Identification of molecular markers and putative candidate genes associated with early seedling vigour traits in rice (Oryza sativa L.)

The early seedling vigour (ESV) is a complex and imperative trait for the development of varieties suitable to direct-seeded rice (DSR) conditions. Identification of molecular markers and candidate genes associated with ESV traits facilitates the effective improvement of DSR varieties using marker-assisted breeding. In the present study, we demonstrated that the molecular markers RM9, and RM246 flanking quantitative trait locus (QTL) germination rate, qGR-1 while RM3 and RM20429 of QTL for seedling vigour index, qVI were found to be associated with the targeted ESV traits through the bulked segregant analysis (BSA) in the F-4 population derived from a cross of BPT5204, a high yielding low ESV variety and MTU3626, a high yielding high ESV variety. In addition, we also attempted to uncover the candidate genes underlying qGR-1 and qVI QTLs for germination rate and seedling vigour index traits employing publicly available databases, respectively. We prioritized peptide deformylase (LOC_Os01g45070), CTP synthase (LOC_Os01g46570) as the putative candidate genes for qGR-1 whereas inorganic H+pyrophosphatase (LOC_Os06g43660) as the candidate gene for qVI QTL based on QTG finder, literature mining, co-expression, gene ontology and homology analysis. In conclusion, the molecular markers and candidate genes identified in the study have immense value for improving ESV traits through MAS and also offer insights into understanding ESV traits.