title: Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map.
abstract: Melon (Cucumis meloL.) is a phenotypically diverse eudicot diploid (2n= 2x= 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. TheFSTbetween accessions ofcantalupensisandinodoruswas 0.23. TheFSTbetweencantalupensisand variousagrestisaccessions was in a range of 0.19-0.53 and betweeninodorusandagrestisaccessions was in a range of 0.21-0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in β-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops.
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University Institute, WV, USA.
authors.forename: Padma
authors.initials: P
authors.lastname: Nimmakayala
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA; Department of Selection and Seed Production, Dnepropetrovsk State Agrarian and Economic UniversityDnepropetrovsk, Ukraine.
authors.forename: Yan R
authors.initials: YR
authors.lastname: Tomason
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University Institute, WV, 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, USA.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Alvarado
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University Institute, WV, 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, USA.
authors.forename: Venkata G
authors.initials: VG
authors.lastname: Vajja
authors.affiliation: Department of Agriculture, Alcorn State University Lorman, MS, USA.
authors.forename: Germania
authors.initials: G
authors.lastname: Salazar
authors.affiliation: Department of Agriculture, Alcorn State University Lorman, MS, USA.
authors.forename: Girish K
authors.initials: GK
authors.lastname: Panicker
authors.affiliation: U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research Service Charleston, SC, USA.
authors.forename: Amnon
authors.initials: A
authors.lastname: Levi
authors.affiliation: U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research Service Charleston, SC, USA.
authors.forename: William P
authors.initials: WP
authors.lastname: Wechter
authors.affiliation: U.S. Agricultural Research Station Salinas, CA, USA.
authors.forename: James D
authors.initials: JD
authors.lastname: McCreight
authors.affiliation: Department of Evolutionary and Environmental Biology, Haifa University Haifa, Israel.
authors.forename: Abraham B
authors.initials: AB
authors.lastname: Korol
authors.affiliation: Department of Evolutionary and Environmental Biology, Haifa University Haifa, Israel.
authors.forename: Yefim
authors.initials: Y
authors.lastname: Ronin
authors.affiliation: Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institute for Food and Agricultural Research and Technology-Universitat Autònoma de Barcelona-Universitat de Barcelona Barcelona, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Garcia-Mas
authors.affiliation: Gus R. Douglass Institute and Department of Biology, West Virginia State University Institute, WV, USA.
authors.forename: Umesh K
authors.initials: UK
authors.lastname: Reddy
keywords: GWAS; fruit firmness; genotyping-by-sequencing; high-resolution genetic map; linkage disequilibrium; melon