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Positional differences of intronic transposons in pAMT affect the pungency level in chili pepper through altered splicing efficiency
Author(s) -
Tanaka Yoshiyuki,
Asano Takaya,
Kanemitsu Yorika,
Goto Tanjuro,
Yoshida Yuichi,
Yasuba Kenichiro,
Misawa Yuki,
Nakatani Sachie,
Kobata Kenji
Publication year - 2019
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.14462
Subject(s) - pungency , transposable element , biology , intron , genetics , rna splicing , allele , gene , mutant , rna , pepper , food science
Summary Capsaicinoids are unique compounds that give chili pepper fruits their pungent taste. Capsaicinoid levels vary widely among pungent cultivars, which range from low pungency to extremely pungent. However, the molecular mechanisms underlying this quantitative variation have not been elucidated. Our previous study identified various loss‐of‐function alleles of the pAMT gene which led to low pungency. The mutations in these alleles are commonly defined by Tcc transposon insertion and its footprint. In this study, we identified two leaky pamt alleles ( pamt L1 and pamt L2 ) with different levels of putative aminotransferase (pAMT) activity. Notably, both alleles had a Tcc transposon insertion in intron 3, but the locations of the insertions within the intron were different. Genetic analysis revealed that pamt L1 , pamt L2 and a loss‐of‐function pamt allele reduced capsaicinoid levels to about 50%, 10% and less than 1%, respectively. pamt L1 and pamt L2 encoded functional pAMT proteins, but they exhibited lower transcript levels than the functional type. RNA sequencing analysis showed that intronic transposons disrupted splicing in intron 3, which resulted in simultaneous expression of functional pAMT mRNA and non‐functional splice variants containing partial sequences of Tcc . The non‐functional splice variants were more dominant in pamt L2 than in pamt L1 . This suggested that the difference in position of the intronic transposons could alter splicing efficiency, leading to different pAMT activities and reducing capsaicinoid content to different levels. Our results provide a striking example of allelic variations caused by intronic transposons; these variations contribute to quantitative differences in secondary metabolite contents.