Lu Xiaotian, Suo Langda, Yan Xiaochun, Li Wenze, Su Yixin, Zhou Bohan, Liu Can, Yang Lepu, Wang Jiayin, Ji De, Cuomu Renqing, Cuoji Awang, Gui Ba, Wang Zhiying, Jiang Wei, Wu Yujiang, Su Rui
Institute of Animal Science, Xizang Academy of Agricultural and Animal Husbandry Science, Lhasa, China.
College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China.
Front Vet Sci. 2024 May 30;11:1409084. doi: 10.3389/fvets.2024.1409084. eCollection 2024.
Northwest Xizang White Cashmere Goat (NXWCG) is the first new breed of cashmere goat in the Xizang Autonomous Region. It has significant characteristics of extremely high fineness, gloss, and softness. Genome-wide association analysis is an effective biological method used to measure the consistency and correlation of genotype changes between two molecular markers in the genome. In addition, it can screen out the key genes affecting the complex traits of biological individuals. The aim of this study was to analyze the genetic mechanism of cashmere trait variation in NXWCG and to discover SNP locus and key genes closely related to traits such as superfine cashmere. Additionally, the key genes near the obtained significant SNPs were analyzed by gene function annotation and biological function mining. In this study, the phenotype data of the four traits (cashmere length, fiber length, cashmere diameter, and cashmere production) were collected. GGP_Goat_70K SNP chip was used for genotyping the ear tissue DNA of the experimental group. Subsequently, the association of phenotype data and genotype data was performed using Gemma-0.98.1 software. A linear mixed model was used for the association study. The results showed that four fleece traits were associated with 18 significant SNPs at the genome level and 232 SNPs at the chromosome level, through gene annotated from genome using assembly ARS1. A total of 107 candidate genes related to fleece traits were obtained. Combined with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, we can find that , , , , , and can be used as important candidate genes for fleece traits of NXWCG. We used Sanger sequencing and suitability chi-square test to further verify the significant loci and candidate genes screened by GWAS, and the results show that the base mutations loci on the five candidate genes, (snp12579, 34,449,796, A → G), (snp41503, 69,173,527, A → G), (snp41082, 67,134,820, G → A), (14:78472665, 78,472,665, G → A), and (12: 9705753, 9,705,753, C → T), significantly affect the fleece traits of NXWCG. The results provide a valuable basis for future research and contribute to a better understanding of the genetic structure variation of the goat.
藏西北白绒山羊（NXWCG）是西藏自治区首个绒山羊新品种。它具有极高细度、光泽度和柔软度等显著特征。全基因组关联分析是一种有效的生物学方法，用于测量基因组中两个分子标记之间基因型变化的一致性和相关性。此外，它还可以筛选出影响生物个体复杂性状的关键基因。本研究的目的是分析藏西北白绒山羊羊绒性状变异的遗传机制，发现与超细羊绒等性状密切相关的SNP位点和关键基因。此外，通过基因功能注释和生物学功能挖掘对获得的显著SNP附近的关键基因进行分析。在本研究中，收集了四个性状（羊绒长度、纤维长度、羊绒直径和产绒量）的表型数据。使用GGP_Goat_70K SNP芯片对实验组耳组织DNA进行基因分型。随后，使用Gemma - 0.98.1软件进行表型数据和基因型数据的关联分析。采用线性混合模型进行关联研究。结果表明，通过使用组装ARS1从基因组中注释基因，四个羊毛性状在基因组水平上与18个显著SNP相关，在染色体水平上与232个SNP相关。共获得107个与羊毛性状相关的候选基因。结合基因本体论和京都基因与基因组百科全书富集分析，我们发现， ， ， ， ， 和 可作为藏西北白绒山羊羊毛性状的重要候选基因。我们使用桑格测序和适合度卡方检验进一步验证GWAS筛选出的显著位点和候选基因，结果表明五个候选基因上的碱基突变位点， （snp12579，34449796，A→G）， （snp41503，69173527，A→G）， （snp41082，67134820，G→A）， （14:78472665，78472665，G→A），和 （12: 9705753，9705753，C→T），显著影响藏西北白绒山羊的羊毛性状。这些结果为未来的研究提供了有价值的依据，有助于更好地理解山羊的遗传结构变异。
