Genetic architecture of seedling stage chilling tolerance in United States rice germplasm

Chilling stress during the seedling stage severely limits rice growth and development, highlighting the need for a deeper understanding of the genetic architecture underlying chilling stress tolerance. In this study, a rice association panel was evaluated for seedling vigor traits under growth-chamber conditions (Experiment 1) and under natural chilling conditions (Experiment 2). Nine stress tolerance indices (STIs) were calculated from Experiment 1 for the seedling traits. Genome-wide association studies (GWAS) were conducted using 872,995 high-density single-nucleotide polymorphisms (SNPs) and four models, including two single-locus (GLM and MLM) and two multi-locus (FarmCPU and BLINK) models. A total of 54 quantitative trait loci (QTLs) associated with seedling morphological traits were identified, with phenotypic variance explained (PVE) ranging from 5.3 to 82.2%. Twenty-eight QTLs were co-localized with previously reported loci, confirming the reliability of the associations, while one novel QTL, qNL2-1, was consistently detected in both Experiment 1 and STI-based analyses. Candidate gene mining within the identified QTL regions revealed several putative genes involved in calcium signaling, transcriptional regulation, and stress response pathways, including calmodulin (CaM)/CaM-like (CML) proteins, calcium-dependent protein kinases (CDPKs), calcineurin B-like (CBL) proteins, CBL-interacting protein kinases (CIPK), and brassinosteroid (BR) signaling proteins. The candidate genes identified in this study could serve as potential targets for enhancing rice chilling tolerance through genomics-assisted breeding strategies.