PLoS ONE (Jan 2022)

Unraveling the genomic regions controlling the seed vigour index, root growth parameters and germination per cent in rice.

  • Saumya Ranjan Barik,
  • Elssa Pandit,
  • Priyadarshini Sanghamitra,
  • Shakti Prakash Mohanty,
  • Abhisarika Behera,
  • Jyotirmayee Mishra,
  • Deepak Kumar Nayak,
  • Ramakrushna Bastia,
  • Arpita Moharana,
  • Auromira Sahoo,
  • Sharat Kumar Pradhan

DOI
https://doi.org/10.1371/journal.pone.0267303
Journal volume & issue
Vol. 17, no. 7
p. e0267303

Abstract

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High seed vigour ensures good quality seed and higher productivity. Early seedling growth parameters indicate seed vigour in rice. Seed vigour via physiological growth parameters is a complex trait controlled by many quantitative trait loci. A panel was prepared representing a population of 274 rice landraces by including genotypes from all the phenotypic groups of sixseedling stage physiological parameters including germination % for association mapping. Wide variations for the six studiedtraits were observed in the population. The population was classified into 3 genetic groups. Fixation indices indicated the presence of linkage disequilibrium in the population. The population was classified into subpopulations and each subpopulation showed correspondence with the 6 physiological traits. A total of 5 reported QTLs viz., qGP8.1 for germination % (GP); qSVII2.1, qSVII6.1 and qSVII6.2 for seed vigour index II (SVII), and qRSR11.1 for root-shoot ratio (RSR) were validated in this mapping population. In addition, 13 QTLs regulating the physiological parameters such as qSVI 11.1 for seed vigour index I; qSVI11.1 and qSVI12.1 for seed vigour index II; qRRG10.1, qRRG8.1, qRRG8.2, qRRG6.1 and qRRG4.1 for rate of root growth (RRG); qRSR2.1, qRSR3.1 and qRSR5.1 for root-shoot ratio (RSR) while qGP6.2 and qGP6.3 for germination %were identified. Additionally, co-localization or co-inheritance of QTLs, qGP8.1 and qSVI8.1 for GP and SVI-1; qGP6.2 and qRRG6.1 for GP and RRG, and qSVI11.1 and qRSR11.1 for SVI and RSR were detected. The QTLs identified in this study will be useful for improvement of seed vigour trait in rice.