Direct and maternal genetic relationships between calving ease, gestation length, milk production, fertility, type, and lifespan of Holstein-Friesian primiparous cows

Genetic evaluation for stillbirth and preweaning mortality in Australian dairy cattle

The welfare of calves is important to both farmers and consumers. Practices that increase the proportion of calves born alive and enable them to thrive through to weaning contribute to improved sustainability. Stillbirths (SB) are calvings where the calf dies at birth or within 24 h after birth. Preweaning mortality (PWM) refers to calves that die after the first day of life but before weaning based on termination data. Both SB and PWM are binary traits characterized by low heritability. Data collection for these traits is incomplete, compared with traits such as milk yield in cows. Despite these challenges, genetic variation can be measured and used to produce breeding tools, such as EBVs, to reduce calf mortality over time. The aim of this study was to compare the performance of various linear models to predict SB and PWM traits in Holstein and Jersey cattle and evaluate their applicability for industry-wide use in the Australian dairy industry. Calving records from around 2.25 million Holstein and Jersey dams were obtained from DataGene's Central Data Repository from the year 2000 onward, to calculate genetic parameters. About 7% of calves were recorded as SB in the period from 2000 to 2021 (n = 1.48 million calvings). The prevalence of PWM was much lower than SB during the same period at 2% (n = 0.89 million calves). Genetic parameters were estimated for SB direct, SB maternal, and PWM using bivariate linear models with calving ease (CE) as the second trait in the model. The heritability of these calf traits was low and varied between 1% and 5% depending on the breed, trait, and model. In Holstein cattle, heritabilities were 2% for PWM and SB direct and 1% for SB maternal, whereas in Jersey cattle heritabilities were 5% for PWM, 2% for SB direct, and 1% for SB maternal. The genetic trends for both SB direct and SB maternal in Holstein cattle indicate improvement in both traits, whereas there was no apparent increase or decrease in PWM in the past 2 decades. The coefficient of genetic variation for SB direct and PWM was between 11.7% and 23.0% in Holstein and Jersey cattle, demonstrating considerable genetic variation in calf survival traits as a first step to using genetic selection to increase the proportion of calves born alive and calves weaned. A focus on improved calf and calving recording practices is expected to increase the reliability of genetic predictions.

Genetic parameters for oocytes and embryo production and their association with linear type traits in dairy Gyr Cattle

In vitro embryo production is one of the main reproductive techniques used in dairy Gyr cattle. In addition, linear type measures are well characterized and have been used in dairy Gyr breed selection for the last 4 decades. The estimation of genetic parameters for the number of aspirated oocytes and in vitro-produced embryos associated with the linear type measures would support genetic progress for animal breeding programs toward embryo production. This study aimed to estimate genetic parameters for aspirated oocytes, embryo in vitro production, and linear type traits, exploring the association between them. The repeatability model was applied to 14,251 ovum pick-up events from 1,916 Gyr donors. A subset of 604 donors from the same group had their body measurements taken. Single- and 2-trait analyses were carried out using the BLUPF90 family programs. Heritability estimates of 0.38, 0.34, and 0.20 were obtained for total oocytes, viable oocytes, and embryos, respectively,-and the heritability of the linear type traits ranged from 0.22 to 0.40. High genetic correlations between total oocytes and viable oocytes (0.99), and between oocytes (total and viable) and embryos (0.83) were obtained. Low to high genetic (-0.07 to 0.92) and phenotypic (0.32 to 0.86) correlations were obtained between the linear type traits. Moreover, low phenotypic correlations (0.01 to 0.13) were observed for oocytes (total and viable) and embryos with the linear type traits, whereas low to moderate genetic correlations (0.07 to 0.42) were observed between the same traits, especially for ilium width (0.42), rump area (0.38), and hip height (0.33). Thus, selection for in vitro production is achievable in Gyr dairy cattle, and superior genetic progress is associated with the selection of oocytes (total and viable). Furthermore, the moderate genetic association between oocytes and embryos with linear type traits, especially ilium width suggests that progress on in vitro embryo production may be achieved by accessing these measurements.

Genetic parameters, GWAS and selection perspective on gestation length in 16 French cattle breeds

In this paper, we present a comprehensive study of gestation length (GL) in 16 cattle breeds by using large genotype and animal record databases. Data included over 20 million gestations since 2000 and genotypes from one million calves. The study addressed the GL variability within and between breeds, estimation of its direct and maternal heritability coefficients, association with fitness and several economic traits, and QTL detection. The breed average GL varied from 279.7 to 294.4 d, in Holstein and Blonde d'Aquitaine breeds, respectively. Standard deviations per breed were similar and ranged from 5.2 to 5.8 d. Direct heritability (i.e., for GL defined as a trait of the calf) was moderate to high (h2 = 0.40 to 0.67), whereas the maternal heritability was low (0.04 to 0.06). Extreme breeding values for GL were strongly associated with a higher mortality during the first 2 d of life and were associated with milk production of dams for dairy breeds and precocity of females. Finally, several QTL were detected affecting GL with cumulated effects up to a few days, and at least 2 QTL were found to be shared between different breeds. Our study highlights the risks that would be associated with selection toward a reduced gestation length. Further genomic studies are needed to identify the causal variants, and their association with juvenile mortality and other economic traits.

Quantitative trait loci exploration and characterization of gestation length in Holstein cattle

Gestation length (GL) is a moderately heritable trait in cattle with economic and management implications. This study aimed to characterize the gestation length of an Argentinian Holstein cattle population, understand contributing factors, and explore the GL effect on production performance. Further objectives were to estimate direct and maternal heritabilities for this trait and to identify genomic regions affecting it. Data consisted of GL records from 45,738 births corresponding to 17,004 Holstein cows and heifers. The effects of age and calving season over GL were analyzed using a Student's t-test for homoscedastic samples. The effects of the GL category (GL shorter than 1.5 SD, within ±1.5 SD, and longer than 1.5 SD from the mean) on production performance were studied by analysis of variance. A single-step genome-wide association study was performed using the BLUPF90 suite of programs with genotypes from 654 Holstein animals on 40,339 SNP. The results showed that the younger the age at calving, the shorter the GL. Moreover, gestations ending in warmer seasons were, in general, statistically shorter than those ending in colder seasons for both heifers and cows. Regarding the effect of GL on production performance, cows with gestation periods within ±1.5 SD from the population mean exhibited the highest 305-day cumulative milk, fat, and protein productions. Direct and maternal heritabilities for GL were 0.42 and 0.03, respectively. We detected a SNP suggestively associated with direct gestation length at 57.7 Mb on Bos taurus autosome 18, a locus included in a region described in the literature as associated with the trait. The information obtained on the environmental and genetic factors affecting GL in Argentinian Holstein cows contributes to characterizing the population in pursuit of improving the performance of national dairy cattle breeding systems.

Estimation of Genetic Parameters for Conformation Traits and Milk Production Traits in Chinese Holsteins

The objective of this study was to explore the genetic parameters of conformation traits and milk production traits in Chinese Holstein cattle and to provide a reference for dairy cattle breeding. We collected the phenotypic data of 23 conformation traits and five milk production traits of Chinese Holsteins and used animal models to estimate the genetic parameters of conformation traits and milk production traits. The estimated heritability of conformation traits ranged from 0.11 (angularity) to 0.37 (heel depth) and the genetic correlation between conformation traits ranged from -0.73 (bone quality and rear leg-rear view) to 0.76 (chest width and loin strength). The heritability of milk production traits ranged from 0.23 (somatic cell score) to 0.50 (305-d milk yield). The estimated values of genetic correlation between conformation traits and milk production traits ranged from -0.56 (heel depth and 305-d milk yield) to 0.57 (udder texture and milk fat percentage). There was a positive genetic correlation between most conformation traits and milk fat percentage, but a weak negative genetic correlation with milk yield. Strengthening the moderately and highly heritable milk production and conformation traits, especially the selection of rear udder traits and body shape total score, will be beneficial in improving the performance of dairy cows.

Success rate of artificial insemination, reproductive performance and economic impact of failure of first service insemination: a retrospective study

Background

A retrospective cohort study using a 10 year artificial insemination (AI) and cow reproductive performance data was conducted to study the success rate of AI; associations between effectiveness of AI and breed, AI season and, number of service per conception, and economic impact of failure of FSC in Dessie town, Dessie zuria and Kutaber districts. A total of 3480 dairy cows’ AI and reproductive performance records which were performed between 2003 and 2013 in the three selected districts of South Wollo were used. The economic losses and costs for cows that failed to conceive at their first AI associated with the larger number of days open were estimated.

Result

The prevalence of conception has a statistically significant difference between breeds of cows (P = 0.019). The non-return rate for first service was 58.54%. The median days to first service (DFS), inter-service interval (ISI) and gestation length (GL) were 126, 30 and 278 days respectively. Whereas, the mean + SD days open, calving interval (CI), number of inseminations (NOI) and number of services per conception (NSPC) were 147.2 ± 60.26, 424.5 ± 60.55, 1.14 ± 0.38 and 1.15 ± 0.39 respectively. Based on AI season there was a significant difference in conception between winter and spring (P = 0.021). There is a 45.04 days extension in the mean calving to conception interval in cows that did not conceive at their first AI but conceived by 2nd and 3rd AI than in cows that did conceive at their first AI. A total of 21,665.3 ETB extra costs was spent on reproductive treatment and other management for cows that failed to conceive at their first AI but conceived by second and third service. In cows that did not conceive totally the owner losses on average 473.7 ETB per cow per day extra costs until the cows will be culled.

Conclusion

Therefore to increase the conception rate and decrease the economic loss the owners of the dairy cows should supervise the cows regularly and should be trained on how to identify cows on estrous, the AI technicians should be trained to conduct the AI service accurately.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03325-1.

Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle

The goal of our study was to identify the SNPs, metabolic pathways (KEGG), and gene ontology (GO) terms significantly associated with calving and workability traits in dairy cattle. We analysed direct (DCE) and maternal (MCE) calving ease, direct (DSB) and maternal (MSB) stillbirth, milking speed (MSP), and temperament (TEM) based on a Holstein-Friesian dairy cattle population consisting of 35,203 individuals. The number of animals, depending on the trait, ranged from 22,301 bulls for TEM to 30,603 for DCE. We estimated the SNP effects (based on 46,216 polymorphisms from Illumina BovineSNP50 BeadChip Version 2) using a multi-SNP mixed model. The SNP positions were mapped to genes and the GO terms/KEGG pathways of the corresponding genes were assigned. The estimation of the GO term/KEGG pathway effects was based on a mixed model using the SNP effects as dependent variables. The number of significant SNPs comprised 59 for DCE, 25 for DSB and MSP, 17 for MCE and MSB, and 7 for TEM. Significant KEGG pathways were found for MSB (2), TEM (2), and MSP (1) and 11 GO terms were significant for MSP, 10 for DCE, 8 for DSB and TEM, 5 for MCE, and 3 for MSB. From the perspective of a better understanding of the genomic background of the phenotypes, traits with low heritabilities suggest that the focus should be moved from single genes to the metabolic pathways or gene ontologies significant for the phenotype.

Genetic and Genomic Analyses of Service Sire Effect on Female Reproductive Traits in Holstein Cattle

Fertility and reproductive performance are key drivers of dairy farm profitability. Hence, reproduction traits have been included in a large majority of worldwide dairy cattle selection indexes. The reproductive traits are lowly heritable but can be improved through direct genetic selection. However, most scientific studies and dairy cattle breeding programs have focused solely on the genetic effects of the dam (GED) on reproductive performance and, therefore, ignored the contribution of the service sire in the phenotypic outcomes. This study aimed to investigate the service sire effects on female reproductive traits in Holstein cattle from a genomic perspective. Genetic parameter estimation and genome-wide association studies (GWAS) were performed for the genetic effect of service sire (GESS) on conception rate (CR), 56-day non-return rate (NRR56), calving ease (CE), stillbirth (SB), and gestation length (GL). Our findings indicate that the additive genetic effects of both sire and dam contribute to the phenotypic variance of reproductive traits measured in females (0.0196 vs. 0.0109, 0.0237 vs. 0.0133, 0.0040 vs. 0.0289, 0.0782 vs. 0.0083, and 0.1024 vs. 0.1020 for GESS and GED heritability estimates for CR, NRR56, CE, SB, and GL, respectively), and these two genetic effects are positively correlated for SB (0.1394) and GL (0.7871). Interestingly, the breeding values for GESS on insemination success traits (CR and NRR56) are unfavorably and significantly correlated with some production, health, and type breeding values (ranging from -0.449 to 0.274), while the GESS values on calving traits (CE, SB, and GL) are usually favorably associated with those traits (ranging from -0.493 to 0.313). One hundred sixty-two significant single-nucleotide polymorphisms (SNPs) and their surrounding protein-coding genes were identified as significantly associated with GESS and GED, respectively. Six genes overlapped between GESS and GED for calving traits and 10 genes overlapped between GESS for success traits and calving traits. Our findings indicate the importance of considering the GESS when genetically evaluating the female reproductive traits in Holstein cattle.

Assessment of Performance and Some Welfare Indicators of Cows in Vietnamese Smallholder Dairy Farms

Smallholder dairy farms (SDFs) are distributed widely across lowland and highland regions in Vietnam, but data on the productivity and welfare status of these cows remains limited. This cross-sectional study was conducted to describe and compare the productivity and welfare status of SDF cows across contrasting regions. It was conducted in autumn 2017 on 32 SDFs randomly selected from four typical but contrasting dairy regions (eight SDFs per region); a south lowland, a south highland, a north lowland, and a north highland region. Each farm was visited over a 24-h period (an afternoon followed by a morning milking and adjacent husbandry activities) to collect data of individual lactating cows (n = 345) and dry cows (n = 123), which included: milk yield and concentrations, body weight (BW), body condition score (BCS, 5-point scale, 5 = very fat), inseminations per conception, and level of heat stress experienced (panting score, 4.5-point scale, 0 = no stress). The high level of heat stress (96% of lactating cows were moderate to highly heat-stressed in the afternoon), low energy corrected milk yield (15.7 kg/cow/d), low percentage of lactating cows (37.3% herd), low BW (498 and 521 kg in lactating and dry cows, respectively), and low BCS of lactating cows (2.8) were the most important productivity and welfare concerns determined and these were most serious in the south lowland. By contrast, cows in the north lowland, a relatively hot but new dairying region, performed similarly to those in the south highland; a region historically considered to be one of the most suitable for dairy cows in Vietnam due to its cool environment. This indicates the potential to mitigate heat stress through new husbandry strategies. Cows in the north highland had the highest BW (535 and 569 kg in lactating and dry cows, respectively) and the highest energy corrected milk yield (19.2 kg/cow/d). Cows in all regions were heat-stressed during the daytime, although less so in the highlands compared to the lowlands. Opportunities for research into improving the productivity and welfare of Vietnamese SDF cows are discussed.

Reproductive Performance in a Selected Sample of Dairy Farms in Una-Sana Canton, Bosnia and Herzegovina

Background

The production of milk and dairy products and their placement on the market represent a constant profit for the farmers/producers in Bosnia and Herzegovina (BH). The profitable operation of the dairy farms is influenced by the reproductive performance of the lactating animals. This study assessed individual animal reproductive characteristics in selected dairy farms and described their reproductive performance indicators.

Results

The median age at first insemination was 493 days (5^th–95^th percentile range 429–840), while the age at first calving was 802 days (5^th–95^th percentile range 708–1168). The median pregnancy proportion at first insemination was 40% (5^th–95^th percentile range 17–62), while the cumulative pregnancy rate calculated at day-60, day-80, day-100, and day-120 showed that approximately 64% of all pregnancies happened before day-120. The calculated interservice intervals showed that approximately 69% of the repeat breeding animals came back to the oestrus in the period of 18 to 24 days. This is an indication of very good oestrus detection in selected dairy farms. The mean number of services per pregnancy was 2.61 (range 1–12). The median calving-to-first-insemination interval was 62.5 days (5^th–95^th percentile range 16–408). The calving-to-conception interval was 101 day (5^th–95^th percentile range 36–506). Finally, the calving interval was 385 days (5^th–95^th percentile range 329–773).

Conclusions

There is a need for an organised, regular, and more comprehensive recording system for the reproduction of dairy cattle among dairy farms in Una-Sana Canton. The calculated reproductive measures indicated an undulant trend in reproductive performance among selected dairy farms in Una-Sana Canton. Knowing the apparent reproductive indicators described in this study, the farmers and veterinary authorities may identify and correct areas in their management that contribute to the reproductive underperformance.

Twinning rate is not genetically correlated with production and reproduction traits in Iranian dairy cows

Context Any interruption to the reproductive system can negatively influence animal performance, and suitable animal-management practices should be adopted that will decrease the occurrence of reproductive problems such as may be the case with twinning. Aims The study was designed to estimate genetic parameters for twinning rate (TR) and to estimate genetic correlations between twinning rate and production and reproductive performances in the first lactation of Iranian Holstein cows. Methods The dataset used in this study was collected by the Animal Breeding Center of Iran during 1991–2013 and consisted of 273742 records of calving type (singleton or twin), 435742 records of 305-day milk yield, 424175 records of milk fat percentage, 253901 records of milk protein percentage, 251558 records of first calving interval, and 153632 records of number of days to first service. A single Gibbs sampling chain with 500000 rounds was generated to run linear and threshold animal models. Key results Posterior mean estimates of heritabilities for traits were: TR 0.0028, milk yield 0.28, milk fat percentage 0.33, milk protein percentage 0.38, first calving interval 0.064, and days to first service 0.061. Genetic correlations between TR and performance traits were negligible and varied from –0.08 (between TR and milk yield) to 0.04 (between TR and protein percentage). Conclusions Diminishing TR by genetic selection is a slow task owing to its low heritability. Negligible genetic correlation between TR and performance traits suggests that selection for decreased TR would not cause a significant decrease in milk production, nor is it likely to have a negative impact on the reproductive performance of dairy cows. Implications Dairy cattle breeders should follow genetic selection programs, especially for milk-production traits, without concern for an increase in twinning rate.

Genetic correlations among selected traits in Canadian Holsteins

In the Canadian dairy industry, there are currently over 80 traits routinely evaluated, and more are considered for potential selection. Particularly, in the last few years, recording has commenced for several new phenotypes required to introduce novel traits with high economic importance into the selection program. However, without a systematic estimation of the genetic correlations that exist among traits, the potential results of indirect selection are unknown. Therefore, 29 traits representative of the trait diversity for first lactation Canadian animals were selected. Their two-by-two genetic correlations were estimated from a dataset of 62 498 first lactation Holstein cows, using a Markov Chain Monte Carlo Gibbs sampling approach. The general tendencies among the groups of traits confirm that production traits are negatively correlated with fertility traits and that functional traits are positively correlated with one another. The association of udder depth with fertility and disease resistance has also been highlighted. This contribution offers a comprehensive overview of current estimates across traits and includes correlations with novel traits that constitute an original addition to the literature. These new estimates can be used for newly developed genomic evaluation models and possibly lead to more accurate estimations of the dairy cows’ overall genetic merit.

Multi-trait meta-analyses reveal 25 quantitative trait loci for economically important traits in Brown Swiss cattle

Background

Little is known about the genetic architecture of economically important traits in Brown Swiss cattle because only few genome-wide association studies (GWAS) have been carried out in this breed. Moreover, most GWAS have been performed for single traits, thus not providing detailed insights into potentially existing pleiotropic effects of trait-associated loci.

Results

To compile a comprehensive catalogue of large-effect quantitative trait loci (QTL) segregating in Brown Swiss cattle, we carried out association tests between partially imputed genotypes at 598,016 SNPs and daughter-derived phenotypes for more than 50 economically important traits, including milk production, growth and carcass quality, body conformation, reproduction and calving traits in 4578 artificial insemination bulls from two cohorts of Brown Swiss cattle (Austrian-German and Swiss populations). Across-cohort multi-trait meta-analyses of the results from the single-trait GWAS revealed 25 quantitative trait loci (QTL; P < 8.36 × 10^− 8) for economically relevant traits on 17 Bos taurus autosomes (BTA). Evidence of pleiotropy was detected at five QTL located on BTA5, 6, 17, 21 and 25. Of these, two QTL at BTA6:90,486,780 and BTA25:1,455,150 affect a diverse range of economically important traits, including traits related to body conformation, calving, longevity and milking speed. Furthermore, the QTL at BTA6:90,486,780 seems to be a target of ongoing selection as evidenced by an integrated haplotype score of 2.49 and significant changes in allele frequency over the past 25 years, whereas either no or only weak evidence of selection was detected at all other QTL.

Conclusions

Our findings provide a comprehensive overview of QTL segregating in Brown Swiss cattle. Detected QTL explain between 2 and 10% of the variation in the estimated breeding values and thus may be considered as the most important QTL segregating in the Brown Swiss cattle breed. Multi-trait association testing boosts the power to detect pleiotropic QTL and assesses the full spectrum of phenotypes that are affected by trait-associated variants.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6066-6) contains supplementary material, which is available to authorized users.

Genetic and nongenetic profiling of milk pregnancy-associated glycoproteins in Holstein cattle

Pregnancy-associated glycoproteins (PAG) are secreted by the trophoblast and are detectable in maternal circulation around the time of attachment of the fetal placenta, as well as in blood and milk throughout gestation. The understanding of the genetic mechanisms controlling PAG levels can confer advantages for livestock breeding programs given the precocity and the ease of obtaining this phenotype from routine pregnancy diagnosis. The aim of this study was to characterize PAG levels by estimating genetic parameters and correlations with other dairy traits, and to identify genomic regions and candidate genes associated with PAG levels in milk. The PAG data consisted of pregnancy diagnoses using commercial assays from 2012 to 2017, and genotype data consisted of 54,123 SNP markers for 2,352 individuals (embryos and dams). The model included contemporary group (herd, year, and season) and embryo age as fixed effects, and random embryonic (direct) and maternal (indirect) genetic effects. Using genomic data, the estimated heritability for direct and maternal genetic effects (± standard deviations) were 0.23 ± 0.05 and 0.11 ± 0.05, respectively. The genetic correlation between these effects was almost zero (0.001 ± 0.06). A preliminary analysis revealed low correlations between milk PAG levels and other dairy traits. The genome-wide association analysis was performed using 2 approaches: single-marker and single-step using all markers. Four genomic regions with direct genetic effects were detected on Bos taurus autosome (BTA) 6, BTA7, BTA19, and BTA29 of the embryonic genome. The BTA29 locus was within the bovine PAG gene cluster, suggesting a cis-regulatory quantitative trait locus on the PAG expression. However, other associations, without an obvious link to PAG expression, could be related to the transportation of PAG and their concentration in milk. Only 1 region from the maternal genome, on BTA4, had a significant indirect effect, where WNT2 is a candidate gene related to placenta vascularization and gestation health. Collectively, our results suggest a moderate genetic control of milk PAG levels from both maternal and fetal genomes, but larger studies are needed to fully evaluate the usefulness of milk PAG in the genetic evaluation of fetal growth and cow fertility.

Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle

Background

Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. Different dairy cattle breeds have different incidence of calving difficulty, with Holstein having the highest dystocia rates and Jersey the lowest. Genomic selection becomes important especially for complex traits with low heritability, where the accuracy of conventional selection is lower. However, for complex traits where a large number of genes influence the phenotype, genome-wide association studies showed limitations. Biological networks could overcome some of these limitations and better capture the genetic architecture of complex traits. In this paper, we characterize Holstein, Brown Swiss and Jersey breed-specific dystocia networks and employ them in genomic predictions.

Results

Marker association analysis identified single nucleotide polymorphisms explaining the largest average proportion of genetic variance on BTA18 in Holstein, BTA25 in Brown Swiss, and BTA15 in Jersey. Gene networks derived from the genome-wide association included 1272 genes in Holstein, 1454 genes in Brown Swiss, and 1455 genes in Jersey. Furthermore, 256 genes in Holstein network, 275 genes in the Brown Swiss network, and 253 genes in the Jersey network were within previously reported dystocia quantitative trait loci. The across-breed network included 80 genes, with 9 genes being within previously reported dystocia quantitative trait loci. The gene-gene interactions in this network differed in the different breeds. Gene ontology enrichment analysis of genes in the networks showed Regulation of ARF GTPase was very significant (FDR ≤ 0.0098) on Holstein. Neuron morphogenesis and differentiation was the term most enriched (FDR ≤ 0.0539) on the across-breed network. Genomic prediction models enriched with network-derived relationship matrices did not outperform regular GBLUP models.

Conclusions

Regions identified in the genome were in the proximity of previously described quantitative trait loci that would most likely affect calving difficulty by altering the feto-pelvic proportion. Inclusion of identified networks did not increase prediction accuracy. The approach used in this paper could be extended to any instance with asymmetric distribution of phenotypes, for example, resistance to disease data.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0606-y) contains supplementary material, which is available to authorized users.

Bayesian estimates of genetic relationship between calving difficulty and productive and reproductive performance in Holstein cows

The objective of present study was to estimate genetic correlations between calving difficulty and productive and reproductive traits in Iranian Holsteins. Calving records from the Animal Breeding Center of Iran, collected from 1991 to 2011 and comprising 183 203 first-calving events of Holstein cows from 1470 herds were included in the dataset. Threshold animal models included direct genetic effect (Model 1) or direct and maternal genetic effects with covariance between them (Model 2) were fitted for the genetic analysis of calving difficulty. Also, linear animal models including direct genetic effect were fitted for the genetic analysis of productive and reproductive performance traits. A set of linear-threshold bivariate models was used for obtaining genetic correlation between calving difficulty and other traits. All analyses were implemented by Bayesian approach via Gibbs sampling methodology. A single Gibbs sampling chain with 300 000 rounds was generated by the TM program. Posterior mean estimates of direct heritabilities for calving difficulty were 0.056 and 0.066, obtained from different models. Also, posterior mean estimate of maternal heritability for this trait was 0.018. Estimate of correlation between direct and maternal genetic effects for calving difficulty was negative (–0.44). Posterior mean estimates of direct heritabilities for milk yield, fat yield, protein yield, days from calving to first service, days open and first calving interval were 0.257, 0.188, 0.235, 0.034, 0.042 and 0.050 respectively. The posterior means of direct genetic correlation between calving difficulty and milk yield, fat yield, protein yield, days from calving to first service, days open and first calving interval were low and equal to –0.135, 0.030, –0.067, –0.010, –0.075 and –0.074 respectively. The results of the current study indicated that exploitable genetic variation in calving difficulty, productive and reproductive traits could be applied in designing future genetic selection plans for Iranian Holsteins.

Genome-wide association studies of fertility and calving traits in Brown Swiss cattle using imputed whole-genome sequences

Background

The detection of quantitative trait loci has accelerated with recent developments in genomics. The introduction of genomic selection in combination with sequencing efforts has made a large amount of genotypic data available. Functional traits such as fertility and calving traits have been included in routine genomic estimation of breeding values making large quantities of phenotypic data available for these traits. This data was used to investigate the genetics underlying fertility and calving traits and to identify potentially causative genomic regions and variants.

We performed genome-wide association studies for 13 functional traits related to female fertility as well as for direct and maternal calving ease based on imputed whole-genome sequences. Deregressed breeding values from ~1000–5000 bulls per trait were used to test for associations with approximately 10 million imputed sequence SNPs.

Results

We identified a QTL on BTA17 associated with non-return rate at 56 days and with interval from first to last insemination. We found two significantly associated non-synonymous SNPs within this QTL region. Two more QTL for fertility traits were identified on BTA25 and 29. A single QTL was identified for maternal calving traits on BTA13 whereas three QTL on BTA19, 21 and 25 were identified for direct calving traits. The QTL on BTA19 co-localizes with the reported BH2 haplotype. The QTL on BTA25 is concordant for fertility and calving traits and co-localizes with a QTL previously reported to influence stature and related traits in Brown Swiss dairy cattle.

Conclusion

The detection of QTL and their causative variants remains challenging. Combining comprehensive phenotypic data with imputed whole genome sequences seems promising. We present a QTL on BTA17 for female fertility in dairy cattle with two significantly associated non-synonymous SNPs, along with five additional QTL for fertility traits and calving traits. For all of these we fine mapped the regions and suggest candidate genes and candidate variants.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4308-z) contains supplementary material, which is available to authorized users.

Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle

Background

Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genotyped using the Illumina Bovine 50 K BeadChip and imputed to the Illumina BovineHD BeadChip (HD). GWAS were performed on 601,717 real and imputed single nucleotide polymorphism (SNP) genotypes using a single-SNP mixed linear model on 4841 Holstein bulls with breeding value predictions and followed by gene identification and in silico functional analyses. The association results were further validated using five scenarios with different numbers of SNPs.

Results

Seven hundred and eighty-two SNPs were significantly associated with calving performance at a genome-wise false discovery rate (FDR) of 5%. Most of these significant SNPs were on chromosomes 18 (71.9%), 17 (7.4%), 5 (6.8%) and 7 (2.4%) and mapped to 675 genes, among which 142 included at least one significant SNP and 532 were nearby one (100 kbp). For body conformation traits, 607 SNPs were significant at a genome-wise FDR of 5% and most of them were located on chromosomes 5 (30%), 18 (27%), 20 (13%), 6 (6%), 7 (5%), 14 (5%) and 13 (3%). SNP enrichment functional analyses for calving traits at a FDR of 1% suggested potential biological processes including musculoskeletal movement, meiotic cell cycle, oocyte maturation and skeletal muscle contraction. Furthermore, pathway analyses suggested potential pathways associated with calving performance traits including tight junction, oxytocin signaling, and MAPK signaling (P < 0.10). The prediction ability of the 1206 significant SNPs was between 78 and 83% of the prediction ability of the BovineSNP50 SNPs for calving performance traits and between 35 and 79% for body conformation traits.

Conclusions

Various SNPs that are significantly associated with calving performance are located within or nearby genes with potential roles in tight junction, oxytocin signaling, and MAPK signaling. Combining the significant SNPs or SNPs within or nearby gene(s) from the HD panel with the BovineSNP50 panel yielded a marginal increase in the accuracy of prediction of genomic estimated breeding values for all traits compared to the use of the BovineSNP50 panel alone.

Electronic supplementary material

The online version of this article (10.1186/s12711-017-0356-8) contains supplementary material, which is available to authorized users.

Comparison of breeding values among cows with exceptional longevity and their contemporary herdmates in German Holsteins

Abstract. The present analysis compares the estimated breeding values (EBVs), relative breeding values (RBVs), and daughter yield deviations (YDs) of cows with exceptional longevity with their contemporary herdmates. In addition, the relative breeding values of their sires were compared among these two daughter groups; the RBVs of the sires were also compared with the proportion of their daughters with exceptional longevity. Data included 5037 sires born between 1963 and 1996 with a total of 61 988 daughter; of these sires, 486 had sired daughters that completed more than nine lactations (exceptional cows) and 4957 sires had sired the contemporary herdmates. Exceptional cows had on average significantly lower EBVs for milk yield, fat and protein yield, and significantly lower YDs for milk and protein yield in the first three lactations, significantly lower RBVs for milk production and type but significantly higher RBVs for somatic cell score and functional longevity. The sires of exceptional cows had significantly higher RBVs for somatic cell count (RZS), functional longevity (RZN), and fitness (RZFit) in comparison to the sires of contemporary herdmates. Correlations among the proportion of exceptional cows per sire and RZN, RZS as well as RZFit were positive, whereas milk production (RZM) showed a negative correlation. An increase in the number of cows with exceptional longevity may be possible through a relative total breeding value with high positive weights for RZN, RZS, and RZFit but negative weights for RZM and type (RZE).

Genotype by environment interaction for livability of dairy calves from first parity cows

Death of calves around parturition is a matter of concern for dairy farmers. Relatively high stillbirth rates and unfavourable trends have been reported for Holstein heifers in the Netherlands and several other countries. In our study, we investigated herd differences, genetic parameters and genotype by environment interaction for heifer calf livability. A large dataset with data from calvings between 1993 and 2012 of Dutch dairy farms was used. There were considerable differences between herds in livability of calves from heifers, with averages ranging from 74% to 95%. Both herds with relatively high and low averages showed the same negative trend between 1993 and 2012, with largest declines in herds with the lowest averages. We found that heritability and genetic variation of first parity livability were substantially larger in herd environments where the likelihood of stillbirth was high v. environments where stillbirth was at a low level. The genetic correlations between herd environment levels were all very close to unity, indicating that ranking of sires was similar for all environments. However, for herds with a relatively high stillbirth incidence selecting sires with favourable breeding values is expected to be twice as profitable as in herds with a relatively low stillbirth incidence.

Maternal aging affects life performance of progeny in a Holstein dairy cow model

The development and life performance of 404 high-producing Holstein dairy cows was studied from birth onwards and during two lactations. The management, environment and parental genetics of the cows were known in detail. Cluster analysis identified four performance ‘types’: high-yielding (HY) cows and persistently high-yielding (PHY) cows, which accounted for 33% of the animals; medium-yielding (MY) cows, 41%; and low-yielding (LY) cows, 26%. Prenatal determinants of the life performance of the progeny were analyzed. Developmental and environmental factors were excluded as determinants of performance (including birth weight, level of passive immunity transfer, growth rate, age at first parturition and reproductive efficiency). Life performance did show minor seasonal effects, with more HY cows but less PHY being born during the cold season (90.1% in HY; 58.3% in PHY v. 81.5%). Instead, the single most important factor influencing life performance of daughters was maternal age. HY cows were born from the youngest mothers (1.89±1.14 parturitions, 3.12±1.42-year old), whereas LY cows were born from the oldest (2.72±1.80 parturitions, 3.97±2.01-year old; P<0.001). Life performance of the dams did not differ among clusters. In addition, metabolic parameters (fat and protein yield) were found to correlate significantly with yields between the first and second lactations (milk yield: r=0.357; fat yield: r=0.211; protein yield: r=0.277; P<0.0001), suggesting the influence of the individual. These results suggest that under optimal health, nutritional and environmental conditions, maternal aging is an important determinant of the life performance of progeny and argue for the need to identify conditions that contribute to health and disease in progeny according to the Developmental Origin of Health and Disease or DOHaD concept. Our findings may help the development of novel management guidelines for dairy farms.