Genome-wide scan for common variants associated with intramuscular fat and moisture content in rainbow trout

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dc.contributor.authorAli, Ali
dc.contributor.authorAl-Tobasei, Rafet
dc.contributor.authorLourenco, Daniela
dc.contributor.authorLeeds, Tim
dc.contributor.authorKenney, Brett
dc.contributor.authorSalem, Mohamed
dc.date.accessioned2021-03-11T20:23:40Z
dc.date.available2021-03-11T20:23:40Z
dc.date.issued2020-08-25
dc.description.abstractGenetic improvement of fillet quality attributes is a priority of the aquaculture industry. Muscle composition impacts quality attributes such as flavor, appearance, texture, and juiciness. Fat and moisture make up about ~ 80% of the tissue weight. The genetic architecture underlying the fat and moisture content of the muscle is still to be fully explored in fish. A 50 K gene transcribed SNP chip was used for genotyping 789 fish with available phenotypic data for fat and moisture content. Genotyped fish were obtained from two consecutive generations produced in the National Center for Cool and Cold Water Aquaculture (NCCCWA) growth-selective breeding program. Estimates of SNP effects from weighted single-step GBLUP (WssGBLUP) were used to perform genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with the studied traits. Using genomic sliding windows of 50 adjacent SNPs, 137 and 178 SNPs were identified as associated with fat and moisture content, respectively. Chromosomes 19 and 29 harbored the highest number of SNPs explaining at least 2% of the genetic variation in fat and moisture content. A total of 61 common SNPs on chromosomes 19 and 29 affected the aforementioned traits; this association suggests common mechanisms underlying intramuscular fat and moisture content. Additionally, based on single-marker GWA analyses, 8 and 24 SNPs were identified in association with fat and moisture content, respectively. SNP-harboring genes were primarily involved in lipid metabolism, cytoskeleton remodeling, and protein turnover. This work provides putative SNP markers that could be prioritized and used for genomic selection in breeding programs.en_US
dc.description.urihttps://doi.org/10.1186/s12864-020-06932-0
dc.identifierhttps://doi.org/10.13016/a4c1-jiid
dc.identifier.citationAli, A., Al-Tobasei, R., Lourenco, D. et al. Genome-wide scan for common variants associated with intramuscular fat and moisture content in rainbow trout. BMC Genomics 21, 529 (2020).en_US
dc.identifier.urihttp://hdl.handle.net/1903/26920
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Agriculture & Natural Resourcesen_us
dc.relation.isAvailableAtAnimal & Avian Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectFat contenten_US
dc.subjectMoistureen_US
dc.subjectGWASen_US
dc.subjectSingle-stepen_US
dc.subjectQTLen_US
dc.titleGenome-wide scan for common variants associated with intramuscular fat and moisture content in rainbow trouten_US
dc.typeArticleen_US

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