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

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 qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, 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.

Automated summary

Seed vigor, an important performance parameter of seed quality, was studied in this research. A panel of genotypes representing different seedling growth parameters was created from 278 germplasm lines and showed a wide variation in traits. The panel was categorized into four genetic structure groups, showing the presence of linkage disequilibrium in the population. Using 143 SSR markers, a moderate to high level of diversity parameters was observed. Analysis methods such as principal component analysis, coordinate analysis, neighbor-joining tree, and cluster analysis showed correspondences between subpopulations and growth parameters. Marker-trait association analysis identified eight novel QTLs that can improve seed vigor in rice.