Single nucleotide polymorphisms, haplotypes and combined genotypes of LAP3 gene in bovine and their association with milk production traits

Leucine aminopeptidase 3 (LAP3) is an aminopeptidase which catalyses the removal of N-terminal amino acids and is involved in protein maturation and degradation. In this study, we detected the polymorphisms of LAP3 gene by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods in 916 individuals from three Chinese cattle breeds including Chinese Holstein, Luxi Yellow and Bohai Black. One novel single nucleotide polymorphism (SNP) (g.24564G>A ss196003366) and four previously deposited SNPs in the GenBank database (g.24794T>G, g.24803T>C, g.24846T>C, g.25415T>C) were detected. Three of the SNPs (g.24794T>G, g.24803T>C, g.24846T>C) were firstly found to be linked completely and regarded as a SNP g.24794M>N by PCR-SSCP and DNA sequencing in the tested breeds. The allelic frequencies and genetic indices of the SNPs were different in three Chinese cattle populations. The SNPs and their genetic effects on milk production traits in Chinese Holsteins were evaluated. Least squares analysis showed that cows with genotype MM had higher fat percentage and protein percentage than genotype NN (P<0.05); and the cows with g.25415T>C-CC genotype had higher protein rate than ones with TT genotype (P<0.05). In addition, eight haplotypes and 23 combined genotypes were identified based on the nine genotypes and the association between combined genotypes and milk production traits were analyzed. Statistic results showed that the cows with genotype combination MAT/MGC have higher protein and fat rate and lower SCS. Our finding demonstrated that the LAP3 gene possibly contributed to conducting association analysis and can be used as molecular marker in milk production traits and other performance for animal breeding.     

Expression analysis, single nucleotide polymorphisms and combined genotypes in candidate genes and their associations with growth and carcass traits in Qinchuan cattle

The apolipoprotein E (ApoE) gene is an important component of plasma lipoprotein, and Fas apoptosis inhibitory molecule (FAIM) is a novel anti-apoptotic gene. In this study, we researched and discussed seven genes in eight different tissues in Qinchuan cattle by quantitative Real-time PCR. The result of analysis showed that ApoE and FAIM ₂ genes had a correlation with muscle and fat. PCR–RFLP was applied to analyze the genetic variations of the ApoE and FAIM ₂ genes and verify the effect on growth and carcass traits in a total of 365 Qinchuan cattles. The result of haplotype analysis showed that nine different haplotypes were identified among the four SNPs in ApoE and FAIM ₂ genes. The statistical analyses indicated that the four SNPs were significant association with growth and carcass traits (P < 0.05, N = 365); and the four SNPs were significant association between nine combined genotypes of candidate genes and growth and carcass traits. Taken together, our results provide the evidence that polymorphisms in candidate genes are associated with growth and carcass traits in Qinchuan cattle, and may be used as a possible candidate for marker-assisted selection and management in beef cattle breeding program.     

奶牛乳铁蛋白基因5’侧翼区遗传多态性及其与乳腺炎关联性分析

牛乳铁蛋白(Lactoferrin,LF)是保护乳腺组织的防御因子之一,是具有多种功能的糖蛋白,关于牛LF基因的多态性研究的报道较多,但其多态性与奶牛乳腺炎相关性的研究较少,文章采用PCR-RFLP、CRS-PCR对268头中国荷斯坦牛LF基因启动子区的-926(G/A)、-915(T/G)、-478(/G)、+72(T/C)突变进行基因型分型,应用最小二乘线性模型分析LF基因多态性与体细胞评分(Somatic cell score,SCS)的相关性,结果表明,新发现+72(T/C)和-478(/G)对SCS有显著影响,而其他两个位点对SCS影响不显著(P>0.05),+72(T/C)的AB基因型是优良基因型,其个体的SCS值均显著低于AA型(P<0.01),BB型个体(P<0.05).-478(/G)位点的C等位基因是优良的等位基因,CC基因型个体的SCS值极显著低于CD、DD基因型个体(P<0.01).因此,LF基因+72(T/C)的AB基因型和-478(/G)位点的CC基因型均是奶牛乳腺炎抗性的优良基因型,可作为分子标记应用于奶牛乳腺炎抗性筛选.     

Single nucleotide polymorphisms (SNPs) in human lactoferrin gene.

The lactoferrin protein possesses antimicrobial and antiviral activities. It is also involved in the modulation of the immune response. In a normal healthy individual, lactoferrin plays a role in the front-line host defense against infection and in immune and inflammatory responses. Whether genomic variations, such as single nucleotide polymorphisms (SNPs), have an effect on the structure and function of lactoferrin protein and whether these variations contribute to the different susceptibility of individuals in response to environmental insults are interesting health-related issues. In this study, the lactoferrin gene was resequenced as part of the Environmental Genome Project of the National Institute of Environmental Health Sciences, which operates within the National Institutes of Health. Ninety-one healthy donors of different ethnicities were used to establish common SNPs in the exons of the lactoferrin gene in the general population. The data will serve as a basis from which study the association of lactoferrin polymorphism and disease.     

Association study of single nucleotide polymorphisms in JAK2 and STAT5B genes and their differential mRNA expression with mastitis susceptibility in Chinese Holstein cattle

The JAK–STAT pathway plays a key role in mediating immune responses. The genetic effects of single nucleotide polymorphisms (SNPs) in JAK2 and STAT5B were investigated for serum cytokines, mastitis indicators and productions traits in a population of 468 Chinese Holstein cattle. Pooled DNA sequencing revealed one SNP (BTA8:g.39645396A>G) in JAK2 and two SNPs (BTA19:g.43673888A>G and BTA19:g.43660093T>C) in STAT5B. A fixed effect model considering the effects of SNPs, parity, herd, season and year of calving was used by way of the general linear model procedure of sas . Genotype frequencies of these SNPs in the population were in Hardy–Weinberg equilibrium (P > 0.05). A novel SNP (g.39645396A>G) in JAK2 was predicted to change the amino acid from lysine to asparagine and was significantly associated with the somatic cell count (SCC) and somatic cell score (SCS), whereas g.43673888A>G in STAT5B was significantly associated with SCC, SCS and interleukin‐4 (IL‐4) (P < 0.05). The dominant effect of g.39645396A>G in JAK2 was significant for SCS, and its additive effect was significant for SCC, whereas the dominant effect of g.43673888A>G in STAT5B was significant for SCS and IL‐4 (P < 0.05). The combination of g.39645396A>G in JAK2 and g.43673888A>G in STAT5B showed a significant effect on SCC, SCS, IL‐4 and TNF‐α (P < 0.05). As for mRNA expression analysis, the AA genotype g.39645396A>G and GG genotype g.43673888A>G indicated higher mRNA expression level and were significantly different from other genotypes (P < 0.05). The results imply that JAK2 and STAT5B genes could be useful candidate genes, and the identified polymorphisms might potentially be strong genetic markers for selection of dairy cattle against mastitis development.     

Single nucleotide polymorphisms and haplotypes in Native American populations

Autosomal DNA polymorphisms can provide new information and understanding of both the origins of and relationships among modern Native American populations. At the same time that autosomal markers can be highly informative, they are also susceptible to ascertainment biases in the selection of the markers to use. Identifying markers that can be used for ancestry inference among Native American populations can be considered separate from identifying markers to further the quest for history. In the current study, we are using data on nine Native American populations to compare the results based on a large haplotype‐based dataset with relatively small independent sets of single nucleotide polymorphisms. We are interested in what types of limited datasets an individual laboratory might be able to collect are best for addressing two different questions of interest. First, how well can we differentiate the Native American populations and/or infer ancestry by assigning an individual to her population(s) of origin? Second, how well can we infer the historical/evolutionary relationships among Native American populations and their Eurasian origins? We conclude that only a large comprehensive dataset involving multiple autosomal markers on multiple populations will be able to answer both questions; different small sets of markers are able to answer only one or the other of these questions. Using our largest dataset, we see a general increasing distance from Old World populations from North to South in the New World except for an unexplained close relationship between our Maya and Quechua samples. Am J Phys Anthropol, 2011. © 2011 Wiley Periodicals, Inc.     

Single nucleotide polymorphisms of myostatin gene in Chinese domestic horses

The myostatin gene (MSTN) is a genetic determinant of skeletal muscle growth. Single nucleotide polymorphisms (SNP) in MSTN are of importance due to their strong associations with horse racing performances. In this study, we screened the SNPs in MSTN gene in 514 horses from 15 Chinese horse breeds. Six SNPs (g.26 T > C, g.156 T > C, g.587A > G, g.598C > T, g.1485C > T, g.2115A > G) in MSTN gene were detected by sequencing and genotyped using PCR-RFLP method. The g.587A > G and g.598C > T residing in the 5′UTR region were novel SNPs identified by this study. The g.2115A > G which have previously been associated with racing performances were present in Chinese horse breeds, providing valuable genetic information for evaluating the potential racing performances in Chinese domestic breeds. The six SNPs together defined thirteen haplotypes, demonstrating abundant haplotype diversities in Chinese horses. Most of the haplotypes were shared among different breeds with no haplotype restricted to a specific region or a single horse breed. AMOVA analysis indicated that most of the genetic variance was attributable to differences among individuals without any significant contribution by the four geographical groups. This study will provide fundamental and instrumental genetic information for evaluating the potential racing performances of Chinese horse breeds.     

Single nucleotide polymorphisms in theRET gene and their correlations with Hirschsprung disease phenotype

Hirschsprung disease (HSCR) is a congenital, heterogeneous disorder, characterized by the absence of intestinal ganglion cells. Recent advances show that the RET gene is a major locus involved in the pathogenesis of HSCR. The aim of this study was to analyse if the HSCR phenotype in the Polish population is associated with the presence of polymorphisms in exons 2, 3, 7, 11, 13, 14 and 15 of the RET gene. Molecular results were compared with clinical and long-term follow-up data in 70 Polish patients with HSCR (84.3% with a short segment and 15.7% with a long segment of aganglionic gut). Single-nucleotide polymorphisms were analysed by using the minisequencing SNaPshot multiplex method. The 135G>A polymorphism in RET exon 2 was overrepresented in HSCR patients, compared with a healthy control group. Moreover, the 135G>A variant was shown to be associated with the severe HSCR phenotype. Two other polymorphisms, 2071G>A in exon 11 and 2712C>G in exon 15, were underrepresented in the patients. The results confirm that these RET polymorphisms play a role in the aetiology of HSCR.     

SNPs of CXCR1 gene and its associations with somatic cell score in Chinese Holstein cattle

Mastitis is one of the most prevalent diseases in dairy cattle; CXCR1 plays a key role in mastitis resistance via IL8 signaling pathway, with the CXCR1 SNPs showing a different degree of mastitis resistance. To investigate the situation of CXCR1 polymorphisms in Chinese Holstein cattle and determine the relationship between the CXCR1 SNPs and mastitis resistance, the CXCR1 SNPs in 610 Chinese Holstein cattle of 30 families were investigated using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique. The results showed that four SNPs, -1830A > G, -1768T > A, -344T > C, and 783C > A were detected at 5' upstream and coding region. The correlation analysis demonstrated that -1830AA, -1768TT, and -344TT correlated significantly with the lowest SCS for each site, respectively. Haplotype analysis revealed Haplo2 (ATTA) correlated significantly with the lowest SCS. These findings indicated a prospect genetic marker of mastitis resistance in dairy cattle.     

荷斯坦牛Nramp1基因遗传多态性及其与乳房炎相关性的研究

利用PCR-SSCP技术检测了344头中国荷斯坦牛Nramp1基因exon 11的基因多态性, 并分析了其不同基因型与乳房炎及产奶量性状的关系。结果表明: 实验群体发现3种基因型AA、AB、BB, 其中A等位基因为优势等位基因, 等位基因频率为0.767, 而B等位基因频率则为0.233。经χ2适合性检验, 群体处于Hardy-Weinberg平衡状态(P>0.05)。测序结果显示: 扩增片段分别在200 bp(C/G)和254 bp(T/G)存在碱基突变, 并导致了氨基酸改变, 分别为丙氨酸替换为脯氨酸(Ala356Pro)、亮氨基酸替换为蛋氨酸(Leu374Met)。通过构建最小二乘线性模型, 进行Nramp1基因多态性与产奶量、体细胞评分(SCS)的相关性分析表明, AA型个体的SCS最小二乘均值显著低于BB﹑AB型(P<0.05), 而AA型﹑AB个体的产奶量最小二乘均值显著高于BB型(P<0.01, P<0.05), AA基因型可作为乳房炎抗性的优良基因型。因此, 可将Nramp1作为奶牛乳房炎候选基因应用于分子标记辅助选择育种。     

Genetic polymorphisms of lipoprotein lipase gene and their associations with growth traits in Xiangxi cattle

Lipoprotein lipase (LPL), involved in the metabolism and transport of lipids, regulate energy balance, fat deposition and growth traits. The objective of this study was to investigate the single nucleotide polymorphisms (SNPs) of LPL gene and to determine their associations between these polymorphisms and growth traits in Xiangxi cattle breed. In this study, six novel SNPs (C355157T, T355169C, T355186G, A355210G, T355348A and T355420C) and one reported SNP (A355427T, has been recorded in dbSNP, ID rs110590698) were detected using polymerase chain reaction and DNA sequencing method. Genotyping and genetic diversity analysis were performed in 240 Xiangxi cattle on the basis of sequence alignment, which indicated that five SNPs (C355157T, 355186G, T355348A, T355420C, A355427T) were in abundant genetic diversity, and the other two SNPs (T355169C and TA355210G) were in low genetic diversity. Linkage disequilibrium analysis showed that 18 different haplotypes were identified in these animals. Moreover, the results of the association between LPL gene polymorphisms and growth traits indicated that the individuals with H1H1 haplotype combination had higher BW and HG than those with other haplotype combinations (P?<?0.05). The animals with CC genotype maintain higher mean values for BW than those with the CT and TT genotypes (P?<?0.05) at T355420C locus. The animals with the AA genotype have lower mean values for WH, BL, HG and BW than those with the AT and TT genotypes at A355427T locus (P?<?0.05). The results suggested that the SNPs of the LPL gene might be useful genetic markers for growth traits in the bovine reproduction and breeding.     

Single nucleotide polymorphisms and disease gene mapping

Single nucleotide polymorphisms are the most important and basic form of variation in the genome, and they are responsible for genetic effects that produce susceptibility to most autoimmune diseases. The rapid development of databases containing very large numbers of single nucleotide polymorphisms, and the characterization of haplotypes and patterns of linkage disequilibrium throughout the genome, provide a unique opportunity to advance association strategies in common disease rapidly over the next few years. Only the careful use of these strategies and a clear understanding of their statistical limits will allow novel genetic determinants for many of the common autoimmune diseases to be determined.     

Single nucleotide polymorphisms in caprine calpastatin gene

The calpains and calpastatin (CAST) make up a major cytosolic proteolytic system, the calpain-calpastatin system, found in mammalian tissues. The relative levels of the components of the calpain-calpastatin system determine the extent of meat tenderization during postmortem storage. Calpastatin (CAST) is a protein inhibitor of the ubiquitous calcium-dependent proteases, μ-calpain, and m-calpain. Polymorphisms in the bovine, ovine and pig CAST gene have been associated with meat tenderness but little is known about how caprine CAST gene may affect goat meat quality traits. In this study we selected different parts of the CAST gene: (1) that have been previously reported to be polymorphic, intron 5 and 12 and 3’UTR; (2) first time explored (exon 3, 7 and 8 and part of intron 7 and 8) to investigate polymorphic status of caprine CAST gene. Using comparative sequencing ten novel SNPs located in exon 3 and intron 5, 7 and 8 were identified. Previously reported SNPs in intron 5, 3’UTR and intron 12 were absent. Sequence analysis revealed a non synonymous amino acid variation in exon 3, which would result in Lys/Arg substitution in the corresponding protein sequence. Considerable variation was detected in intronic regions. Twenty-four InDel were also recognized in intronic regions (15) and 3’UTR (9). All the sequences shared high homology with published bovine and ovine sequences. Three PCR-RFLP loci have been established for further analyzing genetic polymorphism in indigenous goats.     

Single nucleotide polymorphism and haplotype effects associated with somatic cell score in German Holstein cattle

Background

To better understand the genetic determination of udder health, we performed a genome-wide association study (GWAS) on a population of 2354 German Holstein bulls for which daughter yield deviations (DYD) for somatic cell score (SCS) were available. For this study, we used genetic information of 44 576 informative single nucleotide polymorphisms (SNPs) and 11 725 inferred haplotype blocks.

Results

When accounting for the sub-structure of the analyzed population, 16 SNPs and 10 haplotypes in six genomic regions were significant at the Bonferroni threshold of P ≤ 1.14 × 10^-6. The size of the identified regions ranged from 0.05 to 5.62 Mb. Genomic regions on chromosomes 5, 6, 18 and 19 coincided with known QTL affecting SCS, while additional genomic regions were found on chromosomes 13 and X. Of particular interest is the region on chromosome 6 between 85 and 88 Mb, where QTL for mastitis traits and significant SNPs for SCS in different Holstein populations coincide with our results. In all identified regions, except for the region on chromosome X, significant SNPs were present in significant haplotypes. The minor alleles of identified SNPs on chromosomes 18 and 19, and the major alleles of SNPs on chromosomes 6 and X were favorable for a lower SCS. Differences in somatic cell count (SCC) between alternative SNP alleles reached 14 000 cells/mL.

Conclusions

The results support the polygenic nature of the genetic determination of SCS, confirm the importance of previously reported QTL, and provide evidence for the segregation of additional QTL for SCS in Holstein cattle. The small size of the regions identified here will facilitate the search for causal genetic variations that affect gene functions.     

Single nucleotide polymorphism in the promoter region of the lactoferrin gene and its associations with milk performance traits in Polish Holstein-Friesian cows

Bovine lactoferrin (LTF) is a multifunctional small glycoprotein found in milk acting mainly as a defense factor in the mammary gland. Many polymorphisms have been found in the bovine LTF gene but almost none were considered as genetic markers of production traits in dairy cattle. In this study, the promoter fragment of LTF gene containing mutation (G/C) in position +32 has been amplified by PCR followed by genotyping by the SSCP and RFLP method. 358 Polish Holstein-Friesian cows were screened, giving the following frequency of genotypes: 0.628, 0.313 and 0.059 for GG, GC and CC, respectively. GLM (General Linear Model) analysis was applied to evaluate the associations of lactoferrin with milk performance traits, including SCC - somatic cell count. It was found that CC cows show significantly higher (P < or = 0.01) protein content in milk in comparison with GG cows. The values of other milk performance traits were also higher but at non-significant levels. SCC in milk was the lowest in CC cows, but also at a non-significant level.     

Single nucleotide polymorphism in the promoter region of the lactoferrin gene and its associations with milk performance traits in Polish Holstein-Friesian cows

Bovine lactoferrin (LTF) is a multifunctional small glycoprotein found in milk acting mainly as a defense factor in the mammary gland. Many polymorphisms have been found in the bovine LTF gene but almost none were considered as genetic markers of production traits in dairy cattle. In this study, the promoter fragment of LTF gene containing mutation (G/C) in position +32 has been amplified by PCR followed by genotyping by the SSCP and RFLP method. Three hundred fifty-eight Polish Holstein-Friesian cows were screened, giving the following frequency of genotypes: 0.628, 0.313 and 0.059 for GG, GC and CC, respectively. GLM (General Linear Model) analysis was applied to evaluate the associations of lactoferrin with milk performance traits, including SCC (somatic cell count). It was found that CC cows show significantly higher (P ≤ 0.01) protein content in milk in comparison with GG cows. The values of other milk performance traits were also higher but at nonsignificant levels. SCC in milk was the lowest in CC cows, but also at a nonsignificant level. The text was submitted by the authors in English.     

Single nucleotide polymorphisms in the equine transferrin gene

Single nucleotide polymorphisms (SNPs) in exons 13, 15 and 16 of equine transferrin for common, rare and mutant variants were investigated. Compared with previous work a further 13 SNPs have been identified, allowing for the two previously identified clades to be subdivided into 11 groups. A combination of one or more of eight SNPs can be used to classify the equine variants into these 11 groups, since most are co-inherited. Putative sites of glycosylation in exons 13 and 16 showed no polymorphism, suggesting that presence or absence of sugar moieties does not lead to electrophoretic variation between the variants. Using the 26 SNPs currently identified in transferrin it is still not possible to differentiate variants F1 from F2, or D from H2, which represent 75% of the variants occurring in Thoroughbred equine population. This suggests that further SNPs exist in equine transferrin. The significance of the high level of variation in exon 15 is discussed.     

Single nucleotide polymorphisms in the human E-cadherin gene

We report four DNA variants in the gene coding for the cell adhesion molecule E-cadherin. The polymorphisms affect codons 115, 133, 582 and the 3-noncoding region.