肉牛生长性状和肉质性状全基因组关联分析的研究进展

全基因组关联分析(genome-wide association studies,GWAS)是研究家畜复杂经济性状和疾病遗传变异的有效方法,GWAS的核心是挖掘遗传变异与目标表型性状间的关系.随着牛全基因组测序工作完成,海量单核苷酸多态性(single nucleotide polymorphism,SNP)位点被标记...     

Genetic analysis of days open in beef cattle

The aim of this work was to analyse the genetic parameters affecting days open (DO) in beef cattle to evaluate its potential as criterion of selection. The present study characterises DO as a trait with considerable genetic variability, relative to that usually found for reproduction traits, especially for heifers and second calving cows. The estimates of heritability for the trait ranged from 0.091 for cows with 10 or more calvings to 0.197 for second calving cows. The genetic correlations estimated for DO in different parities are situated between 0.9 and 1, showing that the genes affecting the trait are substantially the same across parities of the dam. A substantial permanent environment (around 9%) seems to affect DO performance. Permanent environmental factors seem to be especially important in younger cows. Genetic correlation between DO and calving interval was positive and very high (1.0), while those between DO and gestation length and calving date were negative from low to moderate (−0.089 and −0.308, respectively). DO can be used in improvement programs of beef cattle as an early indicator of reproductive performance of the cow.     

Characterization of two microsatellites in chicken monoamine oxidase A

We surveyed two polymorphic microsatellites in a candidate gene for fear response, monoamine oxidase A ( MAOA ), in chicken. Two hundred and eighty chickens from five breeds (Nagoya, Mikawa, White Leghorn, White Plymouth Rock, and Rhode Island Red) were investigated. A thymine (T) repeat and an adenine (A) repeat were found on MAOA intron 4 ( CMin4T ) and intron 9 ( CMin9A ), respectively. Nine alleles ( 127-bp to 166-bp ) in CMin4T and six alleles ( 184-bp to 198-bp ) in CMin9A were detected. A 128-bp allele in CMin4T was observed in the Nagoya breed only, implying a highly useful marker for discriminating the Nagoya breed from other breeds. In addition, the Mikawa breed had the fixed 127-bp and 198-bp alleles in CMin4T and CMin9A , respectively. The Nagoya breed chickens show densely cowardly behavior, but the Mikawa breed chickens do not show the same behavior. The current results may indicate that MAOA is an informative candidate gene for breed difference.     

Cumulative discounted expressions of dairy and beef traits in cattle production systems

Gene-flow methodology was used to calculate the cumulative discounted expressions (CDE) for annual/lactation, replacement heifer, cull cow, birth, yearling, and slaughter traits in alternative cattle production systems. Generic equations were presented and parameters representing dairy-beef production systems in Ireland and Brazil were inputted. Cumulative discounted expressions using input parameters from a hypothetical purebred dairy production system with poor cow longevity were also calculated. Cumulative discounted expressions were calculated assuming either an initial purebred or crossbred mating within each production system. Absolute and relative differences in CDE existed among trait categories across the three alternative production systems investigated. For example, the CDE of beef-related traits accruing from an initial purebred mating ranged from 0.42 to 0.75 CDE of an annual/lactation trait across the three contrasting systems investigated which differed in various input parameters. Such variation may alter the relative emphasis of traits on overall profitability thereby contributing to genotype by environment interactions. The results of this study highlight the necessity to consider auxiliary traits in sire selection over and above those representing the principal intended use of the sire. This was particularly so for integrated dairy-beef cattle production systems.     

Association between IGF-I, IGF-IR and GHRH gene polymorphisms and growth and carcass traits in beef cattle

Molecular biology techniques are of help in genetic improvement since they permit the identification, mapping and analysis of polymorphisms of genes encoding proteins that act on metabolic pathways involved in economically interesting traits. The somatotrophic axis, which essentially consists of growth hormone releasing hormone (GHRH), growth hormone (GH), insulin-like growth factors I and II (IGF-I and IGF-II), and their associated binding proteins and receptors (GHRHR, GHR, IGF-IR and IGF-IIR), plays a key role in the metabolism and physiology of mammalian growth. The objectives of the present study were to estimate the allele and genotype frequencies of the IGF-I/SnaBI, IGF-IR/TaqI and GHRH/HaeIII gene polymorphisms in different genetic groups of beef cattle and to determine associations between these polymorphisms and growth and carcass traits. For this purpose, genotyping was performed on 79 Nellore animals, 30 Canchim (5/8 Charolais+3/8 Zebu) animals and 275 crossbred cattle originating from the crosses of Simmental (n=30) and Angus (n=245) sires with Nellore females. In the association studies, traits of interest were analyzed using the GLM procedure of SAS and least square means of the genotypes were compared by the Tukey test. Associations of IGF-I/SnaBI genotypes with body weight and subcutaneous backfat were significant (p<0.05), and nearly significant for longissimus dorsi area (p=0.06), with the BB genotype being favorable compared to the AB genotype. No significant associations were observed between this polymorphism and weight gain or carcass yield (P>0.05). The IGF-IR/TaqI and GHRH/HaeIII polymorphisms showed no association with production traits.     

Genetic associations between accumulated productivity, and reproductive and growth traits in Nelore cattle

The total meat yield in a beef cattle production cycle is economically very important and depends on the number of calves born per year or birth season, being directly related to reproductive potential. Accumulated Productivity (ACP) is an index that expresses a cow's capacity to give birth regularly at a young age and to wean animals of greater body weight. Using data from cattle participating in the “Program for Genetic Improvement of the Nelore Breed” (PMGRN — Nelore Brasil), bi-trait analyses were performed using the Restricted Maximum Likelihood method based on an ACP animal model and the following traits: age at first calving (AFC), female body weight adjusted for 365 (BW365) and 450 (BW450) days of age, and male scrotal circumference adjusted for 365 (SC365), 450 (SC450), 550 (SC550) and 730 (SC730) days of age. Median estimated ACP heritability was 0.19 and the genetic correlations with AFC, BW365, BW450, SC365, SC450, SC550 and SC730 were 0.33, 0.70, 0.65, 0.08, 0.07, 0.12 and 0.16, respectively. ACP increased and AFC decreased over time, revealing that the selection criteria genetically improved these traits. Selection based on ACP appears to favor the heaviest females at 365 and 450 days of age who showed better reproductive performance as regards AFC. Scrotal circumference was not genetically associated with ACP.     

Effects of GHR gene polymorphisms on growth and carcass traits in Zebu and crossbred beef cattle

The growth hormone receptor (GHR) is the cell surface receptor for growth hormone (GH) and is required for GH to carry out its effects on target tissues. The objectives of the present study were to estimate the allele and genotype frequencies of the GHR/Alu I gene polymorphism located in the regulatory region in beef cattle belonging to different genetic groups and to determine associations between this polymorphism and growth and carcass traits. Genotyping was performed on 384 animals, including 79 Nellore (Zebu), 30 Canchim (5/8 Charolais + 3/8 Zebu), 30 Simmental × Nellore crossbred and 245 Angus × Nellore crossbred cattle. Alleles Alu I(+), Alu I(−) and Alu I(N)–null allele–were evidenced for the GHR/Alu I polymorphism and the frequency of the Alu I(N) allele was significantly higher than the frequency of the Alu I(+) and Alu I(−) alleles in all genetic groups. Genotype Alu I(N/N) of the GHR/Alu I predominated in Nellore animals, while the Alu I(N/+) and Alu I(N/−) predominated in the other genetic groups. In the association studies, traits of interest were analyzed using the General Linear Model (GLM) procedure of the SAS program and least squares means of the genotypes were compared by the Tukey test. Significant associations (P < 0.05) were observed between the Alu I(N/N) genotype of the GHR/Alu I polymorphism and lower weight gain and body weight at slaughter, although a confounding between genotypes and genetic groups may have occurred.     

Frequencies of PRNP gene polymorphisms in Vietnamese dairy cattle for potential association with BSE

Summary Since 2004, significant associations between bovine spongiform encephalopathy (BSE) susceptibility in cattle and frequencies of insertion/deletion (ins/del; indel) polymorphisms within the bovine prion protein gene (PRNP) have been reported. In this study, we investigated the frequencies of indel polymorphisms within two variable sites, a 23-bp indel polymorphism in the promoter region (23indel) and a 12-bp indel polymorphism in intron 1 region (12indel), in the PRNP in 206 Vietnamese dairy cattle and seven Japanese BSE-affected cattle. In Vietnamese dairy cattle, the frequency distributions of del allele and del/del genotypic polymorphisms in the 23indel site, which are thought to be associated with BSE susceptibility, were significantly higher, whereas the frequencies of del allelic and del/del genotypic polymorphisms in the 12indel site, which have been reported to confer BSE susceptibility, were significantly lower. We have provided evidence that Vietnamese dairy cattle have a unique genetic background in the PRNP gene in comparison with cattle or sires previously reported in other countries.     

澳大利亚2019年肉牛产业发展分析与借鉴

澳大利亚是世界上牛肉出口大国之一,肉牛产业是其重要的支柱产业。我国是澳大利亚重要的牛肉出口国之一,随着我国与澳大利亚自由贸易协议的签订及实施,近几年我国对澳大利亚的牛肉进口量持续快速攀升,2019年跃居澳大利亚牛肉出口国第一位。本文收集汇总了澳大利亚官方发布的相关数据,对2019年澳大利亚肉牛产业发展现状、贸易情况进行追踪,通过分析以期为我国肉牛产业持续健康发展提出借鉴。     

Genome-wide association study identifies genomic loci associated with flight reaction in cattle

Lower flight reaction is closely related to higher production in cattle, but the genetic basis of lower flight reaction is not clearly understood. Here, we sampled a total of 45 Brahman cattles and 166 Yunling cattles with flight distance (FD), and 73 Brahman cattles and 288 Yunling cattles with crush score (CS) and flight speed (FS), whereas there were 45 Brahman cattles and 161 Yunling cattles with all three traits. The FD, CS and FS in Brahman cattle were significantly lower than those in Yunling cattle. The flight reaction traits had negative correlation with conformational traits (e.g., body weight, withers height and body length). Based on SNPs derived from a subset of 162 whole genomes (25 Brahman genomes and 100 Yunling genomes with FD, 30 Brahman and 131 Yunling genomes with CS and FS), genome-wide association study with mixed linear model was performed to test potential associations between flight reaction traits and genomic variants. We identified five, two and two genomic loci suggestively associated with FD, CS and FS, respectively. Five out of five candidate genes for FD (LOC789753, LRP6, CTIF, SLC9A9 and ZEB1) were reported to be related to Alzheimer's disease representing cognitive impairment in human, which was consistent with the finding that cognitive-behavioural intervention decreased the FD of cows to human. In CS, a very strong association locus was assigned to CDH8, a cadherin involved in synaptic adhesion, axon outgrowth and guidance, whose deletion was associated with autism spectrum disorder. In FS, a very strong association locus was assigned to GABRG2, a gamma-aminobutyric acid (a major inhibitory neurotransmitter in brain) receptor, whose polymorphisms were associated with suicidal behaviour in schizophrenia patients. Our findings will provide targets for molecular-marker selection and genetic manipulation of cattle improvement to meeting the growing demand for lower flight reaction to human.     

Clinical and pathological findings associated with congenital hypovitaminosis A in extensively grazed beef cattle

Objective   To determine the cause of exceptionally high mortality (41.4%) in perinatal calves on a beef cattle property 50 km south-west of Julia Creek in north-western Queensland.
Design   Investigations were based on clinical assessment of affected calves and laboratory analysis of pre- and postmortem specimens taken from 12 calves aged from 6 to 36 h of age.
Methods   Associations between gross and histopathological findings and biochemical analyses conducted on serum and tissue samples were examined in relation to clinical observations.
Results   Clinical signs varied, but commonly included mild to severe ataxia, difficulty finding a teat and sucking, blindness (partial or complete, as judged by avoidance of obstacles) and depression with prominent drooping of the head. Gross and histopathological findings included herniation of the cerebellar vermis through the foramen magnum, squamous metaplasia of interlobular ducts in the parotid salivary glands and Wallerian degeneration of the optic nerves. Biochemical analysis of serum and liver samples available from four of the calves revealed low or undetectable levels of both vitamin A and vitamin E.
Conclusion   Although vitamin E is known to have a sparing effect on vitamin A, the role (if any) played by deficiency of this vitamin was uncertain. The combination of clinical signs, postmortem findings, histopathological features and biochemical findings indicate that gestational vitamin A deficiency was highly likely to have been an important contributor to perinatal calf mortalities in this herd.     

宁夏固原市肉牛口蹄疫和布鲁氏菌病血清抗体检测与分析

[目的] 为了调查宁夏固原市肉牛口蹄疫和布鲁氏菌病的流行情况,[方法]通过采集74份不同月龄肉牛血清样本,采用酶联免疫吸附试验(ELISA)对2种疫病抗体进行检测和分析。[结果],抗体阳性率由高到低分别为A型口蹄疫(48.65%)、O型口蹄疫(43.24%)、布鲁氏菌病(12.16%)。混合抗体阳性率中主要以O型和A型口蹄疫混合抗体阳性率最高(58.54%)。O型口蹄疫在西吉县的阳性检出率最高(88.24%),彭阳县最低(6.67%);A型口蹄疫在西吉县阳性检出率最高(82.35%),彭阳县最低(26.67%);布鲁氏菌病在原州区阳性检出率最高(15.00%),泾源县和彭阳县未检出。从不同年龄来看,3种疫病均在＞12月龄的肉牛中阳性率最高,分别为O型口蹄疫69.23%、A型口蹄疫76.92%、布鲁氏菌病15.38%。[结论] 固原市各个县区肉牛养殖地区均出现2种病原感染的情况,以O型和A型口蹄疫混合感染为主。在肉母牛养殖过程中,应加强对以上病原的检疫并采取相应的防控措施。     

Genetic parameters for carcass traits of field progeny and their relationships with feed efficiency traits of their sire population for Japanese Black cattle

Genetic parameters for carcass traits of 1774 field progeny (1281 steers and 493 heifers), and their genetic relationships with feed efficiency traits of their sire population (740 bulls) were estimated with REML. Feed efficiency traits included feed conversion ratio (FCR) and residual feed intake (RFI). RFI was calculated by the residual of phenotypic (RFI_phe) and genetic (RFI_gen) regression from the multivariate analysis of feed intake on metabolic weight and daily gain. Progeny traits were carcass weight (CWT), rib eye area (REA), rib thickness (RBT), subcutaneous fat, yield estimate (YEM), marbling score (MSR), meat quality grade, meat color, fat color, meat firmness and meat texture. The estimated heritability for CWT (0.70) was high and heritabilities for all the other traits were moderate (ranged from 0.32 to 0.47), except for meat and fat color and meat texture which were low (ranged from 0.02 to 0.25). The high genetic correlation (0.62) between YEM and MSR suggests that simultaneous improvement of high carcass yield and beef marbling is possible. Estimated genetic correlations of RFI (RFI_phe and RFI_gen) of sires with CWT (− 0.60 and − 0.53) and MSR (− 0.62 and − 0.50) of their progeny were favorably negative indicating that the selection against RFI of sires may have contributed to produce heavier carcass and increase in beef marbling. The correlated responses in CWT, REA and RBT of progeny were higher to selection against RFI than those to selection against FCR of sires. This study provides evidence that selection against RFI is preferred over selection against FCR in sire population for getting better correlated responses in carcass traits of their progeny.     

A genome‐wide association study for fat‐related traits computed by image analysis in Japanese Black cattle

The objective of this study was to identify genomic regions associated with fat‐related traits using a Japanese Black cattle population in Hyogo. From 1836 animals, those with high or low values were selected on the basis of corrected phenotype and then pooled into high and low groups (n = 100 each), respectively. DNA pool‐based genome‐wide association study (GWAS) was performed using Illumina BovineSNP50 BeadChip v2 with three replicate assays for each pooled sample. GWAS detected that two single nucleotide polymorphisms (SNPs) on BTA7 (ARS‐BFGL‐NGS‐35463 and Hapmap23838‐BTA‐163815) and one SNP on BTA12 (ARS‐BFGL‐NGS‐2915) significantly affected fat percentage (FAR). The significance of ARS‐BFGL‐NGS‐35463 on BTA7 was confirmed by individual genotyping in all pooled samples. Moreover, association analysis between SNP and FAR in 803 Japanese Black cattle revealed a significant effect of SNP on FAR. Thus, further investigation of these regions is required to identify FAR‐associated genes and mutations, which can lead to the development of DNA markers for marker‐assisted selection for the genetic improvement of beef quality.     

Genetic parameters for dry matter, energy and protein intake, and their relationships with performance and carcass traits in Japanese Black cattle

Genetic parameters for feed intake and performance traits of 514 bulls and carcass traits of 22 099 of their progeny, and the relationships of measures of feed intake with performance and carcass traits were estimated. Feed intake traits were dry matter intake (DMI), concentrate intake (CONI), roughage intake, ratio of roughage intake to DMI, metabolizable energy intake (MEI) and digestible crude protein intake (DCPI). Performance traits included daily gain, metabolic weight, live weight at the end of test, dry matter conversion ratio and residual feed intake. Progeny carcass traits were carcass weight, percentage of meat yield, rib eye area (REA), subcutaneous fat, marbling score, meat colour (MCS), fat colour (FCS) and meat quality grade. All the feed intake and performance traits were moderately heritable. The heritabilities for REA and MCS were moderate, and that for FCS was low, while those for the other carcass traits were high. Selection against DMI, CONI and DCPI would reduce excessive intake of feed, but would have undesirable effects on growth and most of the carcass traits. Selection against MEI would lead to improvements in feed efficiency and growth traits. Selection against DCPI would also improve feed efficiency; however, responses in growth traits would decrease. Results indicate that selection against MEI might be better than any other measures of feed intake to improve feed efficiency with simultaneous improvement in growth and most of the carcass traits.     

Linear model vs. survival analysis for genetic evaluation of sires for longevity in Chianina beef cattle

The objective of this study was to compare sire EBVs for longevity in Chianina beef cattle estimated with linear models and survival analysis. Two datasets were created, one considered all data (SURVall), the other only uncensored records (SURVun). The linear models were used to analyze longevity measured as three correlated dichotomous (yes/no) measures of survival in the first three parities (LIN-S3) and as an overall measure of lifespan in months (LIN-LPL). Correlation between sire EBVs from the two survival analyses were 0.85. For LIN-S3 the correlations of EBVs across parities were between 0.69 to 0.93. Medium correlations (from 0.50 to 0.62) were found when only uncensored data (SURVun) were compared to the linear model (LIN-S3). Higher correlations (from 0.71 to 0.93) were found when EBV based on both censored and uncensored data (SURVall) were compared to LIN-S3. Heritability was estimated at 0.11, 0.09 and 0.08 for SURVall, SURVun and LIN-LPL, respectively; and 0.05, 0.02 and 0.02, respectively, for survival in the first three parities according to LIN-S3. Linear and non-linear models differed in many aspects; the most precise EBV were obtained when all data was used in the evaluation.     

Effect of polymorphisms linked to LEP gene on its expression on adipose tissues in beef cattle

In cattle, genetic markers at the leptin (LEP) gene and at those linked to the gene have been described as affecting calving interval (markers LEPSau3AI and IDVGA51), or daily weight gain (BMS1074 and BM1500). This work investigated the effect of these alleles on LEP mRNA levels in cattle subcutaneous and omental adipose tissues. A sample of 137 females of a Brangus‐Ibage beef cattle herd was analysed to evaluate the distribution of the polymorphisms; then, animals having at least one of the IDVGA51*181 (allele 181 at marker IDVGA51; six animals), LEPSau3AI*2 (four), BMS1074*151 (13), BM1500*135 (six) alleles and a control group composed of animals without any of these alleles (four animals) were submitted to surgery to obtain omental and subcutaneous adipose tissues. Leptin mRNA expression was quantified by TaqMan RT‐PCR, using 18S rRNA as internal control and adjusted for the effect of body condition score, through regression analysis. Omental fat had LEP gene expression 33% lower than the subcutaneous tissue. Carriers of IDVGA*181 and BMS1074*151 showed subcutaneous fat leptin mRNA levels higher than the controls. Leptin controls feed intake and coordinates reproduction; therefore, animals with higher LEP gene expression will probably have lower daily weight gain than others with similar forage offer and nutritional condition and probably will also have longer calving interval.     

Association of a single nucleotide polymorphism in ribosomal protein L27a gene with marbling in Japanese Black beef cattle

Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The c2‐11#2 expressed sequence tag (EST) has been previously shown to possess expression difference in musculus longissimus muscle between low‐marbled and high‐marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus, the ribosomal protein L27a (RPL27A) gene containing the c2‐11#2 EST sequence was considered as a positional candidate for the gene responsible for marbling. In the present study, a single nucleotide polymorphism (SNP) in the promoter region of the RPL27A, referred to as g.3109537C>T, was detected between the 2 steer groups. The SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. The effect of genotypes of the SNP on the predicted breeding value for subcutaneous fat thickness was not statistically significant. These findings suggest that the RPL27A SNP may be useful for effective marker‐assisted selection to increase the levels of marbling in Japanese Black beef cattle.     

Copy number variations at LEPR gene locus associated with gene expression and phenotypic traits in Chinese cattle

Current evidences show that copy number variations (CNVs) are linked to complex phenotypic traits. Leptin receptor (LEPR) gene plays a critical role in energy homeostasis and fat development and re‐sequencing of the cattle genome revealed the CNV region (herein referred to as “I3 DNA”) within the LEPR intron 3. In the present study, we qualified copy numbers of I3 DNA within LEPR gene in four cattle breeds (Qinchuan, Nanyang, Jinnan and Xianan) by quantitative PCR, and explored their impacts on LEPR gene expression and phenotypic traits in Qinchuan and Nanyang cattle. The results showed that more individuals in Nanyang are with loss of the I3 DNA copy number than that in the others. Additionally, I3 DNA CNVs exhibited a significant negative correlation with LEPR gene expression (P < 0.05). Association analysis showed that gain/normal copy number types performed better traits of body weight, body height and body length than the loss type in Nanyang. To the best of our knowledge, this is the first evidence of the association between LEPR CNVs and cattle traits, and this may help deep understanding of the function of CNVs which may be promising markers for beef cattle breeding and genetics. © 2015 Japanese Society of Animal Science     

Effects of plasma progesterone concentrations on LH release and ovulation in beef cattle given GnRH

The effects of plasma progesterone concentrations on LH release and ovulation in beef cattle given 100 microg of GnRH im were determined in three experiments. In Experiment 1, heifers were given GnRH 3, 6 or 9 days after ovulation; 8/9, 5/9 and 2/9 ovulated (P<0.02). Mean plasma concentrations of progesterone were lowest (P<0.01) and of LH were highest (P<0.03) in heifers treated 3 days after ovulation. In Experiment 2, heifers received no treatment (Control) or one or two previously used CIDR inserts (Low-P4 and High-P4 groups, respectively) on Day 4 (estrus=Day 0). On Day 5, the Low-P4 group received prostaglandin F(2alpha) (PGF) twice, 12 h apart and on Day 6, all heifers received GnRH. Compared to heifers in the Control and Low-P4 groups, heifers in the High-P4 group had higher (P<0.01) plasma progesterone concentrations on Day 6 (3.0+/-0.3, 3.0+/-0.3 and 5.7+/-0.4 ng/ml, respectively; mean+/-S.E.M.) and a lower (P<0.01) incidence of GnRH-induced ovulation (10/10, 9/10 and 3/10). In Experiment 3, 4-6 days after ovulation, 20 beef heifers and 20 suckled beef cows were given a once-used CIDR, the two largest follicles were ablated, and the cattle were allocated to receive either PGF (repeated 12h later) or no additional treatment (Low-P4 and High-P4, respectively). All cattle received GnRH 6-8 days after follicular ablation. There was no difference between heifers and cows for ovulatory response (77.7 and 78.9%, P<0.9) or the GnRH-induced LH surge (P<0.3). However, the Low-P4 group had a higher (P<0.01) ovulatory response (94.7% versus 61.1%) and a greater LH surge of longer duration (P<0.001). In conclusion, although high plasma progesterone concentrations reduced both GnRH-induced increases in plasma LH concentrations and ovulatory responses in beef cattle, the hypothesis that heifers were more sensitive than cows to the suppressive effects of progesterone was not supported.