Construction of high-density bin map and QTL mapping of horticultural traits from an interspecific cross between Capsicum annuum and Chinese wild Capsicum frutescens

Abstract

Chinese wild pepper (Capsicum frutescens L.) acts as a source of genetic variability for cultivated pepper breeding. High-resolution quantitative train locus (QTL) mapping is essential for identifying genetic regions related to important phenotype variation. In this study, a set of 120 F2 populations derived from a cross between cultivar Capsicum annuum ‘007EA’ and the wild relative Capsicum frutescens ‘P1512’ (Chinese wild pepper) were generated, and genotyping was performed with genotyping-by-sequencing. Next, an interspecific high-density genetic map containing 3708 bins was constructed using a sliding window approach. The genetic distance of the total map was 5601.79 cM, and the average interval between bins was 1.51 cM. Based on the genetic map, a QTL analysis of the pepper horticultural traits was performed. A total of 25 significant QTLs controlling nine horticultural traits were detected on 12 linkage groups (LGs), and contributed values of phenotypic variance explained (PVE) ranging from 1.90% to 59.03%, with LOD scores ranging from 4.2 to 24.6. In addition, the QTLs for the main stem length, flowering date and numbers of leaves were observed at the same position. Next, we mapped a set of significant QTLs for yield-related traits and other horticultural traits in pepper, based on a high-density genetic linkage map, using GBS. These genetic map and markers are valuable genomic resources for marker-assisted selection (MAS) of excellent agronomic traits and will provide a basis for further fine mapping and comparative genomics research involving pepper.

Keywords

• chinese wild pepper
• capsicum frutescens
• interspecific genetic map
• qtl mapping
• genotyping-by-sequencing