Genome-wide association study for calving performance using high-density genotypes in dairy and beef cattle

Background

Calving difficulty and perinatal mortality are prevalent in modern-day cattle production systems. It is well-established that there is a genetic component to both traits, yet little is known about their underlying genomic architecture, particularly in beef breeds. Therefore, we performed a genome-wide association study using high-density genotypes to elucidate the genomic architecture of these traits and to identify regions of the bovine genome associated with them.

Results

Genomic regions associated with calving difficulty (direct and maternal) and perinatal mortality were detected using two statistical approaches: (1) single-SNP (single nucleotide polymorphism) regression and (2) a Bayesian approach. Data included high-density genotypes on 770 Holstein-Friesian, 927 Charolais and 963 Limousin bulls. Several novel or previously identified genomic regions were detected but associations differed by breed. For example, two genomic associations, one each on chromosomes 18 and 2 explained 2.49 % and 3.13 % of the genetic variance in direct calving difficulty in the Holstein-Friesian and Charolais populations, respectively. Imputed Holstein-Friesian sequence data was used to refine the genomic regions responsible for significant associations. Several candidate genes on chromosome 18 were identified and four highly significant missense variants were detected within three of these genes (SIGLEC12, CTU1, and ZNF615). Nevertheless, only CTU1 contained a missense variant with a putative impact on direct calving difficulty based on SIFT (0.06) and Polyphen (0.95) scores. Using imputed sequence data, we refined a genomic region on chromosome 4 associated with maternal calving difficulty in the Holstein-Friesian population and found the strongest association with an intronic variant in the PCLO gene. A meta-analysis was performed across the three breeds for each calving performance trait to identify common variants associated with these traits in the three breeds. Our results suggest that a portion of the genetic variation in calving performance is common to all three breeds.

Conclusion

The genomic architecture of calving performance is complex and mainly influenced by many polymorphisms of small effect. We identified several associations of moderate effect size but the majority were breed-specific, indicating that breed-specific alleles exist for calving performance or that the linkage phase between genotyped allele and causal mutation varies between breeds.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0126-4) contains supplementary material, which is available to authorized users.     

牛α辅肌动蛋白(α-Actinin)1 基因遗传变异与产犊数性状的相关性

为了探讨辅肌动蛋白1(α-actinin1)基因对母牛产犊数的影响,以鲁西单胎牛,鲁西双胎牛,南阳牛,晋南牛,荷斯坦牛,三河牛和延边牛为研究对象,以α-actinin1为影响产犊数的候选基因,分别扩增418 bp和505 bp 2个片段,采用直接测序,RFLP-RsaⅠ和RFLP-Apa Ⅰ方法检测α-actinin1基因的多态性,并将其与产犊数性状进行了关联分析.在内含子15 第227 nt处的碱基发生G→A突变,和内含子10第3 124 nt处发生A→G突变,使其产生酶切多态.对2个酶切多态位点进行基因型分型,χ2检验表明：在G227A位点,除了鲁西单胎牛外,其他群体都已达到Hardy-Weinberg平衡;在A3 124G位点,除了鲁西双胎牛外,其余群体都已经达到Hardy-Weinberg平衡.SAS 9.0的最小二乘拟和一般线性模型分析结果表明：A3 124G位点的AG基因型的产犊数的最小二乘均数极显著（P＜0.01）高于基因型AA;而单倍型组合G G的产犊数的最小二乘均数显著高（P＜0.01）于其它3种单倍型组合.α-actinin1基因有可能作为产犊数性状的候选分子的遗传标记.     

牦牛FSHR 基因部分序列多态性及其与繁殖性状的关联分析

本研究旨在分析牦牛FSHR 基因5’端及第一外显子的多态性,并分析其与繁殖性状的关联性,为从遗传角度上解决牦牛产犊间隔过长的问题提供参考。以4 个种群的667 头牦牛为研究对象,应用PCR-SSCP 方法检测FSHR 基因的多态性,并用最小二乘法分析雌性个体该基因多态性与产犊间隔的关系。结果表明,三个扩增片段共获得牦牛FSHR 基因940 bp 的序列,由5’端和第一外显子组成,与其它哺乳动物的对应序列有较高的同源性。共发现9 处突变位点,其中一处位于开放阅读框内,但属于同义突变。不同种群间的产犊间隔差异显著(P <0. 05);FSHR 基因不同基因型对产犊间隔影响差异不显著(P > 0. 05),但AB、LL、LM、LN 及RT 基因型均有缩短牦牛产犊间隔的趋势。     

Sequencing and alignment of mitochondrial genomes of Tibetan chicken and two lowland chicken breeds

Tibetan chicken lives in high-altitude area and has adapted well to hypoxia genetically. Shouguang chicken and Silky chicken are both lowland chicken breeds. In the present study, the complete mitochondrial genome sequences of the three chicken breeds were all sequenced. The results showed that the mitochondrial DNAs (mtDNAs) of Shouguang chicken and Silky chicken consist of 16784 bp and 16785 bp respectively, and Tibetan chicken mitochondrial genome varies from 16784 bp to 16786 bp. After sequence analysis, 120 mutations, including 4 single nucleotide polymorphisms (SNPs) in tRNA genes, 9 SNPs and 1 insertion in rRNA genes, 38 SNPs and 1 deletion in D-LOOP, 66 SNPs in protein-coding genes, were found. This work will provide clues for the future study on the association between mitochondrial genes and the adaptation to hypoxia.     

中国主要家鹅品种的遗传分化研究

利用PCR和DNA测序技术扩增了15个中国家鹅品种线粒体DNA控制区部分序列（1042bp）。研究结果表明：伊犁鹅与14个品种间的核苷酸分歧度最高,为3．805％～4．067％;不同品种内核苷酸多样度表现出较大的差异,为0～0．116％。除伊犁鹅外的14个家鹅品种中,豁眼鹅与其他品种间的核苷酸分歧度为0．211％～0．272％,明显高于其他品种间的0～0．094％。中国家鹅品种的遗传分化格局与地理分布有关,豁眼鹅的分歧时间较早,遗传漂变是导致豁眼鹅遗传分化的主要因素（Nm=0．02～0．54）,基因流则是另外13个家鹅品种间遗传分化不明显的主要因素（Nm=12．0～65．33）．     

Sequencing and alignment of mitochondrial genomes of Tibetan chicken and two lowland chicken breeds

Tibetan chicken lives in high-altitude area and has adapted well to hypoxia genetically. Shouguang chicken and Silky chicken are both lowland chicken breeds. In the present study, the complete mito-chondrial genome sequences of the three chicken breeds were all sequenced. The results showed that the mitochondrial DNAs (mtDNAs) of Shouguang chicken and Silky chicken consist of 16784 bp and 16785 bp respectively, and Tibetan chicken mitochondrial genome varies from 16784 bp to 16786 bp. After sequence analysis, 120 mutations, including 4 single nucleotide polymorphisms (SNPs) in tRNA genes, 9 SNPs and 1 insertion in rRNA genes, 38 SNPs and 1 deletion in D-LOOP, 66 SNPs in pro-tein-coding genes, were found. This work will provide clues for the future study on the association between mitochondrial genes and the adaptation to hypoxia.Tibetan chicken, lowland chicken, mitochondrial genome, hypoxia.     

Assessment of the post partum Reproductive Performance of the Icelandic Dairy Cow During a 3 Year Period

The time of ovulation, artificial insemination (AI), conception and conception rate were studied in 412 Icelandic dairy cows from 2 different areas during a period of 3 years. To assess these parameters the progesterone level was measured in sequential samples of milk and the status of the genital organs evaluated by monthly rectal palpations. The time and number of AI was recorded and the conception rate calculated and compared with the other parameters. Furthermore, the length of the calving interval and gestation period were determined. The effects of year, season, area, age, herd and parity on these parameters were evaluated. The overall mean for the time of first post partum ovulation was 42 days and varied from 29 to 49 days between herds. This is a considerably longer time than recorded for many other breeds of dairy cows. The effects of season, area and herd were significant for the time of first post partum ovulation. The overall time of first post partum AI and conception were 74 days and 97 days, respectively. In spite of late onset of ovarian activity in Icelandic dairy cows, these two pararmeters are comparable to those of other breeds of cattle. The effects of season, parity and herd were significant for these two parameters. The conception rate to first post partum AI was 59% and the number of AI per conception was 1.6. The time of conception correlated closely (r = 0.5) with the time of first post partum AI, but the conception rate to first AI increased and the number of AI per conception decreased with increasing time of first post partum AI. The calving interval was 382 days and the gestation period was 287 days.     

Genetic parameters for stayability to consecutive calvings in Zebu cattle

Longer-lived cows tend to be more profitable and the stayability trait is a selection criterion correlated to longevity. An alternative to the traditional approach to evaluate stayability is its definition based on consecutive calvings, whose main advantage is the more accurate evaluation of young bulls. However, no study using this alternative approach has been conducted for Zebu breeds. Therefore, the objective of this study was to compare linear random regression models to fit stayability to consecutive calvings of Guzerá, Nelore and Tabapuã cows and to estimate genetic parameters for this trait in the respective breeds. Data up to the eighth calving were used. The models included the fixed effects of age at first calving and year-season of birth of the cow and the random effects of contemporary group, additive genetic, permanent environmental and residual. Random regressions were modeled by orthogonal Legendre polynomials of order 1 to 4 (2 to 5 coefficients) for contemporary group, additive genetic and permanent environmental effects. Using Deviance Information Criterion as the selection criterion, the model with 4 regression coefficients for each effect was the most adequate for the Nelore and Tabapuã breeds and the model with 5 coefficients is recommended for the Guzerá breed. For Guzerá, heritabilities ranged from 0.05 to 0.08, showing a quadratic trend with a peak between the fourth and sixth calving. For the Nelore and Tabapuã breeds, the estimates ranged from 0.03 to 0.07 and from 0.03 to 0.08, respectively, and increased with increasing calving number. The additive genetic correlations exhibited a similar trend among breeds and were higher for stayability between closer calvings. Even between more distant calvings (second v. eighth), stayability showed a moderate to high genetic correlation, which was 0.77, 0.57 and 0.79 for the Guzerá, Nelore and Tabapuã breeds, respectively. For Guzerá, when the models with 4 or 5 regression coefficients were compared, the rank correlations between predicted breeding values for the intercept were always higher than 0.99, indicating the possibility of practical application of the least parameterized model. In conclusion, the model with 4 random regression coefficients is recommended for the genetic evaluation of stayability to consecutive calvings in Zebu cattle.     

Extensive mtDNA diversity in horses revealed by PCR–SSCP analysis

The hypervariable D-loop region of mitochondrial DNA (mtDNA) was amplified with the polymerase chain reaction using total horse DNA samples. Analysis of single strand conformation polymorphism (SSCP) of denatured amplification products was carried out by native polyacrylamide (8%) gel electrophoresis followed by silver staining. As many as 15 distinct SSCP variants were revealed when screening a total of 78 maternally unrelated horses representing five different breeds. All breeds showed a high degree of polymorphism and the estimated probability (PI_mt) that two maternally unrelated individuals have, by chance, identical SSCP variants varied between 0.14 and 0.30. We detected no heteroplasmy or deviations from strict and stable maternal inheritance when examining four maternal lineages, each represented by six to eight horses, separated by up to five generations from a common ancestral mare. The study establishes a simple screening method for detecting equine mtDNA types, which can be applied for tracing maternal genealogies and for association studies.     

Low calving rates in Brahman cross cattle

Summary It is suggested that the low calving rate of crosses between Bos taurus cows and Brahman bulls in the F2 generation, in later generations and in breeds derived from the cross, could be due to the difference between the Bos taurus Y and the Bos indicus Y if this difference is due to a translocation between the Y and an autosome. It is suggested that such a translocation could set up a balanced polymorphism and perpetuate low calving rates against selection.     

Effects of early weaning on reproductive efficiency in beef cows

Six hundred eighty-three mature cows of the Devon, A. Angus, and Hereford breeds were used to investigate the effect of weaning 90 days after calving on the postpartum reproduction (anestrus and pregnancy rate). The calving pariod was 90 days, from September to November (Spring 1976). The breeding period, also of 90 days, began at the end of the calving period and was from December to February (Summer 1977). The calves were separated from their mothers with a mean age of 90 days for the “W” group of cows and 200 days for the “S”.Early weaning increased overall conception in the 90 days breeding period by 43.07% (P < .001) and reduced the postpartum anestrus from 60.42% in the “S” group to 13.79% (difference of 46.63% ? P < .001) in the “W” group.     

Effects of body condition and temporary calf removal on reproductive performance of range cows

The effects of body condition at calving and breeding and temporary calf removal prior to the start of the breeding season on reproductive performance of 323 cows from two breed groups were studied over two breeding seasons. Body condition score at calving was significantly and positively correlated with two body condition indices, which were based on weight-to-height ratio measured at calving and at the start of the breeding season. While the two body condition indices were strongly associated with the age of the cow, the body condition score, based on palpation and visual appraisal, was less affected by the age of the cow. Cows with a body condition score of 3.0 at calving had a shorter calving interval (P<0.02), higher pregnancy rate (P<0.08), and higher number of calves born (P<0.10) than cows which had body condition scores lower than 3.0 at calving. Temporary (48 h) calf removal prior to the start of the breeding season did not have a significant influence on the calving interval, pregnancy rate or the number of calves born nor on the weaning weights of their calves. Differences in reproductive performance between the two breed groups of cows were not significant.     

家鹅线粒体tRNAthr与tRNApro序列与结构分析

本研究采用PCR和DNA测序技术测定了6个中国家鹅品种和2个欧洲鹅品种25个个体线粒体DNA tRNApro（69bp）和tRNAthr（68bp）基因的完整序列,通过对家鹅线粒体基因组的研究,首次报道了家鹅线粒体tRNApro和tRNAthr基因的结构,对鸿雁家鹅、灰雁家鹅、白额雁（Anser albifrons,序列号为AF363031）种间的tRNApro和tRNAthr基因的二级结构及序列的变异特征进行了分析,并通过家鸡（Gallus gallus domesticus,序列号为NC001323）与鸿雁家鹅间tRNApro和tRNAthr基因二级结构的比较,初步进行了鸡形目与雁形目两个目间tRNApro和tRNAthr基因二级结构及序列变异的分析。结果表明：家鹅tRNApro和tRNAthr基因均可折叠成标准的三叶草形二级结构; 2个tRNA基因三叶草结构的氨基酸臂、反密码子环在鸿雁、灰雁和白额雁种间以及鸡形目与雁形目两个目间没有发生变异,具有高度的保守性。本研究的结果将为进一步探讨家鹅线粒体DNA tRNApro和tRNAthr基因序列与结构、功能的关系奠定基础。所测定的基因序列已登录国际GenBank数据库,序列号为AY427800～AY427805和AY427812～AY427814。     

Productivity of Thai Brahman and Simmental-Brahman crossbred (Kabinburi) cattle in central Thailand

The productivity of the new crossbred cattle Kabinburi (K) was compared to that of Thai Brahman (TB) using 756 production records from K cattle and 1,316 production records from TB cattle kept at three locations in Thailand. The data were analyzed for the effect of breeds and locations. The ambient temperature, the humidity, the Temperature–Humidity Index (THI) and the rainfall of the three locations were different. Lamphayaklang Livestock Research and Breeding Center (LP) had the highest rainfall/year followed by Nongkwang Livestock Research and Breeding Center (NK), and Prachinburi Livestock Breeding Station (PC). Kabinburi cattle had a higher bodyweight at birth as well as at 200, 400 and 600 days of age than TB cattle. Furthermore, K heifers gave birth to their first calf at a younger age and had a shorter calving interval than TB cows. Thai Brahman cattle kept at LP had significantly higher bodyweight at 400 and 600 days than the animals kept at NK, but bodyweight at birth and 600 days of age were not significantly different. Thai Brahman cattle kept at LP were younger at first calving and had a shorter calving interval than the animals kept at NK. K cattle kept at NK were heavier at birth and at 200, 400 and 600 days of age than the animals kept at PC. Furthermore, Kabinburi cows kept at NK were younger at first calving (P < 0.01), but the calving interval was not different between the two groups kept at NK or PC.     

Mitochondrial sequence reveals high levels of gene flow between breeds of domestic sheep from Asia and Europe

Sequence variation present within the mitochondrial genome was used to investigate genetic diversity within sheep breeds from Asia and Europe. Comparison of 2027 bp of sequence from 121 animals revealed 44 phylogenetically informative nucleotide positions and a single insertion/deletion. A total of 57 haplotypes were observed which formed two distinct clades. Type A haplotypes were found in breeds from Asia (India, Indonesia, Mongolia, and Tibet), while type B haplotypes were observed at the highest frequency in breeds sourced from Europe (nine breeds from Austria, Aland, Finland, Spain, and northwestern Russia). The distribution of haplotypes indicates sheep appear to have the weakest population structure and the highest rate of intercontinental dispersal of any domestic animal reported to date. Only 2.7% of the sequence variation observed was partitioned between continents, which is lower than both goat (approximately 10%) and cattle (approximately 50%). Diagnostic restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) tests which distinguish type A and B haplotypes were used to test an additional 223 animals from 17 breeds of European and Asian origin. A mixture of the two lineages was found in every breed except Suffolk and the Indian Garole, indicating introgression has played a major part during breed development and subsequent selection.     

Association between alphas1-, beta- and kappa-casein loci in two Italian cattle breeds.

The genetic polymorphism alphas1-, beta- and kappa-caseins was examined by gel electrophoresis in two Italian breeds, Valdostana and Piedmont. The results obtained from acid and basic migration show that the gene frequencies of the two breeds are very similar. Non independent assortment of genotypes among these milk protein loci was also studied. Results of analyses carried out on loci pairs showed that the genetic complex alphas1-CnB - beta-CnA2 was the most common in both breeds. In addition, the measure of linkage disequilibrium or gametic association (denoted delta) showed a close association between alphas1-Cn and beta-Cn, and between beta-Cn and kappa-Cn. No significant association was found between alphas1-Cn and kappa-Cn. This is in line with the model proposed by Grosclaude et al. (1973).     

Prevalence of, and risk factors associated with, perinatal calf mortality in pasture-based Holstein-Friesian cows

Recent publications indicate that the prevalence of perinatal mortality has increased in some dairy industries and an increased proportion of this loss is not associated with the traditional risk factors for perinatal mortality. The objectives of this study were to establish the prevalence of perinatal mortality (calf death within 24 h of calving) in Irish dairy herds and to determine the current significance of putative risk factors in pasture-based management systems. A total of 182 026 records of full-term calvings from Holstein-Friesian dams served by artificial insemination (AI) sires of seven breeds in herds of 20 calvings or more per year were available from the Irish national breeding database over 4 years (2002 to 2005). The prevalence of perinatal mortality was 4.29% (7.7% in primiparae and 3.5% in pluriparae). The likelihood of perinatal mortality increased between 2002 and 2005 and was greatest in June and in winter. There was an interaction (P < 0.001) between the effect of calving assistance and parity with the effect of dystocia on perinatal mortality being greater in primiparae. The odds of perinatal mortality were greater in male (OR = 1.12; P < 0.001) and in twin calves (OR = 5.70-13.36; P < 0.001) and in dams that had perinatal mortality at the previous calving (OR = 4.21; P < 0.001). The logit of the probability of perinatal mortality increased by 0.099 per unit increase in sire predicted transmitting ability (PTA) for direct perinatal mortality. The probability of perinatal mortality increased at an increasing rate in primiparae as animals calved at a younger age relative to the median age at first calving. The only herd-level factor examined, herd size did not affect the odds of perinatal mortality. These data indicate that the prevalence of perinatal mortality in this cattle population is similar to that in other pasture-based dairy systems worldwide. The putative exposures and attributes traditionally associated with perinatal mortality were associated with perinatal mortality in this pasture-based dairy cow population. The practical implication of these results is that as many of the significant risk factors are largely not under management control (year of calving, month of calving, twin calving, primiparity, previous perinatal mortality and foetal gender), herd owners must focus on the significant determinants under their control (age at first calving, sire genetic merit for direct perinatal mortality and both the extent of calving supervision and the degree of assistance), in order to reduce the prevalence of perinatal mortality and improve perinatal welfare.     

Molecular phylogeny of Indian horse breeds with special reference to Manipuri pony based on mitochondrial D-loop

Manipuri pony is the geographically distant breed of horse from the five recognized horse breeds found in the Indian subcontinent. The phylogenetic relationship of Manipuri pony with the other breeds is unknown. The diversity in the mitochondrial (mt) DNA D-loop region is employed as an important tool to understand the origin and genetic diversification of domestic horses and to examine genetic relationships among breeds around the world. This study was carried out to understand the maternal lineages of Manipuri pony using the 247 bp region of the mtDNA D-loop. The dataset comprised of eleven numbers of self developed sequences of Manipuri pony, 59 and 35 number of retrieved sequences of Indian horse breeds and other worldwide breeds respectively. A total of 35 haplotypes was identified with a high level of genetic diversity in the Indian breeds. A total of seven major mtDNA haplogroups (A–G) was identified in the Indian horse breeds that indicated the abundance of mtDNA diversity and multiple origins of maternal lineages in them. The majority of the studied sequences of Indian breeds (33.3 %) were grouped into haplogroup D and least (3.9 %) in haplogroup E. The Manipuri breed showed the least F_ST distance (0.03866) with the most diverged Indian breeds and with Thoroughbred horse among the worldwide. This study indicated a close association between Manipuri pony and Thoroughbred.     

Mitochondrial haplotypes reveal a strong genetic structure for three Indian sheep breeds

This survey represents the first characterization of mitochondrial DNA diversity within three breeds of Indian sheep (two strains of the Deccani breed, as well as the Bannur and Garole breeds) from different geographic regions and with divergent phenotypic characteristics. A 1061-bp fragment of the mitochondrial genome spanning the control region, a portion of the 12S rRNA gene and the complete phenyl tRNA gene, was sequenced from 73 animals and compared with the corresponding published sequence from European and Asian breeds and the European Mouflon (Ovis musimon). Analysis of all 156 sequences revealed 73 haplotypes, 52 of which belonged to the Indian breeds. The three Indian breeds had no haplotypes in common, but one Indian haplotype was shared with European and other Asian breeds. The highest nucleotide and haplotype diversity was observed in the Bannur breed (0.00355 and 0.981 respectively), while the minimum was in the Sangamneri strain of the Deccani breed (0.00167 and 0.882 respectively). All 52 Indian haplotypes belonged to mitochondrial lineage A. Therefore, these Indian sheep are distinct from other Asian and European breeds studied so far. The relationships among the haplotypes showed strong breed structure and almost no introgression among these Indian breeds, consistent with Indian sheep husbandry, which discourages genetic exchange between breeds. These results have implications for the conservation of India's ovine biodiversity and suggest a common origin for the breeds investigated.