# Mapping of quantitative trait loci for early seed germination using whole-genome resequencing chromosome segment substitution lines of aus Kasalath in the background of japonica Nipponbare

## TL;DR

This study identifies genetic regions linked to early seed germination in rice using advanced genomic techniques.

## Contribution

The study identifies six stable QTLs for seed germination and highlights two candidate genes using CSSLs and whole-genome resequencing.

## Key findings

- Six stable QTLs for early seed germination were identified across two years of evaluation.
- The qSV-1 locus on chromosome 1 was found to be the most consistent for germination traits.
- C3H10 and OsOFP3 were identified as primary candidate genes within the qSV-1 interval.

## Abstract

Direct-seeding systems in rice require cultivars with enhanced seed vigor to ensure rapid and uniform germination. In this study, a population of 42 chromosome segment substitution lines (CSSLs) derived from aus Kasalath in the japonica Nipponbare background, coupled with whole-genome resequencing data, was analyzed to identify quantitative trait loci (QTLs) associated with early seed germination. Phenotypic traits, including germination percentage (GP), germination rate (GR), and germination index (GI), were measured over two consecutive years to ensure robustness. Six stable QTLs were identified, with qSV-1 on chromosome 1 (30.10–30.94 Mb) emerging as the most consistent across evaluations for GP and GI. Functional annotation and gene expression analyses of the 840-kb qSV-1 interval pinpointed C3H10 and OsOFP3 as the primary candidate genes for further investigation. This study underscores the effectiveness of whole-genome resequencing paired with the CSSL platform for precise QTL identification, thereby providing critical genetic resources for improving seed vigor through marker-assisted breeding and functional genomics.