Nucleotide sequencing and DNA polymorphism studies of BMP 15 gene in Corriedale and local Kashmir valley sheep (Ovis aries)

The families of TGF-β proteins are the most important growth factors in the ovary for growth and differentiation of early ovarian follicles. Three related oocyte-derived members of the transforming growth factor-β superfamily, namely GDF9, BMP15 and BMPR-IB have been shown to be essential for follicular growth and ovulation. The objective of the present study was to detect the incidence of mutation in intronic portion of BMP 15 gene in Corriedale and local Kashmir valley sheep breeds. Blood samples were collected from 85 ewes and genomic DNA was extracted using the modified phenol chloroform method. The quantity and quality of extracted DNA was examined using spectrophotometry and gel electrophoresis, respectively. A fragment with the size of 356 bp was amplified using polymerase chain reaction (PCR) with a pair of specific primers. The amplified PCR products were digested with Mph11031 restriction enzyme. In the presence of mutation at this locus, the Mph11031 enzyme cannot recognize the restriction site. However, here in the absence of mutations, the enzyme recognizes one restriction site and divides the amplified fragment into two fragments of 152 and 204 bp. The 356 bp fragment was also analyzed for polymorphism by SSCP technique. The results indicated two different banding patterns AA and AB for this fragment. Later on two different allelic forms A and B were confirmed by nucleotide sequencing. The 356 bp nucleotide sequence was subjected to alignment analysis and it was observed that sequence similarity of this fragment with that of other sheep and Jining grey goat was more than 97.8%. Phylogenetic analysis revealed that both designated A and B alleles as well as published sequence of sheep form a common cluster indicating their evolutionary closeness. The origin of Jining grey goat was located some distance away from the sheep. The overall frequencies of AA and AB genotypes were 0.79 and 0.21. The breed wise frequencies were 0.78 and 0.22 in Corriedale sheep and the frequencies in Kashmir valley sheep were 0.80 and 0.20 for AA and AB genotypes, respectively. The overall allelic frequencies of A and B alleles were 0.89 and 0.11 whereas allelic frequencies Corriedale sheep was 0.89 and 0.11 and that of Kashmir valley sheep were 0.90 and 0.10.     

Amplification and sequence analysis of the full length toxR gene in Vibrio harveyi

This study was focused on obtaining the complete gene sequence of the toxR gene in V. harveyi by using toxR-targeted PCR to amplify 5' and 3' regions flanking the 576-bp Vibrio harveyi (NBRC 15634) toxR gene fragment previously amplified using degenerate PCR. To obtain the 5' flanking sequences, a forward PCR primer (VhtoxRpv) was designed based on known sequences upstream of toxR in V. parahaemolyticus and V. vulnificus. The reverse primer (VctoxR2R) was based on the sequence of the 576-bp Vibrio harveyi toxR fragment. The resulting 750-bp amplicon was sequenced, providing the 5' sequences of the V. harveyi (NBRC 15634) toxR gene. The 3' flanking region was amplified using a primer pair toxRS1 and toxRS2 based on V. parahaemolyticus and V. vulnificus toxR and toxS, resulting in a 900-bp amplicon that contained the remaining 3' sequences of the V. harveyi NBRC 15634 toxR. This paper reports, for the first time, a complete 882-bp nucleotide sequence for toxR in Vibrio harveyi. Sequence analysis and alignment revealed that the complete toxR gene in V. harveyi shares 87% sequence similarity with toxR of V. parahaemolyticus, 84% similarity with V. fluvialis, 83% with V. vulnificus and partial sequence of V. campbellii. The phylogenetic trees revealed wider divergence in toxR compared to 16S rRNA genes, so that V. harveyi could easily be distinguished from V. campbellii and V. parahaemolyticus.     

牛α1-AT基因5’侧翼区新SNPS的鉴定及其与产奶性状的相关性

以中国荷斯坦奶牛(Chinese Holstein dairy cattle)为对象,以α1 抗胰蛋白酶基因(α1-AT)为候选基因,扩增5′侧翼区668 bp和999 bp的片段并进行测序.首次发现,在+3 142 bp处P1和+4 408 bp处P2分别发生C-T、T-C突变.随后采用PCR-RFLP方法对随机采自6个牛场,共计294头牛进行了检测,遗传变异和产奶性状分析结果显示：2个位点的等位基因在群体中都有分布,且处于中度多态.P1位点A和B等位基因的频率分别为50.34%和49.66%; AA、AB和BB基因型频率分别为23.81%、53.06%和23.13%;P2位点E和F等位基因的频率分别为30.61%和69.39%, EE、EF和FF基因型频率分别为11.90%、37.41%和50.68%. χ2适合性检验表明,该群体在P1位点的突变达到Hardy-Weinberg平衡状态（P>0.05）,在P2位点未达到平衡.基因与产奶性状关联分析表明,AB基因型个体产奶量与脂蛋比显著高于AA基因型个体(P＜0.05);FF基因型个体乳蛋白率显著高于EF基因型个体(P＜0.05);9种单倍型组合与乳脂率、乳蛋白率、体细胞数、产奶量及脂蛋比均存在不同程度相关性.     

红鳍东方鲀(Takifugu rubripes)MC4R基因的多态性分析

采用PCR-SSCP(single strand conformation polymorphism)技术和DNA测序方法分析红鳍东方鲀MC4R(Melanocortin-4receptor)基因编码区多态性。在MC4R基因编码区48 nt和264 nt均发生了碱基的转换突变(G→A),两个突变位点分别位于M1和M2引物扩增产物中。引物M1扩增产物SSCP分析得到两种基因型:AA基因型和AB基因型,并且AA基因型和A等位基因频率明显高于AB基因型和B等位基因。引物M2扩增产物也得到两种基因型:CC基因型和CD基因型,CC基因型和C等位基因频率明显高于CD基因型和D等位基因。遗传变异结果分析表明,两个突变位点均属于低度多态性,而且群体遗传杂合度较低,反映了该群体的遗传一致性较高。     

甘肃肉羊新品种选育群GDF9基因外显子2多态性及其与产羔性状关联分析

根据GenBank发布的绵羊GDF9基因外显子2的序列设计4对引物,采用PCR-SSCP技术分析GDF9基因外显子2在甘肃内羊新品种选育群羊中的单核苷酸多态性,并与产羔性状进行关联分析.结果表明,GDF9基因的扩增片段在所检测的新品种群羊中存在PCR-SSCP多态性,检测到3种基因型(AA、AB和BB),而在32只无角陶赛特母羊群中只检测到AA和AB基因型.测序结果显示,GDF9基因编码区第978位碱基发生A→G突变,但没有导致氨基酸的改变;第994位碱基发生G→A突变,导致Ⅴ变成Ⅰ(缬氨酸→异亮氨酸).新品种选育群羊产羔数的最小二乘均值关系为AB＞ AA＞ BB,统计分析结果初步表明3种基因型之间差异不显著(P＞0.05).故该区域可能不是影响新品种群羊繁殖力的功能结构区城.     

猪MyoG基因3''''端PCR-SSCP遗传多态性及其遗传效应

采用PCR—SSCP方法对长白猪、大白猪、杜洛克猪、山西黑猪和马身猪共636头猪的肌细胞生成素（Myogenin,简称MyoG）基因3’端的遗传多态性进行检测,分析MyoG基因对猪的初生体质量、断奶体质量、6月龄体质量和背膘厚的影响。根据已发表的猪MyoG基因3’端侧翼序列设计3对引物,发现F1／R1引物对扩增的片段有多态性。统计结果发现：长白、大白、杜洛克猪种B基因为优势基因,其基因频率分别为0．8807、0．7256和0．8581：山西黑猪种4基因为优势基因,其基因频率为0．9359;马身猪种只检测到4基因。χ^2独立性检验表明,基因型分布在外来猪种（长白猪、大白猪、杜洛克猪）与地方猪种（山西黑猪、马身猪）间存在极显著差异（P〈0．01）。固定效应模型分析结果表明,初生体质量基因型闻差异显著（P〈0．05）,而断奶体质量、6月龄体质量和背膘厚基因型闻差异不显著（P〉0．05）。最小二乘分析结果表明,BB基因型与其它2种基因型比较有较大的初生质量,同似和AB型比较差异极显著（P〈0．01）。因此,推测MyoG基因对个体的初生体质量存在一足的影响,选择带有B等位基因的个体有望提高个体的初生体质量。     

FSHβ 基因PCR-SSCP多态性及其与济宁青山羊高繁殖力关系的研究

采用PCR-SSCP技术检测促卵泡素b亚基(follicle-stimulating hormone β, FSHβ)基因5′调控区、外显子1和外显子2在高繁殖力山羊品种(济宁青山羊)和低繁殖力山羊品种(辽宁绒山羊、波尔山羊、安哥拉山羊)中的单核苷酸多态性, 同时研究该基因对济宁青山羊高繁殖力的影响。结果表明: 山羊与绵羊的FSHβ 基因该段核苷酸序列同源性为98%。9对引物中, 只有P9的扩增片段存在多态性。P9的扩增片段在济宁青山羊和辽宁绒山羊中检测到AA、AB和AC 3种基因型; 在波尔山羊中检测到AA、CC和AC 3种基因型; 在安哥拉山羊中检测到AA、BB、CC、AB、AC和BC共6种基因型。测序分析发现BB型与AA型相比在外显子2的第94 bp处有G→A突变, 并引起氨基酸改变(丙氨酸→苏氨酸); CC型与AA型相比在外显子2的第174 bp有一处C→T沉默突变。济宁青山羊AA、AB和AC基因型频率分别为0.686、0.137和0.177。AA基因型济宁青山羊产羔数最小二乘均值比AB基因型的多0.78只(P<0.05), 比AC基因型的多0.64只(P<0.05)。     

黑曲霉糖化酶高产和低产菌株糖化酶基因调控区的克隆及其分析比较

以PCR合成的糖化酶高产菌株黑曲霉(Asp. Niger)T21糖化酶基因5’近端非编码区588bp(EcoRI-BamHI)的序列为探针,从T21染色体DNA中克隆到近2.0kb的糖化酶基因5’端非编码区序列,并以此序列为探针从糖化酶低产菌株黑曲霉3.795(T21的诱变出发株)的染色体DNA中克隆到1.5kb的糖化酶基因5’端非编码区序列。该二序列的分析测定结果表明,其结构特征与文献报道的黑曲霉糖化酶基因5’端非编码区的基本一致,被称为“核心启动子”(Core promoter)的TATAAAT框及GCAAT框,分别在翻译起始点的-109bp及-178bp处。此外,在曲霉amdS,amyB基因中已发现有调控功能的CCAAT序列存在于-449bp和-799bp处。高产和低产菌株糖化酶基因5’端非编码区序列的分析比较结果表明,有9个部位的碱基发生了变化。此实验结果为进一步研究黑曲霉糖化酶基因在转录水平上的调控规律打下了基础。     

Cloning of the gene for the thyrotropin beta subunit in the Japanese crested ibis,Nipponia nippon

We isolated a putative gene for the thyrotropin beta subunit (TSHbeta) from two types of genomic libraries of the Japanese crested ibis, Nipponia nippon. Exon-intron structure was deduced by comparing the determined sequence with those of TSH beta cDNA of other birds. The deduced amino acid sequence shows extensive similarities to those of the other birds, which assures our assumption that the acquired nucleotide sequence represents the TSHbeta gene. The assembled genomic fragment is 4192 bp in size and consists of 1937 bp of putative 5' flanking region followed by exon-intron structure with three exons and two introns, similar to those observed in rat, human and goldfish counterparts. Locations of introns are also similar to those in mammals and goldfish. Comparison of the 5' flanking region of the ibis TSHbeta gene with those of mammals reveals that several regulatory sequences, such as negative thyroid hormone responsive element (nTRE), Pit-1 responsive element, and AP-1 responsive element, which were characterized in mammalian TSHbeta genes, are also found in the promoter region. This is the first report on the exon-intron structure and 5' flanking region of the TSHbeta gene in an avian species.     

Isolation and nucleotide sequence of a mouse histidine tRNA gene.

We have sequenced a 1307 base pair mouse genomic DNA fragment which contains a histidine tRNA gene. The sequence of the putative mouse histidine tRNA differs from the published sequence of sheep liver histidine tRNA by a single base change in the D-loop. It does not contain an unpaired 5' terminal G residue, as reported for Drosophila and sheep histidine tRNAs. The gene does not contain introns. The 3' flanking region contains a typical RNA polymerase III termination site of 6 consecutive T residues. 523 residues after the 3' end of the his tRNA coding region, the mouse DNA contains a sequence 72% homologous to part of the consensus sequence of the B1 (alu) family.     

FGF5基因对内蒙古绒山羊绒毛性状的影响

根据FGF5基因已知DNA序列设计了2对引物, 采用PCR-SSCP和PCR-RFLP技术, 在内蒙古绒山羊群体中进行基因多态性检测, 结果发现FGF5基因外显子1存在限制性内切酶BglⅠ多态位点。对其不同基因型个体PCR回收产物进行测序, 测序结果发现该SNP是由碱基序列C→T的突变而引起的。基因型和基因频率统计, 该实验群体以等位基因A具有明显的优势, χ2检验表明该SNP位点的基因频率处于Hardy-Weinberg平衡状态; 对该SNP与绒毛性状关联分析, 表明该SNP对绒纤维伸直长度(P<0.01)和含绒量(P<0.05)有显著影响, 而对其他各绒毛性状的影响不显著(P>0.05)。AB基因型个体绒纤维伸直长度(P<0.01)和含绒量(P<0.05)显著高于AA基因型个体。     

IGFBP-3基因多态性及其与中国美利奴羊部分羊毛性状的关联性分析

采用PCR-SSCP方法对中国美利奴羊和哈萨克羊中IGFBP-3基因的多态性进行了检测, 并对不同基因型与中国美利奴羊部分羊毛性状间的关联性进行了分析。结果在位于内含子1区的一段178 bp的扩增产物经SSCP分析后出现了3种基因型, 基因型AA、AB和BB及等位基因A、B在中国美利奴羊中的频率分别为0.70、0.24、0.06和0.82、0.18; 在哈萨克羊中的频率分别为0.87、0.13、0.00和0.93、0.07。序列分析发现: 在该序列的122位碱基表现多态性 (g.122 G>T)。所研究的两个群体在该位点上均处于Hardy-Weinberg不平衡状态(P<0.01)。不同基因型对部分羊毛性状有一定的影响: 不同基因型个体在剪毛后体重和净毛率上没有明显差异。AA、AB及BB基因型个体的羊毛伸直长度逐渐变短, 其中AA与AB基因型之间差异极显著(P<0.01)。AA型个体的剪毛量和羊毛密度要明显低于AB型(P<0.01)和BB型个体(P<0.05); 羊毛纤维直径则明显高于AB型(P<0.01)和BB型(P<0.05)个体。     

耐辐射奇球菌超氧化物歧化酶基因的克隆与序列分析

By using a 453 bp length gene fragment of superoxide dismutase(SOD)as a probe,which was firstly amplified from Deinococcus radiodurans genomic DNA by PCR with degenerate oligonucleotide primers corresponding to the conservative regions of known SODs,a putative SOD gene was identified from the database of D.radiodurans whole genome.Its 636 bp length open reading frame and 5′ and 3′ flanking sequence was determined.The conventional E.coli ribosomal and RNA polymerase binding sites were found upstream from SOD encoding region and an inverted repeat sequence downstream of the termination codon.The deduced 211 amino acid sequence of the structural gene showed a high similarity to other manganese and iron containing SODs in normally conserve regions.     

羊BLG基因5′和3′调控区克隆及其调控GFP基因在乳腺细胞的表达

乳球蛋白 (ＢＬＧ)是反刍家畜的一种主要乳清蛋白质。将外源基因置于ＢＬＧ 5′调控区下游 ,能够控制外源基因在动物乳腺的组织特异性表达。现已清楚在ＢＬＧ 5′端有多个乳核因子 1(ＮＦ1)和转录因子Ｓｔａｔ5的识别位点 ,此外还存在多个激素作用位点[1 ] 。具有这些调控成分的ＢＬＧ 5′翼端 (5′ｆｌａｎｋｉｎｇ)能够控制外源基因在乳腺的表达 ,但受整合位点、外源基因结构以及转基因拷贝数及其排列方式的影响[2 ] 。研究结果表明 ,仅含有 5′调控区的乳腺表达构件 ,还不能使外源基因的表达达到内源性ＢＬＧ的表达水平 ,因为在 5′远端(…     

Prolactin Receptor as a Candidate Gene for Prolificacy of Small Tail Han Sheep

DNA polymorphism of the ovine prolactin receptor gene (PRLR) was investigated and used to study its effect on litter size in sheep. By means of PRLR gene sequence homology between sheep and human, three primer pairs were designed for polymerase chain reaction (PCR) amplification within intron 1 and exon 10 of the PRLR gene in sheep. In these parts of the gene the single nucleotide polymorphisms were detected by PCR-single strand conformation polymorphism (SSCP) in 314 Small Tail Han ewes. These poly-morphisms were used to study the associations with litter size. The results indicated that there were three genotypes (AA, AB and BB) detected by three primer pairs. For three primer pairs the frequency of allele A was 0.96, 0.79, 0.68; and the frequency of allele B was 0.04, 0.21, 0.32, respectively. The frequency of genotype AA was 0.93, 0.62, 0.51; the frequency of genotype AB was 0.06, 0.34, 0.34; the frequency of genotype BB was 0.01, 0.04, 0.15, respectively. The Small Tail Han ewes with genotype BB or AB had 0.64–0.76 or 0.44–0.54 more lambs than those with genotype AA, respectively. These results preliminarily showed that the prolactin receptor locus is either a major gene that influences the prolificacy in Small Tail Han sheep or is in close linkage with such a gene.     

Prolactin receptor as a candidate gene for prolificacy of small tail han sheep

DNA polymorphism of the ovine prolactin receptor gene (PRLR) was investigated and used to study its effect on litter size in sheep. By means of PRLR gene sequence homology between sheep and human, three primer pairs were designed for polymerase chain reaction (PCR) amplification within intron 1 and exon 10 of the PRLR gene in sheep. In these parts of the gene the single nucleotide polymorphisms were detected by PCR-single strand conformation polymorphism (SSCP) in 314 Small Tail Han ewes. These poly-morphisms were used to study the associations with litter size. The results indicated that there were three genotypes (AA, AB and BB) detected by three primer pairs. For three primer pairs the frequency of allele A was 0.96, 0.79, 0.68; and the frequency of allele B was 0.04, 0.21, 0.32, respectively. The frequency of genotype AA was 0.93, 0.62, 0.51; the frequency of genotype AB was 0.06, 0.34, 0.34; the frequency of genotype BB was 0.01, 0.04, 0.15, respectively. The Small Tail Han ewes with genotype BB or AB had 0.64-0.76 or 0.44-0.54 more lambs than those with genotype AA, respectively. These results preliminarily showed that the prolactin receptor locus is either a major gene that influences the prolificacy in Small Tail Han sheep or is in close linkage with such a gene.     

κ中国荷斯坦奶牛κ-酪蛋白基因第四外显子多态性与产奶性状的关联分析

摘要: 以544头中国荷斯坦奶牛为研究对象, 以k-酪蛋白基因为产奶性状的候选基因, 扩增779 bp的片段, 结合测序结果采用PCR-RFLP方法来检测k-酪蛋白基因3个位点的多态性。结果在exon 4的第10 891 bp、10 927 bp和10 988 bp处分别发生了T/C、C/A错义突变和G/A同义突变, 据此分别选择了TaqⅠ、HindⅢ、 PstⅠ等 3种限制性内切酶检测了其多态性。发现3个位点的A、B等位基因在群体中都有分布, 且处于低度多态; A 和B 等位基因的频率分别为86.03%和13.97%; AA, AB和BB基因型频率分别为73.71%, 24.63%和1.66%; c2适合性检验表明, 该群体在这3个位点的突变达到Hardy-Weinberg平衡状态(P > 0.05); BB和AB基因型个体乳脂率显著高于AA基因型个体(P<0.05), AB基因型个体脂蛋白比显著高于AA基因型个体(P < 0.05), 但不同基因型对产奶量和乳蛋白率没有显著影响; 3个位点的酶切多态性在所研究群体中是紧密连锁的。说明在中国荷斯坦奶牛群体中, κ-酪蛋白B等位基因可作为改良奶牛乳脂率性状的分子遗传标记。     

DNA sequence of the porcine α-lactalbumin 5' flanking region and single-base polymorphisms within this region

The 5' flanking region of the α-lactalbumin (α-LA) gene was sequenced for the Duroc, Yorkshire and Meishan breeds of swine to identify potential sequence variants within this regulatory region of the porcine α-LA gene. The sequenced region of the gene encompasses 391 bp 5' of the translation start site to 11 bp 3' of the translation start site. Within this sequence of the porcine α-LA gene two single-base pair differences were detected. One variant occurs at position – 178 and the other at position – 235 from the translation start site. Each of the variations can be detected by a restriction fragment length polymorphism within a polymerase chain reaction amplified product. The polymorphisms at the – 178 and – 235 positions appear to be genetically linked in the animals that have been analysed.     

Association between PCR-SSCP of growth differentiation factor 9 gene and high prolificacy in Small Tail Han sheep

Small Tail Han sheep that has significant characteristics of high prolificacy and nonseasonal ovulatory activity is an excellent local sheep breed in P.R. China. The lambing percentage averaged 260% in Small Tail Han sheep. Growth differentiation factor 9 (GDF9) gene, which was essential for growth and differentiation of early ovarian follicles, was considered as a possible candidate gene for litter size in Small Tail Han sheep. The genetic polymorphism of a part of the GDF9 gene was detected in 130 ewes of Small Tail Han sheep by PCR-SSCP. The results indicated that there were two genotypes (AA and AB) detected by two primer pairs. In both exon 1 and exon 2 of the GDF9 gene in Small Tail Han sheep, frequencies of AA genotype were 0.846 and 0.908, frequencies of AB genotype were 0.154 and 0.092, frequencies of A allele were 0.923 and 0.954, and frequencies of B allele were 0.077 and 0.046, respectively. The results of chi2 fitness test indicated that both exon 1 and exon 2 of the GDF9 gene were in Hardy-Weinberg equilibrium (p > 0.05) in Small Tail Han sheep. Least squares means of litter size in the first and the second parity for genotype AA were 0.30 (p <0.05) and 0.77 (p <0.0001) more than those for genotype AB detected in exon 1 of the GDF9 gene in Small Tail Han sheep, respectively. Fragments detected in exon 2 of the GDF9 gene had no significant effect (p > 0.05) on litter size in both the first and the second parity in Small Tail Han sheep. Litter size in sheep is lowly heritable, expressed only in females, and manifested relatively late in life. Access to genetic markers would thus be advantageous in selection programs.     

Polymorphism of insulin-like growth factor 1 gene and its association with litter size in Small Tail Han sheep

The insulin-like growth factor 1 (IGF1) gene was studied as a candidate gene for high prolificacy in sheep. Polymorphisms of 5' regulatory region and all four exons of IGF1 gene were detected in Small Tail Han (n?=?277), Hu (n?=?58), Texel (n?=?48) and Dorset (n?=?46) sheep by PCR-RFLP and PCR-SSCP analysis. A microsatellite polymorphic site and a restriction fragment length polymorphism were shown in the 5' regulatory region of IGF1 gene. The ewes with genotype 123/123?bp had 0.81 (P??0.05) in Small Tail Han sheep. These results preliminarily indicated that these polymorphisms of IGF1 gene could be used in molecular marker-assisted selection for sheep breeding programs.