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04 12, 2023;14 (4):

Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice.

Shakti Prakash Mohanty, Deepak Kumar Nayak, Priyadarsini Sanghamitra, Saumya Ranjan Barik, Elssa Pandit, Abhisarika Behera, Dipti Ranjan Pani, Shibani Mohapatra, Reshmi Raj K R, Kartik Chandra Pradhan, Chita Ranjan Sahoo, Mihir Ranjan Mohanty, Chinmayee Behera, Alok Kumar Panda, Binod Kumar Jena, Lambodar Behera, Prasanta K Dash, Sharat Kumar Pradhan
Author Information
  1. Shakti Prakash Mohanty: ICAR-National Rice Research Institute, Cuttack 753006, India.
  2. Deepak Kumar Nayak: ICAR-National Rice Research Institute, Cuttack 753006, India.
  3. Priyadarsini Sanghamitra: ICAR-National Rice Research Institute, Cuttack 753006, India.
  4. Saumya Ranjan Barik: ICAR-National Rice Research Institute, Cuttack 753006, India. ORCID
  5. Elssa Pandit: Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756020, India. ORCID
  6. Abhisarika Behera: ICAR-National Rice Research Institute, Cuttack 753006, India.
  7. Dipti Ranjan Pani: ICAR-National Bureau of Plant Genetic Resources, Base Center, Cuttack 753006, India.
  8. Shibani Mohapatra: ICAR-National Rice Research Institute, Cuttack 753006, India. ORCID
  9. Reshmi Raj K R: ICAR-National Rice Research Institute, Cuttack 753006, India.
  10. Kartik Chandra Pradhan: College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India.
  11. Chita Ranjan Sahoo: Directorate of Research, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India. ORCID
  12. Mihir Ranjan Mohanty: Regional Research and Technology Transfer Station (RRTTS), Odisha University of Agriculture & Technology, Jeypore 764001, India.
  13. Chinmayee Behera: Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, SOA University, Bhubaneswar 753001, India.
  14. Alok Kumar Panda: Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India. ORCID
  15. Binod Kumar Jena: Krishi Vigyan Kendra, Odisha University of Agriculture & Technology, Rayagada 765022, India.
  16. Lambodar Behera: ICAR-National Rice Research Institute, Cuttack 753006, India.
  17. Prasanta K Dash: ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110012, India.
  18. Sharat Kumar Pradhan: ICAR-National Rice Research Institute, Cuttack 753006, India. ORCID
PMID: 37107660 DOI: 10.3390/genes14040902

Abstract

Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker-trait association analysis detected eight novel QTLs, namely , , and for absolute growth rate (AGR); , and for relative shoot growth (RSG); and for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), , was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice.

Keywords

absolute growth rate association mapping germination rate indica rice relative growth rate relative shoot growth

References

  1. BMC Genet. 2020 Jul 14;21(1):76 [PMID: 32664865]
  2. Nat Biotechnol. 2012 Jan 22;30(2):174-8 [PMID: 22267009]
  3. Bioinformatics. 2007 Oct 1;23(19):2633-5 [PMID: 17586829]
  4. Mol Genet Genomics. 2019 Aug;294(4):963-983 [PMID: 30963249]
  5. PLoS One. 2016 Aug 05;11(8):e0160027 [PMID: 27494320]
  6. J Zhejiang Univ Sci B. 2010 Dec;11(12):958-64 [PMID: 21121075]
  7. J Exp Bot. 2016 Feb;67(3):567-91 [PMID: 26585226]
  8. Planta. 2014 Jun;239(6):1309-19 [PMID: 24668487]
  9. Bioinformatics. 2012 Oct 1;28(19):2537-9 [PMID: 22820204]
  10. Bioinformatics. 2005 May 1;21(9):2128-9 [PMID: 15705655]
  11. PLoS One. 2016 Mar 31;11(3):e0152406 [PMID: 27031620]
  12. Genes Genomics. 2019 Jan;41(1):95-105 [PMID: 30242741]
  13. C R Biol. 2015 Oct;338(10):650-9 [PMID: 26321658]
  14. Annu Rev Plant Biol. 2012;63:507-33 [PMID: 22136565]
  15. Mol Ecol. 2005 Jul;14(8):2611-20 [PMID: 15969739]
  16. BMC Plant Biol. 2020 Feb 4;20(1):57 [PMID: 32019504]
  17. PLoS One. 2022 Jul 26;17(7):e0267303 [PMID: 35881571]
  18. PLoS One. 2014 Dec 23;9(12):e115732 [PMID: 25536503]
  19. Rice (N Y). 2015 Dec;8(1):51 [PMID: 26054243]
  20. Rice (N Y). 2019 Sep 4;12(1):69 [PMID: 31485824]
  21. Sci Rep. 2019 Sep 5;9(1):12810 [PMID: 31488854]
  22. Theor Appl Genet. 2011 Oct;123(6):869-79 [PMID: 21681488]
  23. BMC Plant Biol. 2022 Dec 29;22(1):620 [PMID: 36581797]
  24. PLoS One. 2019 Dec 17;14(12):e0214979 [PMID: 31846460]
  25. Molecules. 2019 Jun 14;24(12): [PMID: 31207950]
  26. Front Plant Sci. 2019 Dec 13;10:1582 [PMID: 31921238]
  27. Front Plant Sci. 2021 Jul 27;12:672618 [PMID: 34386025]
  28. Physiol Mol Biol Plants. 2020 Oct;26(10):1989-2003 [PMID: 33088044]
  29. Front Plant Sci. 2018 Dec 21;9:1909 [PMID: 30622552]
  30. Planta. 2015 May;241(5):1027-50 [PMID: 25805338]
  31. Front Plant Sci. 2017 Apr 25;8:552 [PMID: 28487705]
  32. Theor Appl Genet. 2002 Oct;105(5):745-753 [PMID: 12582488]
  33. J Integr Plant Biol. 2014 Aug;56(8):749-59 [PMID: 24571491]
  34. PLoS One. 2021 Mar 1;16(3):e0246232 [PMID: 33647046]
  35. Phytopathology. 2016 Jul;106(7):710-8 [PMID: 26976728]
  36. Theor Appl Genet. 2015 Jun;128(6):1103-15 [PMID: 25805315]
  37. Sci Rep. 2020 Dec 16;10(1):22103 [PMID: 33328509]
  38. Genetics. 2000 Jun;155(2):945-59 [PMID: 10835412]
  39. New Phytol. 2020 Jul;227(1):65-83 [PMID: 32129897]
  40. Nucleic Acids Res. 1980 Oct 10;8(19):4321-5 [PMID: 7433111]
  41. Nat Genet. 2006 Feb;38(2):203-8 [PMID: 16380716]
  42. Philos Trans R Soc Lond B Biol Sci. 2007 Jun 29;362(1482):1009-21 [PMID: 17347106]

MeSH Term

Seedlings
Germination
Oryza
Quantitative Trait Loci
Genomics
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 2

Word Cloud

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