中国美利奴羊（新疆型）毛品质性状全基因组关联分析

发布时间：2018-05-10 16:27

本文选题：中国美利奴羊(新疆型) + 毛品质性状　；参考：《石河子大学》2017年博士论文

【摘要】：细羊毛产量和质量决定了羊毛的经济价值,关系到羊毛产业的生产效益。发现和鉴定影响细羊毛产量和品质性状的基因或标记,是利用标记辅助选择策略开展细毛羊遗传育种的前提。本研究以中国美利奴羊(新疆型)为主要研究对象,围绕羊毛纤维直径和自然长度、伸直长度、伸直率等毛品质性状和产毛量,利用全集因组SNPs数据信息,结合连锁不平衡(Linkage Disequilibrium,LD)和全基因组关联分析(Genome-Wide Association Studies,GWAS)的方法,筛选和鉴定影响细毛羊上述主要毛品质性状的基因、标记和染色体的区域,为细毛羊分子育种奠定基础。1、中国美利奴羊(新疆型)是以生产优质细毛著称的品种,而对于该品种的LD研究尚未见深入报道。本研究利用635只中国美利奴羊(新疆型)的Illumina OvineSNP50 BeadChip分型数据,用Plink进行质量控制,标准设定为SNP检出率大于0.95,样本检测率大于0.95,最小等位基因频率大于0.05,哈代温伯格平衡检验显著性水平大于0.000001,去除性染色体,质控后,对26条常染色体上的46062个SNPs位点的分布和特征进行统计分析,根据连锁不平衡平方相关系数(r2)分别对常染色体组和每条常染色体进行计算,证实在中国美利奴羊(新疆型)0-10kb物理距离范围内属于中度连锁(r2≥0.25),并对每一条染色体上的连锁不平衡进行计算,其中r2最大的前四条染色体分别是OAR25和OAR24、OAR18、OAR10,在这些区域共注释与毛囊发育相关的基因47个;在LD分析的基础上,对中国美利奴羊(新疆型)七个世代(2000世代、1000世代、500世代、100世代、50世代、10世代、5世代)的有效群体大小(Effective population size,Ne)进行了估计,研究发现,中国美利奴羊有效群体大小随着世代的增加而减少,在50世代下降速度最快,这与该品种在上世纪七十年代大规模选育的历史相吻合;同时,中国美利奴羊(新疆型)在第十个世代,有效群体含量呈下降趋势,近期(五个世代)有效群体大小范围介于140.36到183.33只,从而证明了中国美利奴羊(新疆型)在近15年内有效群体在逐渐减少,须加大对这一品种遗传多样性的保护,这为中国美利奴羊(新疆型)群体的科学保护提供了理论依据。2、采用Illumina OvineSNP50 BeadChip基因芯片技术,首先,对中国美利奴羊(新疆型)和德国美利奴羊728只个体进行了SNP分型分析,完成了其中728只个体的羊毛纤维直径、364只个体的羊毛自然长度、伸直率、伸直长度以及产毛量性状的测量和整理;其次,对表型性状进行正态分布检验,发现伸直长度和产毛量符合正态分布,自然长度和纤维直径、伸直率不符合正态分布,对不符合正态分布的表型进行BoxCox分析,使其符合正态分布;再次,对研究群体进行主成份分析(Principal Component Analysis,PCA)发现在选择的资源群体中有分层现象,这可能给分析结果带来假阳性,为了得到准确的结果,对校正后的自然长度和质控后的SNPs分别构建广义线性模型(Generalized linear model,GLM)和混合线性模型(Mixed liner model,MLM),通过分位数-分位数(Quantile-Quantile,Q-Q)图,发现混合线性模型的观测值和期望值的基线吻合性优于广义线性模型,从而说明了混合线性模型更适合本研究的资源群体;然后,通过混合线性模型进行分析,得到35个显著的SNPs(P值0.05/47025=10-5.97),在SNPs附近共检测到41个基因,潜在相关的SNPs共38个(取最显著关联的SNPs标记的-log10(P值)下降3为潜在相关的SNPs标记);最后,选择s33115.1位点分别在中国美利奴羊(新疆型)和德国美利奴羊进行群体验证:在两个群体中,AA基因型对应的伸直长度与AB和BB两种基因型对应的伸直长度差异显著,AB和BB基因型对应的伸直长度之间差异不显著,两个群体中,基因型频率都以BB型为主,AA型频率最低,证明了该分析和全基因组关联分析的结果一致。本论文基于Illumina OvineSNP50 BeadChip基因芯片,建立了中国美利奴羊(新疆型)连锁不平衡和全基因组关联分析的技术平台,获得了中国美利奴羊(新疆型)SNPs图谱和其分布特征,在此基础上,筛选和挖掘与细毛羊羊毛品质性状相关的候选基因或标记,这为进一步研究和挖掘中国美利奴羊(新疆型)毛品质性状相关的候选基因或标记的分子调控机制奠定了基础。
[Abstract]:The production and quality of fine wool determines the economic value of wool, which is related to the production benefit of wool industry. The discovery and identification of genes or markers affecting the yield and quality of fine wool is the premise of using marker assisted selection strategy to carry out genetic breeding of fine wool sheep. The study is based on the Chinese Merino sheep (Xinjiang type) as the main research object. Wool fiber diameter and natural length, elongation length, elongation rate and other wool quality traits and wool yield were used to screen and identify the main wool quality of fine wool sheep by means of Linkage Disequilibrium, LD and whole genome association analysis (Genome-Wide Association Studies, GWAS) in complete set of SNPs data. The genes, markers and chromosomes of the traits have laid the foundation for the breeding of fine wool sheep, and the Chinese Merino sheep (Xinjiang type) is famous for producing fine fine hair, while the LD study of this breed has not been reported in depth. This study uses the Illumina OvineSNP50 BeadChip typing data of 635 Chinese Merino sheep (Xinjiang type). Using Plink for quality control, the standard set is that the detection rate of SNP is greater than 0.95, the sample detection rate is greater than 0.95, the minimum allele frequency is more than 0.05, the Hardy Weinberg balance test is more significant than 0.000001, and the distribution and characteristics of 46062 SNPs loci on the 26 autosomes are statistically analyzed. The linkage disequilibrium square correlation coefficient (R2) was used to calculate the autosomes and each autosomes respectively. It was proved that in the physical distance range of the Chinese Merino sheep (Xinjiang type), the 0-10kb physical distance was a moderate linkage (R2 > 0.25), and the linkage disequilibrium on each chromosome was calculated, of which the largest four chromosomes of the R2 were OAR25, respectively. A total of 47 genes related to hair follicle development were annotated with OAR24, OAR18, OAR10, and on the basis of LD analysis, the effective population size (Effective population size, Ne) of seven generations (2000, 1000, 500, 100, 50, 10, 5) of Chinese Merino sheep (Xinjiang type) was estimated. The effective population size of Chinese Merino sheep decreased with the increase of generation and the fastest decline in the 50 generation, which coincided with the history of large-scale breeding in 70s of last century. At the same time, the Chinese Merino sheep (Xinjiang type) was in tenth generations, the effective population showed a decline trend, and the recent (five generation) effective population size. The range of 140.36 to 183.33 only proves that the effective population of the Chinese Merino sheep (Xinjiang type) is gradually decreasing in the last 15 years. It is necessary to increase the protection of the genetic diversity of this breed. This provides a theoretical basis for the scientific protection of the Chinese Merino sheep (Xinjiang type) group by.2, using the Illumina OvineSNP50 BeadChip gene chip technology, First, 728 individuals of the Chinese Merino sheep (Xinjiang type) and German Merino sheep were analyzed by SNP typing. The wool fiber diameter of 728 of them, the natural length of 364 wool, the straightening rate, the elongation length and the wool yield were measured and arranged. Secondly, the normal distribution of the phenotypic characters was tested and the extension was found. The direct length and wool yield conforms to the normal distribution, the natural length and fiber diameter, the elongation does not conform to the normal distribution, and the BoxCox analysis of the phenotypes that do not conform to the normal distribution makes it conform to the normal distribution; thirdly, the principal component analysis (Principal Component Analysis, PCA) of the study group is found to be stratified among the selected resource groups. In order to get the exact result, the generalized linear model (Generalized linear model, GLM) and the mixed linear model (Mixed liner model, MLM) are constructed respectively for the corrected natural length and the SNPs after the quality control, and the mixed linear model is found by the fractional number of quantiles (Quantile-Quantile, Q-Q), and the mixed linear model is found. The baseline agreement between the observed values and the expected values is better than that of the generalized linear model, which shows that the mixed linear model is more suitable for the resource groups of this study. Then, 35 significant SNPs (P values 0.05/47025=10-5.97) are obtained by the mixed linear model, and 41 genes are detected near SNPs, and the potential related SNPs is 38. The -log10 (P value) of the significantly associated SNPs markers decreased by 3 for the potentially related SNPs markers. Finally, the selection of s33115.1 loci in Chinese Merino sheep (Xinjiang type) and German Merino sheep showed that the extension length corresponding to the AA genotype corresponding to the two genotypes of AB and BB was significantly different in the two populations, AB and BB. There was no significant difference between the length of the genotypes. Among the two groups, the genotype frequency was BB type and the AA type was the lowest. It proved that the analysis was consistent with the result of the whole genome association analysis. Based on the Illumina OvineSNP50 BeadChip gene chip, the linkage disequilibrium and full base of the Chinese Merino sheep (Xinjiang type) were established. Based on the technical platform of group association analysis, the SNPs map and its distribution characteristics of Chinese Merino sheep (Xinjiang type) were obtained. On this basis, the candidate genes or markers related to the quality traits of fine wool sheep wool were screened and excavated. This is the candidate genes or markers related to the wool quality traits of the Chinese Merino sheep (Xinjiang type). The mechanism of molecular regulation has laid the foundation.

【学位授予单位】：石河子大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：S826

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