Quantitative trait loci and genome-wide association study identifies novel loci for plant height in pepper (Capsicum spp.)

Abstract

Plant height (PH) is a key trait that influences photosynthetic efficiency, early maturity, lodging resistance, and crop yield. The development of plant factories and mechanical harvesting has increased the demand for peppers ( Capsicum spp.) with suitable plant architecture. In this study, we performed quantitative trait locus (QTL) analysis and genome-wide association studies (GWAS) to determine the genetic basis of PH in pepper. For QTL analyses, 117 F 2 individuals derived by crossing C. annuum ‘Jeju’ and ‘Micropep’ were used for PH analysis. Another population of 154 F 2 plants derived from crossing C. annuum ‘Takanotsume’ and ‘Micropep’ was used to analyze main stem length (MSL), number of main stem nodes (NMSN), and average node length of the main stem (ANLMS). Of these, 153 individuals were used for genetic map construction and QTL mapping. After genotyping-by-sequencing and filtering, 1,066 SNPs from the JM population and 1,446 from the TM population were retained for bin-map construction. QTL mapping was conducted with 451 bin markers for JM and 518 for TM. The GWAS used 25,126 SNPs on chromosomes 1–12 in the core collection. Composite interval mapping revealed QTLs for PH on chromosomes 1 and 11 in the JM population. QTL analysis in the TM population identified a significant NMSN QTL on chromosome 3 and a significant MSL QTL on chromosome 1. GWAS additionally identified significant SNPs for PH, NMSN, ANLMS, and MSL in the core collection. Genes near these SNPs were predicted, based on sequence similarity to characterized genes in other species, to include transcription factors, cell-wall-remodeling proteins, metabolic enzymes, and developmental regulators. Neither of the significant TM QTLs overlapped an LD block containing significant GWAS SNPs for the corresponding trait. These findings provide linkage regions, association signals, and predicted candidate genes for plant height and main stem traits in pepper, which will require validation in independent populations before they can be used in breeding.