Association between single nucleotide polymorphisms (SNPs) and milk production traits in Italian Brown cattle

Italian Brown is a cattle breed largely exploited in the production of many dairy products in Italy, including typical and traditional cheeses. For this reason, the improvement of selection methods is of economic relevance while a deeper understanding of the genetic mechanisms regulating milk production is of general scientific interest. We selected a total of 561 samples, representing virtually all Italian Brown bull population, to test for association between milk production traits and 29 known genes harbouring 106 single nucleotide polymorphisms (SNPs). After filtering, a total of 31 SNPs in 22 candidate genes and 473 bulls were retained. Associations between each SNP and milk traits were tested by a mixed model approach, obtaining seven significantly associated SNPs, two of which (in β-Lactoglobulin) associated with all traits, and four (in Chemokin receptor I, αs1 casein, k casein, fatty acid synthase, thyroid hormone responsive and Oxytocin prepropetide genes) associated with at least one trait.     

单核苷酸多态性(SNPs)——第三代DNA分子标记

单核苷酸多态性 (SNPs)是指染色体基因组水平上由单个核苷酸变异引起的DNA序列多态性 ,具有分布广、密度高、多态性丰富等特点 ,且易于实现自动化检测 ,被公认为是最新的第 3代DNA分子标记。其在基因作用机理、疾病的研究及动物育种等领域具有广泛的应用前景。本文简要介绍了 6种高通量的SNPs检测技术 :基因芯片、TaqMan、变性高效液相色谱、双色荧光偏振检测入侵、基质辅助激光解吸附电离飞行时间质谱及单碱基延伸标签阵列的原理及其优、缺点。     

Evolution of the genetic variability of eight French dairy cattle breeds assessed by pedigree analysis

A pedigree analysis was performed on eight French dairy cattle breeds to assess their change in genetic variability since a first analysis completed in 1996. The Holstein, Normande and Montbéliarde breeds are selected internationally with over hundreds of thousands cows registered in the performance recording system. Three breeds are internationally selected but with limited numbers of cows in France (Brown Swiss, French Simmental and French Red Pied). The last two remaining breeds (Abondance and Tarentaise) are raised at regional level. The effective numbers of ancestors of cows born between 2004 and 2007 varied between 15 (Abondance and Tarentaise) and 51 (French Red Pied). The effective population sizes (classical approach) varied between 53 (Abondance) and 197 (French Red Pied). This article also compares the genetic variability of the ex situ (collections of the French National Cryobank) and in situ populations. The results were commented in regard to the recent history of gene flows in the different breeds as well as the existence of more or less stringent bottlenecks. Our results showed that whatever the size of the breeds, their genetic diversity impoverished quite rapidly since 1996 and they all could be considered as quite poor from a genetic diversity point of view. It shows the need for setting up cryobanks as gene reservoirs as well as sustainable breeding programmes that include loss of genetic diversity as an integrated control parameter.     

Combined use of principal component analysis and random forests identify population‐informative single nucleotide polymorphisms: application in cattle breeds

The genetic identification of the population of origin of individuals, including animals, has several practical applications in forensics, evolution, conservation genetics, breeding and authentication of animal products. Commercial high‐density single nucleotide polymorphism (SNP) genotyping tools that have been recently developed in many species provide information from a large number of polymorphic sites that can be used to identify population‐/breed‐informative markers. In this study, starting from Illumina BovineSNP50 v1 BeadChip array genotyping data available from 3711 cattle of four breeds (2091 Italian Holstein, 738 Italian Brown, 475 Italian Simmental and 407 Marchigiana), principal component analysis (PCA) and random forests (RFs) were combined to identify informative SNP panels useful for cattle breed identification. From a PCA preselected list of 580 SNPs, RFs were computed using ranking methods (Mean Decrease in the Gini Index and Mean Accuracy Decrease) to identify the most informative 48 and 96 SNPs for breed assignment. The out‐of‐bag (OOB) error rate for both ranking methods and SNP densities ranged from 0.0 to 0.1% in the reference population. Application of this approach in a test population (10% of individuals pre‐extracted from the whole data set) achieved 100% of correct assignment with both classifiers. Linkage disequilibrium between selected SNPs was relevant (r² > 0.6) only in few pairs of markers indicating that most of the selected SNPs captured different fractions of variance. Several informative SNPs were in genes/QTL regions that affect or are associated with phenotypes or production traits that might differentiate the investigated breeds. The combination of PCA and RF to perform SNP selection and breed assignment can be easily implemented and is able to identify subsets of informative SNPs useful for population assignment starting from a large number of markers derived by high‐throughput genotyping platforms.     

Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags

We have collected more than 190 000 porcine expressed sequence tags (ESTs) from full‐length complementary DNA (cDNA) libraries and identified more than 2800 single nucleotide polymorphisms (SNPs). In this study, we tentatively chose 222 SNPs observed in assembled ESTs to study pigs of different breeds; 104 were selected by comparing the cDNA sequences of a Meishan pig and samples of three‐way cross pigs (Landrace, Large White, and Duroc: LWD), and 118 were selected from LWD samples. To evaluate the genetic variation between the chosen SNPs from pig breeds, we determined the genotypes for 192 pig samples (11 pig groups) from our DNA reference panel with matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry. Of the 222 reference SNPs, 186 were successfully genotyped. A neighbor‐joining tree showed that the pig groups were classified into two large clusters, namely, Euro‐American and East Asian pig populations. F‐statistics and the analysis of molecular variance of Euro‐American pig groups revealed that approximately 25% of the genetic variations occurred because of intergroup differences. As the F_IS values were less than the F_ST values_, the clustering, based on the Bayesian inference, implied that there was strong genetic differentiation among pig groups and less divergence within the groups in our samples.     

Milk protein polymorphisms in cattle (Bos indicus), mithun (Bos frontalis) and yak (Bos grunniens) breeds and their hybrids indigenous to Bhutan

In the current study, milk protein variation was examined in cattle (Bos indicus), mithun (Bos frontalis), yak (Bos grunniens) and their hybrid populations in Bhutan to estimate genetic variability, conduct genetic characterization and assess the possibility of gene flow between mithun and cattle. Isoelectric focusing of 372 milk samples from 11 populations detected four molecular types of β‐lactoglobulin (A, B, E and M), five molecular types of α_S1‐casein (A, B, C, E and X) and three molecular types of k‐casein (A, B and X). Mithun and yak shared alleles but were found to exhibit different allele frequencies for the proteins studied. The degree of genetic variability within populations was measured by average heterozygosity and ranged from 24–40% in cattle, 26% for yak and 33% for mithun. We also resolved the traditional mithun and cattle hybridization system via principal component analysis. Our results suggested secondary introgression of mithun genes to the village Thrabum population, and a close genetic relationship between Bhutanese indigenous cattle and Indian cattle.     

Stearoyl CoA desaturase (SCD) gene polymorphisms in Italian cattle breeds.

Stearoyl CoA desaturase (SCD) is the key enzyme involved in the endogenous synthesis of conjugated linoleic acid (CLA) in ruminants. Changes in the enzymatic activity as a result of SCD gene polymorphism and regulation have been hypothesized to cause diet-independent variations of CLA content in milk. Evidences for the direct influence of SCD polymorphism on fatty acid composition of milk and beef have also been reported. To evaluate genetic differences because of breed and/or selection goal, we investigated the polymorphism of three previously reported single nucleotide polymorphisms located in exon 5 of the SCD gene in 11 cattle breeds raised in Italy and selected for different production goals. Results obtained: (i) evidenced a high variability in the allele frequencies across breeds; (ii) detected three novel haplotypes, one of which is private to indigenous beef breeds, and (iii) showed a significant association between haplotypes and selective goal.     

Gene and haplotype polymorphisms of the Prion gene (PRNP) in Japanese Brown, Japanese native and Holstein cattle

Polymorphisms in the prion protein gene ( PRNP ) are known to be associated with transmissible spongiform encephalopathies in human, sheep and goats. There is tentative association between PRNP promoter polymorphism and bovine spongiform encephalopathy (BSE) susceptibility in cattle. In this study, we genotyped for six bovine PRNP polymorphic sites including a 23-bp indel in the promoter, a 12-bp indel in the intron 1, two nonsynonymous single nucleotide polymorphisms (SNPs), octapeptide repeats in the coding region and a 14-bp indel in the 3'-untranslated region in 178 animals representing Japanese Brown, Kuchinoshima feral, Mishima, Japanese Shorthorn and Holstein. In 64 Japanese Brown cattle, three indel sites were polymorphic. All of the six sites were monomorphic in Kuchinoshima. The 23-bp and 12-bp indel sites were polymorphic in Mishima cattle. The 23-bp and 14-bp indel sites were polymorphic in Japanese Shorthorn cattle. Both SNP sites were monomorphic in all cattle examined in this study. At the 23-bp indel site, the genotype frequencies of Japanese Brown and Holstein breeds were similar to that of BSE affected cattle. We estimated 12 different haplotypes from these genotypic data. A '23-12-K6S14+' haplotype was the major haplotype in all populations, whose frequencies ranged from 0.50 to 1.00.     

Multiple marker effects of single nucleotide polymorphisms in three genes,AKIRIN2, EDG1 and RPL27A,for marbling development in Japanese Black cattle

Marbling in beef, measured by Beef Marbling Standard (BMS) number, is an economically important trait for beef cattle breeding and markets in Japan. We previously detected three single nucleotide polymorphisms (SNPs) associated with BMS number of Japanese Black in Oita prefecture: c.*188G>A in AKIRIN2, g.1471620G>T in EDG1 and g.3109537C>T in RPL27A. Here, we carried out single and multiple marker association analyses for the three SNPs in a different commercial Japanese Black population of 892 genotyped animals. The single marker analyses with the model including a single SNP showed significant associations of all SNPs with BMS number. The multiple marker analysis with the model including the main effects of the three SNPs and their interactions detected only significant main effects of g.1471620G>T and g.3109537C>T and a significant interaction between c.*188G>A and g.1471620G>T. These findings suggest the presence of inter‐allelic interactions among genes affecting the development of beef marbling. For effective marker‐assisted selection for BMS number, interactions among these markers need to be considered.     

Genetic correlations between categorical morphological traits in Nelore cattle by applying Bayesian analysis under a threshold animal model

In this study, Bayesian analysis under a threshold animal model was used to estimate genetic correlations between morphological traits (body structure, finishing precocity and muscling) in Nelore cattle evaluated at weaning and yearling. Visual scores obtained from 7651 Nelore cattle at weaning and from 4155 animals at yearling, belonging to the Brazilian Nelore Program, were used. Genetic parameters for the morphological traits were estimated by two‐trait Bayesian analysis under a threshold animal model. The genetic correlations between the morphological traits evaluated at two ages of the animal (weaning and yearling) were positive and high for body structure (0.91), finishing precocity (0.96) and muscling (0.94). These results indicate that the traits are mainly determined by the same set of genes of additive action and that direct selection at weaning will also result in genetic progress for the same traits at yearling. Thus, selection of the best genotypes during only one phase of life of the animal is suggested. However, genetic differences between morphological traits were better detected during the growth phase to yearling. Direct selection for body structure, finishing precocity and muscling at only one age, preferentially at yearling, is recommended as genetic differences between traits can be detected at this age.     

Estimation of (co)variance components for birth weight in Nellore cattle using alternative data editing criteria

The aim of this study was to estimate the (co)variance components and breeding values for birthweight (BW) in Nellore cattle by considering or not identical weights that exhibit a high frequency within the contemporary group (CG). A total of 175,258 BW records of Nellore cattle born between 2002 and 2018 were used. The CG was formed by farm, year of birth, sex and feeding regime at birth. CGs with more than 16% of identical BW values were eliminated, generating a data file called BWd. Another file was created without removing these animals (BWt). A mixed linear model was used for statistical analysis, which included fixed and random effects. In both data files analysed, single-trait analysis was performed by Bayesian inference. The mean direct and maternal heritability for BW and the correlation between direct and maternal effects were 0.27, 0.07 and −0.07 for BWt, respectively, and 0.30, 0.093 and −0.07 for BWd. This method should affect the estimation of genetic merits of animals for BW, providing greater safety in the choice of sires.     

Genetic differentiation between subpopulations of Swedish mountain (Fjäll and Fjällnära) cattle

ABSTRACT

The Swedish Mountain (Fjäll) cattle and the subpopulation Fjällnära originates from northern Sweden. They are differentiated from both traditional and commercial cattle from southern Sweden. We analysed data from the GGP HD150k SNP array and investigated genetic diversity and differences between Fjäll and Fjällnära, and between different groups of Fjällnära. We found that the Fjällnära can be divided into four groups, which are differentiated from each other and from the other Fjäll cattle. We also compared allele frequencies between different groups of Fjäll and Fjällnära for some of the functional SNPs included in the SNP array. Interestingly, the B allele of Beta lactoglobulin has a very high frequency (94%) in the Fjällnära cattle, which is significantly different from the frequency in the Fjäll cattle (60%). Comparing older samples of Fjäll cattle with more recent samples, we found a significant increase in the frequency of the B allele in Fjäll cattle.     

Application of highly differentiated SNPs between Japanese Black and Holstein to a breed assignment test between Japanese Black and F1 (Japanese Black x Holstein) and Holstein

Two taurine breeds, Japanese Black and Holstein, established from geographically distant origins and selected for different uses, beef and dairy, were extensively genotyped using a genome‐wide single nucleotide polymorphism (SNP) chip with more than 1000 animals of each breed. The genetic structure was examined by principal component analysis, in which the first principal component clearly separated the two breeds and explained more than 15% of the variance. Highly differentiated SNPs were detected throughout the genome, some of which were clustered within small regions on BTA4 (79.2–79.7 Mb, Btau4.0) and BTA26 (22.2–23.6 Mb). A breed assignment test was developed using 18 highly differentiated SNPs to distinguish Japanese Black from F₁ (Japanese Black × Holstein) and Holstein. The error rate that an F₁ or Holstein animal is misjudged as Japanese Black was expected to be < 0.8%, while the error rate that a Japanese Black animal is misjudged as F₁ or Holstein was expected to be < 0.001%. This test provides a reliable and powerful method to detect breed label falsification in retail beef.     

Prevalence and characteristics of Shiga toxin-producing Escherichia coli (STEC) from cattle in Korea between 2010 and 2011

A total of 156 Shiga-like toxin producing Escherichia coli (STEC) were isolated from fecal samples of Korean native (100/568, 18%) and Holstein dairy cattle (56/524, 11%) in Korea between September 2010 and July 2011. Fifty-two STEC isolates (33%) harbored both of shiga toxin1 (stx1) and shiga toxin2 (stx2) genes encoding enterohemolysin (EhxA) and autoagglutinating adhesion (Saa) were detected by PCR in 83 (53%) and 65 (42%) isolates, respectively. By serotyping, six STEC from native cattle and four STEC from dairy cattle were identified as O-serotypes (O26, O111, O104, and O157) that can cause human disease. Multilocus sequence typing and pulsed-field gel electrophoresis patterns highlighted the genetic diversity of the STEC strains and difference between strains collected during different years. Antimicrobial susceptibility tests showed that the multidrug resistance rate increased from 12% in 2010 to 42% in 2011. Differences between isolates collected in 2010 and 2011 may have resulted from seasonal variations or large-scale slaughtering in Korea performed to control a foot and mouth disease outbreak that occurred in early 2011. However, continuous epidemiologic studies will be needed to understand mechanisms. More public health efforts are required to minimize STEC infection transmitted via dairy products and the prevalence of these bacteria in dairy cattle.     

基于微卫星标记的中国斑翅山鹑遗传多样性及遗传结构分析

斑翅山鹑(Perdix dauuricae)是具有很高经济价值的猎用禽.为了获得其群体遗传多样性及遗传变异信息,为我国斑翅山鹑进一步有效保护和合理利用提供科学依据,本研究共采用了8个微卫星标记位点对分布于我国北方的斑翅山鹑23个地理种群285个个体进行了群体遗传多样性及遗传结构分析.结果表明,我国斑翅山鹑为遗传多样性较丰富的群体,且每一群体均表现出较高的遗传多样性,其中柴达木盆地地区的种群拥有最高的遗传多样性.遗传分化分析显示组间及组内种群间均表现为遗传分化显著,遗传分化系数(FST)值表明大部分种群间表现出显著的遗传分化.系统树构建和贝叶斯聚类分析结果均显示斑翅山鹑23个地理种群被分化为明显的两个组群.另外,通过BOTTLENECK对各地理种群的分析显示斑翅山鹁种群曾经历过近期瓶颈效应.本研究结果表明,柴达木盆地地区种群、华北平原地区种群、静宁种群、张家川种群以及六盘山地区种群应予以相应关注,以保证有足够的种群大小来保持这些种群的遗传多样性.     

Comparison of voluntary feed intake, rumen passage and degradation kinetics between crossbred Brahmam cattle (Bos indicus) and swamp buffaloes (Bubalus bubalis) fed a fattening diet based on corn silage

Three crossbred tropical cattle and three crossbred buffaloes, fitted with rumen cannulas, were used to investigate the differences in feed intake, digestibility and parameters with rumen degradation kinetics between cattle and buffalo fed a fattening diet in the Philippines. The animals were fed a diet consisting of 50% corn silage (CS), 30% brewer's grain (BG) and 20% concentrate mixture (CM) on a dry matter (DM) basis, at a level of 3% bodyweight (BW) as DM. Total DM intake (DMI) and rumen fill were greater (P < 0.05) for buffaloes than for cattle, but significant differences were not detected between the animal species when those were expressed as percentage of BW. The DMI per metabolic body size for BG and CM were greater for buffaloes than for cattle (P < 0.05), whereas that of CS did not differ between the species (P > 0.05). The weight proportion of consumed feedstuffs differed between cattle and buffaloes (P < 0.05), although nutrient intake per total DMI did not differ significantly (P > 0.05) between the animal species. Nutrients digestibility was higher (P < 0.05) for buffaloes than for cattle. Ruminal passage rate constant of feed particles and rumen fluid did not differ (P > 0.05) between the animal species. Higher DM degradation rate constant and effective degradability with CS were prominent for buffaloes than for cattle (P < 0.05). Degradation parameters did not differ (P > 0.05) between cattle and buffaloes, neither with BG nor CM. The results indicate that the greater digestibility with DM and energy for buffaloes are ascribable to greater effective degradability of CS fed ad libitum level.     

运用贝叶斯方法估计中国美利奴羊(新疆型)毛用性状及繁殖性状的遗传参数

为了解中国美利奴羊（新疆型）近年来遗传结构的变化趋势以及探讨毛用性状与繁殖性状的遗传关系,需要进一步研究这些性状的遗传力以及它们之间的关系。本研究收集额敏县聚鑫细毛羊养殖专业合作社1985-2018年中国美利奴羊（新疆型）共计9 428只羊毛生产记录和1987-2018共计5 887只年繁殖记录,运用BLUPF90软件结合Gibbs抽样方法,利用单性状模型对中国美利奴（新疆型）毛用性状（细度支数、等级、总评分、毛长、污毛重和鉴定时体重）和繁殖性状（配种次数、妊娠天数、胎产羔数和总产羔数）进行方差组分和遗传力估计,利用双性状模型分析毛用性状与繁殖性状之间的遗传相关与表型相关。结果显示,中国美利奴羊（新疆型）毛用性状细度支数、等级、总评分、毛长、污毛重、鉴定时体重的遗传力估计值分别为0.471±0.020、0.088±0.030、0.114±0.018、0.426±0.025、0.328±0.041、0.317±0.046;繁殖性状配种次数、妊娠天数、胎产羔数及总产羔数的遗传力估计值分别为0.056±0.009、0.022±0.010、0.120±0.018、0.163±0.016;毛用性状与胎产羔数、总产羔数之间的遗传相关范围为-0.031~0.286,鉴定时体重与胎产羔数（0.286）、总产羔数（0.204）遗传相关最高,细度支数与胎产羔数（-0.143）、总产羔数（-0.048）呈负的遗传相关;毛用性状与胎产羔数、总产羔数之间的表型相关范围为-0.210~0.216,毛长与总产羔数（0.216）表型相关最高,细度支数与胎产羔数（-0.137）、总产羔数（-0.210）呈显著负表型相关。本研究结果发现,毛用性状与繁殖性状之间存在一定的关系,这一结果可为今后制定中国美利奴羊育种规划提供数据基础,为选育优质高产、繁殖性能好的细毛羊提供理论依据,从而进一步提高细毛羊产业经济效益。     

Myophosphorylase deficiency (glycogen storage disease Type V) in a herd of Charolais cattle in New Zealand: Confirmation by PCR-RFLP testing

AIM: To describe a disease of muscle in Charolais calves and confirm the putative diagnosis of inherited myophosphorylase deficiency.

METHODS: Variously stained paraffin sections of muscle prepared from affected calves were used to describe the lesions. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) test was developed and applied to affected calves, their sires, dams and other individuals.

RESULTS: The lesions were those of rhabdomyolysis of skeletal muscles and sub-sarcolemmal spaces in normal fibres. The PCR-RFLP test confirmed the expected mutation for phosphorylase deficiency of Charolais cattle in two affected calves. In addition, sires, dams and other closely-related individuals of four affected calves tested as heterozygous for the mutation. Other apparently unrelated animals also tested as heterozygous.

CONCLUSIONS: The diagnosis of myophosphorylase deficiency was confirmed. The PCR-RFLP test is suitable for use in controlling this recessively-inherited disorder as it can diagnose heterozygous individuals that are otherwise clinically normal.     

Polymorphisms in the bovine hemoglobin‐beta gene provide evidence for gene‐flow between wild species of Bos (Bibos) and domestic cattle in Southeast Asia

The electrophoretic variation in bovine hemoglobin‐beta (HBB) is one of the most investigated genetic markers. The presence of a unique HBB variant, HBB^X, in Southeast Asian cattle has been reputed as a sign of gene‐flow from wild bovine species. In this study, we analyzed the DNA sequences of HBB genes in domestic and wild bovine species to verify this belief. Isoelectric focusing of HBB chain revealed that the HBB^X in domestic cattle had dimorphism and was separated into HBB^X1 and HBB^X2. The HBB^X1 had the same DNA sequence of the common HBB variant in gayal (Bos gaurus frontalis), while some of the HBB^X2 were identical with that of Cambodian banteng (Bos javanicus birmanicus). As a result, we confirmed that the bovine HBB variants can be a good indicator of introgression between wild and domestic cattle. The HBB^X1 was always predominant to HBB^X2 in the continental populations, suggesting that the gaur had contributed to the gene pool of domestic cattle in this region much more than the banteng. On the other hand, the mitochondrial DNA analysis could not detect gene‐flow from wild species. Autosomal markers that can trace the phylogeny between alleles are suitable for the assessment of bovine interspecific introgression.     

Two single nucleotide polymorphisms in the promoter of the ovine myostatin gene (MSTN) and their effect on growth and carcass muscle traits in New Zealand Romney sheep

Myostatin is a negative regulator of muscle growth and development in mammals, and variation in ovine myostatin gene (MSTN) has been demonstrated to be associated with variation in the muscularity of sheep. Polymerase chain reaction–single‐stranded conformational polymorphism (PCR–SSCP) was used to look for single nucleotide polymorphisms (SNPs) in a 304‐bp amplicon from the promoter region of ovine MSTN. Sequence analyses revealed two previously identified SNPs (c.?2449G/C and c. ?2379T/C) that resulted in three haplotypes (H₁ (c.[?2449G; ?2379C]), H₂ (c.[?2449C; ?2379C]) and H₃ (c.[?2449G; ?2379T]). The effect of these SNPs on growth and carcass traits was investigated in 357 NZ Romney lambs. General linear mixed‐effect models revealed that sheep with the genotype c.?2449GC had a higher loin meat yield (p = 0.032) and proportion loin yield (p = 0.028), than those with the genotype c.?2449GG. The genotype c.?2379CC was associated with an increase in three weight traits: birthweight (p = 0.003), tailing weight (p = 0.009) and weaning weight (p = 0.028), when compared with the genotype c.?2379TC, but it was not found to have an association with growth rate. This suggests that c.?2379T/C has an effect that originates at, or before birth. Haplotype H₃ was associated with a decrease in birthweight (p = 0.002), tailing weight (p = 0.003) and weaning weight (p = 0.011). Haplotype H₂ was associated with increased loin yield (p = 0.012) and proportion loin yield (p = 0.002). The SNPs may have value as genetic markers for improved Romney breeding.