本文關(guān)鍵詞： 牛乳成分 候選基因 全基因組關(guān)聯(lián)分析 轉(zhuǎn)錄組測(cè)序 遺傳效應(yīng)分析　出處：《中國(guó)農(nóng)業(yè)大學(xué)》2016年博士論文　論文類(lèi)型：學(xué)位論文

【摘要】：挖掘與鑒定影響奶牛乳成分性狀的關(guān)鍵基因或致因突變是實(shí)施奶牛低脂高蛋白新品系分子培育的前提與基礎(chǔ)。本研究旨在利用基因組學(xué)、轉(zhuǎn)錄組學(xué)、生物信息學(xué)、統(tǒng)計(jì)遺傳學(xué)等技術(shù),鑒定影響奶牛乳成分性狀(乳脂肪酸和乳蛋白)的候選基因及SNPs,進(jìn)而對(duì)其進(jìn)行大群體遺傳效應(yīng)分析,以確定真正的致因基因或是遺傳效應(yīng)較大的基因。利用全基因組關(guān)聯(lián)分析(GWAS)鑒定牛乳脂肪酸含量候選基因。以北京地區(qū)18個(gè)牛場(chǎng)的21頭公牛家系的784頭中國(guó)荷斯坦母牛為研究群體,以Illumina BovineSNP50芯片為基因型,氣相色譜法獲得22個(gè)脂肪酸性狀的含量為表型,采用PLINK軟件進(jìn)行GWAS。分析共發(fā)現(xiàn)84個(gè)全基因組顯著水平SNPs和314個(gè)潛在顯著SNPs同18個(gè)脂肪酸性狀關(guān)聯(lián),主要位于BTA5、10、14、17和26上；一些顯著SNPs位于或距離很近同已知影響乳成分性狀的DGAT1、FASN、 SCD等18個(gè)功能基因；結(jié)合乳成分QTL區(qū)域及基因功能注釋,提出了20個(gè)新的候選基因：HTR1B、 CPM、 PRKG1、 MINPP1、 LIPJ、LIPK、EHHADH, MOGAT1、 ECHS1、 STAT1、 SORBS1、 NFKB2、 AGPAT3、CHUK、OSBPL8、PRLR、IGF1R、ACSL3、GHR和OXCT1,影響C10:0、C12:0、C14:0、C14：1、C14指數(shù)、C18:0、C18:1n9c、C18指數(shù)、SFA、UFA和SFA/UFA。利用轉(zhuǎn)錄組測(cè)序(RNA-Seq)鑒定牛乳蛋白性狀候選基因。以2個(gè)泌乳期(泌乳高峰期和干奶期)下6頭高乳蛋白率和6頭低乳蛋白率的中國(guó)荷斯坦�；铙w取樣的乳腺組織為研究對(duì)象進(jìn)行RNA-Seq,在牛已注釋的27,544個(gè)基因中,約有20,000個(gè)基因在乳腺組織廣泛表達(dá)。結(jié)果分別鑒定到高峰期下高低蛋白組、干奶期下高低蛋白組、泌乳期比較組差異表達(dá)基因157、497和5,488個(gè)。整合分析確定了10個(gè)影響乳蛋白性狀的已知候選基因：WAP、NARS、MARS、GARS、CDO1、 GATM、INSR、IGF1R、IGFBP3 和CRIM1;并提出10個(gè)新的候選基因：SERPINA1、CLU、CNTFR、 ERBB2、NEDD4L、ANG、GALE、HSPA8、LPAR6和CD14。針對(duì)以上鑒定到的乳成分性狀候選基因,挑選5個(gè)影響乳脂肪酸含量的候選基因SCD、FASN、 PPARGC1A、 ABCG2和IGF1于13個(gè)牛場(chǎng)的13個(gè)公牛家系的346頭中國(guó)荷斯坦母牛群體中進(jìn)行遺傳效應(yīng)分析。結(jié)果驗(yàn)證了功能基因FASN、SCD及PPARGC1A對(duì)牛乳脂肪酸含量的效應(yīng)導(dǎo)致了其臨近SNPs在GWAS中的顯著；揭示了SCD主要影響中長(zhǎng)鏈不飽和脂肪酸,特別是C14：1和C14指數(shù)性狀；FASN、PPARGC1A、ABCG2和IGFl主要影響中鏈飽和脂肪酸和長(zhǎng)鏈不飽和脂肪酸。挑選4個(gè)影響乳蛋白性狀的候選基因于17個(gè)牛場(chǎng)的17個(gè)公牛家系的1,027頭中國(guó)荷斯坦母牛群體中開(kāi)展遺傳效應(yīng)分析,從基因組水平驗(yàn)證了4個(gè)候選基因SERPINA1、GALE、HSPA8和ERBB2對(duì)奶牛乳蛋白性狀的顯著遺傳效應(yīng)。本研究進(jìn)一步明確并縮小了影響乳成分性狀的基因組區(qū)域,為后續(xù)基因精細(xì)定位揭示致因基因或突變提供了基礎(chǔ)；提出的影響乳脂肪酸和乳蛋白性狀的已知和新的候選基因,為深入闡明乳脂乳蛋白合成代謝調(diào)控機(jī)制提供了基礎(chǔ),為后續(xù)開(kāi)展分子標(biāo)記輔助選擇等育種措施培育低脂高蛋白奶牛新品系提供了基因來(lái)源和原動(dòng)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.
【學(xué)位授予單位】：中國(guó)農(nóng)業(yè)大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類(lèi)號(hào)】：S823
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本文編號(hào)：1443788