Integrating Meta-QTL mapping and RNA-seq analysis identifies candidate genes for cold tolerance at rice seedling stage

Cold stress severely limits rice growth and yield. To overcome the limitations of traditional QTL mapping, this study employed an integrated Meta-QTL and RNA-seq approach to systematically identify cold tolerance genes in rice seedlings. We meta-analyzed 553 QTLs from 28 published studies (2005-2023), yielding 41 robust meta-QTLs with an average confidence interval of 2.08 Mb across all 12 chromosomes. Parallel transcriptome analysis of seedlings under cold stress identified 14,692 differentially expressed genes (DEGs). Integrative analysis pinpointed 34 high-confidence candidate genes within the meta-QTL intervals, including known 13 stress-responsive genes and 21 previously uncharacterized loci. qRT-PCR validated their dynamic expression under cold stress. This work provides precise genetic targets and a validated framework for breeding cold-tolerant rice, enhancing our understanding of the genetic architecture underlying cold adaptation.