Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity [version 1; referees: 2 approved]

Access to sheep genome sequences significantly improves the chances Background of identifying genes that may influence the health, welfare, and productivity of these animals. : A public, searchable DNA sequence resource for U.S. sheep was created Methods 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. : The genomes had a combined average read depth of 16, and an average WGS Results 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 ( bone GDF9), morphogenetic protein 15 ( ), and bone morphogenetic protein receptor 1B ( BMP15 ). In the 96 U.S. rams, nine missense variants encoding 11 protein variants BMPR1B were identified. However, only one was previously reported to affect litter size ( V371M, Finnsheep). Two missense variants in were identified that GDF9 BMP15 had not previously been reported: R67Q in Dorset, and L252P in Dorper and White Dorper breeds. Also, two novel missense variants were identified in : M64I BMPR1B 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 and are predicted to interfere with their function. BMP15 BMPR1B However, preliminary analyses of litter sizes in small samples did not reveal a correlation with variants in and with daughters of these rams. BMP15 BMPR1B : Collectively, this report describes a new resource for discovering protein Conclusions variants and identifies alleles for further testing of their effects on litter size in in silico U.S. breeds. This article is included in the Global Open Data for gateway. Agriculture and Nutrition 1 1 1 1 1 1