|NIMMAKAYALA, PADMA - West Virginia State University|
|SAHI, BHAGARATHI - West Virginia State University|
|ABBURI, VENKATA - West Virginia State University|
|LOPEZ-ORTIZ, CARLOS - West Virginia State University|
|KSHETRY, ARJUN OJHA - West Virginia State University|
|SHINDE, SUHAS - West Virginia State University|
|DAVENPORT, BRITTANY - West Virginia State University|
|REDDY, UMESH - West Virginia State University|
Submitted to: Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/30/2021
Publication Date: 7/3/2021
Citation: Nimmakayala, P., Sahi, B., Abburi, V.L., Lopez-Ortiz, C., Kshetry, A., Shinde, S., Davenport, B., Stommel, J.R., Reddy, U. 2021. Exploration into natural variation for genes associated with fruit shape and size among Capsicum chinense collections. Genomics. 113:3002-3014. https://doi.org/10.1016/j.ygeno.2021.06.041.
Interpretive Summary: The Habanero pepper belongs to the species Capsicum chinense and is considered one of the most important pepper species because of high market demand due to its aroma and flavor. Fruit size and shape are important determinants for suitability of Habanero and related C. chinense relatives for culinary applications. However, little knowledge is available on the genetic control of fruit shape in this species. Using a diverse C. chinense plant collection, we examined variation in DNA of the respective plants and conducted an analysis to associate this DNA variation with fruit shape attributes. We identified DNA markers that are associated with fruit shape and the number of locules within the fruit. These genetic markers are valuable for characterizing and preserving pepper genetic diversity and will be useful to plant breeders since they will improve the efficiency of breeding new pepper cultivars.
Technical Abstract: Phenotypic diversity within cultivated Capsicum chinense is particularly evident for fruit shape and size; however, genetic analysis of fruit shape variation in C. chinense is absent. To unravel the genetic mechanism underlying fruit shape variation, we identified 43,081 single nucleotide polymorphisms (SNPs) from diverse collections of C. chinense by using genotyping by sequencing. In our GWAS, we selected 12 SNPs associated with locule number trait and 8 SNP markers associated with other fruit shape traits such as perimeter, area, obovoid, ellipsoid and morphometrics (5y, 6y and 7y). The SNPs in CLAVATA1, WD-40, auxin receptor, AAA type ATPase family protein, and RNA polymerase III genes were the major markers identified for fruit locule number from our GWAS results. Furthermore, we found SNPs in tetratricopeptiderepeat thioredoxin-like 3, enhancer of ABA co-receptor 1, subunit of exocyst complex 8 and pleiotropic drug resistance proteins associated with various fruit shape traits.