GWAS-informed genomic selection for cold tolerance in pepper (Capsicum annuum L.).

backgroundBreeding for cold tolerance in pepper (Capsicum annuum L.) is critical to mitigate yield losses caused by unpredictable temperature fluctuations associated with climate change. However, genetic improvement of this trait is hindered by challenges in accurate phenotyping, particularly at the adult stage, and by its complex genetic architecture involving numerous minor-effect loci. While genomic selection (GS) offers a promising solution to accelerate genetic gain, its predictive ability is often limited by statistical noise from uninformative markers within whole-genome marker sets. This study aimed to overcome this limitation by developing a robust phenotypic index and implementing a genome-wide association study (GWAS)-informed GS strategy.

resultsWe phenotyped 192 pepper accessions from a core collection for cold tolerance using a visual survival score (Surv) and a newly developed composite cold-tolerance index (CTI). Both CTI (h

conclusionsOur study demonstrates that assessing cold tolerance via the CTI helps overcome the limitations of discrete survival scoring. By turning ordinal data into a continuous spectrum, the CTI can unmask hidden genetic variation. In addition, GWAS identified candidate genomic regions and genes associated with cold response, and nested CV and LOOCV showed that GWAS-selected marker sets could achieve higher prediction accuracy than the full marker set and random marker sets of the same marker number. This integrated framework offers a practical approach for interpreting the genetic basis of adult-stage cold tolerance in pepper and improving the efficiency of genomic prediction models for complex abiotic stress traits.