Genetic insights into cold tolerance in cotton: GWAS identified GhPRL1 gene responsible for cold tolerance in cotton at seedling stage

Cold stress during the seedling emergence stage severely affects the growth and development of cotton (Gossypium hirsutum), leading to reduced yield and plant health. Despite its importance, the molecular mechanisms underlying cold tolerance in cotton remain poorly understood. In this study, we analyzed 302 cotton accessions from the Cotton Research Institute in Anyang, China, to assess phenotypic and genetic responses to cold stress. Statistical analysis revealed significant reductions in primary root length (PRL) under cold stress, with a notable increase in genetic variation in root growth. Genome-wide association studies (GWAS) identified key genetic loci associated with cold tolerance, particularly on chromosome A11, where a cluster of SNPs exhibited strong associations with PRL. Fine mapping revealed high linkage disequilibrium in this region, indicating evolutionary selection for cold tolerance. Among the candidate genes, Gh_A11G315100 (GhPRL1) was identify as a major gene linked to cold tolerance. Virus-Induced Gene Silencing (VIGS) of GhPRL1 confirmed its essential role in maintaining plant health under cold stress, with GhPRL1-silenced plants showing greater phenotypic damage, increased ion leakage, and reduced antioxidant activity. This study provides valuable insights into the genetic basis of cold tolerance in cotton and identifies GhPRL1 as a critical target for future breeding efforts aimed at enhancing cold resilience.