發(fā)布時(shí)間：2018-05-10 16:27

  本文選題：中國(guó)美利奴羊(新疆型) + 毛品質(zhì)性狀��； 參考：《石河子大學(xué)》2017年博士論文

【摘要】：細(xì)羊毛產(chǎn)量和質(zhì)量決定了羊毛的經(jīng)濟(jì)價(jià)值,關(guān)系到羊毛產(chǎn)業(yè)的生產(chǎn)效益。發(fā)現(xiàn)和鑒定影響細(xì)羊毛產(chǎn)量和品質(zhì)性狀的基因或標(biāo)記,是利用標(biāo)記輔助選擇策略開展細(xì)毛羊遺傳育種的前提。本研究以中國(guó)美利奴羊(新疆型)為主要研究對(duì)象,圍繞羊毛纖維直徑和自然長(zhǎng)度、伸直長(zhǎng)度、伸直率等毛品質(zhì)性狀和產(chǎn)毛量,利用全集因組SNPs數(shù)據(jù)信息,結(jié)合連鎖不平衡(Linkage Disequilibrium,LD)和全基因組關(guān)聯(lián)分析(Genome-Wide Association Studies,GWAS)的方法,篩選和鑒定影響細(xì)毛羊上述主要毛品質(zhì)性狀的基因、標(biāo)記和染色體的區(qū)域,為細(xì)毛羊分子育種奠定基礎(chǔ)。1、中國(guó)美利奴羊(新疆型)是以生產(chǎn)優(yōu)質(zhì)細(xì)毛著稱的品種,而對(duì)于該品種的LD研究尚未見深入報(bào)道。本研究利用635只中國(guó)美利奴羊(新疆型)的Illumina OvineSNP50 BeadChip分型數(shù)據(jù),用Plink進(jìn)行質(zhì)量控制,標(biāo)準(zhǔn)設(shè)定為SNP檢出率大于0.95,樣本檢測(cè)率大于0.95,最小等位基因頻率大于0.05,哈代溫伯格平衡檢驗(yàn)顯著性水平大于0.000001,去除性染色體,質(zhì)控后,對(duì)26條常染色體上的46062個(gè)SNPs位點(diǎn)的分布和特征進(jìn)行統(tǒng)計(jì)分析,根據(jù)連鎖不平衡平方相關(guān)系數(shù)(r2)分別對(duì)常染色體組和每條常染色體進(jìn)行計(jì)算,證實(shí)在中國(guó)美利奴羊(新疆型)0-10kb物理距離范圍內(nèi)屬于中度連鎖(r2≥0.25),并對(duì)每一條染色體上的連鎖不平衡進(jìn)行計(jì)算,其中r2最大的前四條染色體分別是OAR25和OAR24、OAR18、OAR10,在這些區(qū)域共注釋與毛囊發(fā)育相關(guān)的基因47個(gè);在LD分析的基礎(chǔ)上,對(duì)中國(guó)美利奴羊(新疆型)七個(gè)世代(2000世代、1000世代、500世代、100世代、50世代、10世代、5世代)的有效群體大小(Effective population size,Ne)進(jìn)行了估計(jì),研究發(fā)現(xiàn),中國(guó)美利奴羊有效群體大小隨著世代的增加而減少,在50世代下降速度最快,這與該品種在上世紀(jì)七十年代大規(guī)模選育的歷史相吻合;同時(shí),中國(guó)美利奴羊(新疆型)在第十個(gè)世代,有效群體含量呈下降趨勢(shì),近期(五個(gè)世代)有效群體大小范圍介于140.36到183.33只,從而證明了中國(guó)美利奴羊(新疆型)在近15年內(nèi)有效群體在逐漸減少,須加大對(duì)這一品種遺傳多樣性的保護(hù),這為中國(guó)美利奴羊(新疆型)群體的科學(xué)保護(hù)提供了理論依據(jù)。2、采用Illumina OvineSNP50 BeadChip基因芯片技術(shù),首先,對(duì)中國(guó)美利奴羊(新疆型)和德國(guó)美利奴羊728只個(gè)體進(jìn)行了SNP分型分析,完成了其中728只個(gè)體的羊毛纖維直徑、364只個(gè)體的羊毛自然長(zhǎng)度、伸直率、伸直長(zhǎng)度以及產(chǎn)毛量性狀的測(cè)量和整理;其次,對(duì)表型性狀進(jìn)行正態(tài)分布檢驗(yàn),發(fā)現(xiàn)伸直長(zhǎng)度和產(chǎn)毛量符合正態(tài)分布,自然長(zhǎng)度和纖維直徑、伸直率不符合正態(tài)分布,對(duì)不符合正態(tài)分布的表型進(jìn)行BoxCox分析,使其符合正態(tài)分布;再次,對(duì)研究群體進(jìn)行主成份分析(Principal Component Analysis,PCA)發(fā)現(xiàn)在選擇的資源群體中有分層現(xiàn)象,這可能給分析結(jié)果帶來(lái)假陽(yáng)性,為了得到準(zhǔn)確的結(jié)果,對(duì)校正后的自然長(zhǎng)度和質(zhì)控后的SNPs分別構(gòu)建廣義線性模型(Generalized linear model,GLM)和混合線性模型(Mixed liner model,MLM),通過(guò)分位數(shù)-分位數(shù)(Quantile-Quantile,Q-Q)圖,發(fā)現(xiàn)混合線性模型的觀測(cè)值和期望值的基線吻合性優(yōu)于廣義線性模型,從而說(shuō)明了混合線性模型更適合本研究的資源群體;然后,通過(guò)混合線性模型進(jìn)行分析,得到35個(gè)顯著的SNPs(P值0.05/47025=10-5.97),在SNPs附近共檢測(cè)到41個(gè)基因,潛在相關(guān)的SNPs共38個(gè)(取最顯著關(guān)聯(lián)的SNPs標(biāo)記的-log10(P值)下降3為潛在相關(guān)的SNPs標(biāo)記);最后,選擇s33115.1位點(diǎn)分別在中國(guó)美利奴羊(新疆型)和德國(guó)美利奴羊進(jìn)行群體驗(yàn)證:在兩個(gè)群體中,AA基因型對(duì)應(yīng)的伸直長(zhǎng)度與AB和BB兩種基因型對(duì)應(yīng)的伸直長(zhǎng)度差異顯著,AB和BB基因型對(duì)應(yīng)的伸直長(zhǎng)度之間差異不顯著,兩個(gè)群體中,基因型頻率都以BB型為主,AA型頻率最低,證明了該分析和全基因組關(guān)聯(lián)分析的結(jié)果一致。本論文基于Illumina OvineSNP50 BeadChip基因芯片,建立了中國(guó)美利奴羊(新疆型)連鎖不平衡和全基因組關(guān)聯(lián)分析的技術(shù)平臺(tái),獲得了中國(guó)美利奴羊(新疆型)SNPs圖譜和其分布特征,在此基礎(chǔ)上,篩選和挖掘與細(xì)毛羊羊毛品質(zhì)性狀相關(guān)的候選基因或標(biāo)記,這為進(jìn)一步研究和挖掘中國(guó)美利奴羊(新疆型)毛品質(zhì)性狀相關(guān)的候選基因或標(biāo)記的分子調(diào)控機(jī)制奠定了基礎(chǔ)。
[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.

【學(xué)位授予單位】：石河子大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2017
【分類號(hào)】：S826

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2 李建華;綿羊NOS基因的克隆及其在布魯氏菌侵染過(guò)程中的作用[D];石河子大學(xué);2015年

3 于常江;綿羊EIF3L、EIF3H、EEF1D基因克隆表達(dá)及對(duì)羊毛生長(zhǎng)相關(guān)因子的影響[D];塔里木大學(xué);2017年

4 趙玉民;中國(guó)美利奴羊育成母羊能量和蛋白質(zhì)需要研究[D];延邊大學(xué);2005年

5 馬依拉·吐爾遜;6個(gè)KRT基因在中國(guó)美利奴羊（新疆型）中的遺傳多態(tài)性及其與毛性狀的關(guān)聯(lián)性分析[D];新疆農(nóng)業(yè)大學(xué);2013年

6 艾買提·買買提;5個(gè)KAP基因在中國(guó)美利奴羊（新疆型）群體中的多態(tài)性及其與毛性狀關(guān)聯(lián)性分析[D];新疆農(nóng)業(yè)大學(xué);2013年

7 段新華;中國(guó)美利奴羊及其它三個(gè)綿羊品種的RAPD分析[D];新疆農(nóng)業(yè)大學(xué);2002年

8 努爾比亞·吾布力;應(yīng)用MTDFREML法和動(dòng)物模型BLUP對(duì)中國(guó)美利奴羊（新疆型）遺傳參數(shù)估計(jì)和遺傳評(píng)定[D];新疆農(nóng)業(yè)大學(xué);2012年

9 朱二勇;BMPR-IB基因作為新疆幾種綿羊多胎性能候選基因的研究[D];新疆農(nóng)業(yè)大學(xué);2006年

10 溫青娜;哈薩克羊和中國(guó)美利奴羊DRB1基因SSCP多態(tài)性與細(xì)粒棘球蚴病遺傳抗性的關(guān)聯(lián)分析[D];石河子大學(xué);2010年

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