中国荷斯坦牛乳成分性状候选基因的鉴定及其遗传效应分析

发布时间：2018-01-19 10:34

  本文关键词： 牛乳成分 候选基因 全基因组关联分析 转录组测序 遗传效应分析　出处：《中国农业大学》2016年博士论文　论文类型：学位论文

【摘要】：挖掘与鉴定影响奶牛乳成分性状的关键基因或致因突变是实施奶牛低脂高蛋白新品系分子培育的前提与基础。本研究旨在利用基因组学、转录组学、生物信息学、统计遗传学等技术,鉴定影响奶牛乳成分性状(乳脂肪酸和乳蛋白)的候选基因及SNPs,进而对其进行大群体遗传效应分析,以确定真正的致因基因或是遗传效应较大的基因。利用全基因组关联分析(GWAS)鉴定牛乳脂肪酸含量候选基因。以北京地区18个牛场的21头公牛家系的784头中国荷斯坦母牛为研究群体,以Illumina BovineSNP50芯片为基因型,气相色谱法获得22个脂肪酸性状的含量为表型,采用PLINK软件进行GWAS。分析共发现84个全基因组显著水平SNPs和314个潜在显著SNPs同18个脂肪酸性状关联,主要位于BTA5、10、14、17和26上；一些显著SNPs位于或距离很近同已知影响乳成分性状的DGAT1、FASN、 SCD等18个功能基因；结合乳成分QTL区域及基因功能注释,提出了20个新的候选基因：HTR1B、 CPM、 PRKG1、 MINPP1、 LIPJ、LIPK、EHHADH, MOGAT1、 ECHS1、 STAT1、 SORBS1、 NFKB2、 AGPAT3、CHUK、OSBPL8、PRLR、IGF1R、ACSL3、GHR和OXCT1,影响C10:0、C12:0、C14:0、C14：1、C14指数、C18:0、C18:1n9c、C18指数、SFA、UFA和SFA/UFA。利用转录组测序(RNA-Seq)鉴定牛乳蛋白性状候选基因。以2个泌乳期(泌乳高峰期和干奶期)下6头高乳蛋白率和6头低乳蛋白率的中国荷斯坦牛活体取样的乳腺组织为研究对象进行RNA-Seq,在牛已注释的27,544个基因中,约有20,000个基因在乳腺组织广泛表达。结果分别鉴定到高峰期下高低蛋白组、干奶期下高低蛋白组、泌乳期比较组差异表达基因157、497和5,488个。整合分析确定了10个影响乳蛋白性状的已知候选基因：WAP、NARS、MARS、GARS、CDO1、 GATM、INSR、IGF1R、IGFBP3 和CRIM1;并提出10个新的候选基因：SERPINA1、CLU、CNTFR、 ERBB2、NEDD4L、ANG、GALE、HSPA8、LPAR6和CD14。针对以上鉴定到的乳成分性状候选基因,挑选5个影响乳脂肪酸含量的候选基因SCD、FASN、 PPARGC1A、 ABCG2和IGF1于13个牛场的13个公牛家系的346头中国荷斯坦母牛群体中进行遗传效应分析。结果验证了功能基因FASN、SCD及PPARGC1A对牛乳脂肪酸含量的效应导致了其临近SNPs在GWAS中的显著；揭示了SCD主要影响中长链不饱和脂肪酸,特别是C14：1和C14指数性状；FASN、PPARGC1A、ABCG2和IGFl主要影响中链饱和脂肪酸和长链不饱和脂肪酸。挑选4个影响乳蛋白性状的候选基因于17个牛场的17个公牛家系的1,027头中国荷斯坦母牛群体中开展遗传效应分析,从基因组水平验证了4个候选基因SERPINA1、GALE、HSPA8和ERBB2对奶牛乳蛋白性状的显著遗传效应。本研究进一步明确并缩小了影响乳成分性状的基因组区域,为后续基因精细定位揭示致因基因或突变提供了基础；提出的影响乳脂肪酸和乳蛋白性状的已知和新的候选基因,为深入阐明乳脂乳蛋白合成代谢调控机制提供了基础,为后续开展分子标记辅助选择等育种措施培育低脂高蛋白奶牛新品系提供了基因来源和原动力。
[Abstract]:It is the premise and foundation of molecular cultivation of dairy cow low fat and high protein new line to excavate and identify the key genes or cause mutation that affect dairy cow milk composition character. This study aims to utilize genomics and transcriptome. Bioinformatics, statistical genetics and other techniques were used to identify candidate genes and SNPs that affect milk composition traits (milk fatty acids and milk proteins) of dairy cows, and then to analyze their genetic effects in large populations. To identify the true cause genes or genes with larger genetic effects. GWASA using genome-wide association analysis. To identify the candidate genes for fatty acid content in milk, 784 Chinese Holstein cows from 21 bull families in 18 cattle farms in Beijing were studied. The phenotype of 22 fatty acid characters was obtained by gas chromatography using Illumina BovineSNP50 microarray as genotype. A total of 84 genomic significant level SNPs and 314 potentially significant SNPs were found to be associated with 18 fatty acid traits, mainly located in BTA5. 10, 14, 17 and 26; Some significant SNPs were located in or close to the same 18 functional genes as DGAT1FASN, SCD and so on, which were known to affect milk component traits. In combination with the QTL region and gene function annotation of milk components, 20 new candidate genes, namely: HTR1B, CPM, PRKG1, MINPP1, LIPJNLIPK, were proposed. EHHADH, MOGAT1, ECHS1, STAT1, SORBS1, NFKB2, AGPAT3,CHUK,OSBPL8,PRLR. IGF1RU ACSL3 / GHR and OXCT1 affect C10: 0, C12: 0, C14: 0, C14: 1, C14, C18: 0, C181: 1n9c. C18 index SFA. UFA and SFA-UFA.Identification of milk protein candidate genes by RNA-Seq. two lactation periods (peak lactation and dry milk). RNA-Seq was performed on the breast tissues of 6 Chinese Holstein cattle with high milk protein rate and six low milk protein rates. Of the 27,544 annotated genes, about 20,000 genes were widely expressed in breast tissues. There were 157,497 and 5,488 differentially expressed genes in the lactation period comparison group. Ten known candidate genes that affect milk protein traits were identified by integration analysis: WAPN NARSSMARS. GARSU CDO1, GATMNSRIGF1RP3-IGFBP3 and CRIM1; Ten new candidate genes, namely: SERPINA1 / CLU CNTFR, ERBB2 / NEDD4L / ANGGALE / HSPA8, were proposed. LPAR6 and CD14. five candidate genes, SCDFASN, PPARGC1A, which affect the content of fatty acid in milk, were selected according to the above identified candidate genes for milk component traits. The genetic effects of ABCG2 and IGF1 were analyzed in 346 Chinese Holstein cows from 13 cattle families in 13 cattle farms. The results confirmed the functional gene FASN. The effects of SCD and PPARGC1A on the content of fatty acids in milk resulted in the significant presence of SNPs in GWAS. It was revealed that SCD mainly affected the middle and long chain unsaturated fatty acids, especially C14: 1 and C14 index. FASN,PPARGC1A. ABCG2 and IGFl mainly affected middle chain saturated fatty acids and long chain unsaturated fatty acids. Four candidate genes affecting milk protein traits were selected from 17 bull families in 17 cattle farms. Genetic effect analysis was carried out in 027 Chinese Holstein cows. Four candidate genes SERPINA1Gale were verified at genomic level. The significant genetic effects of HSPA8 and ERBB2 on dairy cow milk protein traits. It provides a basis for the subsequent gene fine mapping to reveal the cause gene or mutation. The known and new candidate genes which affect the characteristics of milk fatty acids and milk proteins provide the basis for further elucidation of the regulation mechanism of the synthesis and metabolism of milk fat milk proteins. It provides the gene source and motive force for breeding low fat and high protein dairy cow by molecular marker-assisted selection.
【学位授予单位】：中国农业大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S823
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本文编号：1443788