Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires  

作　　者：Gerson A.Oliveira Júnior Daniel J.A.Santos Aline S.M.Cesar Solomon A.Boison Ricardo V.Ventura Bruno C.Perez JoséF.Garcia JoséBento S.Ferraz Dorian J.Garrick 

机构地区：[1]Department of Veterinary Medicine,University of São Paulo(USP),Faculty of Animal Science and Food Engineer,Pirassununga,SP,Brazil [2]Department of Animal Bioscience,Center for Genetic Improvement of Livestock,University of Guelph,Guelph,ON,Canada [3]Department of Animal and Avian Sciences,University of Maryland,College Park,Maryland,USA [4]Department of Animal Science,University of São Paulo(USP),Piracicaba,SP,Brazil [5]Department of Sustainable Agricultural Systems,University of Natural Resources and Life Sciences,Vienna,Austria [6]Department of Animal Nutrition and Production,School of Veterinary Medicine and Animal Science,University of São Paulo(USP),Pirassununga,Brazil [7]Department of Support,Production and Animal Health,School of Veterinary Medicine,São Paulo State University(Unesp),Araçatuba,SP,Brazil [8]School of Agriculture,Massey University,Ruakura Ag Centre,Hamilton,New Zealand

出　　处：《Journal of Animal Science and Biotechnology》2020年第2期303-315,共13页畜牧与生物技术杂志（英文版）

基　　金：supported by the“Fundação de Amparoà Pesquisa do Estado de São Paulo”(FAPESP),under project numbers 2012/50533-2,2013/12097-9,2014/07566-2,2015/12396-1.

摘　　要：Background:Impaired fertility in cattle limits the efficiency of livestock production systems.Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection.In this study,we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore(Bos indicus)heifers.Methods:The dataset comprised of 1337 heifers genotyped using a GeneSeek®Genomic Profiler panel(74677 SNPs),representing the daughters from 78 sires.After performing marker quality control,64800 SNPs were retained.Haplotypes carried by each sire at six previously identified QTL on BTAs 5,14 and 18 for heifer pregnancy and BTAs 8,11 and 22 for antral follicle count were constructed using findhap software.The significance of the contrasts between the effects of every two paternally-inherited haplotype alleles were used to identify sires that were heterozygous at each QTL.Whole-genome sequencing data localized to the haplotypes from six sires and 20 other ancestors were used to identify sequence variants that were concordant with the haplotype contrasts.Enrichment analyses were applied to these variants using KEGG and MeSH libraries.Results:A total of six(BTA 5),six(BTA 14)and five(BTA 18)sires were heterozygous for heifer pregnancy QTL whereas six(BTA 8),fourteen(BTA 11),and five(BTA 22)sires were heterozygous for number of antral follicles’QTL.Due to inadequate representation of many haplotype alleles in the sequenced animals,fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14,which had 641 and 3733 concordant candidate sequence variants,respectively.The KEGG“Circadian rhythm”and“Neurotrophin signaling pathway”were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA 14.Among the concordant sequence variants,0.2%and 0.3%were classified as missense variants for BTAs 5 and 14,respectively,highlighting the genes MTERF2

关 键 词：Antral follicles Causal variants HAPLOTYPE Heifer pregnancy WGS 

分 类 号：S823[农业科学—畜牧学]