| China has a long history of sheep domestication and rich resources of sheep breeds, in which short fat-tailed sheep are widely distributed. According to archaeological and genetic research, Small-Tailed Han sheep, Hu sheep, Duolang sheep, Tan sheep and other breeds are derived from Mongolian sheep. However, after a long period of domestication and adaptation to the environment, these breeds have been variation in many phenotypic traits with Mongolian sheep. Highlighted on the reproductive performance, Mongolian sheep belonging to seasonal estrous, lambing rate of only about 103% while Small-Tailed Han sheep, Hu sheep and duolang sheep are year-round estrous, lambing rate is more than 200%. The genetic basis of the phenotypic diversity being lack of systematic studies on genome-wide level, this research performed pooled whole-genome resequencing of 3 short fat-tailed breeds: Small-Tailed Han sheep, Duolang sheep and Mongolian sheep which range spans a large space and the main findings are as follows:(1) The research have generated 43.2-fold coverage of the sheep genome using pools of genomic DNA representing 3 breeds of short fat-tailed sheep. We report more than 13, 209,060 single nucleotide polymorphisms and almost 912,131 InDel.(2) In the protein coding regions (CDS) of Small-Tailed Han sheep, Mongolian sheep and Duolang sheep,90,853/90,720/56,804 SNP in total were indentified respectively, of which synonymous SNP 36,820/37,449/21,029, missense SNP 54,033/53,271/35,775 (located inside 11,063/11,421/7,724 genes), stop gained SNP 2,474/2,421/1,786 (located inside 1,789/1,810/1,192 genes), respectively.(3) Because Small-Tailed Han sheep and Duolang sheep are year-round estrous and prolificacy while Mongolian sheep is seasonal estrous and singleton, we indentified 797 genes containing missence SNP both in Small-Tailed Han sheep and Duolang sheep but not in Mongolian sheep. We searched for significantly overrepresented gene ontology terms among these genes and identified several categories, in which one conspicuous cluster relates to the term reproduction and 15 genes belonging to this category (12 genes belonging to GO: 0007283 spermatogenesis). KEGG pathway were also significantly enriched, of which, "Progesterone-mediated oocyte maturation" containing 7 genes (RPS6KA3, MAD2L1, CCNB2, GNAI2, ADCY5, PIK3R5, CDC25B) may be related to the reproductive traits of short fat-tailed sheep.(4) By applying the thresholds Z(HP)<-4 and/or Z(FST)> 4, we identified 108 regions in the Small-Tailed Han sheep genome with extremely low levels of heterozygosity and 65 regions with strongly elevated FST values. In total,136 unique autosomal regions containing 774 protein coding genes were identified by the two approaches combined. While thresholds Z(HP)<-3 and/or Z(FST)> 3 were used for the analysis of the X chromosome, and 9 regions containing 24 protein coding genes were identified. In the whole genome of Small-Tailed Han sheep,145 regions with total length of 45.3 Mb, accounting for 1.74% of the total genome, were identified.(5) We searched for significantly overrepresented gene ontology terms among the genes in the genomic regions under selection of Small-Tailed Han sheep and identified 8 categories: developmental process, cellular process, multicellular organismal process, biological regulation, metabolic process, reproduction, localization and growth. KEGG pathway were also significantly enriched, involved "Endometrial cancer" "Prostate cancer" that might be assosiated with the reproductive traits of short fat-tailed sheep potentially.(6) Genes related to reproduction in the genomic regions under selection of Small-Tailed Han sheep are a total of 25, of which there are 8 genes attributed to only selection in Small-Tailed Han sheep(MMP14, PMCH, HMGCR, SLC6A3, PRL, OXT, TSSK3, FLT1),5 to selection both in Small-Tailed Han sheep and Duolang sheep (ADAM2, GAMT, NR3C1, DAZAP1, ADAM29),1 to only selection in Mongolian sheep (HOXA10), and 5 to selection in all 3 breeds (DMRTB1, RQCD1, FGF9, ABCB9, YBX2). |
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