Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map
Nimmakaya, Padma (West Virginia University. Department of Biology)
Tomason, Yan R. (West Virginia University. Department of Biology)
Abburi, Venkata L. (West Virginia University. Department of Biology)
Alvarado, Alejandra (West Virginia University. Department of Biology)
Saminathan, Thangasamy (West Virginia University. Department of Biology)
Vajja, Venkata G. (West Virginia University. Department of Biology)
Salazar, Germania (Alcorn State University. Department of Agriculture)
Panicker, Girish K. (Alcorn State University. Department of Agriculture)
Levi, Amnon (United States Department of Agriculture. U. S. Vegetable Laboratory)
Wechter, William P. (United States Department of Agriculture. U. S. Vegetable Laboratory)
McCreight, James D. (United States Department of Agriculture. U.S. Agricultural Research Station)
Korol, Abraham B. (Universiṭat Ḥefah. Department of Evolutionary and Environmental Biology)
Ronin, Yefim (Universiṭat Ḥefah. Department of Evolutionary and Environmental Biology)
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica)
Reddy, Umesh K. (West Virginia University. Department of Biology)

Date:	2016
Abstract:	Melon (Cucumis melo L. ) 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. The FST between accessions of cantalupensis and inodorus was 0. 23. The FST between cantalupensis and various agrestis accessions was in a range of 0. 19-0. 53 and between inodorus and agrestis accessions 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.
Note:	Ajuts: Funding support is provided by Gus R. Douglass Institute (Evans Allen Project to Nimmakayala) and USDA-NIFA (2010-02247 and 2012-02511).
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Genotyping-by-sequencing ; High-resolution genetic map ; Linkage disequilibrium ; Melon ; GWAS ; Fruit firmness
Published in:	Frontiers in plant science, Vol. 7 (Sep. 2016) , art. 1437, ISSN 1664-462X

DOI: 10.3389/fpls.2016.01437
PMID: 27713759

15 p, 7.0 MB

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