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• W2740089724 abstract "<ns4:p><ns4:italic>Background</ns4:italic>: Access to sheep genome sequences significantly improves the chances of identifying genes that may influence the health, welfare, and productivity of these animals. </ns4:p><ns4:p> <ns4:italic>Methods</ns4:italic>: A public, searchable DNA sequence resource for U.S. sheep was created with whole genome sequence (WGS) of 96 rams. The animals shared minimal pedigree relationships and represent nine popular U.S. breeds and a composite line. The genomes are viewable online with the user-friendly Integrated Genome Viewer environment, and may be used to identify and decode gene variants present in U.S. sheep.</ns4:p><ns4:p> <ns4:italic>Results</ns4:italic>: The genomes had a combined average read depth of 16, and an average WGS genotype scoring rate and accuracy exceeding 99%. The utility of this resource was illustrated by characterizing three genes with 14 known coding variants affecting litter size in global sheep populations: growth and differentiation factor 9 (<ns4:italic>GDF9), </ns4:italic>bone morphogenetic protein 15 (<ns4:italic>BMP15</ns4:italic>), and bone morphogenetic protein receptor 1B (<ns4:italic>BMPR1B</ns4:italic>). In the 96 U.S. rams, nine missense variants encoding 11 protein variants were identified. However, only one was previously reported to affect litter size (<ns4:italic>GDF9</ns4:italic> V371M, Finnsheep). Two missense variants in <ns4:italic>BMP15</ns4:italic> were identified that had not previously been reported: R67Q in Dorset, and L252P in Dorper and White Dorper breeds. Also, two novel missense variants were identified in <ns4:italic>BMPR1B</ns4:italic>: M64I in Katahdin, and T345N in Romanov and Finnsheep breeds. Based on the strict conservation of amino acid residues across placental mammals, the four variants encoded by <ns4:italic>BMP15 </ns4:italic>and <ns4:italic>BMPR1B</ns4:italic> are predicted to interfere with their function. However, preliminary analyses of litter sizes in small samples did not reveal a correlation with variants in <ns4:italic>BMP15</ns4:italic> and <ns4:italic>BMPR1B</ns4:italic> with daughters of these rams. </ns4:p><ns4:p> <ns4:italic>Conclusions</ns4:italic>: Collectively, this report describes a new resource for discovering protein variants <ns4:italic>in silico</ns4:italic> and identifies alleles for further testing of their effects on litter size in U.S. breeds.</ns4:p>" @default.
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• W2740089724 date "2017-08-02" @default.
• W2740089724 modified "2023-10-09" @default.
• W2740089724 title "Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity" @default.
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• W2740089724 doi "https://doi.org/10.12688/f1000research.12216.1" @default.
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