Genetic parameters for linear type traits including locomotion in Italian Jersey cattle breed

Genome-Wide Association Study on Body Conformation Traits in Xinjiang Brown Cattle

Body conformation traits are linked to the health, longevity, reproductivity, and production performance of cattle. These traits are also crucial for herd selection and developing new breeds. This study utilized pedigree information and phenotypic (1185 records) and genomic (The resequencing of 496 Xinjiang Brown cattle generated approximately 74.9 billion reads.) data of Xinjiang Brown cattle to estimate the genetic parameters, perform factor analysis, and conduct a genome-wide association study (GWAS) for these traits. Our results indicated that most traits exhibit moderate to high heritability. The principal factors, which explained 59.12% of the total variance, effectively represented body frame, muscularity, rump, feet and legs, and mammary system traits. Their heritability estimates range from 0.17 to 0.73, with genetic correlations ranging from -0.53 to 0.33. The GWAS identified 102 significant SNPs associated with 12 body conformation traits. A few of the SNPs were located near previously reported genes and quantitative trait loci (QTLs), while others were novel. The key candidate genes such as LCORL, NCAPG, and FAM184B were annotated within 500 Kb upstream and downstream of the significant SNPs. Therefore, factor analysis can be used to simplify multidimensional conformation traits into new variables, thus reducing the computational burden. The identified candidate genes from GWAS can be incorporated into the genomic selection of Xinjiang Brown cattle, enhancing the reliability of breeding programs.

Association of Production and Selected Dimensional Conformation Traits in Holstein Friesian Cows

The objective of this study was to estimate the heritability of dairy production traits and that for dimensional traits and to calculate the correlation between the two heritability values in a Holstein Friesian cow herd bred in Hungary. Data of 15,032 Holstein Friesian cows born in the period 2008-2018 from 666 sires were collected for the study in 6 large dairy herds. Among the conformation traits, stature (ST), chest width (CW), body depth (BD), and rump width (RW), and for production traits, in the first lactation of cows, the 305-day milk yield (MY), milk butterfat yield (FY), and milk protein yield (MY) were evaluated. Heritability estimates of ST, CW, BD, and RW were 0.49, 0.25, 0.31, and 0.30, and those of MY, FY, and PY were 0.40, 0.35, and 0.30, respectively. BD and RW had no phenotypic (b = -0.01) or genetic (b = 0.00-0.01) change. The production traits (MY, FY, PY) increased to a greater extent (b = 2.2-43.3) than the examined conformation traits over time. Consequently, it is indicated that the selection for dairy production did not result in an increase in the studied dimensional traits.

Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle

Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the future profitability of the dairy sector. Registered body conformation traits are reliable and cost-effective tools for use in national cattle breeding selection programs. These traits are significantly related to the production, longevity, mobility, health, fertility, and environmental adaptation of dairy cows. Therefore, they can be considered indirect indicators of economically important traits in dairy cows. Utilizing efficacious genetic methods, such as genome-wide association studies (GWASs), allows for a deeper understanding of the genetic architecture of complex traits through the identification and application of genetic markers. In the current review, we summarize information on candidate genes and genomic regions associated with body conformation traits in dairy cattle worldwide. The manuscript also reviews the importance of body conformation, the relationship between body conformation traits and other traits, heritability, influencing factors, and the genetics of body conformation traits. The information on candidate genes related to body conformation traits provided in this review may be helpful in selecting potential genetic markers for the genetic improvement of body conformation traits in dairy cattle.

Genetic relationships of body condition score and locomotion with production, type and fertility traits in Holstein-Friesian cows

New traits are sought to add in breeding goals to prevent worsening health and fertility of Polish Holstein-Friesian cows. The objectives of this study were to estimate genetic parameters for body condition score (BCS) and locomotion (LOC) and their relationship with other type traits, milk and fertility traits, and to show genetic trends for BCS and LOC in Polish Holstein-Friesian population. Data on 317 028 Holstein-Friesian cows, born from 2010 through 2015 in 11 792 herds, were collected. All cows were scored for BCS and 43% of them for LOC. All records comprised lactational yields of milk, fat and protein, content of fat and protein and somatic cell count from the first three lactations, stature, five composite and 16 linear conformation traits, and four fertility traits. Genetic parameters were estimated using a Bayesian method with Gibbs Sampling, generating 100 000 samples in each of four steps: BCS and LOC with five composite conformation traits, BCS and LOC with 16 linear conformation traits, BCS and LOC with production traits, and BCS and LOC with four fertility traits. The linear model for BCS and LOC contained fixed effects of herd-year-season-classifier and lactation stage, fixed linear and quadratic regressions on age at calving, fixed linear regression on the percentage of Holstein-Friesian genes, and random additive genetic effect. Breeding values for BCS and LOC were calculated using the same model as used for estimation of genetic parameters. Genetic trends for BCS and LOC, defined as regression coefficients of mean breeding value on birth year, were examined. BCS was a moderately heritable trait (0.19) and was genetically correlated with non-return rate until 56 days after first insemination for cows (-0.32) and with days open (-0.22), so selection for BCS might have a favourable correlated effect on fertility. LOC, lowly heritable (0.06), was relatively strongly genetically correlated with feet-and-legs traits (from 0.48 to 0.93, ignoring sign) and could be included in a selection subindex for feet-and-legs. The positive trend for LOC indicated substantial progress towards the highest genetic value (optimum at the end of the scale), while the small trend for BCS showed a tendency to stabilise the average value in the middle of the scale (optimum for BCS). The estimates of the genetic parameters for BCS and LOC indicate that both traits could contribute to more effective selection to improve fertility (BCS) and legs health (LOC) in the Polish dairy cattle population.

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.

Factor Analysis of Genetic Parameters for Body Conformation Traits in Dual-Purpose Simmental Cattle

Simple Summary

Body conformation traits are closely related to economically important characteristics and should be considered in cattle breeding programs. A variety of body conformation traits recorded by classifiers can complicate the analysis process. Factor analysis can reduce the number of variables by combining two or more variables into a single factor, which has biological significance. The results of this study could be used by breeders to define conformation indexes and implement genetic assessments for conformation traits in dual-purpose breeds.

Abstract

In this study, we estimated the genetic parameters for 6 composite traits and 27 body conformation traits of 1016 dual-purpose Simmental cattle reared in northwestern China from 2010 to 2019 using a linear animal mixed model. To integrate these traits, a variety of methods were used as follows: (1) genetic parameters estimates for composite and individual body conformation traits based on the pedigree relationship matrix (A) and combined genomic-pedigree relationship matrix (H); (2) factor analysis to explore the relationships among body conformation traits; and (3) genetic parameters of factor scores estimated using A and H, and the correlations of EBVs of the factor scores and EBVs of the composite traits. Heritability estimates of the composite traits using A and H were low to medium (0.07–0.47). The 24 common latent factors explained 96.13% of the total variance. Among factors with eigenvalues ≥ 1, F1 was mainly related to body frame, muscularity, and rump; F2 was related to feet and legs; F3, F4, F5, and F6 were related to teat placement, teat size, udder size, and udder conformation; and F7 was related to body frame. Single-trait analysis of factor scores yielded heritability estimates that were low to moderate (0.008–0.43 based on A and 0.04–0.43 based on H). Spearman and Pearson correlations, derived from the best linear unbiased prediction analysis of composite traits and factor scores, showed a similar pattern. Thus, incorporating factor analysis into the morphological evaluation to simplify the assessment of body conformation traits may improve the genetics of dual-purpose Simmental cattle.

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

BACKGROUND

Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits.

RESULTS

SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117).

CONCLUSIONS

Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.