Genome-wide association study reveals candidate genes controlling root system architecture in pepper (Capsicum annuum L.)

Although plant growth habits play a pivotal role in horticultural productivity, research has predominantly concentrated on aboveground organs, with root system architecture (RSA) frequently overlooked due to the inherent difficulty of accessing subterranean structures in situ. In this study, we quantified RSA in 137 pepper (Capsicum annuum L.) accessions by analyzing images of four-week-old seedlings grown in a paper-based medium, measuring primary root length (PRL), sum of lateral roots (SLR), number of lateral roots (NLR), and total root length (TRL) in 137 accessions. A genome-wide association study (GWAS) identified three significant SNPs for RSA on chromosomes 4, 6, and 9. Linkage disequilibrium and epistasis analyses identified candidate genes associated with RSA, including Root System-Inducible 1 (RSI-1), Small-Intrinsic Protein 1-2 (SIP1-2), and G-type lectin S-receptor-like serine/threonine protein kinase (SRK). We further evaluated associations between RSA and aboveground traits by analyzing growth-related traits at 2 and 6 months, as well as RGB image–based drought tolerance indices. Correlation analyses revealed positive associations between RSA and the 2-month traits, first internode length, whereas associations with 6-month traits and drought indices were weak or non-significant. To utilize GWAS data, we performed genomic prediction (GP) using GWAS-derived SNPs and achieved a prediction accuracy of 0.63, indicating moderate predictive power for TRL. Taken together, these findings provide genetic insights into root development in pepper and establish a genetic framework for future efforts to incorporate RSA traits into breeding programs.