背景:绒山羊产业是内蒙古自治区畜牧业的主要支柱之一,在地方经济发展中发挥着不可替代的作用。随着饲养方式和环境的变化,内蒙古绒山羊生产的羊绒呈现粗化趋势,羊绒产量不能满足人们的消费需求。然而,这些变化背后的遗传基础还没有完全理解。我们测量了羊绒性状,包括羊绒产量(CY),羊绒直径(CD),羊绒厚度(CT),和连续四年的羊毛长度(FL)特征,并利用新的基因组学工具对内蒙古绒山羊4个绒类性状进行全基因组关联研究,推断与绒类性状相关的基因组区域和功能位点,构建显著影响绒类性状的单倍型。
结果:我们估计了内蒙古绒山羊绒类性状的遗传参数。羊绒产量的遗传力,羊绒直径,内蒙古绒山羊的绒长性状为0.229、0.359和0.250,属于中等遗传力性状(0.2〜0.4)。羊绒厚度性状的低遗传力为0.053。我们在不同染色体上检测到151个全基因组与4个羊绒性状显著相关的SNPs,它们非常接近392个基因的染色体(位于基因内或±500kb内)。Notch3,BMPR1B,CCNA2与成纤维细胞和滤泡干细胞有直接的功能关联,在毛囊的生长发育中起着重要作用。基于GO功能注释和KEGG富集分析,潜在的候选基因与毛囊发生和发育的途径相关(Notch,P13K-Akt,TGF-β,细胞周期,Wnt,MAPK)。我们计算内蒙古绒山羊群体的有效等位基因数为1.109-1.998,大多数SNP的优势基因型为野生型,57个SNP的多态性信息含量较低(0
G,chr10_g.82715068T>C,chr1_g.124483769C>T,chr24_g.12811352C>T,chr6_g.114111249A>G,在验证群体中,chr6_g.115606026T>C的基因分型显着(P<0.05)。
结论:结论:单个SNP对表型的遗传影响很小,SNP更倾向于整体继承。通过从与羊绒性状显著相关的SNP构建单倍型,这将有助于揭示内蒙古绒山羊绒类性状的复杂和潜在的因果变异。这将是羊绒山羊基因组学和育种的宝贵资源。
BACKGROUND: The cashmere goat industry is one of the main pillars of animal husbandry in Inner Mongolia Autonomous Region, and plays an irreplaceable role in local economic development. With the change in feeding methods and environment, the cashmere produced by Inner Mongolia cashmere goats shows a tendency of coarser, and the cashmere yield can not meet the consumption demand of people. However, the genetic basis behind these changes is not fully understood. We measured cashmere traits, including cashmere yield (CY), cashmere diameter (CD), cashmere thickness (CT), and fleece length (FL) traits for four consecutive years, and utilized Genome-wide association study of four cashmere traits in Inner Mongolia cashmere goats was carried out using new genomics tools to infer genomic regions and functional loci associated with cashmere traits and to construct
haplotypes that significantly affect cashmere traits.
RESULTS: We estimated the genetic parameters of cashmere traits in Inner Mongolia cashmere goats. The heritability of cashmere yield, cashmere diameter, and fleece length traits of Inner Mongolia cashmere goats were 0.229, 0.359, and 0.250, which belonged to the medium heritability traits (0.2 ~ 0.4). The cashmere thickness trait has a low heritability of 0.053. We detected 151 genome-wide significantly associated SNPs with four cashmere traits on different chromosomes, which were very close to the chromosomes of 392 genes (located within the gene or within ± 500 kb). Notch3, BMPR1B, and CCNA2 have direct functional associations with fibroblasts and follicle stem cells, which play important roles in hair follicle growth and development. Based on GO functional annotation and KEGG enrichment analysis, potential candidate genes were associated with pathways of hair follicle genesis and development (Notch, P13K-Akt, TGF-beta, Cell cycle, Wnt, MAPK). We calculated the effective allele number of the Inner Mongolia cashmere goat population to be 1.109-1.998, the dominant genotypes of most SNPs were wild-type, the polymorphic information content of 57 SNPs were low polymorphism (0 < PIC < 0.25), and the polymorphic information content of 79 SNPs were moderate polymorphism (0.25 < PIC < 0.50). We analyzed the association of SNPs with phenotypes and found that the homozygous mutant type of SNP1 and SNP3 was associated with the highest cashmere yield, the heterozygous mutant type of SNP30 was associated with the lowest cashmere thickness, the wild type of SNP76, SNP77, SNP78, SNP80, and SNP81 was associated with the highest cashmere thickness, and the wild type type of SNP137 was associated with the highest fleece length. 21 haplotype blocks and 68 haplotype combinations were constructed.
Haplotypes A2A2, B2B2, C2C2, and D4D4 were associated with increased cashmere yield,
haplotypes E2E2, F1F1, G5G5, and G1G5 were associated with decreased cashmere fineness,
haplotypes H2H2 was associated with increased cashmere thickness,
haplotypes I1I1, I1I2, J1J4, L5L3, N3N2, N3N3, O2O1, P2P2, and Q3Q3 were associated with increased cashmere length. We verified the polymorphism of 8 SNPs by KASP, and found that chr7_g.102631194A > G, chr10_g.82715068 T > C, chr1_g.124483769C > T, chr24_g.12811352C > T, chr6_g.114111249A > G, and chr6_g.115606026 T > C were significantly genotyped in verified populations (P < 0.05).
CONCLUSIONS: In conclusion, the genetic effect of single SNP on phenotypes is small, and SNPs are more inclined to be inherited as a whole. By constructing
haplotypes from SNPs that are significantly associated with cashmere traits, it will help to reveal the complex and potential causal variations in cashmere traits of Inner Mongolia cashmere goats. This will be a valuable resource for genomics and breeding of the cashmere goat.