Genome-wide association studies for feedlot and growth traits in cattle

A genome wide-association study for production traits in cattle was carried out using genotype data from the 10K Affymetrix (Santa Clara, CA) and the 50K Illumina (San Diego, CA) SNP chips. The results for residual feed intake (RFI), BW, and hip height in 3 beef breed types (Bos indicus, Bos taurus, and B. indicus × B. taurus), and for stature in dairy cattle, are presented. The aims were to discover SNP associated with all traits studied, but especially RFI, and further to test the consistency of SNP effects across different cattle populations and breed types. The data were analyzed within data sets and within breed types by using a mixed model and fitting 1 SNP at a time. In each case, the number of significant SNP was more than expected by chance alone. A total of 75 SNP from the reference population with 50K chip data were significant (P < 0.001) for RFI, with a false discovery rate of 68%. These 75 SNP were mapped on 24 different BTA. Of the 75 SNP, the 9 most significant SNP were detected on BTA 3, 5, 7, and 8, with P ≤ 6.0 × 10(-5). In a population of Angus cattle divergently selected for high and low RFI and 10K chip data, 111 SNP were significantly (P < 0.001) associated with RFI, with a false discovery rate of 7%. Approximately 103 of these SNP were therefore likely to represent true positives. Because of the small number of SNP common to both the 10K and 50K SNP chips, only 27 SNP were significantly (P < 0.05) associated with RFI in the 2 populations. However, other chromosome regions were found that contained SNP significantly associated with RFI in both data sets, although no SNP within the region showed a consistent effect on RFI. The SNP effects were consistent between data sets only when estimated within the same breed type.     

Preweaning growth of F1 tropically adapted beef cattle breeds x Angus and reproductive performance of their Angus dams in arid rangeland

The objective of this study was to determine the preweaning performance of F1 Brahman (Bos indicus)-, Senepol (Bos taurus)-, and Tuli (Sanga)-Angus calves under semiarid south Texas conditions and to evaluate the reproductive performance of their Angus dams. Four hundred eighty-nine records collected over 4 yr were analyzed. The statistical model for performance traits included the effects of breed of sire, year, sex, age of dam, and breed of sire x year. Year effects were important (P < 0.05) for performance traits but could be explained, at least partially, by differences between years in rainfall patterns. Brahman F1 calves were 13% less (P < 0.05) vigorous at birth, 4.7 kg heavier (P < 0.05) at birth, 13.5 kg heavier (P < 0.05) at weaning, 0.25 units lower (P < 0.05) in body condition score (BCS) at weaning, and 1.75 units greater (P < 0.05) in frame score (scores of 1 to 9) at weaning than Tuli and Senepol F1 calves. Senepol F1 calves were intermediate (P < 0.05) between the Brahman and Tuli F1 calves for birth and weaning weight but had 11% more (P < 0.05) vigor at birth than the other two crossbreds. Tuli and Senepol F1 were similar (P > 0.05) in BCS and frame size at weaning. Males were 3.3 kg heavier (P = 0.12) at birth than females, especially for the F1 Brahman males that were 4.5 kg heavier (P < 0.05) than their counterparts. Brahman F1 weaned 19.9 kg heavier (P < 0.05) than the average of the other two F1 in the year of the greatest rainfall (1994), whereas the average advantage in other years was 11.4 kg. This difference gave rise to a breed of sire x year interaction (P < 0.003). Brahman F1 were heavier at every measurement and appeared to be later-maturing and more able to excel under good forage conditions than the other two F1 breed types; Senepol and Tuli F1 were similar (P > 0.05) in these respects but appeared to be more competitive in relative growth rate to the Brahman F1 calves in years of greater nutritional stress. Angus females were observed to have a relatively low reproductive rate and high apparent fetal loss at the first (27.5%) and second (19.2%) compared with the third or later pregnancy (11.2%). Angus females that gave birth to Brahman F1 calves had 20.1% lower (P < 0.05) pregnancy rates in the succeeding year than those that had given birth to the other two breeds.     

Relationship between nutrition and reproduction in beef cattle

The primary nutrient consideration for optimum reproductive performance in beef cattle is energy. Low energy intake delays the onset of puberty in heifers and bulls. Heifers should reach approximately 66 per cent of mature body weight by 14 to 15 months of age and be bred 30 days prior to breeding the main cow herd. Body conditioning scores (BCS) (1 = emaciated, 9 = obese) should be used to evaluate pregnant cows entering their third trimester. Cows should calve with body conditioning score 5 to 7. Forage quality and environmental factors influence maximum dry matter intake and nutrient requirements and must be considered in the clinical setting. Crude protein dietary content should be 11 to 12 per cent for lactating beef cattle. Mineral (calcium, phosphorus, magnesium, potassium, sulfur, sodium, chloride) nutrition is not a major cause of decreased reproductive performance in beef cattle. Trace mineral deficiencies (particularly selenium, copper, and zinc) can cause decreased reproductive performance. Diagnosis of these trace mineral deficiencies can be confirmed by elemental analysis of blood or tissues.     

Pregnancy rate per cycle is heritable and reduces with cycle in naturally mated tropically adapted beef cows

Pregnancy in cattle is the outcome of the complex process of initiation of cycling, fertilization, maternal recognition of pregnancy and foeto-placental development. Though much is known about initiation of cycling and associated risk factors, there are virtually no data on pregnancy rate per cycle for naturally mated cattle, especially for extensively managed, tropically adapted genotypes, which this study aimed to determine. Tropical composite (Bos indicus and African Sanga crosses with Bos taurus) and Brahman cattle (n = 2,181) of known pedigree in four-year groups at four sites were mated annually for 84 days. Body condition, ovarian function, pregnancies, calving and lactation were monitored through six full reproductive cycles using 4–8 weekly ultrasound of the reproductive tract outside the calving period and daily monitoring during calving. From this, dates of commencement of cycling and conception in each year were estimated for each animal, enabling calculation of established pregnancy for consecutive 21-day periods while cycling and of pregnancies within four months of calving while lactating (P4M). Pregnancy per 21-day period (cycle) during mating for cycling animals averaged 63%, 71%, 41% and 28% in four consecutive cycles. Pregnant per cycle was 2%–11% higher in tropical composites than in Brahmans. The only other consistently significant risk to becoming pregnant was if cycling commenced later than three weeks before mating commenced. P4M averaged 62% and was lower for cows in sub-optimal body condition and in first-parity and later-calving cows. Pregnant per cycle was moderately heritable (~20%), while heritability was moderate to high (33%) for P4M. Selection for pregnant per cycle could be achieved indirectly by selection for P4M, a trait that is readily measured.     

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...     

Estimates of covariances between reproduction and growth in Australian beef cattle

Estimates of covariance components between scrotal circumference, serving capacity, days to calving, and yearling and final weight were obtained for Hereford, Angus, and Zebu cross cattle in temperate and tropical Australia. Analyses were carried out by REML employing a derivative-free algorithm and fitting bivariate animal models. Aspects of modeling and computational requirements related to the use of this method are discussed. Estimates of heritabilities agreed closely with those from univariate analyses, being low for female reproductive performance and moderate to high for male reproduction and growth. Estimates of genetic correlation between male and female fertility traits were low but favorable, being -.25, -.28, and -.41 between scrotal circumference and days to calving for Herefords, Angus, and Zebu crosses, respectively. Genetic correlations between male reproductive traits and weights ranged from .24 to .52 for the temperate breeds and were higher (.65 to .69) for Zebu crosses. Phenotypic correlations between scrotal circumference and weights were similar for all breeds, ranging from .32 to .47, whereas serving capacity and weights were phenotypically unrelated. Estimates of correlations between days to calving and weights were less consistent. Phenotypically, there was little association between the two traits. Genetic correlations for Zebu crosses were negative and low to moderate (-.36 to -.66) and estimates for Angus were close to zero.     

Evaluation of tropically adapted straightbred and crossbred cattle: postweaning gain and feed efficiency when finished in a temperate climate

Beef cows in the subtropical USA must be adapted to the stressors of the environment, typically supplied by using Brahman (Br) breeding. Calves produced in the region, however, are usually grown and finished in more temperate regions, and have a perceived reputation for poor ADG and feed efficiency during finishing. Compromised fertility and carcass quality often associated with the Br have increased interest in tropically adapted Bos taurus breed types. The objective of this study was to evaluate 3 breeds [An = Angus (Bos taurus, temperate); Br (B. indicus, tropical); and Ro = Romosinuano (B. taurus, tropical)] and all possible crosses during various segments of post-weaning growth, and for feed efficiency during the finishing phase. Steer calves (n = 473) born over 3 yr were weaned in late September, backgrounded for at least 21 d (BKG), shipped 2,025 km to El Reno, OK, in October, fed a preconditioning diet for 28 d (RCV), grazed wheat (Triticum aestivum L.) pasture from November to May (WHT), finished on a conventional feedlot diet (FIN), and serially harvested after approximately 95, 125, and 150 d on feed. Body weight and ADG during each segment were tested using a mixed model that included calf age at weaning, year (Y), breed of sire (SB), breed of dam (DB), and interactions. In addition, winter treatment (continuous wheat or reduced grazing of wheat with supplement) was included for the wheat and feedlot phases. Sire within SB × SB [and pen (barn × year) for feedlot phase] were considered random. The SB × DB interaction was significant for all traits (P < 0.01) except exit velocity taken at weaning and ADG during FIN, but both traits were affected by 3-way interactions with Y or harvest group. Tropically-adapted purebred steers had greater (P < 0.01) ADG than AnAn through weaning and BKG in FL but the reverse was true during the RCV and WHT segments. Similar, but less pronounced results were noted for F(1) steers with 100% tropical influence compared with those with only 50%. Heterosis was numerically greater for most traits for An × Br (11 to 64%) compared with An × Ro and Br × Ro (3 to 42%), which were similar. In a subset of the steers (n = 261), G:F was not influenced by level of tropical breeding, but tropically adapted steers were more efficient (P < 0.05) by residual feed intake. No heterosis was evident. These data show that in temperate zones, winter is the period when productivity of tropically adapted cattle is compromised.     

Genome-wide association studies for osteochondrosis in French Trotter horses

A genome-wide association study for osteochondrosis (OC) in French Trotter horses was carried out to detect QTL using genotype data from the Illumina EquineSNP50 BeadChip assay. Analysis data came from 161 sire families of French Trotter horses with 525 progeny and family sizes ranging from 1 to 20. Genotypes were available for progeny (n = 525) and sires with at least 2 progeny (n = 98). Radiographic data were obtained from progeny using at least 10 views to reveal OC. All radiographic findings were described by at least 2 veterinary experts in equine orthopedics, and severity indices (scores) were assigned based on the size and location of the lesion. Traits used were a global score, the sum of all severity scores lesions (GM, quantitative measurement), and the presence or absence of OC on the fetlock (FM), hock (HM), and other sites (other). Data were analyzed using 2 mixed models including fixed effects, polygenic effects, and SNP or haplotype cluster effects. By combining results with both methods at moderate evidence of association threshold P < 5 × 10(-5), this genome-wide association study displayed 1 region for GM on the Equus caballus chromosome (ECA) 13, 2 for HM on ECA 3 and 14, and 1 for other on ECA 15. One region on ECA 3 for HM represented the most significant hit (P = 3 × 10(-6)). By comparing QTL between traits at a decreased threshold (P < 5 × 10(-4)), the 4 QTL detected for GM were associated to a QTL detected for FM or HM but never both. Another interesting result was that no QTL were found in common between HM and FM.     

Aspects of reproduction in female Bos indicus cattle: a review

SUMMARY Differences occur between female Bos indicus and Bos taurus cattle in various aspects of reproductive physiology and behaviour. These may be associated with different natural and human selection pressures, compounded by strong genotype-environment interactions. B indicus cattle are better adapted for tropical environments (despite overall poor cattle reproductive rates in these regions) which tend to be more stressful for B taurus genotypes. Conversely, B taurus cattle generally show superior reproductive and productive traits under more favoured, temperate conditions. Despite genotype-environment effects, B indicus females are generally considered to take longer to achieve puberty and to have longer gestation lengths, exhibit prolonged postpartum anoestrus, show greater seasonality of reproductive traits (tending to be long-day breeders), display a shorter, less overt oestrus as well as less tendency to allow riding behaviour by subordinate females. Some groups appear to have increased losses both during pregnancy and in the neonatal period. On the positive side, B indicus females respond well to managerial and nutritional interventions, tend to have greater reproductive longevity and they generally exhibit strong maternal traits. Culling of infertile females and selection for greater male scrotal circumference and sex-drive, in conjunction with the use of target weights, body condition scoring and weaning stratagems can improve reproductive rates in B indicus females.     

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.     

Reproductive and leptospiral studies on beef cattle in central Queensland

The effect of rainfall on reproductive performance in beef cattle and the effects of rainfall and soil type on the prevalence of leptospirosis in beef cattle in inland central Queensland are described. Low annual rainfall produced a significant (P less than 0.05) decrease in calf branding rates. Leptospirosis (due to serovar hardjo) was serologically more prevalent after rain and on farms with high water holding capacity soils but there was no significant difference in branding rates between cattle on high or low water holding capacity soils. As a secondary mid-year rainfall peak is a feature of the area, leptospirosis due to serovar hardjo will tend to spread when most of the breeding herd is in the last trimester of pregnancy. The prevalence of leptospirosis due to serovar pomona is significantly lower in the region.     

Candidate genes for male and female reproductive traits in Canchim beef cattle

Background: Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals.Results: Associated SNPs were observed for scrotal circumference at 420 d of age(435 SNPs), followed by scrotal circumference at 210 d of age(12 SNPs), age at first calving(six SNPs), and age at second calving(four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction.Conclusions: Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless,the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, al relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program.     

Genome wide association study on beef production traits in Marchigiana cattle breed

A genomewide association study was carried out on a sample of Marchigiana breed cattle to detect markers significantly associated with carcass and meat traits. Four hundred and nine young bulls from 117 commercial herds were genotyped by Illumina 50K BeadChip assay. Eight growth and carcass traits (average daily gain, carcass weight, dressing percentage, body weight, skin weight, shank circumference, head weight and carcass conformation) and two meat quality traits (pH at slaughter and pH 24 h after slaughter) were measured. Data were analysed with a linear mixed model that included fixed effects of herd, slaughter date, fixed covariables of age at slaughter and SNP genotype, and random effects of herd and animal. A permutation test was performed to correct SNP genotype significance level for multiple testing. A total of 96 SNPs were significantly associated at genomewide level with one or more of the considered traits. Gene search was performed on genomic regions identified on the basis of significant SNP position and level of linkage disequilibrium. Interesting loci affecting lipid metabolism (SOAT1), bone (BMP4) and muscle (MYOF) biology were highlighted. These results may be useful to better understand the genetic architecture of growth and body composition in cattle.     

肉牛微量元素铜的营养

铜是人和动物所必需的微量元素,大量的试验研究已证实,铜具有广泛的生物学作用,它与畜禽的生长性能、免疫功能等都有密切的联系。铜的缺乏对畜禽的造血功能、神经系统、骨骼、结缔组织和被毛的生长发育等均会造成不同程度的不良影响。     

Hip dysplasia in beef cattle

A bilateral hip lameness has been found in young beef bulls of the Hereford, Aberdeen Angus, Galloway and Charolais breeds in the United Kingdom, North America and Australia. The incidence is usually small and sporadic, but up to half of the male animals on one farm may be affected clinically by the time they are one year old. Clinical lameness begins at three months to two years old, and very occasionally up to three years of age; some calves are obviously affected at birth. Aberdeen Angus cattle tend to be affected earlier than other breeds. Clinical evidence of the condition is almost entirely confined to the male.