Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity

Author:

Heaton Michael P.ORCID,Smith Timothy P.L.,Freking Bradley A.,Workman Aspen M.ORCID,Bennett Gary L.,Carnahan Jacky K.,Kalbfleisch Theodore S.

Abstract

Background:  Access to sheep genome sequences significantly improves the chances of identifying genes that may influence the health, welfare, and productivity of these animals.   Methods:  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. Results:  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 (GDF9), bone morphogenetic protein 15 (BMP15), and bone morphogenetic protein receptor 1B (BMPR1B).  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 (GDF9 V371M, Finnsheep).  Two missense variants in BMP15 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 BMPR1B:  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 BMP15 and BMPR1B are predicted to interfere with their function.  However, preliminary analyses of litter sizes in small samples did not reveal a correlation with variants in BMP15 and BMPR1B with daughters of these rams.  Conclusions: Collectively, this report describes a new resource for discovering protein variants in silico and identifies alleles for further testing of their effects on litter size in U.S. breeds.

Funder

U.S. Department of Agriculture

Publisher

F1000 Research Ltd

Subject

General Pharmacology, Toxicology and Pharmaceutics,General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3