Genetic models for breed quality and navel development scores and its associations with growth traits in beef cattle

Genetic analysis of growth, visual scores, height, and carcass traits in Nelore cattle

Covariance components were estimated for growth traits (BW, birth weight; WW, weaning weight; YW, yearling weight), visual scores (BQ, breed quality; CS, conformation; MS, muscling; NS, navel; PS, finishing precocity), hip height (HH), and carcass traits (BF, backfat thickness; LMA, longissimus muscle area) measured at yearling. Genetic gains were obtained and validation models on direct and maternal effects for BW and WW were fitted. Genetic correlations of growth traits with CS, PS, MS, and HH ranged from 0.20 ± 0.01 to 0.94 ± 0.01 and were positive and low with NS (0.11 ± 0.01 to 0.20 ± 0.01) and favorable with BQ (0.14 ± 0.02 to 0.37 ± 0.02). Null to moderate genetic correlations were obtained between growth and carcass traits. Genetic gains were positive and significant, except for BW. An increase of 0.76 and 0.72 kg is expected for BW and WW, respectively, per unit increase in estimated breeding value (EBV) for direct effect and an additional 0.74 and 1.43, respectively, kg per unit increase in EBV for the maternal effect. Monitoring genetic gains for HH and NS is relevant to maintain an adequate body size and a navel morphological correction, if necessary. Simultaneous selection for growth, morphological, and carcass traits in line with improve maternal performance is a feasible strategy to increase herd productivity.

Genetic parameters and genetic trends of conformation and management traits in Dairy Gir cattle

ABSTRACT The objective of this study was to estimate genetic parameters and genetic trends of different conformation and management traits regularly measured within the context of the National Dairy Gir Breeding Program (PNMGL). The estimation of genetic and residual variances for each trait was performed using average information restricted maximum likelihood (AI-REML) procedure in AIREMLF90 program software. The population was divided into three subpopulations constituted by measured females (with phenotype records), all females, and males. Linear regressions were applied for each trait, considering two periods of birth (1st period: 1938-1996; 2nd period: 1997-2012). The estimated heritability of conformation and management traits varied from 0.01 to 0.53, denoting a perspective of genetic improvement through selection and corrective matings for purebred Dairy Gir populations. The average genetic changes in conformation and management traits were, in general, variable and inexpressive, showing that the selection of Dairy Gir may have had been directed essentially to increase milk yield. The analysis of the two periods of birth indicated that some linear traits present progress (although inexpressive) in the 2nd period (more recent period).

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

Background

CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.

Results

Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics V_ST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs.

Conclusion

For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07808-7.

Genetic associations between mature size and condition score of Nelore cows, and weight, subjective scores and carcass traits as yearlings

The size and body condition of female livestock is critical for improving production efficiency. However, we know little about how height and body condition score in mature beef cattle are genetically related to traits observed when the animals are younger. In the present study, we used data from 321650 Nelore cattle, first, to compare genetic parameters and breeding values on the basis of different models employing weight (MW), height (MH) and body condition score (BCS) of mature cows (3–17 years old). Next, we estimated the genetic correlations between the three traits and assorted yearling traits (YW, weight; YC; conformation score; YP, precocity score; YM, muscling score; YN, navel score; LMA, longissimus muscle area; BF, back fat thickness). Finally, we obtained the expected direct responses to selection for MW, MH and BCS of cows and correlated responses for these traits when the selection was applied to yearling traits. For MW and MH, single-trait Bayesian analyses were used to evaluate the effects of including BCS when defining contemporary groups (BCS included, CG1; BCS not included, CG2). For BCS trait, linear and threshold animal models were compared. After, bi-trait analyses that included MW, MH or BCS with yearling traits were performed. The CG1 scenario resulted in a higher heritability for MW (0.45 ± 0.02) than did CG2 (0.39 ± 0.02). Both scenarios yielded the same heritability estimates for MH (0.35 ± 0.02). Sires’ rank correlations between predicted breeding values under CG1 and CG2 were 0.60–0.92 for MW and 0.90–0.98 for MH, considering different selection intensities. Thus, only for MW genetic evaluations, the incorporation of BCS in the definition of the contemporary groups is indicated. For BCS trait, the same sires were selected regardless of the model (linear or threshold). Genetic correlations between MW and five yearling traits (YW, YC, YP, YM and YN) ranged from 0.18 ± 0.03 to 0.84 ± 0.01. The MH had a higher and positive genetic association with YW (0.64 ± 0.02) and YC (0.54 ± 0.03), than with YN (0.18 ± 0.03). However, MH was negatively and lowly genetically correlated with YP (–0.08 ± 0.03) and YM (–0.14 ± 0.03). The BCS had positive genetic associations with all yearling traits, particularly with YP (0.61 ± 0.06) and YM (0.60 ± 0.07). Mature size and carcass traits exhibited a low to moderate negative genetic correlations. However, BCS had positive genetic associations with LMA (0.38 ± 0.12) and BF (0.32 ± 0.14). Despite a shorter generation interval, selection at the yearling stage will result in a slower genetic progress per generation than does direct selection for cow MW, MH or BCS. Moreover, using YW and YC as selection criteria will increase cattle size at maturity without altering BCS. Last, LMA or BF-based selection will reduce mature size, while improving BCS, as a correlated response.

Threshold and linear models for genetic evaluation of visual scores in Hereford and Braford cattle

Data from 127539 Hereford and Braford cattle were used to compare estimates of genetic parameters for navel, conformation, precocity, muscling and size visual scores at yearling, using linear and threshold animal models. In a second step, these models were cross-validated using a multinomial logistic regression in order to quantify the association between phenotype and genetic merit for each trait. For navel score, higher heritability was obtained with the threshold model (0.42 ± 0.02) in relation to the linear model (0.22 ± 0.02). However, similar heritability was estimated in both models for conformation, precocity, muscling and size, with values of 0.18 ± 0.01, 0.19 ± 0.01, 0.19 ± 0.01 and 0.26 ± 0.01, respectively, using linear model, and of 0.19 ± 0.01, 0.19 ± 0.01, 0.20 ± 0.01, and 0.29 ± 0.01, respectively, using threshold model. For navel score, Spearman correlations between sires’ breeding values predicted using linear and threshold models ranged from 0.60 (1% of the best sires are selected) to 0.96 (all sires are selected). For conformation, precocity, muscling and size scores, low changes in sires’ rank are expected using these models (Spearman correlations >0.86), regardless of the proportion of sires selected. Except for navel with the linear model, the direction of the associations between phenotype and genetic merit were in accordance with its expectation, as there were increases in the phenotype per unit of change in the breeding value. Thus, the threshold model would be recommended to perform genetic evaluation of navel score in this population. However, linear and threshold models showed similar predictive ability for conformation, precocity, muscling and size scores.

Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus

Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 × 10^-9) was found on chromosome 5 spanning positions 47.9-48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a ∼6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding.