Identification and Candidate Gene Analysis of qCTS11-TK9, a Novel Major Quantitative Trait Locus Associated with Chilling Tolerance in Rice Seedlings.

Chilling stress can severely damage rice and lead to yield losses. The genetic mechanisms underlying responses of rice to chilling stress are complex and can vary depending on the genetic background, developmental stage, and experimental conditions. In this study, we used the chilling stress-tolerant japonica variety Taiken 9 (TK9) and the chilling stress-sensitive indica variety Taichung Sen 17 (TCS17) to investigate the genetic basis of chilling tolerance in rice seedlings. A BC₃-derived backcross inbred line, NSY1051070, which inherited high chilling tolerance from TK9 within the genetic background of TCS17, was developed through recurrent backcross breeding. A major quantitative trait locus (QTL), qCTS11-TK9, was identified in the distal region of the long arm of chromosome 11 by using F₂ and F₃ populations derived from the cross between TCS17 and NSY1051070. High-resolution linkage analysis delimited qCTS11-TK9 to a 191-kb genomic region containing 16 annotated putative genes in the rice reference genome. Expression and sequence analyses revealed three candidate genes responsible for chilling tolerance in NSY1051070: LOC_Os11g42790, LOC_Os11g42800, and LOC_Os11g42850. Our findings unveiled a novel major QTL associated with chilling tolerance in rice seedlings. The discovery of qCTS11-TK9 highlights a new source of seedling-stage chilling tolerance, and the markers developed in this study may aid future breeding programs.