黄牛NPM1、SREBP1c基因的克隆、SNPs检测及其与生长性状的关系
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摘要
本研究分别以南阳牛、秦川牛、郏县红牛、中国荷斯坦牛4个群体共1035份血样和秦川牛的组织样为材料,分别提取基因组DNA和RNA。
     运用反转录PCR、DNA测序和DNA序列分析,对牛的核仁磷酸蛋白1(NPM1)基因的CDS序列进行了克隆、鉴定与序列分析。
     运用黄牛混合DNA池测序技术和PCR-SSCP、PCR-RFLP、Forced PCR-RFLP相结合的方法,分析了黄牛核仁磷酸蛋白1(NPM1)基因(1个外显子构成)和固醇调节元件结合蛋白1(SREBP1c)基因(21个外显子构成)共2个候选基因22个外显子和20个内含子的遗传变异;并对南阳牛、秦川牛和郏县红牛3个群体在上述基因的SNPs位点与其生长性状进行了相关分析;以检验候选基因的SNPs位点对3个黄牛群体生长发育的遗传效应,以期发现对重要经济性状具有显著效应的遗传标记。为中国黄牛的高效选育和分子标记数据库的建立、种质资源保存与利用提供遗传学依据。
     本研究得到了以下结果:
     1.黄牛NPM1基因的克隆、鉴定及生物信息学分析
     利用反转录PCR(RT-PCR)技术,对牛NPM1基因进行克隆,将得到的片段重组到pGM-T载体进行序列测定。获得了一个长为885bp的cDNA片断。通过氨基酸序列分析发现,牛NPM1基因的该片段由1个外显子组成,编码295个氨基酸。与其他动物同源性比较表明,该基因与猪、犬、人、猕猴、大鼠、小鼠、原鸡和斑马鱼在氨基酸序列上分别有92.1%、91.9%、92.0%、90.7%、89.1%、88.5%、72.2%、52.8%的同源性。组织表达谱分析表明,黄牛NPM1基因在肾脏,肝脏,肺,小肠,脾脏和肌肉组织中广泛表达。
     2. NPM1基因SNPs检测及其与南阳牛、秦川牛和郏县红牛生长性状的关联分析
     运用黄牛混合DNA池测序法寻找牛NPM1基因的SNPs,在整个编码区(1个外显子:885 bp)共检测到6个SNPs和第634bp~645bp之间一处12-bp的缺失突变。其中,236C>G和636A>C为错义突变,其它4个SNPs为同义突变,并且489G>A, 516G>A, 624T>C, 630T>C和636A>C 5个SNPs为连锁突变。
     关联分析结果显示,在南阳牛群体中,不同基因型对初生重、6月龄个体的体长、6月龄和12月龄个体胸围、12月龄个体的体重和体长、18月龄体重显著相关,突变型个体大于野生型(P<0.05)。在秦川牛群体中,不同基因型对体重、胸围、腰角宽、胸深、体高、体斜长和十字部高,共11项指标显著相关,突变型个体大于野生型(P<0.05)。在郏县红牛群体中,不同基因型对6月龄体重和平均日增重、12月龄胸围、24月龄个体坐骨端宽显著相关,突变型个体大于野生型(P<0.01或者P<0.05)。
     3. SREBP1c基因SNPs检测及其与南阳牛、秦川牛和郏县红牛生长性状的关联分析
     运用黄牛混合DNA池测序法寻找牛SREBP1c基因的SNPs,共检测到7个SNPs和内含子7区域一处84-bp的缺失突变。其中,9807G>A、10914G>A、12020 C>T和13603 T>C为4个错义突变,10781C>G为同义突变。
     关联分析结果显示,在南阳牛群体中,不同基因型对初生重,6、12、18月龄体重和平均日增重,24月龄体重显著相关,野生型个体大于突变型个体(P<0.05)。在秦川牛群体中,不同基因型对体重、荐高、体高、体斜长、胸围、管围、坐骨端宽、腰角宽、十字部高、胸深和胸宽显著相关,突变杂合型个体大于野生型(P<0.01或者P<0.05)。在郏县红牛群体中,不同基因型对6月龄体重、体斜长、平均日增重、胸围和坐骨端宽,12月龄体重、胸围、坐骨端宽,18和24月龄的体斜长、体重和胸围,18月龄的平均日增重显著相关,突变杂合型个体大于野生型(P<0.05)。
In this study, 1035 blood samples from 4 cattle populations- Nanyang, Qinchuan, Jiaxian Red, and Chinese Holstein were collected to extract genomic DNA, and some tissues samples from Qinchuan were taken to extract total RNA.
     The clone, identification and sequence analysis to the CDS of bovine Nucleophosmin 1 (NPM1) gene by reverse transcription PCR, DNA sequencing and DNA sequence analysis.
     Genetic variation of NPM1 and SREBP1c genes were detected by DNA sequencing, PCR-SSCP, PCR-RFLP and Forced PCR-RFLP techniques 22 exons and 20 introns in the 2 candidate genes, and association analysis were carried out to evaluate the effects of genotypes of candidate genes on growth traits of three Chinese cattle (Nanyang, Qinchuan and Jiaxian Red). The objects were to discovery the hereditary characteristics and to explore molecular markers with significant effects on economic important traits for efficient selection and improvement of Chinese cattle, and to provide genetic information for foundation of molecular marker database, protection and usage of breed resource of Chinese cattle. The results were as follows:
     1. The clone identification and bioinformatics analysis of bovine NPM1 gene
     Bovine NPM1 gene cDNA by RT-PCR, the product was cloned in pGM-T vector. The sequencing result showed that the fragment sequence coincided with the prediction, which is 885 bp long. The analysis of amino acid sequence indicated that cattle NPM1 gene consisted 1 exon and coded 295 amino acids. Homologous comparison with some animals indicated that cattle NPM1 cDNA shared 92.1%、91.9%、92.0%、90.7%、89.1%、88.5%、72.2%、52.8% similarity in nucleic acid sequence with Sus scrofa, Canis familiaris, Homo sapiens, Macaca mulatta, Rattus norvegicus, Mus musculus, Gallus gallus and danio rerio. Bovine NPM1 gene cDNA was found in kidny, muscle, liver, small intestine, spleen and lung tissues by the analysis of its expression in various tissues.
     2. SNPs detection of NPM1 gene and their assosiation between growth traits in Nanyang, Qinchuan and Jiaxian Red cattle
     SNPs were detected in the exon from 4 cattle breeds in China. Comparison between the nucleotide sequences of the bovine NPM1 gene and the above sequences revealed 6 SNPs and 12-bp deletion in the coding region nt634bp~645bp of the NPM1 gene. Moreover, the SNPs at nt489, nt516, nt624, nt630 and nt636 are linked completely. The 236C>G and 636A>C were 2 missense mutations. While variation at the other 4 SNPs were synonymous mutations.
     In Nanyang cattle population, different genotypes were significantly associated with the body length of 6 month, heart girth of 6, 12 month, body weight and body length of 12 month, body weight of 12 month, of which the mutational individuals were higher than wildtypes (P<0.05). In Qinchuan cattle population, different genotypes were significantly associated with the body weight, heart girth, hip width, chest depth, withers length, body length and height at hip cross, of which the mutational individuals were higher than wildtypes (P<0.05). In Jiaxian Red cattle population, different genotypes were significantly associated with the body weight and average daily gain of 6 month, heart girth of 12 month, hucklebone width of 24 month, of which the mutational individuals were higher than wildtypes.
     3. SNPs detection of SREBP1c gene and their assosiation between growth traits in Nanyang, Qinchuan and Jiaxian Red cattle
     SNPs were detected in the SREBP1c gene from four cattle breeds in China. Comparison between the nucleotide sequences of the bovine NPM1 gene and the above sequences revealed 7 SNPs and 84-bp deletion in intron 7. Moreover, the SNPs at 9807G>A、10914G>A、12020 C>T and 13603 T>C were missense mutations, 10781C>G is synonymous mutations, 10649 T>G and 13475 T>C is nonsense mutation.
     In Nanyang cattle population, different genotypes were significantly associated with brith weight, the body weight and average daily gain of 6, 12 and 18 month, body weight of 24 month. of which the mutational individuals were higher than wildtypes (P<0.05). In Qinchuan cattle population, different genotypes were significantly associated with the body weight, height at sacrum, withers length, body length, heart girth, circumference of cannon bone, hucklebone width, hip width, height at hip cross, chest depth and chest width, of which the mutational individuals were higher than wildtypes (P<0.01 or P<0.05). In Jiaxian Red cattle population, different genotypes were significantly associated with the body weight, body height, average daily gain, heart girth and hucklebone width of 6 month, body weight, heart girth and hucklebone width of 6 month, body weight, body height and heart girth of 18 and 24 month, average daily gain of 18 month. of which the mutational individuals were higher than wildtypes (P<0.05).
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