The Association Between Genomic Heterozygosity and Carcass Merit in Cattle

Sire mating advice framework for cattle to recommend which beef bull to mate to individual dairy females

A decision-support tool or system is a computerized information system used to support decision making in a business; one central component to profitable dairy cattle production systems is the appropriate mating of bulls and females. Although tools have been described to aid mating decisions between dairy bulls and dairy females, or between beef bulls and beef females, there is a void of such tools that recommend which beef bull to mate to individual dairy females. The objective of the present study was to develop and validate a framework, founded on linear programming, to aid herd-level mating decisions where the bull-female mating is tailored based on complementarity and compatibility of both mates; consideration in the process was given to the genetic merit of both mates for a series of traits as well as the life history of the female herself. Traits considered in the linear function to be maximized in the linear programming procedure were those related to calving performance traits (i.e., calving dystocia, perinatal mortality, and gestation length) and subsequent beef performance (i.e., docility, feed intake, and carcass merit); each trait was weighted in the linear function by its respective economic importance. First, a calibration and validation dataset from a national database were generated using data truncated on calendar year to validate predictions of progeny performance. Expected performance of progeny was based on a combination of estimated genetic merit and nongenetic effects that would be available at the time of mating. The direction of the associations in the validation population was in line with expectations and, in many instances, the extent of the association was close to expectation. Using real dairy cow data of 284,334 cows from 1,535 herds, 6 randomly chosen candidate beef bulls of multiple breeds were selected per herd for mating assignments to all cows, each with an equal number of matings. Bull-cow matings were assigned either at random or using the developed linear programming framework. Although the mean expected genetic merit of the hypothetical progeny was the same for both scenarios (as expected), the bull-cow assignments proposed by the linear programming mating framework were assortative in nature. Bulls with a greater genetic risk of dystocia in their progeny were, on average, recommended for mating to cows that, genetically, were less likely to experience calving dystocia based on their direct and maternal estimates of genetic merit. Similarly, where possible, bulls that genetically were expected to produce, on average, heavy and more conformed carcass progeny were mated to cows whose progeny were expected to have lighter and less conformed carcasses based on the genetic merit inherited from the cow. A case study of one large dairy herd illustrating in more detail how the linear programming-based mating algorithm operates is also presented especially in relation to assortative mating for calving dystocia and carcass merit. The validated linear programming-based mating decision-support tool presented in this study describes a digital framework for aiding decision making in beef-on-dairy herd breeding programs.

Selection signatures associated with adaptation in South African Drakensberger, Nguni, and Tuli beef breeds

In the present study 1,709 cattle, including 1,118 Drakensberger (DRB), 377 Nguni (NGI), and 214 Tuli (TUL), were genotyped using the GeneSeek® Genomic Profiler™ 150 K bovine SNP panel. A genomic data set of 122,632 quality-filtered single nucleotide polymorphisms (SNPs) were used to identify selection signatures within breeds based on conserved runs of homozygosity (ROH) and heterozygosity (ROHet) estimated with the detectRUNS R package. The mean number of ROH per animal varied across breeds ranging from 36.09 ± 12.82 (NGI) to 51.82 ± 21.01 (DRB), and the mean ROH length per breed ranged between 2.31 Mb (NGI) and 3.90 Mb (DRB). The smallest length categories i.e., ROH < 4 Mb were most frequent, indicating historic inbreeding effects for all breeds. The ROH based inbreeding coefficients (FROH) ranged between 0.033 ± 0.024 (NGI) and 0.081 ± 0.046 (DRB). Genes mapped to candidate regions were associated with immunity (ADAMTS12, LY96, WDPCP) and adaptation (FKBP4, CBFA2T3, TUBB3) in cattle and genes previously only reported for immunity in mice and human (EXOC3L1, MYO1G). The present study contributes to the understanding of the genetic mechanisms of adaptation, providing information for potential molecular application in genetic evaluation and selection programs.

Assessment of genome complementarity in three beef-on-dairy crossbreds reveals sire-specific effects on production traits with comparable rates of genomic inbreeding reduction

BACKGROUND

Crossbreeding beef bulls with dairy cows can improve the economic value and fitness of calves not entering dairy production owing to increased meat yield and heterosis. However, outcrossing might reduce the dosage of alleles that confer local adaptation or result in a higher risk of dystocia due to increased calf size. Given the clear phenotypic differences between beef breeds, the varying phylogenetic distances between beef and dairy breeds, and the genomic variations within breeds, the attainable economic and fitness gains of calves will strongly depend on the selection of sires for crossing. Thus, the aim of this study was to assess genome complementarity between Angus (AAN), Limousin (LIM), or Simmental (SIM) beef bulls and Brown Swiss (BSW) dairy cows by quantifying genomic inbreeding reduction in F1 crosses and identifying genes potentially under BSW-specific selection that might be affected by outcrossing.

RESULTS

Low-pass sequencing data from 181 cows, 34 bulls, and 301 of their F1 progeny, and body weight and carcass composition measurements of 248 F1s were obtained. The high genomic inbreeding levels detected in the BSW cows were substantially reduced in the crossbreds, with only minor differences between the sire breeds. In the BSW cows, 585 candidate genes under selection were identified, overrepresenting genes associated with milk, meat and carcass, and production traits. Only a few genes were strongly differentiated at nonsynonymous variants between the BSW and beef breeds, including four tightly clustered genes (FAM184B, NCAPG, DCAF16, and LCORL) nearly fixed for alternate alleles in the BSW cows but mostly heterozygous or homozygous for the reference alleles in the AAN and LIM bulls. The alternate allele dosage at these genes significantly correlated with reduced carcass weight and protein mass in F1s.

CONCLUSION

Some of the few genes that were highly divergent between the BSW and beef breeds at nonsynonymous variants were likely under strong selection for reduced carcass weight in the BSW breed, potentially due to trade-offs between beef and dairy productions. As alleles with opposing effects still segregate in beef cattle, marker-assisted selection of mating pairs may be used to modulate the desired phenotypes and simultaneously decrease genomic inbreeding.

Breed of origin analysis in genome-wide association studies: enhancing SNP-based insights into production traits in a commercial Brangus population

BACKGROUND

Carcass weight (HCW) and marbling (MARB) are critical for meat quality and market value in beef cattle. In composite breeds like Brangus, which meld the genetics of Angus and Brahman, SNP-based analyses have illuminated some genetic influences on these traits, but they fall short in fully capturing the nuanced effects of breed of origin alleles (BOA) on these traits. Focus on the impacts of BOA on phenotypic features within Brangus populations can result in a more profound understanding of the specific influences of Angus and Brahman genetics. Moreover, the consideration of BOA becomes particularly significant when evaluating dominance effects contributing to heterosis in crossbred populations. BOA provides a more comprehensive measure of heterosis due to its ability to differentiate the distinct genetic contributions originating from each parent breed. This detailed understanding of genetic effects is essential for making informed breeding decisions to optimize the benefits of heterosis in composite breeds like Brangus.

OBJECTIVE

This study aims to identify quantitative trait loci (QTL) influencing HCW and MARB by utilizing SNP and BOA information, incorporating additive, dominance, and overdominance effects within a multi-generational Brangus commercial herd.

METHODS

We analyzed phenotypic data from 1,066 genotyped Brangus steers. BOA inference was performed using LAMP-LD software using Angus and Brahman reference sets. SNP-based and BOA-based GWAS were then conducted considering additive, dominance, and overdominance models.

RESULTS

The study identified numerous QTLs for HCW and MARB. A notable QTL for HCW was associated to the SGCB gene, pivotal for muscle growth, and was identified solely in the BOA GWAS. Several BOA GWAS QTLs exhibited a dominance effect underscoring their importance in estimating heterosis.

CONCLUSIONS

Our findings demonstrate that SNP-based methods may not detect all genetic variation affecting economically important traits in composite breeds. BOA inclusion in genomic evaluations is crucial for identifying genetic regions contributing to trait variation and for understanding the dominance value underpinning heterosis. By considering BOA, we gain a deeper understanding of genetic interactions and heterosis, which is integral to advancing breeding programs. The incorporation of BOA is recommended for comprehensive genomic evaluations to optimize trait improvements in crossbred cattle populations.

Population structure and identification of genomic regions associated with productive traits in five Italian beef cattle breeds

Italy has a long history in beef production, with local breeds such as Marchigiana, Chianina, Romagnola, Maremmana, and Podolica which produce high-quality meat. Selection has improved meat production, precocity, growth ability and muscle development, but the genetic determinism of such traits is mostly unknown. Using 33K SNPs-data from young bulls (N = 4064) belonging to these five Italian breeds, we demonstrated that the Maremmana and Podolica rustic breeds are closely related, while the specialised Marchigiana, Chianina, and Romagnola breeds are more differentiated. A genome-wide association study for growth and muscle development traits (average daily gain during the performance test, weight at 1 year old, muscularity) was conducted in the five Italian breeds. Results indicated a region on chromosome 2, containing the myostatin gene (MSTN), which displayed significant genome-wide associations with muscularity in Marchigiana cattle, a breed in which the muscle hypertrophy phenotype is segregating. Moreover, a significant SNP on chromosome 14 was associated, in the Chianina breed, to muscularity. The identification of diverse genomic regions associated with conformation traits might increase our knowledge about the genomic basis of such traits in Italian beef cattle and, eventually, such information could be used to implement marker-assisted selection of young bulls tested in the performance test.

Mean breed performance of the progeny from beef-on-dairy matings

Gains through breeding can be achieved through a combination of both between-breed and within-breed selection. Two suites of traits of particular interest to dairy producers when selecting beef bulls for mating to dairy females are calving-related attributes and the expected value of the subsequent calf, the latter usually being a function of expected carcass value. Estimated breed effects can be informative, particularly in the absence of across-breed genetic evaluations. The objective of the present study was to use a large national database of the progeny from beef-on-dairy matings to estimate the mean breed effects of the used beef sires. Calving performance (i.e., gestation length, calving difficulty score, and perinatal morality) as well as calf value were investigated; a series of slaughter-related traits (i.e., carcass metrics and age at slaughter) of the prime progeny were also investigated. Phenotypic data on up to 977,037 progeny for calving performance, 79,903 for calf price and 103,175 for carcass traits (including dairy × dairy progeny for comparative purposes) were used; sire breeds represented were Holstein-Friesian, Angus, Aubrac, Belgian Blue, Charolais, Hereford, Limousin, Salers, and Simmental. Large interbreed differences existed. The mean gestation length of male calves from beef sires varied from 282.3 d (Angus) to 287.4 d (Limousin) which were all longer than the mean of 280.9 d for Holstein-Friesian sired male calves. Relative to a Holstein-Friesian sire, the odds of dystocia varied from 1.43 (Angus) to 4.77 (Belgian Blue) but, once adjusted for both the estimated maternal genetic merit of the dam and direct genetic merit of the calf for calving difficulty, the range in odds ratios shrunk. A difference of €125.4 existed in calf sale price between the progeny of the different beef breeds investigated which represented over twice the residual standard deviation in calf price within the day of sale-Angus was the cheapest while Charolais calves were, on average, the most expensive calves. Mean carcass weight of steers, not adjusted for age at slaughter or carcass fat, varied from 327.1 kg (Angus) to 363.2 kg (Belgian Blue) for the beef breeds with the mean carcass weight of Holstein-Friesian steer progeny being 322.4 kg. Belgian Blues had, on average, the best carcass conformation with the Herefords and Angus having the worst of all beef breeds. Angus and Hereford steers were slaughtered the youngest of all beef breeds but just 9 d younger than the average of all other beef breeds yet 24 d younger than Holstein-Friesian sired progeny. Clear breed differences in calving and carcass performance exist among beef breeds mated to dairy females. Those breeds excelling in calving performance were not necessarily the best for carcass merit.

Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs

BACKGROUND

In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment of how inbreeding is reflected in the genome is still an issue. The aim of this research was to study the usefulness of genomic information for the assessment of genetic diversity in the highly endangered Gochu Asturcelta pig breed. Pedigree depth varied from 0 (founders) to 4 equivalent discrete generations (t). Four homozygosity parameters (runs of homozygosity, FROH; heterozygosity-rich regions, FHRR; Li and Horvitz's, FLH; and Yang and colleague's FYAN) were computed for each individual, adjusted for the variability in the base population (BP; six individuals) and further jackknifed over autosomes. Individual increases in homozygosity (depending on t) and increases in pairwise homozygosity (i.e., increase in the parents' mean) were computed for each individual in the pedigree, and effective population size (Ne) was computed for five subpopulations (cohorts). Genealogical parameters (individual inbreeding, individual increase in inbreeding, and Ne) were used for comparisons.

RESULTS

The mean F was 0.120 ± 0.074 and the mean BP-adjusted homozygosity ranged from 0.099 ± 0.081 (FLH) to 0.152 ± 0.075 (FYAN). After jackknifing, the mean values were slightly lower. The increase in pairwise homozygosity tended to be twofold higher than the corresponding individual increase in homozygosity values. When compared with genealogical estimates, estimates of Ne obtained using FYAN tended to have low root-mean-squared errors. However, Ne estimates based on increases in pairwise homozygosity using both FROH and FHRR estimates of genomic inbreeding had lower root-mean-squared errors.

CONCLUSIONS

Parameters characterizing homozygosity may not accurately depict losses of variability in small populations in which breeding policy prohibits matings between close relatives. After BP adjustment, the performance of FROH and FHRR was highly consistent. Assuming that an increase in homozygosity depends only on pedigree depth can lead to underestimating it in populations with shallow pedigrees. An increase in pairwise homozygosity computed from either FROH or FHRR is a promising approach for characterizing autozygosity.

Detection of Genomic Imprinting for Carcass Traits in Cattle Using Imputed High-Density Genotype Data

Genomic imprinting is an epigenetic phenomenon defined as the silencing of an allele, at least partially, at a given locus based on the sex of the transmitting parent. The objective of the present study was to detect the presence of SNP-phenotype imprinting associations for carcass weight (CW), carcass conformation (CC) and carcass fat (CF) in cattle. The data used comprised carcass data, along with imputed, high-density genotype data on 618,837 single nucleotide polymorphisms (SNPs) from 23,687 cattle; all animal genotypes were phased with respect to parent of origin. Based on the phased genotypes and a series of single-locus linear models, 24, 339, and 316 SNPs demonstrated imprinting associations with CW, CC, and CF, respectively. Regardless of the trait in question, no known imprinted gene was located within 0.5 Mb of the SNPs demonstrating imprinting associations in the present study. Since all imprinting associations detected herein were at novel loci, further investigation of these regions may be warranted. Nonetheless, knowledge of these associations might be useful for improving the accuracy of genomic evaluations for these traits, as well as mate allocations systems to exploit the effects of genomic imprinting.