Subramanian A (2016) Association of lignin and FLEXIBLE CULM 1 (FC1) ortholog in imparting culm strength and lodging resistance in kodo millet (Paspalum scrobiculatum L.). Mol Breeding 36(11):149
  290. Sreenivasulu N, Miranda M, Prakash HS, Wobus U, Weschke W (2004) Transcriptome changes in foxtail millet genotypes at high salinity: identification and characterization of a PHGPX gene specifically up-regulated by NaCl in a salt-tolerant line. J Plant Physiol 161(4):467���477 [PMID: 15128034]
  291. Srivastava S, Arya C (2021) Millets: malnutrition and nutrition security. Millets and millet technology. Springer, Singapore, pp 81���100
  292. Su Z, Di Y, Li J, Wang X, Zhang F, Yi H (2023) Identification and functional analysis of miR156 family and its target genes in foxtail millet (Setaria italica). Plant Growth Regul 99(1):149���160
  293. Sukumaran S, Li X, Li X, Zhu C, Bai G, Perumal R, Tuinstra MR, Prasad PV, Mitchell SE, Tesso TT, Yu J (2016) QTL mapping for grain yield, flowering time, and stay-green traits in sorghum with genotyping-by-sequencing markers. Crop Sci 56(4):1429���1442
  294. Sun M, Huang D, Zhang A, Khan I, Yan H, Wang X, Zhang X, Zhang J, Huang L (2020) Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing. BMC Plant Biol 20(1):323 [PMID: 32640987]
  295. Sun M, Yan H, Zhang A, Jin Y, Lin C, Luo L, Wu B, Fan Y, Tian S, Cao X, Wang Z (2023) Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets. Plant Biotechnol J 21(11):2348���2357 [PMID: 37530223]
  296. Suresh BV, Choudhary P, Aggarwal PR, Rana S, Singh RK, Ravikesavan R, Prasad M, Muthamilarasan M (2022) De novo transcriptome analysis identifies key genes involved in dehydration stress response in kodo millet (Paspalum scrobiculatum L.). Genomics 114(3):110347 [PMID: 35337948]
  297. Tadesse Y, Sagi L, Swennen R, Jacobs M (2003) Optimisation of transformation conditions and production of transgenic sorghum (Sorghum bicolor) via microparticle bombardment. Plant Cell, Tissue Organ Cult 75(1):1���18
  298. Tao YZ, Hardy A, Drenth J, Henzell RG, Franzmann BA, Jordan DR, Butler DG, McIntyre CL (2003) Identifications of two different mechanisms for sorghum midge resistance through QTL mapping. Theor Appl Genet 107:116���122 [PMID: 12835937]
  299. Tao Y, Zhao X, Wang X, Hathorn A, Hunt C, Cruickshank AW, van Oosterom EJ, Godwin ID, Mace ES, Jordan DR (2020) Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals. Plant Biotechnol J 18(4):1093���1105 [PMID: 31659829]
  300. Taylor MG, Vasil IK (1991) Histology of, and physical factors affecting, transient GUS expression in pearl millet (Pennisetum glaucum (L.) R. Br.) embryos following microprojectile bombardment. Plant Cell Rep 10:120���125 [PMID: 24221489]
  301. Taylor MG, Vasil V, Vasil IK (1993) Enhanced GUS gene expression in cereal/grass cell suspensions and immature embryos using the maize uhiquitin-based plasmid pAHC25. Plant Cell Rep 12:491���495 [PMID: 24196107]
  302. Thulasinathan T, Jain P, Yadav AK, Kumar V, Sevanthi AM, Solanke AU (2022) Current status of bioinformatics resources of small millets. Omics of climate resilient small millets. Springer, Singapore, pp 221���234
  303. Tian T, You Q, Zhang L, Yi X, Yan H, Xu W, Su Z (2016) SorghumFDB: sorghum functional genomics database with multidimensional network analysis. Database 2016:baw099 [PMID: 27352859]
  304. Tiecoura K, Bi SG, Dinant M, Ledou L (2015) In vitro transformation of pearl millet (Pennisetum glaucum (L.) R. BR.): selection of chlorsulfuron-resistant plants and long term expression of the gus gene under the control of the emu promoter. Afr J Biotech 14(46):3112���3123
  305. Usha S, Jyothi MN, Sharadamma N, Dixit R, Devaraj VR (2015) Identification of microRNAs and their targets in Finger millet by high throughput sequencing. Gene 574(2):210���216 [PMID: 26255946]
  306. Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A, Srivastava RK (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol 35(10):969���976 [PMID: 28922347]
  307. Veena M, Melvin P, Prabhu SA, Shailasree S, Shetty HS, Kini KR (2016) Molecular cloning of a coiled-coil-nucleotide-binding-site-leucine-rich repeat gene from pearl millet and its expression pattern in response to the downy mildew pathogen. Mol Biol Rep 43:117���128 [PMID: 26842722]
  308. Vengadessan V, Rai KN, Kannan Bapu JR, Hash CT, Bhattacharjee R, Senthilvel S, Vinayan MT (2013) Nepolean T (2013) Construction of genetic linkage map and QTL analysis of sink-size traits in pearl millet (Pennisetum glaucum). Int Sch Res Not 1:471632
  309. Vetriventhan M, Azevedo VC, Upadhyaya HD, Nirmalakumari A, Kane-Potaka J, Anitha S, Ceasar SA, Muthamilarasan M, Bhat BV, Hariprasanna K, Bellundagi A (2020) Genetic and genomic resources, and breeding for accelerating improvement of small millets: current status and future interventions. Nucleus 63:217���239
  310. Visarada KB, Padmaja PG, Saikishore N, Pashupatinath E, Royer M, Seetharama N, Patil JV (2014) Production and evaluation of transgenic sorghum for resistance to stem borer. In Vitro Cell Dev Biol Plant 50:176���189
  311. Wang S, Gao LZ (2016) The complete chloroplast genome of an irreplaceable dietary and model crop, foxtail millet (Setaria italica). Mitochondrial DNA A DNA Mapp Seq Anal 27(6):4442���4443 [PMID: 26486605]
  312. Wang MZ, Pan YL, Li C, Liu C, Zhao Q, Ao GM, Yu JJ (2011) Culturing of immature inflorescences and Agrobacterium-mediated transformation of foxtail millet (Setaria italica). Afr J Biotech 10(73):16466���16479
  313. Wang M, Li P, Li C, Pan Y, Jiang X, Zhu D, Zhao Q, Yu J (2014) SiLEA14, a novel atypical LEA protein, confers abiotic stress resistance in foxtail millet. BMC Plant Biol 14(1):290 [PMID: 25404037]
  314. Wang Y, Li L, Tang S, Liu J, Zhang H, Zhi H, Jia G, Diao X (2016) Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet. BMC Genet 17:57 [PMID: 27068810]
  315. Wang J, Wang Z, Du X, Yang H, Han F, Han Y, Yuan F, Zhang L, Peng S, Guo E (2017a) A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq. PLoS ONE 12(6):e0179717 [PMID: 28644843]
  316. Wang Y, Li Z, Pan J, Li Y, Wang Q, Guan YA, Liu W (2017b) Cloning and functional analysis of the SiRLK35 gene in Setaria italic L. Yi Chuan= Hereditas 39(5):413���422 [PMID: 28487273]
  317. Wang P, Wang H, Wang Y, Ren F, Liu W (2018a) Analysis of bHLH genes from foxtail millet (Setaria italica) and their potential relevance to drought stress. PLoS ONE 13(11):e0207344 [PMID: 30412624]
  318. Wang T, Song H, Zhang B, Lu Q, Liu Z, Zhang S, Guo R, Wang C, Zhao Z, Liu J, Peng R (2018b) Genome-wide identification, characterization, and expression analysis of superoxide dismutase (SOD) genes in foxtail millet (Setaria italica L.). 3 Biotech. 8(12):486 [PMID: 30498660]
  319. Wang J, Yang Y, Liao L, Xu J, Liang X, Liu W (2019a) Genome-wide identification and functional characterization of the phosphate transporter gene family in Sorghum. Biomolecules 9(11):670 [PMID: 31671617]
  320. Wang Z, Wang J, Peng J, Du X, Jiang M, Li Y, Han F, Du G, Yang H, Lian S, Yong J (2019b) QTL mapping for 11 agronomic traits based on a genome-wide Bin-map in a large F2 population of foxtail millet (Setaria italica (L.) P. Beauv). Mol Breeding 39(2):18
  321. Wang H, Wang R, Liu B, Yang Y, Qin L, Chen E, Zhang H, Guan Y (2020a) QTL analysis of salt tolerance in Sorghum bicolor during whole-plant growth stages. Plant Breeding 139(3):455���465
  322. Wang T, Song H, Wei Y, Li P, Hu N, Liu J, Zhang B, Peng R (2020b) High throughput deep sequencing elucidates the important role of lncRNAs in Foxtail millet response to herbicides. Genomics 112(6):4463���4473 [PMID: 32763352]
  323. Wang H, Hao D, Wang X, Zhang H, Yang P, Zhang L, Zhang B (2021) Genome-wide identification and expression analysis of the SNARE genes in Foxtail millet (Setaria italica) reveals its roles in drought stress. Plant Growth Regul 95:355���369
  324. Wang H, Tang S, Zhi H, Xing L, Zhang H, Tang C, Wang E, Zhao M, Jia G, Feng B, Diao X (2022a) The boron transporter SiBOR1 functions in cell wall integrity, cellular homeostasis, and panicle development in foxtail millet. Crop J 10(2):342���353
  325. Wang L, Liu Y, Gao L, Yang X, Zhang X, Xie S, Chen M, Wang YH, Li J, Shen Y (2022b) Identification of candidate forage yield genes in sorghum (Sorghum bicolor L.) using integrated genome-wide association studies and RNA-Seq. Front Plant Sci 12:3115
  326. Wang L, Fu H, Zhao J, Wang J, Dong S, Yuan X, Li X, Chen M (2023) Genome-wide identification and expression profiling of glutathione S-transferase gene family in foxtail millet (Setaria italica L.). Plants 12(5):1138 [PMID: 36904001]
  327. Weiss T, Wang C, Kang X, Zhao H, Elena Gamo M, Starker CG, Crisp PA, Zhou P, Springer NM, Voytas DF, Zhang F (2020) Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis. Plant J 104(3):828���838 [PMID: 32786122]
  328. Wu Y, Huang Y (2008) Molecular mapping of QTLs for resistance to the greenbug Schizaphis graminum (Rondani) in Sorghum bicolor (Moench). Theor Appl Genet 117(1):117���124 [PMID: 18414829]
  329. Wu E, Lenderts B, Glassman K, Berezowska-Kaniewska M, Christensen H, Asmus T, Zhen S, Chu U, Cho MJ, Zhao ZY (2014) Optimized Agrobacterium-mediated sorghum transformation protocol and molecular data of transgenic sorghum plants. In Vitro Cell Dev Biol Plant 50:9���18 [PMID: 26316679]
  330. Wu D, Shen E, Jiang B, Feng Y, Tang W, Lao S, Jia L, Lin HY, Xie L, Weng X, Dong C (2022) Genomic insights into the evolution of Echinochloa species as weed and orphan crop. Nat Commun 13:689 [PMID: 35115514]
  331. Xie LN, Ming CH, Min DH, Lu FE, Xu ZS, Zhou YB, Xu DB, Li LC, Zhang XH (2017) The NAC-like transcription factor SiNAC110 in foxtail millet (Setaria italica L. confers tolerance to drought and high salt stress through an ABA independent signaling pathway. J Integr Agric 16(3):559���571
  332. Xie H, Hou J, Fu N, Wei M, Li Y, Yu K, Song H, Li S, Liu J (2021) Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica. BMC Genomics 22(1):556 [PMID: 34281524]
  333. Xing G, Jin M, Qu R, Zhang J, Han Y, Han Y, Wang X, Li X, Ma F, Zhao X (2022) Genome-wide investigation of histone acetyltransferase gene family and its responses to biotic and abiotic stress in foxtail millet (Setaria italica [L.] P. Beauv). BMC Plant Biol 22(1):292 [PMID: 35701737]
  334. Xue C, Zhi H, Fang X, Liu X, Tang S, Chai Y, Zhao B, Jia G, Diao X (2016) Characterization and fine mapping of SiDWARF2 (D2) in foxtail millet. Crop Sci 56(1):95���103
  335. Yadav R, Bidinger F, Hash C, Yadav Y, Yadav O, Bhatnagar S, Howarth C (2003) Mapping and characterisation of QTL�� E interactions for traits determining grain and stover yield in pearl millet. Theor Appl Genet 106:512���520 [PMID: 12589552]
  336. Yadav CB, Bonthala VS, Muthamilarasan M, Pandey G, Khan Y, Prasad M (2015a) Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Res 22(1):79���90 [PMID: 25428892]
  337. Yadav CB, Muthamilarasan M, Pandey G, Prasad M (2015b) Identification, characterization and expression profiling of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in foxtail millet. Plant Mol Biol Report 33:43���55
  338. Yadav A, Khan Y, Prasad M (2016a) Dehydration-responsive miRNAs in foxtail millet: genome-wide identification, characterization and expression profiling. Planta 243:749���766 [PMID: 26676987]
  339. Yadav CB, Muthamilarasan M, Dangi A, Shweta S, Prasad M (2016b) Comprehensive analysis of SET domain gene family in foxtail millet identifies the putative role of SiSET14 in abiotic stress tolerance. Sci Rep 6(1):32621 [PMID: 27585852]
  340. Yadav CB, Tokas J, Yadav D, Winters A, Singh RB, Yadav R, Gangashetty PI, Srivastava RK, Yadav RS (2021) Identifying anti-oxidant biosynthesis genes in pearl millet [Pennisetum glaucum (L.) R. Br.] using genome���wide association analysis. Front Plant Sci 12:599649 [PMID: 34122460]
  341. Yadav CB, Srivastava RK, Beynon S, Englyst K, Gangashetty PI, Yadav RS (2022) Genetic variability and genome-wide marker association studies for starch traits contributing to low glycaemic index in pearl millet. Food Energy Secur 11(1):e341
  342. Yan H, Sun M, Zhang Z, Jin Y, Zhang A, Lin C, Wu B, He M, Xu B, Wang J, Qin P (2023) Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nat Genet 55:507���518 [PMID: 36864101]
  343. Yang R, Chen M, Sun JC, Yu Y, Min DH, Chen J, Xu ZS, Zhou YB, Ma YZ, Zhang XH (2019) Genome-wide analysis of LIM family genes in foxtail millet (Setaria italica L.) and characterization of the role of SiWLIM2b in drought tolerance. Int J Mol Sci 20(6):1303 [PMID: 30875867]
  344. Yang Y, Cheng J, Han H, Sun R, Li Y, Zhang Y, Han Y, Zhang H, Li X (2023) Genome-wide identification of the HKT transcription factor family and their response to salt stress in foxtail millet (Setaria italica). Plant Growth Regul 99(1):113���123
  345. Ye CY, Lin Z, Li G, Wang YY, Qiu J, Fu F, Zhang H, Chen L, Ye S, Song W, Jin G (2014) Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species. PLoS ONE 9(11):e113657 [PMID: 25427255]
  346. Yi F, Xie S, Liu Y, Qi X, Yu J (2013) Genome-wide characterization of microRNA in foxtail millet (Setaria italica). BMC Plant Biol 13(1):212 [PMID: 24330712]
  347. Yinghui L, Jingjuan Y, Qian Z, Dengyun Z, Guangming A (2005) Genetic transformation of millet (Tetaria italica) by Agrobacterium-mediated. Nong Ye Sheng Wu Ji Shu Xue Bao= J Agric Biotechnol 13(1):32���37
  348. Yoshitsu Y, Takakusagi M, Abe A, Takagi H, Uemura A, Yaegashi H, Terauchi R, Takahata Y, Hatakeyama K, Yokoi S (2017) QTL-seq analysis identifies two genomic regions determining the heading date of foxtail millet, Setaria italica (L.) P. Beauv. Breed Sci 67(5):518���527 [PMID: 29398946]
  349. You Q, Zhang L, Yi X, Zhang Z, Xu W, Su Z (2015) SIFGD: Setaria italica functional genomics database. Mol Plant 8(6):967���970 [PMID: 25676456]
  350. Yu H, Cong L, Zhu Z, Wang C, Zou J, Tao C, Shi Z, Lu X (2015) Identification of differentially expressed microRNA in the stems and leaves during sugar accumulation in sweet sorghum. Gene 571(2):221���230 [PMID: 26117170]
  351. Yu TF, Zhao WY, Fu JD, Liu YW, Chen M, Zhou YB, Ma YZ, Xu ZS, Xi YJ (2018) Genome-wide analysis of CDPK family in foxtail millet and determination of SiCDPK24 functions in drought stress. Front Plant Sci 26(9):651
  352. Yuan J, Wei H, Liu Y, Dong Z (2013) Agrobacterium-mediated transformation of millet [Setaria italica (L.)] using mature seeds. Res J Biotechnol 8:83���90
  353. Yue J, Li C, Liu Y, Yu J (2014) A remorin gene SiREM6, the target gene of SiARDP, from foxtail millet (Setaria italica) promotes high salt tolerance in transgenic Arabidopsis. PLoS ONE 9(6):e100772 [PMID: 24967625]
  354. Zeifman L, Hertog S, Kantorova V, Wilmoth J (2022) A world of 8 billion
  355. Zhang L, Zheng Y, Jagadeeswaran G, Li Y, Gowdu K, Sunkar R (2011) Identification and temporal expression analysis of conserved and novel microRNAs in Sorghum. Genomics 98(6):460���468 [PMID: 21907786]
  356. Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W, Tao Y (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30(6):549���554 [PMID: 22580950]
  357. Zhang K, Fan G, Zhang X, Zhao F, Wei W, Du G, Feng X, Wang X, Wang F, Song G, Zou H (2017a) Identification of QTLs for 14 agronomically important traits in Setaria italica based on SNPs generated from high-throughput sequencing. G3 7(5):1587���1594 [PMID: 28364039]
  358. Zhang Y, Linghu J, Wang D, Liu X, Yu A, Li F, Zhao J, Zhao T (2017b) Foxtail millet CBL4 (SiCBL4) interacts with SiCIPK24, modulates plant salt stress tolerance. Plant Mol Biol Report 35:634���646
  359. Zhang H, Xiao W, Yu W, Yao L, Li L, Wei J, Li R (2018) Foxtail millet SiHAK1 excites extreme high-affinity K uptake to maintain K homeostasis under low K or salt stress. Plant Cell Rep 37:1533���1546 [PMID: 30030611]
  360. Zhang W, Zhi H, Tang S, Zhang H, Sui Y, Jia G, Wu C, Diao X (2021) Identification of no pollen 1 provides a candidate gene for heterosis utilization in foxtail millet (Setaria italica L.). Crop J 9(6):1309���1319
  361. Zhang B, Guo Y, Wang H, Wang X, Lv M, Yang P, Zhang L (2022a) Identification and characterization of Shaker K channel gene family in foxtail millet (Setaria italica) and their role in stress response. Front Plant Sci 13:907635 [PMID: 35755660]
  362. Zhang D, Tang S, Xie P, Yang D, Wu Y, Cheng S, Du K, Xin P, Chu J, Yu F, Xie Q (2022b) Creation of fragrant sorghum by CRISPR/Cas9. J Integr Plant Biol 64(5):961���964 [PMID: 35142064]
  363. Zhang S, Wang J, He W, Kan S, Liao X, Jordan DR, Mace ES, Tao Y, Cruickshank AW, Klein R, Yuan D (2023a) Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution. BMC Plant Biol 23(1):91 [PMID: 36782130]
  364. Zhang Y, Zhang C, Man X, Men Y, Ren X, Li X, Han L, Sun Z, Yang Y, Hou S, Han Y (2023b) Functional characterization of the SiFPGS2 gene of foxtail millet in folate accumulation and root development. Plant Growth Regul 99(1):137���147
  365. Zhao ZY, Cai T, Tagliani L, Miller M, Wang N, Pang H, Rudert M, Schroeder S, Hondred D, Seltzer J, Pierce D (2000) Agrobacterium-mediated sorghum transformation. Plant Mol Biol 44:789���798 [PMID: 11202440]
  366. Zhao J, Wang G, Li Y, Zhao G, Wang Z, Cheng K, Wang Y, Yu A (2019) Identification NADP-ME gene of foxtail millet and its response to stress. Sci Agric Sin 52(22):3950���3963
  367. Zhao J, Mantilla Perez MB, Hu J, Salas Fernandez MG (2016a) Genome���wide association study for nine plant architecture traits in sorghum. Plant Genome 9(2):plantgenome2015-06
  368. Zhao W, Liu YW, Zhou JM, Zhao SP, Zhang XH, Min DH (2016b) Genome-wide analysis of the lectin receptor-like kinase family in foxtail millet (Setaria italica L.). Plant Cell Tissue Organ Cult 127:335���346
  369. Zhao J, Yu A, Du Y, Wang G, Li Y, Zhao G, Wang X, Zhang W, Cheng K, Liu X, Wang Z (2019) Foxtail millet (Setaria italica (L.) P. Beauv) CIPKs are responsive to ABA and abiotic stresses. PLoS ONE 14(11):e0225091 [PMID: 31714948]
  370. Zhao Z, Liu D, Cui Y, Li S, Liang D, Sun D, Wang J, Liu Z (2020) Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genomics 21:853 [PMID: 33261549]
  371. Zhao W, Zhang LL, Xu ZS, Fu L, Pang HX, Ma YZ, Min DH (2021a) Genome-wide analysis of MADS-Box genes in foxtail millet (Setaria italica L.) and functional assessment of the role of SiMADS51 in the drought stress response. Front Plant Sci 12:659474 [PMID: 34262576]
  372. Zhao Z, Tang S, Zhang Y, Yue J, Xu J, Tang W, Sun Y, Wang R, Diao X, Zhang B (2021b) Evolutionary analysis and functional characterization of SiBRI1 as a Brassinosteroid receptor gene in foxtail millet. BMC Plant Biol 21(1):291 [PMID: 34167462]
  373. Zhi H, He Q, Tang S, Yang J, Zhang W, Liu H, Jia Y, Jia G, Zhang A, Li Y, Guo E (2021) Genetic control and phenotypic characterization of panicle architecture and grain yield-related traits in foxtail millet (Setaria italica). Theor Appl Genet 134(9):3023���3036 [PMID: 34081150]
  374. Zhu C, Ming C, Zhao-Shi X, Lian-Cheng L, Xue-Ping C, You-Zhi M (2014) Characteristics and expression patterns of the aldehyde dehydrogenase (ALDH) gene superfamily of foxtail millet (Setaria italica L.). PLoS ONE 9(7):e101136 [>PMCID: ]
  375. Zou G, Zhai G, Feng Q, Yan S, Wang A, Zhao Q, Shao J, Zhang Z, Zou J, Han B, Tao Y (2012) Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods. J Exp Bot 63(15):5451���5462 [PMID: 22859680]
  376. Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R (2019) The genome of broomcorn millet. Nat Commun 10(1):436 [PMID: 30683860]

MeSH Term

Millets
Plant Breeding
Climate Change
Crops, Agricultural
Genomics
Biodiversity
Food Security
Agriculture
Multiomics

Word Cloud

Created with Highcharts 10.0.0resourcesbreedingIYoMmilletglobalproductionmulti-omics"resiliencefoodsecurityMilletsnutritionalagricultureYearinterventionsmolecularadvancedgoalsclimatechangesustainablecropbiodiversitychallengesclimate-resilientissuespotentialenhance2023genetictraitCRISPR/Cas9InternationalMilletMAINCONCLUSION:Leveragingvitalpositionessential"nutricerealresourcealigningalleviatingstraincerealboostingadvancingimprovementnutritionagrariansustainabilitydemandadoptionnutrient-richcropssupportgrowingpopulationamidstshiftingenvironmentalconditionsalsoreferred"ShreeAnnaemergepromisingsolutionaddressbolsteringimprovingnutrientfosteringconservationharshenvironmentsdensityculturalsignificancedietaryqualityindexmadevaluableassetsRecognizingpivotalroleUnitedNationsdesignated"InternationalemphasizingcontributionenhancementScientificprogressinvigoratedeffortsgenomicyieldingwealthtechnologiesadvancementsofferopportunitiestackleprevailinganti-nutritionalfactorssensoryacceptabilitytoxincontaminationancillaryimprovementsreviewprovidescomprehensiveoverviewninemajorspeciesfocusingimpactwithinframeworkincludewholepan-genomeelucidatingadaptiveresponsesabioticstressorsorganelle-basedstudiesrevealingevolutionarymarkerslinkeddesirabletraitsefficientQTLanalysisfacilitatingselectionfunctionalgenediscoverybiotechnologicalregulatoryncRNAsmodulationweb-basedplatformsstakeholdercommunicationtissueculturetechniquesmodificationintegratedomicsapproachesenabledpreciseapplicationtechnologyAligningseventhematicareasoutlinedcatalyzestransformativechangesutilizationtherebycontributingenhancedconsequencesRealizingvisionary:acceleratingadvancesmultiomicsMolecularMulti-omicsPan-genomeWeb

Similar Articles

Cited By