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Title: Genome-wide differentiation of various melon horticultural groups for use in genome wide association study for fruit firmness and construction of a high resolution genetic map

Author
item NIMMAKAYALA, P - West Virginia State University
item TOMASSON, Y - West Virginia State University
item ABBURI, V - West Virginia State University
item SAMINATHAN, T - West Virginia State University
item RODRIGGUEZ, A - West Virginia State University
item VAJJA, V - West Virginia State University
item SALAZAR, G - West Virginia State University
item GIRISH, P - West Virginia State University
item Levi, Amnon
item Wechter, William - Pat
item McCreight, James - Jim
item KOROL, A - West Virginia State University
item RONIN, Y - West Virginia State University
item GARCIA-MAS, J - West Virginia State University
item REDDY, U - West Virginia State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/8/2016
Publication Date: 9/22/2016
Citation: Nimmakayala, P., Tomasson, Y., Abburi, V.K., Saminathan, T., Rodrigguez, A.G., Vajja, V.G., Salazar, G., Girish, P., Levi, A., Wechter, W.P., McCreight, J.D., Korol, A., Ronin, Y., Garcia-Mas, J., Reddy, U. 2016. Genome-wide differentiation of various melon horticultural groups for use in genome wide association study for fruit firmness and construction of a high resolution genetic map. Frontiers in Plant Science. 7:1437. doi:org/10.3389/fpls.2016.01437.

Interpretive Summary: Melon is an important vegetable crop in the United States and throughout the world. There is a continuous need to improve melon varieties for fruit quality and for enhancing vitamin and nutritional content. The USDA, ARS, maintains a large number of melon accessions collected throughout the world. These accessions are named United States plant introductions (PIs) and they represent wide genetic diversity and are considered useful sources for enhancing disease resistance and fruit quality in existing melon varieties. In this study, ARS scientists at Charleston collaborated with scientists from West Virginia State University, using advanced genomic tools and genetic analysis software to find genes that affect melon fruit quality and ripening. The data in this study should be useful for seed company breeders and researchers that employ DNA markers in their breeding programs, and who are focused on improving melon fruit quality and disease resistance.

Technical Abstract: We generated 13,789 single nucleotide plymorphism (SNP) markers from 97 melon accessions using genotyping by sequencing and anchored them to chromosomes to understand genome-wide fixation index between various melon morphotypes and linkage disequilibrium (LD) decay for inodorus and cantalupensis, the two leading economically important groups. In the current research, we focused to understand genome-wide footprints of divergence underlying formation of inodorus and cantalupensis in comparison with the highly diverse subspecies agrestis. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. Our study further resolved a strong selective sweep and high LD on chromosomes 11 and 5 indicating importance of these chromosomes in genetic differentiation. A high-resolution genetic map with 7,153 loci was constructed in the current study, which could be used to understand colinearity with the genome sequence. Genome-wide segregation distortion and recombination rate across various chromosomes were also characterized. Various quantitative trait loci (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 '-D-xylosidase and histidine kinase, genes that were previously characterized for fruit ripening and softening on other crops.