Assignment of the locus for arachnomelia syndrome to bovine chromosome 23 in Simmental cattle

Arachnomelia syndrome is a lethal inherited malformation mainly of the limbs, vertebral column and skull in cattle, which poses a severe impairment to farmers and breeders. Recently, a number of cases of arachnomelia syndrome have occurred in the Simmental breed and some sires with excellent breeding values had been shown to be carriers of the disease. We herein report the genetic mapping of the mutation underlying arachnomelia in cattle. The disease was mapped using a two-stage genome scan. A first round autosomal genome-wide screening using a limited number of cases identified three chromosomal regions with lod-scores > 1. The position of the arachnomelia syndrome locus was identified to be on BTA 23 by genotyping an additional, independent set of animals with markers that provided positive lod-scores in the course of the initial genome-wide screen. Using a denser set of regional microsatellites, the locus could be mapped to a region about 9 cM in length. The most significant linkage signal with arachnomelia syndrome was obtained with marker NRKM-17 (lod-score > 20) using a recessive model. Interestingly, different genes seem to be responsible for the disease in Brown Swiss and Simmental breeds, as arachnomelia syndrome was mapped to a different location in Brown Swiss. The results provide sufficient information for the development of a genetic test system and also allow the identification of positional candidate genes.     

Genome-wide detection of selective signatures in Simmental cattle

Artificial selection has greatly improved the beef production performance and changed its genetic basis. High-density SNP markers provide a way to track these changes and use selective signatures to search for the genes associated with artificial selection. In this study, we performed extended haplotype homozygosity (EHH) tests based on Illumina BovineSNP50 (54 K) Chip data from 942 Simmental cattle to identify significant core regions containing selective signatures, then verified the biological significance of these identified regions based on some commonly used bioinformatics analyses. A total of 224 regions over the whole genome in Simmental cattle showing the highest significance and containing some important functional genes, such as GHSR, TG and CANCNA2D1 were chosen. We also observed some significant terms in the enrichment analyses of second GO terms and KEGG pathways, indicating that these genes are associated with economically relevant cattle traits. This is the first detection of selection signature in Simmental cattle. Our findings significantly expand the selection signature map of the cattle genome, and identify functional candidate genes under positive selection for future genetic research.     

Establishment and characterization of a fibroblast line from Simmental cattle

A fibroblast line (named SCF36) from ear marginal tissue of Simmental cattle was established successfully by direct culture of explants and cell cryopreservation techniques. Biological analysis showed that the population doubling time of the thawed cells was 42.8 h. The average viability of the cells was 96.8% before freezing and 91.5% after thawing. Measurements of lactic dehydrogenase and malic dehydrogenase isoenzymes showed no cross-contamination of this cell line with other species. Karyotyping showed that the frequency of cells with chromosome number 2n = 60 was more than 90%. Tests for bacteria, fungi, viruses and mycoplasmas were negative. The efficiencies of expression of enhanced green, yellow and red fluorescent protein genes (pEGFP-N₃, pEYFP-N₁ and pDsRed1-N₁) were between 11.3% and 28.8% after transfection; fluorescence was well distributed in the cytoplasm and nucleus except for some cryptomeric vesicles. This Simmental cattle fibroblast line not only contains the germline of this important cattle breed, which is preserved at the cellular level, but valuable material has also been provided for genomic, postgenomic and somatic cloning research. Moreover, the establishment of these methods may provide both technical and theoretical support for preserving the genetic resources of other livestock and poultry at the cellular level.     

Accuracies of genomic prediction for twenty economically important traits in Chinese Simmental beef cattle

Genomic prediction has been widely utilized to estimate genomic breeding values (GEBVs) in farm animals. In this study, we conducted genomic prediction for 20 economically important traits including growth, carcass and meat quality traits in Chinese Simmental beef cattle. Five approaches (GBLUP, BayesA, BayesB, BayesCπ and BayesR) were used to estimate the genomic breeding values. The predictive accuracies ranged from 0.159 (lean meat percentage estimated by BayesCπ) to 0.518 (striploin weight estimated by BayesR). Moreover, we found that the average predictive accuracies across 20 traits were 0.361, 0.361, 0.367, 0.367 and 0.378, and the averaged regression coefficients were 0.89, 0.86, 0.89, 0.94 and 0.95 for GBLUP, BayesA, BayesB, BayesCπ and BayesR respectively. The genomic prediction accuracies were mostly moderate and high for growth and carcass traits, whereas meat quality traits showed relatively low accuracies. We concluded that Bayesian regression approaches, especially for BayesR and BayesCπ, were slightly superior to GBLUP for most traits. Increasing with the sizes of reference population, these two approaches are feasible for future application of genomic selection in Chinese beef cattle.     

Accuracy of direct genomic breeding values for nationally evaluated traits in US Limousin and Simmental beef cattle

Background

In national evaluations, direct genomic breeding values can be considered as correlated traits to those for which phenotypes are available for traditional estimation of breeding values. For this purpose, estimates of the accuracy of direct genomic breeding values expressed as genetic correlations between traits and their respective direct genomic breeding values are required.

Methods

We derived direct genomic breeding values for 2239 registered Limousin and 2703 registered Simmental beef cattle genotyped with either the Illumina BovineSNP50 BeadChip or the Illumina BovineHD BeadChip. For the 264 Simmental animals that were genotyped with the BovineHD BeadChip, genotypes for markers present on the BovineSNP50 BeadChip were extracted. Deregressed estimated breeding values were used as observations in weighted analyses that estimated marker effects to derive direct genomic breeding values for each breed. For each breed, genotyped individuals were clustered into five groups using K-means clustering, with the aim of increasing within-group and decreasing between-group pedigree relationships. Cross-validation was performed five times for each breed, using four groups for training and the fifth group for validation. For each trait, we then applied a weighted bivariate analysis of the direct genomic breeding values of genotyped animals from all five validation sets and their corresponding deregressed estimated breeding values to estimate variance and covariance components.

Results

After minimizing relationships between training and validation groups, estimated genetic correlations between each trait and its direct genomic breeding values ranged from 0.39 to 0.76 in Limousin and from 0.29 to 0.65 in Simmental. The efficiency of selection based on direct genomic breeding values relative to selection based on parent average information ranged from 0.68 to 1.28 in genotyped Limousin and from 0.51 to 1.44 in genotyped Simmental animals. The efficiencies were higher for 323 non-genotyped young Simmental animals, born after January 2012, and ranged from 0.60 to 2.04.

Conclusions

Direct genomic breeding values show promise for routine use by Limousin and Simmental breeders to improve the accuracy of predicted genetic merit of their animals at a young age and increase response to selection. Benefits from selecting on direct genomic breeding values are greater for breeders who use natural mating sires in their herds than for those who use artificial insemination sires. Producers with unregistered commercial Limousin and Simmental cattle could also benefit from being able to identify genetically superior animals in their herds, an opportunity that has in the past been limited to seed stock animals.     

Genome-wide association study identifies loci and candidate genes for meat quality traits in Simmental beef cattle

Improving meat quality is the best way to enhance profitability and strengthen competitiveness in beef industry. Identification of genetic variants that control beef quality traits can help breeders design optimal breeding programs to achieve this goal. We carried out a genome-wide association study for meat quality traits in 1141 Simmental cattle using the Illumina Bovine HD 770K SNP array to identify the candidate genes and genomic regions associated with meat quality traits for beef cattle, including fat color, meat color, marbling score, longissimus muscle area, and shear force. In our study, we identified twenty significant single-nucleotide polymorphisms (SNPs) (p < 1.47 × 10^?6) associated with these five meat quality traits. Notably, we observed several SNPs were in or near eleven genes which have been reported previously, including TMEM236, SORL1, TRDN, S100A10, AP2S1, KCTD16, LOC506594, DHX15, LAMA4, PREX1, and BRINP3. We identified a haplotype block on BTA13 containing five significant SNPs associated with fat color trait. We also found one of 19 SNPs was associated with multiple traits (shear force and longissimus muscle area) on BTA7. Our results offer valuable insights to further explore the potential mechanism of meat quality traits in Simmental beef cattle.     

Association of SCD1 and DGAT1 SNPs with the intramuscular fat traits in Chinese Simmental cattle and their distribution in eight Chinese cattle breeds

Intramuscular fat (IMF) is a key parameter for evaluation of nutritional quality of beef, with its endogenous synthesis regulated by stearoyl CoA desaturase (SCD1) and diacylglycerol-acyl transferase 1 (DGAT1) genes in cattle. The object of this research was to evaluate the effect of SCD1 and DGAT1 polymorphisms on IMF trait in beef cattle and to estimate the frequency distribution of SNPs in the two genes in Chinese cattle populations. The SCD1 and DGAT1 polymorphisms were detected by PCR-single strand conformation polymorphism (PCR-SSCP) method in Chinese Simmental cattle and their associations with IMF traits were analyzed using the general linear model (GLM). The frequency distribution of SNPs in SCD1 and DGAT1 genes were detected by PCR-SSCP method and analyzed in seven other cattle populations. The results showed significant associations of SNPs SCD1-878, SCD1-762, and DGAT1 10433 and 10434 with IMF (%) and shearing force values (SFV; kg) in Chinese Simmental cattle. A haplotype combining SCD1-878C, SCD1-762T, and DGAT1 10433 and 10434-GC had the highest IMF, marbling score and shearing force. The polymorphic investigation indicated that the frequency of SCD1-878C or SCD1-762T was significantly higher in Chinese southern cattle (Leiqiong, Yunnan High pump, BMY or Minnan Cattle) than in Chinese northern cattle (Chinese Simmental, Luxi Cattle, Bohai Black or Chinese Holstein), while the frequency of DGAT1 10433 and 10434-GC in Chinese indigenous breed (Leiqiong, Yunnan High pump, BMY, Luxi Cattle, Bohai Black, or Minnan Cattle) was significantly lower than breeds with imported blood (Chinese Simmental or Chinese Holstein). These findings demonstrated that both the SCD1 and DGAT1 SNPs were prospect genetic markers for IMF traits, and the SCD1 SNPs could be used as a genetic marker for southern or northern blood in Chinese cattle.     

Analyses of the genetic relationships between lactose,somatic cell score,and growth traits in Simmental cattle

Lactose and somatic cell score (SCS) are major economic traits of milk. However, for many countries, they are typically not directly considered in the national genetic evaluation of Simmental cattle. This study aimed to estimate the genetic relationships between lactose, SCS, and growth traits of Simmental cattle to provide information for the national genetic evaluation of the selection of traits of this cattle population. The data of 1781 animals with 6519 records obtained over a period of 41 years (1975–2016) were collected from Xinjiang Hutubi Farm, China. The analyzed traits included 305 days of milk yield (305MY), milk fat percentage (MFP), milk protein percentage (MPP), milk lactose percentage (MLP), total solids (TS), SCS, body height (BH), body length (BL), chest girth (CG), abdominal circumference (AC), rump width (RW), rump length (RL), leg circumference (LC), and cannon circumference (CC). The multiple-trait repeatability model was adopted to estimate (co)variance components using the average information-restricted maximum likelihood method implemented using the DMU statistical package. The heritability estimates for milk components and growth traits ranged from 0.09 (SCS) to 0.51 (BH). Genetic correlations for milk components ranged from 0.03 ± 0.14 (MFP and MLP) to 0.81 ± 0.08 (MFP and MPP). Genetic correlation between MLP and SCS was moderate and negative (− 0.50 ± 0.15) compared with that among other traits. Genetic correlations between the milk components and growth traits ranged from 0.00 ± 0.07 (305MY and RW) to − 0.64 ± 0.15 (MLP and BL). Genetic correlations of BL, LC, RW, and RL with MLP were moderate to high and negative ranging from − 0.39 to − 0.64. Somatic cell score showed the highest correlation with BL (0.41) followed by LC (0.21). An increase in MLP would result in an increase in 305MY or TS and a decrease in BL, LC, RW, and RL. Additionally, a decrease in SCS would occur with the selection of increased MLP and reduced BL. We conclude that selection based on easily and inexpensively measured growth traits could improve the milk quality from Simmental cattle.     

New markers on bovine Chromosome 1 are closely linked to the polled gene in Simmental and Pinzgauer cattle

In this study, four new markers located on bovine Chromosome 1 were tested for linkage with the polled condition in the Simmental and Pinzgauer breeds. The microsatellites INRA212 (D1S42) and the gene for keratin-associated protein 8 (KAP8) show significant linkage with polled at θ= 0.00 (Lod = 6.92), and θ= 0.033 (Lod = 6.52) respectively. The microsatellite INRA117 (D1S20) and the gene for interferon-α receptor (IFNAR) show maximum Lod scores of 2.1 and 1.8 at a recombination rate of zero. Received: 22 July 1996 / Accepted: 8 December 1996     

Mitochondrial abundance and function in skeletal muscle and liver from Simmental beef cattle divergent for residual feed intake

Cellular mitochondrial function has been suggested to contribute to variation in feed efficiency (FE) among animals. The objective of this study was to determine mitochondrial abundance and activities of various mitochondrial respiratory chain complexes (complex I (CI) to complex IV (CIV)) in liver and muscle tissue from beef cattle phenotypically divergent for residual feed intake (RFI), a measure of FE. Individual DM intake (DMI) and growth were measured in purebred Simmental heifers (n = 24) and bulls (n = 28) with an initial mean BW (SD) of 372 kg (39.6) and 387 kg (50.6), respectively. All animals were offered concentrates ad libitum and 3 kg of grass silage daily, and feed intake was recorded for 70 days. Residuals of the regression of DMI on average daily gain (ADG), mid-test BW^0.75 and backfat (BF), using all animals, were used to compute individual RFI coefficients. Animals were ranked within sex, by RFI into high (inefficient; top third of the population), medium (middle third of population) and low (efficient; bottom third of the population) terciles. Statistical analysis was carried out using the MIXED procedure of SAS v 9.3. Overall mean ADG (SD) and daily DMI (SD) for heifers were 1.2 (0.4) and 9.1 (0.5) kg, respectively, and for bulls were 1.8 (0.3) and 9.5 (1.02) kg, respectively. Heifers and bulls ranked as high RFI consumed 10% and 15% more (P < 0.05), respectively, than their low RFI counterparts. There was no effect of RFI on mitochondrial abundance in either liver or muscle (P > 0.05). An RFI × sex interaction was apparent for CI activity in muscle. High RFI animals had an increased activity (P < 0.05) of CIV in liver tissue compared to their low RFI counterparts; however, the relevance of that observation is not clear. Our data provide no clear evidence that cellular mitochondrial function within either skeletal muscle or hepatic tissue has an appreciable contributory role to overall variation in FE among beef cattle.     

The influence of animals from embryo transfer on the genetic evaluation of growth in Simmental beef cattle by using multi-trait models

The weight records from Simmental beef cattle were used in a genetic evaluation of growth with or without the inclusion of animals obtained by embryo transfer. A multi-trait model in which embryo transfer individuals were excluded (MTM1) contained 29,510 records from 10,659 animals, while another model without exclusion of these animals (MTM2) contained 62,895 weight records from 23,160 animals. The weight records were adjusted for ages of 100, 205, 365, 450, 550 and 730 days. The (co)variance components and genetic parameters were estimated by the restricted maximum likelihood method. The (co)variance components were similar in both models, except for maternal permanent environment variance. Direct heritabilities (h²_d) in MTM1 were 0.04, 0.11, 0.20, 0.27, 0.31 and 0.42, while in MTM2 they were 0.11, 0.11, 0.17, 0.21, 0.22 and 0.26 for 100, 205, 365, 450, 550 and 730 days of age, respectively. Estimates of h²_d in MTM1 were higher than in MTM2 for the weight at 365 days of age. Genetic correlations between weights in both models ranged from moderate to high, suggesting that these traits may be determined mainly by the same genes. Animals from embryo transfer may be included in the genetic evaluation of Simmental beef cattle in Brazil; this inclusion may provide potential gains in accuracy and genetic gains by reducing the interval between generations.     

A genome‐wide association study suggests several novel candidate genes for carcass traits in Chinese Simmental beef cattle

A genome‐wide association study (GWAS) was conducted for two carcass traits in Chinese Simmental beef cattle. The experimental population consisted of 1301 individuals genotyped with the Illumina BovineHD SNP BeadChip (770K). After quality control, 671 990 SNPs and 1217 individuals were retained for the GWAS. The phenotypic traits included carcass weight and bone weight, which were measured after the cattle were slaughtered at 16 to 18 months of age. Three statistical models—a fixed polygene model, a random polygene model and a composite interval mapping polygene model—were used for the GWAS. The genome‐wide significance threshold after Bonferroni correction was 7.44E‐08 (= 0.05/671 990). In this study, we detected eight and seven SNPs significantly associated with carcass weight and bone weight respectively. In total, 11 candidate genes were identified within or close to these significant SNPs. Of these, we found several novel candidate genes, including PBX1, GCNT4, ALDH1A2, LCORL and WDFY3, to be associated with carcass weight and bone weight in Chinese Simmental beef cattle, and their functional roles need to be verified in further studies.     

A genome‐wide scan for copy number variations using high‐density single nucleotide polymorphism array in Simmental cattle

Copy number variations (CNVs) have recently been identified as promising sources of genetic variation, complementary to single nucleotide polymorphisms (SNPs). As a result, detection of CNVs has attracted a great deal of attention. In this study, we performed genome‐wide CNV detection using Illumina Bovine HD BeadChip (770k) data on 792 Simmental cattle. A total of 263 CNV regions (CNVRs) were identified, which included 137 losses, 102 gains and 24 regions classified as both loss and gain, covering 35.48 Mb (1.41%) of the bovine genome. The length of these CNVRs ranged from 10.18 kb to 1.76 Mb, with an average length of 134.78 kb and a median length of 61.95 kb. In 136 of these regions, a total of 313 genes were identified related to biological functions such as transmembrane activity and olfactory transduction activity. To validate the results, we performed quantitative PCR to detect nine randomly selected CNVRs and successfully confirmed seven (77.6%) of them. Our results present a map of cattle CNVs derived from high‐density SNP data, which expands the current CNV map of the cattle genome and provides useful information for investigation of genomic structural variation in cattle.     

西门塔尔牛产奶性状的微卫星标记分析

通过对西门塔尔牛育种核心群6个父系组成的150头母牛产奶性状的测定,结合微卫星标记技术,于4条染色体上选择12个微卫星位点进行产奶性状的微卫星标记分析,研究各位点对乳脂、乳蛋白、乳糖、干物质和奶中体细胞数的遗传效应。结果表明： 12个位点都具有高度多态性,杂合度（H）在0.64～0.86之间,多态信息含量（PIC）也达到0.60以上,最高者ILST093的多态信息含量为0.85;位点ILST093对奶中体细胞数有显著性影响(P<0.05),位点BMS711对乳脂率有显著性影响(P<0.05),位点BM1905与奶中乳糖含量呈显著相关(P<0.05),位点BM6438与五个产奶性状均无相关性。     

甘肃西门塔尔牛甘州类群MSTN基因外显子多态性分析

采用PCR-SSCP方法检测50头甘肃西门塔尔牛甘州类群MSTN基因3个外显子的遗传多态性,并对群体内各等位基因进行测序,旨为探讨西门塔尔牛MSTN基因与肉质性状关联等方面的研究提供理论依据。结果显示,甘肃西门塔尔牛甘州类群MSTN基因3个外显子中,外显子2受B、C等位基因控制,形成BB、CC和BC 3种基因型,基因型频率分别为0.22(11/50)、0.64(32/50)、0.14(7/50);外显子1和外显子3分别受A等位基因与D等位基因控制,形成AA和DD基因型,基因型频率均为1(50/50)。序列分析表明,甘肃西门塔尔牛甘州类群MSTN基因3个外显子中,外显子2在第41 bp处发生了C→T的突变,但并没有导致氨基酸发生改变,属于同义突变;外显子1和3均无突变。统计结果表明,甘肃西门塔尔牛甘州类群MSTN基因3个外显子中,外显子2为中度多态,其余均无变化。     

西门塔尔牛产奶性状的微卫星标记遗传效应分析

在4条染色体上选择12个微卫星标记对西门塔尔牛育种核心群6个父系组成的150头母牛产奶性状(包括乳脂、乳蛋白、乳糖、干物质含量和奶中体细胞数)进行分子标记遗传效应分析.结果表明:12个微卫星位点都具有高度多态性,杂合度(H)均在0.64～0.86之间,多态信息含量(PIC)达0.60以上,最高为0.85(ILST093);位点ILST093对奶中体细胞数有显著性影响(P＜0.05);BMS711对乳脂率有显著性影响(P＜0.05);BM1905与奶中乳糖含量呈显著相关(P＜0.05);BM6438与5个产奶性状均无相关性.