An 18.5-kbp Deletion in the Genomic Region, Including the Pun1, is Responsible for Non-pungency Traits in the Japanese Sweet Pepper ‘Sampo Oamanaga’ (Capsicum annuum)

Capsaicinoids are compounds that generate the characteristic pungent taste of chili peppers, the presence or absence of which determines the utilization of the chili peppers as spices or vegetables. Loss of pungency is a qualitative trait resulting from dysfunction in any of four capsaicinoid biosynthesis genes (Pun1, pAMT, CaKR1, and CaMYB31). However, the lack of pungency in sweet peppers cannot be explained by known mutation alleles in these four genes. Herein, we report a novel dysfunctional allele of Pun1, which encodes acyltransferase 3 (capsaicin synthase), in a Japanese sweet pepper, ‘Sampo Oamanaga’. Firstly, PCR genotyping of ‘Sampo Oamanaga’ Pun1 showed that it was not a known mutant allele. We also performed whole-genome resequencing and found a large genomic deletion around the ‘Sampo Oamanaga’ Pun1 (XM_016704778.1). We then examined the precise size and breakpoint of the Pun1-deletion region via de novo assembly and Sanger sequencing analysis. We found an 18.5-kbp deletion, including the Pun1, on chromosome 2, and we designated this novel allele pun1⁵. The genotypic effects of pun1⁵ were investigated using F₂ progeny derived from a ‘Sampo Oamanaga’ (pun1⁵/pun1⁵) × pungent cultivar ‘Takanotsume’ (Pun1/Pun1) cross. Only pun1⁵-homozygous F₂ plants showed non-pungency; co-segregation between Pun1 genotypes and pungency traits was observed. These results demonstrated that the deficiency of pungency in ‘Sampo Oamanaga’ is associated with the pun1⁵ allele. The present study is the first to discover a large genomic deletion, including a gene among dysfunctional pun1 alleles, and provides new insights into the regulation mechanism of pungency in chili peppers.