Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty
Doyle, Jennifer L. ; Berry, Donagh P. ; Veerkamp, Roel F. ; Carthy, Tara R. ; Walsh, Siobhan W. ; Evans, Ross D. ; Purfield, Deirdre C. - \ 2020
Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
cattle - genome-wide association study - linear type traits - sequence - single nucleotide polymorphism - skeletal
Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.
Associations of conformation and locomotive characteristics in growing gilts with osteochondrosis at slaughter
Koning, D.B. de; Grevenhof, E.M. van; Laurenssen, B.F.A. ; Hazeleger, W. ; Kemp, B. - \ 2015
Journal of Animal Science 93 (2015)1. - ISSN 0021-8812 - p. 93 - 106.
linear type traits - leg weakness - exterior traits - genetic correlations - epiphyseal growth - pigs - cartilage - sows - lesions - pathogenesis
Osteochondrosis (OC) and abnormalities in conformation and locomotive characteristics (CLC) have been associated with premature culling in sows. Several CLC have been suggested to be associated with OC and might help as an in vivo indicator for and increased risk of having OC. The aim of this study was to investigate associations of OC with CLC assessed at several ages in growing gilts from 2 separate experiments over the effects of dietary restriction (Exp. 1) and floor type (Exp. 2) on OC prevalence. In Exp. 1, gilts (n = 211) were subjectively assessed for CLC at, on average, 4, 9, 11, 16, and 24 wk of age. In Exp. 2, gilts (n = 212) were subjectively assessed for CLC at, on average, 4, 9, 11, 16, and 22 wk of age. Assessment was done on 10 conformation and 2 locomotive characteristics using a 9-point grading scale by 2 observers. At, on average, 27 wk of age in Exp. 1 and 24 wk of age in Exp. 2, gilts were slaughtered and the knee, elbow, and hock joints were macroscopically assessed for OC. The CLC most frequently associated with OC were O shape or X shape of the hind legs, straight or bowed hind legs, and straight or sickled hock. X-shaped hind legs were associated with OC at slaughter in the knee joint at 4, 9, and 24 wk of age and at the animal level (all joints taken together) at 4, 9, and 16 wk of age. Straight or bowed hind legs were associated with OC at slaughter in the knee joint at 4 and 11 wk of age; in the hock joint at 11 wk of age; and at the animal level at 4, 9, 11, and 22 wk of age. Straight or sickled hock was associated with OC at slaughter in the knee joint at 4 wk of age, in the hock joint at 9 and 22 wk of age, and at the animal level at 9 and 22 wk of age. Results show that several CLC assessed at several ages were associated with OC, but consistent associations of a type of CLC in every assessment could not be found. The associations of CLC with OC are, therefore, difficult to be used as an in vivo indicator of increased risk for OC.
Genetic parameters across lactation for feed intake, fat and protein corrected milk, and live weight in first parity Holstein cattle
Manzanilla Pech, C.I.V. ; Veerkamp, R.F. ; Calus, M.P.L. ; Zom, R.L.G. ; Knegsel, A. van; Pryce, J.E. ; Haas, Y. de - \ 2014
Journal of Dairy Science 97 (2014)9. - ISSN 0022-0302 - p. 5851 - 5862.
body condition score - dry-matter intake - random regression-models - negative-energy balance - linear type traits - dairy-cattle - live weight - covariance functions - cows - efficiency
Breeding values for dry matter intake (DMI) are important to optimize dairy cattle breeding goals for feed efficiency. However, generally, only small data sets are available for feed intake, due to the cost and difficulty of measuring DMI, which makes understanding the genetic associations between traits across lactation difficult, let alone the possibility for selection of breeding animals. However, estimating national breeding values through cheaper and more easily measured correlated traits, such as milk yield and liveweight (LW), could be a first step to predict DMI. Combining DMI data across historical nutritional experiments might help to expand the data sets. Therefore, the objective was to estimate genetic parameters for DMI, fat- and protein-corrected milk (FPCM) yield, and LW across the entire first lactation using a relatively large data set combining experimental data across the Netherlands. A total of 30,483 weekly records for DMI, 49,977 for FPCM yield, and 31,956 for LW were available from 2,283 Dutch Holstein-Friesian first-parity cows between 1990 and 2011. Heritabilities, covariance components, and genetic correlations were estimated using a multivariate random regression model. The model included an effect for year-season of calving, and polynomials for age of cow at calving and days in milk (DIM). The random effects were experimental treatment, year-month of measurement, and the additive genetic, permanent environmental, and residual term. Additive genetic and permanent environmental effects were modeled using a third-order orthogonal polynomial. Estimated heritabilities ranged from 0.21 to 0.40 for DMI, from 0.20 to 0.43 for FPCM yield, and from 0.25 to 0.48 for LW across DIM. Genetic correlations between DMI at different DIM were relatively low during early and late lactation, compared with mid lactation. The genetic correlations between DMI and FPCM yield varied across DIM. This correlation was negative (up to -0.5) between FPCM yield in early lactation and DMI across the entire lactation, but highly positive (above 0.8) when both traits were in mid lactation. The correlation between DMI and LW was 0.6 during early lactation, but decreased to 0.4 during mid lactation. The highest correlations between FPCM yield and LW (0.3–0.5) were estimated during mid lactation. However, the genetic correlations between DMI and either FPCM yield or LW were not symmetric across DIM, and differed depending on which trait was measured first. The results of our study are useful to understand the genetic relationship of DMI, FPCM yield, and LW on specific days across lactation.
Associations between osteochondrosis and conformation and locomotive characteristics in pigs
Koning, D.B. de; Grevenhof, E.M. van; Laurenssen, B.F.A. ; Ducro, B.J. ; Heuven, H.C.M. ; Groot, P.N. de; Hazeleger, W. ; Kemp, B. - \ 2012
Journal of Animal Science 90 (2012)3. - ISSN 0021-8812 - p. 4752 - 4763.
swine breeding herds - linear type traits - leg weakness - genetic-parameters - exterior traits - danish-landrace - housing systems - finishing pigs - growth rate - sows
Conformation and locomotive characteristics (CLC), i.e., leg conformation and gait movement patterns, may be associated with osteochondrosis (OC) in pigs. Osteochondrosis and CLC increase the risk of premature culling. This study investigated whether CLC have an explanatory value, over the previously modelled effects of sex, feeding, and housing conditions, on the occurrence and severity of OC in several joints and at the animal level. At 154 to 156 d of age, 267 pigs were subjectively scored on 9 conformation and 2 locomotive characteristics. Scoring was performed on a 9-point linear grading scale. For conformation characteristics, score 5 indicated normal conformation and scores 1 and 9 indicated severe deviations from normal. For the locomotive characteristics, score 1 indicated normal locomotion and score 9 indicated severe deviation from normal. At 161 to 176 d of age, pigs were slaughtered and joints were dissected for macroscopic evaluation of OC status. Results showed that swaying hindquarters and a stiffer gait were associated with higher scores for OC in, respectively, the femoropatellar (P = 0.018) and tarsocrural joint (P = 0.005); smaller inner claws as compared to the outer claws of the front legs was associated with lower scores for OC than equally sized claws in the femoropatellar joint (P = 0.021) and on animal level (P = 0.010); steep and weak pasterns of the front legs were associated with higher scores for OC in the elbow joint (P = 0.004) and on animal level (P = 0.018); X-shaped hind legs was associated with higher scores for OC on animal level (P = 0.037); and steep and weak pasterns of the hind legs were associated with lower scores for OC than normal conformation in the tarsocrural joint (P = 0.05). This study found several CLC that were associated with OC in several joints and at an animal level. This study showed that certain CLC might be used as indicators of OC and included in the criteria for selection of replacement animals for the breeding herd.
Genetics and genomics to improve fertility in high producing dairy cows
Veerkamp, R.F. ; Beerda, B. - \ 2007
Theriogenology 68 (2007)suppl. 1. - ISSN 0093-691X - p. S266 - S273.
body condition score - quantitative trait loci - linear type traits - milk-production - energy-balance - random regression - herd environment - calving interval - holstein cattle - luteal activity
Improving dairy cow fertility by means of genetic selection is likely to become increasingly important, since it is now well established that declining fertility cannot only be arrested by improved management. Profit margins per kg milk produced are decreasing, therefore farmers need to reduce cost and increase herd size. This restricts the labor input per cow and the disposable cost of getting a cow pregnant, whilst at the same time hormone treatments have become less acceptable. This makes it unlikely that additional management interventions will maintain fertility at acceptable levels in the near future. Genetic improvement seems the obvious solution. Effective selection tools are available in most Western countries using traditional breeding value estimation procedures. Also, in addition to gene assisted selection using individual genes or QTL, high throughput Single Nucleotide Polymorphism (SNP) technology allows genetic improvement of fertility based on information from the whole genome (tens of thousands SNP per animal), i.e. genomic selection. Simulation studies have shown that genomic selection improves the accuracy of selecting juvenile animals compared with traditional breeding methods and compared with selection using information from a few genes or QTL only. Research in the areas genomics and proteomics promise to make genetic selection even more effective. The genomic and proteomics technologies combined with the bioinformatics tools that support the interpretation of gene functioning and protein expression facilitate an exciting starting point for the development of new management strategies and tools for the improvement of reproductive performance.
Phenotypic relationships between longevity, type traits and production in Chianina beef cattle
Forobasco, F. ; Groen, A.F. ; Bozzi, R. ; Arendonk, J.A.M. van; Filippini, F. ; Boettcher, P. ; Bijma, P. - \ 2004
Journal of Animal Science 82 (2004)6. - ISSN 0021-8812 - p. 1572 - 1580.
linear type traits - herd life - genetic-parameters - breed
Longevity is an increasingly important trait in beef cattle. Increased longevity decreases costs for the farmer and increases revenue. The objective of this research was to investigate the phenotypic relationship between type traits and longevity in Chianina beef cattle, and the relationship between production and longevity, to analyze the effect of voluntary culling. Data included records on reproductive, productive, and type traits provided by the National Association of Italian Beef Cattle Breeders from 6,395 Chianina cows. The average length of productive life was 1,829 d. The herd-year had a strong effect on the risk of culling. The effects of 22 type traits were analyzed. All the muscularity traits analyzed were highly significant (P <0.01) and as a group had the largest, effect on longevity followed by dimension, refinement, and leg traits. Cows that calved before 35 mo of age had a lower probability of being culled than cows calving after 35 mo of age. Variation in herd size had a strong effect on risk ratio, with lower risk for intermediate classes. Cows with approximately one calf per year remained in the herd longer than did cows with fewer calves. Straight-legged animals had a 59% greater probability of being replaced than cows with a moderate angle to the hock, whereas sickle-legged animals had only a 3% higher probability of being culled than average cows. Udder conformation had no effect on longevity. In summary, results of this study indicate that herd-year effects and muscularity traits were the most important factors for longevity for Chianina cows among the factors studied.
Genetic relationships among Body condition score, Body weight, Milk yield and Fertility in Dairy Cows
Berry, D.P. ; Buckley, F. ; Dillon, P. ; Evans, R.D. ; Rath, M. ; Veerkamp, R.F. - \ 2003
Journal of Dairy Science 86 (2003)6. - ISSN 0022-0302 - p. 2193 - 2204.
linear type traits - reproductive-performance - calving interval - breeding objectives - female fertility - luteal activity - energy-balance - holstein cows - feed-intake - cattle
Genetic (co)variances between body condition score (BCS), body weight (BW), milk production, and fertility-related traits were estimated. The data analyzed included 8591 multiparous Holstein-Friesian cows with records for BCS, BW, milk production, and/or fertility from 78 seasonal calving grass-based farms throughout southern Ireland. Of the cows included in the analysis, 4402 had repeated records across the 2 yr of the study. Genetic correlations between level of BCS at different stages of lactation and total lactation milk production were negative (-0.51 to -0.14). Genetic correlations between BW at different stages of lactation and total lactation milk production were all close to zero but became positive (0.01 to 0.39) after adjusting BW for differences in BCS. Body condition score at different stages of lactation correlated favorably with improved fertility; genetic correlations between BCS and pregnant 63 d after the start of breeding season ranged from 0.29 to 0.42. Both BW at different stages of lactation and milk production tended to exhibit negative genetic correlations with pregnant to first service and pregnant 63 d after the start of the breeding season and positive genetic correlations with number of services and the interval from first service to conception. Selection indexes investigated illustrate the possibility of continued selection for increased milk production without any deleterious effects on fertility or average BCS, albeit, genetic merit for milk production would increase at a slower rate
Genetic Parameters for Body condition score, Body weigth, Milk yield and Fertility estimated using random regression models
Berry, D.P. ; Buckley, F. ; Dillon, P. ; Evans, R.D. ; Rath, M. ; Veerkamp, R.F. - \ 2003
Journal of Dairy Science 86 (2003)11. - ISSN 0022-0302 - p. 3704 - 3717.
friesian dairy-cattle - linear type traits - energy-balance - reproductive-performance - covariance functions - live weight - calving interval - luteal activity - feed-intake - cows
Genetic (co)variances between body condition score (BCS), body weight (BW), milk yield, and fertility were estimated using a random regression animal model extended to multivariate analysis. The data analyzed included 81,313 BCS observations, 91,937 BW observations, and 100,458 milk test-day yields from 8725 multiparous Holstein-Friesian cows. A cubic random regression was sufficient to model the changing genetic variances for BCS, BW, and milk across different days in milk. The genetic correlations between BCS and fertility changed little over the lactation; genetic correlations between BCS and interval to first service and between BCS and pregnancy rate to first service varied from -0.47 to -0.31, and from 0.15 to 0.38, respectively. This suggests that maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in midlactation when the genetic variance for BCS is largest. Selection for increased BW resulted in shorter intervals to first service, but more services and poorer pregnancy rates; genetic correlations between BW and pregnancy rate to first service varied from -0.52 to -0.45. Genetic selection for higher lactation milk yield alone through selection on increased milk yield in early lactation is likely to have a more deleterious effect on genetic merit for fertility than selection on higher milk yield in late lactation