Identification of qCTB2 for Booting‐Stage Cold Tolerance From the Highly Tolerant Rice Landrace “Lijiangxintuanheigu” ( Oryza sativa L.)

Under increasing climate variability and the expansion of rice cultivation into marginal cold‐prone environments, low temperature has become a major constraint on yield stability and sustainable rice production. Rice is particularly vulnerable to transient cold stress during reproductive development, and cold injury at the booting stage often causes severe and irreversible yield losses. Improving booting‐stage cold tolerance through genetic approaches is therefore essential for safeguarding food security in high‐latitude rice‐growing regions. In this study, we developed a recombinant inbred line (RIL) population of 144 lines derived from a cross between the highly cold‐tolerant landrace Lijiangxintuanheigu (LTH) and the northern elite japonica cultivar Shennong 265 (SN265) to dissect the genetic basis of booting‐stage cold tolerance. Using spikelet sterility as the primary indicator, we conducted quantitative trait locus (QTL) mapping under controlled cold‐stress conditions across two consecutive years. In total, nine QTLs associated with spikelet sterility were identified on chromosomes 2, 3, 4, 6, 7, and 11, each explaining 10.56%–32.49% of the phenotypic variance. Among these loci, a major‐effect QTL on chromosome 2, designated qCTB2 , was consistently detected across years and mapping methods and was subsequently validated using near‐isogenic lines derived from a residual heterozygous line. Interaction‐effect analysis revealed strong additive and complementary effects between qCTB2 and other favorable loci, highlighting its central role in pyramiding‐based breeding strategies. Comparative mapping and sequence comparison indicated that qCTB2 is unlikely to be allelic to the known cold‐tolerance‐related gene LGS1 , suggesting that qCTB2 likely represents an independent locus contributing to booting‐stage cold tolerance. Overall, this study identifies a robust major‐effect locus, qCTB2 , and demonstrates its additive and complementary interactions with other loci, providing a practical genetic framework for pyramiding‐based improvement of booting‐stage cold tolerance and yield stability in high‐latitude rice production systems under increasing climate variability.