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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #344782

Research Project: Genetic and Genomic Basis of Vegetable and Fruit Biology, Quality and Nutrient Content

Location: Plant, Soil and Nutrition Research

Title: Genome-wide linkage disequilibrium mapping to the candidate gene level in melon (Cucumis melo)

Author
item GUR, AMIT - Agricultural Research Organization Of Israel
item TZURI, GALIL - Agricultural Research Organization Of Israel
item MEIR, AYALA - Agricultural Research Organization Of Israel
item PORTNOY, VITALY - Agricultural Research Organization Of Israel
item KATZIR, NURIT - Agricultural Research Organization Of Israel
item SCHAFFER, ARTHUR - Agricultural Research Organization Of Israel
item Li, Li
item BURGER, JOSEPH - Agricultural Research Organization Of Israel
item TADMOR, YAAKOV - Agricultural Research Organization Of Israel

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2017
Publication Date: 8/29/2017
Citation: Gur, A., Tzuri, G., Meir, A., Portnoy, V., Katzir, N., Schaffer, A., Li, L., Burger, J., Tadmor, Y. 2017. Genome-wide linkage disequilibrium mapping to the candidate gene level in melon (Cucumis melo). Scientific Reports. https://doi.org/10.1038/s41598-017-09987-4.
DOI: https://doi.org/10.1038/s41598-017-09987-4

Interpretive Summary: Cucumis melo is highly diverse for fruit traits. This provides great breeding and genetic research opportunities, including genome-wide association (GWA) analysis. By using a collection of 177 accessions and genotyped with 23,931 SNPs, this paper evaluated the potential of GWA for trait mapping in melon and demonstrated the potential of the diverse collections and GWA for mapping of several Mendelian traits to narrow intervals overlapping with known causative genes. It provides a first proof-of-concept for the potential of association genetics for high resolution mapping to a candidate-gene level in melon.

Technical Abstract: Cucumis melo is highly diverse for fruit traits providing wide breeding and genetic research opportunities, including genome-wide association (GWA) analysis. We used a collection of 177 accessions representing the two C. melo subspecies and 11 horticultural groups for detailed characterization of fruit trait variation and evaluation of the potential of GWA for trait mapping in melon. Through genotyping-by-sequencing, 23,931 informative SNPs were selected for genome-wide analyses. We found that linkage-disequilibrium decays at ~100 Kb in this collection and that population structure effect on association results varies between traits. We mapped several monogenic traits to narrow intervals overlapping with known causative genes, demonstrating the potential of diverse collections and GWA for mapping Mendelian traits to a candidate-gene level in melon. We further report on mapping of fruit shape quantitative trait loci (QTLs) and comparison with multiple previous QTL studies. Expansion of sample size and a more balanced representation of taxonomic groups might improve efficiency for simple trait dissection. But, as in other plant species, integrated linkage association multi-allelic approaches are likely to produce better combination of statistical power, diversity capture and mapping resolution in melon. Our data can be utilized for selection of the most appropriate accessions for such approaches.