Multi-Omics Techniques for Soybean Molecular Breeding.

Pan Cao, Ying Zhao, Fengjiao Wu, Dawei Xin, Chunyan Liu, Xiaoxia Wu, Jian Lv, Qingshan Chen, Zhaoming Qi
Author Information
  1. Pan Cao: College of Agriculture, Northeast Agricultural University, Harbin 150030, China.
  2. Ying Zhao: College of Agriculture, Northeast Agricultural University, Harbin 150030, China.
  3. Fengjiao Wu: College of Agriculture, Northeast Agricultural University, Harbin 150030, China.
  4. Dawei Xin: College of Agriculture, Northeast Agricultural University, Harbin 150030, China. ORCID
  5. Chunyan Liu: College of Agriculture, Northeast Agricultural University, Harbin 150030, China.
  6. Xiaoxia Wu: College of Agriculture, Northeast Agricultural University, Harbin 150030, China.
  7. Jian Lv: Department of Innovation, Syngenta Biotechnology China, Beijing 102206, China.
  8. Qingshan Chen: College of Agriculture, Northeast Agricultural University, Harbin 150030, China.
  9. Zhaoming Qi: College of Agriculture, Northeast Agricultural University, Harbin 150030, China. ORCID

Abstract

Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, Soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of Soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite Soybean varieties with specific oil compositions to meet various end-use targets. The assembly of Soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in Soybean research. It facilitated advances in Soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in Soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate Soybean breeding in the future. This review will be of interest not only to Soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.

Keywords

References

  1. Proteomics. 2011 May;11(9):1619-29 [PMID: 21413150]
  2. Nature. 1953 Apr 25;171(4356):737-8 [PMID: 13054692]
  3. Annu Rev Plant Biol. 2022 May 20;73:67-92 [PMID: 35138880]
  4. Theor Appl Genet. 2012 Aug;125(3):503-15 [PMID: 22476873]
  5. PeerJ. 2021 Mar 1;9:e10772 [PMID: 33717671]
  6. PLoS One. 2013;8(3):e59270 [PMID: 23555009]
  7. Mol Genet Genomics. 2004 Jul;271(6):651-7 [PMID: 15221456]
  8. Trends Plant Sci. 2022 Jun;27(6):549-563 [PMID: 35248492]
  9. Plant Cell Physiol. 2008 Aug;49(8):1135-49 [PMID: 18625610]
  10. Bioinformatics. 2002;18 Suppl 2:S241-8 [PMID: 12386008]
  11. BMC Plant Biol. 2020 Mar 26;20(1):127 [PMID: 32216758]
  12. BMC Plant Biol. 2010 Sep 09;10:195 [PMID: 20828382]
  13. Nat Biotechnol. 2000 Nov;18(11):1157-61 [PMID: 11062433]
  14. Protein Pept Lett. 2010 Mar;17(3):319-31 [PMID: 19508212]
  15. Curr Opin Plant Biol. 2022 Apr;66:102167 [PMID: 35016139]
  16. Sci China Life Sci. 2020 Dec;63(12):1938-1941 [PMID: 32902773]
  17. Plant Signal Behav. 2016 Aug 2;11(8):e1215792 [PMID: 27471796]
  18. BMC Genomics. 2010 Feb 24;11:136 [PMID: 20181280]
  19. J Proteomics. 2021 Jan 6;230:103999 [PMID: 33017647]
  20. BMC Plant Biol. 2010 Aug 05;10:160 [PMID: 20687943]
  21. Food Chem. 2015 Apr 1;172:105-16 [PMID: 25442530]
  22. Plant J. 2016 Jun;86(6):530-44 [PMID: 27062090]
  23. Emerg Top Life Sci. 2022 Apr 15;6(2):163-173 [PMID: 35293572]
  24. Nature. 2008 Oct 23;455(7216):1054-6 [PMID: 18948945]
  25. Nat Methods. 2022 May;19(5):534-546 [PMID: 35273392]
  26. Plant Physiol. 2013 Mar;161(3):1251-64 [PMID: 23314941]
  27. Nature. 2010 Jan 14;463(7278):178-83 [PMID: 20075913]
  28. Front Plant Sci. 2016 Jul 19;7:1044 [PMID: 27486466]
  29. J Proteomics. 2018 Feb 10;172:201-215 [PMID: 29133124]
  30. Plant Methods. 2022 Mar 27;18(1):38 [PMID: 35346267]
  31. Food Chem. 2013 Dec 1;141(3):2052-9 [PMID: 23870927]
  32. BMC Plant Biol. 2016 Jan 19;16:20 [PMID: 26786479]
  33. Annu Rev Plant Biol. 2003;54:669-89 [PMID: 14503007]
  34. J Integr Plant Biol. 2014 Sep;56(9):826-36 [PMID: 24942044]
  35. Curr Biol. 2022 Apr 25;32(8):1728-1742.e6 [PMID: 35263616]
  36. Curr Opin Biotechnol. 2022 Jun;75:102693 [PMID: 35151979]
  37. Nucleic Acids Res. 2014 Aug;42(14):8845-60 [PMID: 25053837]
  38. J Proteomics. 2019 Apr 30;198:1-10 [PMID: 30170112]
  39. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4759-64 [PMID: 17360597]
  40. Plant Physiol. 2005 Apr;137(4):1397-419 [PMID: 15824287]
  41. Plant Genome. 2021 Nov;14(3):e20157 [PMID: 34595846]
  42. PLoS One. 2014 Jan 27;9(1):e86153 [PMID: 24475082]
  43. Methods Mol Biol. 2007;358:273-86 [PMID: 17035691]
  44. Plant J. 2014 Jun;78(5):742-52 [PMID: 24330272]
  45. Sensors (Basel). 2020 Jan 01;20(1): [PMID: 31906262]
  46. Front Plant Sci. 2016 Feb 23;7:180 [PMID: 26941754]
  47. Plant Methods. 2013 Jun 13;9(1):17 [PMID: 23758798]
  48. Mol Aspects Med. 2018 Feb;59:36-46 [PMID: 28754496]
  49. Plant Physiol. 2008 Sep;148(1):504-18 [PMID: 18599654]
  50. Nat Biotechnol. 2014 Oct;32(10):1045-52 [PMID: 25218520]
  51. Natl Sci Rev. 2020 May 27;7(11):1776-1786 [PMID: 34691511]
  52. Plant Methods. 2019 Aug 20;15:97 [PMID: 31452673]
  53. Plant Cell Physiol. 2012 Jun;53(6):1154-70 [PMID: 22470059]
  54. Plant Physiol. 2022 Feb 4;188(2):726-737 [PMID: 35235661]
  55. Sci Rep. 2017 Feb 13;7:42478 [PMID: 28211897]
  56. Annu Rev Plant Biol. 2013;64:267-91 [PMID: 23451789]
  57. Front Plant Sci. 2019 Jun 03;10:714 [PMID: 31214228]
  58. Sci Rep. 2019 Oct 1;9(1):14089 [PMID: 31575995]
  59. Plant Methods. 2021 May 5;17(1):50 [PMID: 33952294]
  60. Plant Methods. 2022 Feb 2;18(1):13 [PMID: 35109882]
  61. Food Chem. 2014 Jun 15;153:258-64 [PMID: 24491728]
  62. Food Chem. 2020 Apr 25;310:125914 [PMID: 31835223]
  63. Nat Genet. 2010 Dec;42(12):1053-9 [PMID: 21076406]
  64. Proteome Sci. 2013 Mar 26;11(1):12 [PMID: 23531047]
  65. Chin Med. 2022 Apr 8;17(1):45 [PMID: 35395803]
  66. Funct Plant Biol. 2013 Feb;41(1):68-79 [PMID: 32480967]
  67. J Proteomics. 2017 Jun 6;162:62-72 [PMID: 28435105]
  68. Plant Mol Biol. 2006 Feb;60(3):377-87 [PMID: 16514561]
  69. J Agric Food Chem. 2022 Mar 23;70(11):3375-3390 [PMID: 35275483]
  70. Plant Cell Environ. 2018 Sep;41(9):2109-2127 [PMID: 29486529]
  71. Science. 2009 Jul 24;325(5939):380-1 [PMID: 19628831]
  72. Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22032-7 [PMID: 21131573]
  73. Plant Phenomics. 2021 Jun 23;2021:9846470 [PMID: 34250507]
  74. Nat Rev Genet. 2011 Feb;12(2):87-98 [PMID: 21191423]
  75. Plant Methods. 2017 Apr 8;13:23 [PMID: 28405214]
  76. Plant Cell Rep. 2021 Dec;40(12):2303-2323 [PMID: 34427748]
  77. Plant Physiol. 2010 Apr;152(4):2078-87 [PMID: 20118269]
  78. Trends Biotechnol. 2011 Jun;29(6):267-75 [PMID: 21435731]
  79. J Exp Bot. 2015 Jan;66(1):391-402 [PMID: 25336687]
  80. BMC Genomics. 2022 Mar 31;23(1):250 [PMID: 35361112]
  81. Crit Rev Biotechnol. 2013 Mar;33(1):23-39 [PMID: 22364373]
  82. Plant Mol Biol. 2002 Jan;48(1-2):155-71 [PMID: 11860207]
  83. Plant Phenomics. 2021 Jul 28;2021:9834746 [PMID: 34396150]
  84. Planta. 1981 Oct;153(1):64-74 [PMID: 24276708]
  85. Nat Commun. 2019 Mar 14;10(1):1216 [PMID: 30872580]
  86. Mol Plant. 2020 Sep 7;13(9):1247-1249 [PMID: 32745560]
  87. Mol Cell Proteomics. 2012 Nov;11(11):1140-55 [PMID: 22843990]
  88. BMC Plant Biol. 2010 Jul 26;10:153 [PMID: 20653984]
  89. BMC Genomics. 2016 Feb 09;17:102 [PMID: 26861168]
  90. Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):E6710-E6719 [PMID: 28739919]
  91. Plant Phenomics. 2021 Jun 28;2021:9892570 [PMID: 34286285]
  92. Front Plant Sci. 2016 Dec 09;7:1842 [PMID: 28018382]
  93. Sci China Life Sci. 2018 Aug;61(8):871-884 [PMID: 30062469]
  94. Ann Bot. 2014 Jun;113(7):1107-20 [PMID: 24769535]
  95. Artif Intell Life Sci. 2022 Dec;2: [PMID: 36211981]
  96. Cell. 2020 Jul 9;182(1):162-176.e13 [PMID: 32553274]
  97. New Phytol. 2014 Mar;201(4):1192-1204 [PMID: 24261563]
  98. Plant J. 2019 Dec;100(5):1066-1082 [PMID: 31433882]
  99. Mol Plant Pathol. 2018 Sep;19(9):2177-2186 [PMID: 29665235]
  100. Plant Methods. 2020 Jun 01;16:78 [PMID: 32514286]
  101. Plant Cell Physiol. 2008 Sep;49(9):1263-71 [PMID: 18701524]
  102. Phytochem Anal. 2010 Jan-Feb;21(1):33-47 [PMID: 19927296]
  103. J Genet Eng Biotechnol. 2021 Aug 27;19(1):128 [PMID: 34448979]
  104. Nat Genet. 2017 May;49(5):773-779 [PMID: 28319089]
  105. Proteomics. 2019 Apr;19(7):e1800379 [PMID: 30784187]
  106. Mol Breed. 2021 Jan 7;41(1):3 [PMID: 37309527]
  107. Genome Biol. 2022 Mar 25;23(1):83 [PMID: 35337374]
  108. Plant Mol Biol. 2008 Aug;67(6):567-80 [PMID: 18528765]
  109. Front Plant Sci. 2021 Jul 28;12:691838 [PMID: 34394145]
  110. Front Neurol. 2022 Jan 31;12:792227 [PMID: 35173667]
  111. Theor Appl Genet. 2020 Apr;133(4):1189-1200 [PMID: 31960089]
  112. Sci Rep. 2020 Apr 27;10(1):7055 [PMID: 32341432]

Grants

  1. YQ2021C011/Natural Science Foundation of Heilongjiang-Outstanding Youth Foundation

MeSH Term

DNA Shuffling
Genomics
Plant Breeding
Proteomics
Glycine max

Word Cloud

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