Efficient QTL mapping strategy for agronomical traits in pepper (Capsicum annuum)

Abstract

Majority of agronomical traits including plant height, fruit weight, and contents of secondary metabolites are quantitative traits. Identification of quantitative trait locus (QTL) controlling agronomical traits is important for marker-assisted breeding and understanding the mechanism for the traits. To detect the QTLs controlling agronomical traits in pepper (Capsicum annuum), we constructed an ultra-high-density bin map using 120 recombinant inbred lines (RILs) from intraspecific cross (C. annuum Perennial × C. annuum Dempsey). Reads from resequencing of RILs were aligned to the C. annuum CM334 reference genome, and single nucleotide polymorphisms (SNPs) were called. Due to the low coverage (1×) of the reads, there were large number of missing data. Therefore, linked SNPs in one window were combined as bin by sliding window approach and this method could improve the genetic map. The total map length of the bin map was 1,372 cM, and the average interval between 2,578 bins was 0.53 cM. Also for accurate QTL mapping, we evaluated the phenotype repetitively in three different environments. Using the ultra-high-density bin map and the phenotypic data from three different environments, 32 major QTLs were mapped and they controlled plant architecture, leaf, and fruit related traits. Rapid genotyping by resequencing, improvement of genetic map by sliding window approach, and repetitive phenotyping can facilitate efficient QTL mapping for agronomical traits.