Abstract
SummaryCapsaicinoids are unique compounds produced only in peppers (Capsicum spp.). Several studies using classical quantitative trait loci (QTLs) mapping and genomewide association studies (GWAS) have identified QTLs controlling capsaicinoid content in peppers; however, neither the QTLs common to each population nor the candidate genes underlying them have been identified due to the limitations of each approach used. Here, we performed QTL mapping and GWAS for capsaicinoid content in peppers using two recombinant inbred line (RIL) populations and one GWAS population. Whole‐genome resequencing and genotyping by sequencing (GBS) were used to construct high‐density single nucleotide polymorphism (SNP) maps. Five QTL regions on chromosomes 1, 2, 3, 4 and 10 were commonly identified in both RIL populations over multiple locations and years. Furthermore, a total of 109 610 SNPs derived from two GBS libraries were used to analyse the GWAS population consisting of 208 C. annuum‐clade accessions. A total of 69 QTL regions were identified from the GWAS, 10 of which were co‐located with the QTLs identified from the two biparental populations. Within these regions, we were able to identify five candidate genes known to be involved in capsaicinoid biosynthesis. Our results demonstrate that QTL mapping and GBS‐GWAS represent a powerful combined approach for the identification of loci controlling complex traits.
Highlights
Hot peppers (Capsicum spp.) contain capsaicinoids, unique compounds that produce a burning sensation called pungency
Due to the nonfunctional pun1 allele of the paternal line ‘Dempsey’, the ‘PD’ recombinant inbred line (RIL) population created in this cross had a 1:1 segregation ratio of pungency, comprising 56 pungent and 64 nonpungent RILs
Capsaicinoid content was evaluated from plants grown in three different environments
Summary
Hot peppers (Capsicum spp.) contain capsaicinoids, unique compounds that produce a burning sensation called pungency. CS functions in the final step of capsaicinoid biosynthesis, and the expression of Pun is detected only in the fruits (Stewart et al, 2005, 2007). Most nonpungent pepper cultivars have nonfunctional Pun alleles, containing a deletion (pun1), a frameshift mutation (pun12) or an early stop codon (pun13) (Stellari et al, 2010; Stewart et al, 2005, 2007). Mutations in another gene, Putative Aminotransferase (pAMT), convert biosynthesis of capsaicinoids into that of capsinoids, which are about 1000 times less pungent than capsaicinoids (Lang et al, 2009). The expression levels of these genes correlate with the capsaicinoid content, but allelic variations affecting capsaicinoid biosynthesis have been identified only for Pun and pAMT (Koeda et al, 2015)
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