Identification Of Key Regulatory Genes For Litter Size Trait In Chuanzhong Black Goat By Genome Resequencing

China is a large country of goat production.Goat industry fills an important niche in animal husbandry.Kidding rate is a very important economic trait,but its regulatory mechanism is not clear.Whole genome sequencing can analyze the genetic basis of phenotypic variation of livestock and have great potential use in marker assisted selection.Chuanzhong black goat(CBG)is a local Chinese breed famous for its high fecundity and meat performance.Therefore,the high fecundity(HF)CBG(n = 6)does that produce 4 – 6 kids per doe kidding and low fecundity(LF)does(n = 6)that produce only one kid per doe kidding chosen were chosen in this study.Jugular blood samples were collected to extract genomic DNA.The 350 bp double-terminal sequencing library was constructed,and then the whole genome of 12 libraries were resequenced by Illumina Hi Seq PE150 platform to screen the key candidate genes regulating the litter size.The main results were shown as the followings.(1)A total of 431.50 Gb clean data were obtained from the genome resequencing study of 12 Chuanzhong black goats.Through mutation detection and annotation,7771417 single nucleotide polymorphisms(SNPs)were detected in HF group and8935907 SNPs were detected in LF group.Settings reached both the maximum ZFst value of top 5% and the minimum ZHp value of top 5% as candidate regions,and a total of 130 strong selection signals were annotated in the regions with low heterozygosity and high genetic differentiation.Among them,84,59 and 13 genes were annotated in HF group,LF group and shared windows,respectively.GO enrichment analysis and KEGG pathway showed that 19 candidate genes were involved in the regulation of reproduction,reproduction and embryonic development of CBG,including 11 HF group-specific candidate genes(ADCY10,DRD1,HS6ST1,IGFBP7,MSX2,NOG,NPHP4,PAPPA,PRLHR,TDRP and XYLT1),and five strong selection signal genes(ANXA5,IGF1,EDNRA,FANCL and TAC1)in LF group,and three window genes(AKR1B3,HDAC4 and OPRM1)in HF group shared with LF group.At the same time,most of the GO terms such as G-protein-coupled receptor activity,hormone response and neuropeptide signal pathway contain these 19 candidate genes.In addition,KEGG pathways such as metabolic pathways,neuroactive ligand-receptor interaction,glycosaminoglycan biosynthesis-heparan sulfate/heparin,calcium signaling pathway,c AMP signaling pathway and folate biosynthesis may play an important role in the regulation of fecundity in CBG.(2)BMPR1B,GDF9 and BMP15 genes were located on chromosome 6,7 and X,respectively.Mutations in the candidate genes associated with fecundity in sheep were not detected in CBG.However,the BMPR1 B gene intron,5’UTR and 3’UTR regions contained 154,1 and 2 SNPs,respectively,and the BMP15 intron and 5’UTR regions each contain 1 SNP site.In these SNPs,the number of transitions(A/G and C/T)is far more than that of transversions(A/C,A/T,G/C and G)./T)number.The number of conversions was 117,of which 2 occurred in the 3’UTR region of the BMPR1 B gene and the 5’UTR region of the BMP15 gene.The number of transversions was 42 and one of them occurred in the BMP15 sequence.In conclusion,based on the genome resequencing analysis of CBG,it was found11 HF group-specific candidate genes.Mutations in the candidate genes associated with fecundity in sheep were not detected,however,a total of 159 novel SNPs were found in BMPR1 B and BMP15.These findings expand our understanding of genetic mechanism of goat fecundity,which would be potentially applied to improve reproductive performance by marker assisted selection.