title: Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L.
abstract: Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS 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). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Padma
authors.initials: P
authors.lastname: Nimmakayala
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Venkata L
authors.initials: VL
authors.lastname: Abburi
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Thangasamy
authors.initials: T
authors.lastname: Saminathan
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Suresh B
authors.initials: SB
authors.lastname: Alaparthi
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Aldo
authors.initials: A
authors.lastname: Almeida
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Brittany
authors.initials: B
authors.lastname: Davenport
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Marjan
authors.initials: M
authors.lastname: Nadimi
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Davidson
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Krittika
authors.initials: K
authors.lastname: Tonapi
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Lav
authors.initials: L
authors.lastname: Yadav
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Malkaram
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Gopinath
authors.initials: G
authors.lastname: Vajja
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Gerald
authors.initials: G
authors.lastname: Hankins
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Harris
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-321, Republic of Korea.
authors.forename: Minkyu
authors.initials: M
authors.lastname: Park
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-321, Republic of Korea.
authors.forename: Doil
authors.initials: D
authors.lastname: Choi
authors.affiliation: Genetic Improvement of Fruits and Vegetables Laboratory (USDA, ARS), Beltsville, MD-20705, USA.
authors.forename: John
authors.initials: J
authors.lastname: Stommel
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA.
authors.forename: Umesh K
authors.initials: UK
authors.lastname: Reddy
mesh_terms: D002211:Capsaicin / Q000031:analogs & derivatives* / Q000378:metabolism; D002212:Capsicum / Q000235:genetics / Q000378:metabolism; D005638:Fruit / Q000235:genetics / Q000378:metabolism; D055106:Genome-Wide Association Study; D020641:Polymorphism, Single Nucleotide
chemical_list: D002211:Capsaicin; C012906:dihydrocapsaicin