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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Genetic Improvement for Fruits & Vegetables Laboratory » Research » Publications at this Location » Publication #320784

Research Project: Quality Enhancement and Disease Resistance Development in Tomato and Pepper

Location: Genetic Improvement for Fruits & Vegetables Laboratory

Title: Genome-wide diversity and association mapping for capsaicinoids and fruit weight in Capsicum annuum L

Author
item NIMMAKAYALA, PADMA - West Virginia State University
item ABURRIE, VENKATA - West Virginia State University
item SAMINATHAN, THANGASAMY - West Virginia State University
item ALAPARTHI, SURESH - West Virginia State University
item ALMEIDA, ALDO - West Virginia State University
item HYMA, KATIE - Cornell University - New York
item MITCHELL, SHARON - Cornell University - New York
item DAVENPORT, BRITTANY - West Virginia State University
item TONAPI, KRITTIKA - West Virginia State University
item YADAV, LAV - West Virginia State University
item HANKINS, GERALD - West Virginia State University
item MALKARAM, SRIDHAR - West Virginia State University
item Stommel, John
item PARK, MINKYU - Seoul National University
item CHOI, DOIL - Seoul National University
item RATHINASABAPATHI, BALA - University Of Florida
item REDDY, UMESH - West Virginia State University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/2016
Publication Date: 11/30/2016
Citation: Nimmakayala, P., Aburrie, V.L., Saminathan, T., Alaparthi, S.B., Almeida, A., Hyma, K., Mitchell, S., Davenport, B., Tonapi, K., Yadav, L., Hankins, G., Malkaram, S., Stommel, J.R., Park, M., Choi, D., Rathinasabapathi, B., Reddy, U. 2016. Genome-wide diversity and association mapping for capsaicinoids and fruit weight in Capsicum annuum L. Scientific Reports. 6:38081.

Interpretive Summary: The domestication of Capsicum annuum, the most popular species of pepper, has resulted in increased fruit size and fruit pungency. In this study, we used a diverse collection of domesticated and wild peppers to identify genes associated with these domestication related attributes. Using DNA analysis together with fruit weight and pungency measurements, we identified multiple DNA sequences in pepper that were associated with these traits. Some of these DNA sequences were unique to pepper and others were similar to previously discovered fruit development related genes from other plants. These research results will benefit other scientists studying crop domestication and also benefit researchers working to identify genes that can be used to improve the efficiency of developing improved pepper varieties.

Technical Abstract: Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of domesticated and wild C. annuum to generate 66,960 SNPs using genotyping by sequencing. Principal component analysis and identity by state were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Selfed accessions were grown in three replications during two seasons (2011 and 2012). GWAS revealed 14 SNPs commonly associated with capsaicin and dihydrocapsaicin content and 15 associated with fruit weight in both years. Five associated SNPs for capsaicin and three for fruit weight were nonsynonymous and significant after correction for false discovery rate and were homologous to known fruit-development genes in tomato and other plants. When scanning pairwise fixation index distribution of domesticated and wild accessions across the genome, we identified a segment of 177 Mb on chromosome 11 that was under strong selection sweep. Of 659 genes located in this sweep area, 30 were under high linkage disequilibrium, with reduced nucleotide diversity levels. Annotation of the genes in the sweep coupled with GWAS revealed their important roles in domestication.