Identification of gene-specific polymorphisms and association with capsaicin pathway metabolites in Capsicum annuum L. collections.
Pepper (Capsicum annuum L.) is an economically important crop with added nutritional value. Production of capsaicin is an important quantitative trait with high environmental variance, so the development of markers regulating capsaicinoid accumulation is important for pepper breeding programs. In this study, we performed association mapping at the gene level to identify single nucleotide polymorphisms (SNPs) associated with capsaicin pathway metabolites in a diverse Capsicum annuum collection during two seasons. The genes Pun1, CCR, KAS and HCT were sequenced and matched with the whole-genome sequence draft of pepper to identify SNP locations and for further characterization. The identified SNPs for each gene underwent candidate gene association mapping. Association mapping results revealed Pun1 as a key regulator of major metabolites in the capsaicin pathway mainly affecting capsaicinoids and precursors for acyl moieties of capsaicinoids. Six different SNPs in the promoter sequence of Pun1 were found associated with capsaicin in plants from both seasons. Our results support that CCR is an important control point for the flux of p-coumaric acid to specific biosynthesis pathways. KAS was found to regulate the major precursors for acyl moieties of capsaicinoids and may play a key role in capsaicinoid production. Candidate gene association mapping of Pun1 suggested that the accumulation of capsaicinoids depends on the expression of Pun1, as revealed by the most important associated SNPs found in the promoter region of Pun1.
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America.
Umesh K
UK
Reddy
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America.
Aldo
A
Almeida
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America.
Venkata L
VL
Abburi
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America.
Suresh Babu
SB
Alaparthi
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America.
Desiree
D
Unselt
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America.
Gerald
G
Hankins
Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Minkyu
M
Park
Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Doil
D
Choi
Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, West Virginia, United States of America.
Padma
P
Nimmakayala
D001483:Base Sequence; D002211:Capsaicin / Q000378:metabolism*; D002212:Capsicum / Q000737:chemistry* / Q000235:genetics; D002874:Chromosome Mapping; D017931:DNA Primers / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D056726:Genetic Association Studies; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D055442:Metabolome; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA
D017931:DNA Primers; D002211:Capsaicin