Management of lethal recessive alleles in beef cattle through the use of mate selection software

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.

Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects

Background

Warmblood fragile foal syndrome (WFFS) is a monogenetic defect caused by a recessive lethal missense point mutation in the procollagen‐lysine, 2‐oxoglutarate 5‐dioxygenase 1 gene (PLOD1, c.2032G>A). The majority of homozygous WFFS horses are aborted during gestation. Clinical signs of affected horses include fragile skin, skin and mucosa lacerations, hyperextension of the articulations, and hematomas. In spite of its harmful effect, a relatively high frequency of WFFS carriers has been found in Warmblood horses, suggesting a heterozygote advantage. Thus, in this study our aims were to: (1) estimate the frequency of WFFS carriers in the Swedish Warmblood breed (SWB), (2) estimate the effect of WFFS carrier genotype on performance traits in two SWB subpopulations bred for different disciplines, and (3) simulate the potential effects of balancing selection and different selection strategies on the frequency of carriers.

Methods

In total, 2288 SWB sport horses born between 1971 and 2020 were tested for the WFFS mutation and had estimated breeding values (EBV) for ten traditional evaluating and 50 linear descriptive traits.

Results

The frequency of WFFS carriers calculated from a pool of 511 randomly selected SWB horses born in 2017 was equal to 7.4% and ranged from 0.0 to 12.0% among the whole set of tested SWB horses, starting from 1971 till 2020. The effect of the WFFS carrier genotype was significant for several EBV mainly related to movements and dressage traits and especially for horses not bred for the show jumping discipline. Using simulation, we showed that balancing selection can maintain a recessive lethal allele in populations such as the SWB breed over generations and that the frequency is expected to slowly decrease in absence of balancing selection. Finally, we showed that selection against carrier sires can result in a more rapid decrease of the frequency of the mutant allele over time.

Conclusion

Further research is needed to confirm the apparent association between equine performance and the WFFS carrier genotype. Identification of such associations or new causative mutations for horse performance traits can serve as new tools in horse breeding to select for healthy, sustainable, and better performing horses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00693-4.

How to achieve a higher selection plateau in forest tree breeding? Fostering heterozygote × homozygote relationships in optimal contribution selection in the case study of Populus nigra

In breeding, optimal contribution selection (OCS) is one of the most effective strategies to balance short- and long-term genetic responses, by maximizing genetic gain and minimizing global coancestry. Considering genetic diversity in the selection dynamic-through coancestry-is undoubtedly the reason for the success of OCS, as it avoids preliminary loss of favorable alleles. Originally formulated with the pedigree relationship matrix, global coancestry can nowadays be assessed with one of the possible formulations of the realized genomic relationship matrix. Most formulations were optimized for genomic evaluation, but few for the management of coancestry. We introduce here an alternative formulation specifically developed for genomic OCS (GOCS), intended to better control heterozygous loci, and thus better account for Mendelian sampling. We simulated a multigeneration breeding program with mate allocation and under GOCS for twenty generations, solved with quadratic programming. With the case study of Populus nigra, we have shown that, although the dynamic was mainly determined by the trade-off between genetic gain and genetic diversity, better formulations of the genomic relationship matrix, especially those fostering individuals carrying multiple heterozygous loci, can lead to better short-term genetic gain and a higher selection plateau.

Infertility due to defective sperm flagella caused by an intronic deletion in DNAH17 that perturbs splicing

Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed at a semen collection center. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P = 4.22 × 10-15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1: c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.

Comparison of Genetic Merit for Weight and Meat Traits between the Polled and Horned Cattle in Multiple Beef Breeds

Breeding for polled animals is deemed the most practical solution to eradicate horns naturally and circumvent management costs and risks on health and welfare. However, there has been a historical reluctance by some farmers to select polled animals due to perceived lower productivity of their calves. This study has compared estimated breeding values (EBVs) between horned and polled animals (N = 2,466,785) for 12 production and carcass traits to assess historical (before 2000) and recent (2000-2018) genetic implications of poll breeding. Older generations of the polled animals in most breeds had significantly lower (Bonferroni-corrected p = 0.05) genetic merits for live (birth to maturity) and carcass weights, milk, meat quality, and fat content traits. Substantial gains of genetic potential were achieved during 2000 to 2018 in each breed, such that polled animals have significantly improved for the majority of traits studied. Generally, polled cohorts showed advantageous EBVs for live and carcass weights irrespective of the lower birth weights in some breeds. While Polled Brahman showed inferior production parameters, the poll genetics' effect size (d) and correlation (r) were very small on recent birth weight (d = -0.30, r = -0.08), 200 days (-0.19, -0.05), 400 days (-0.06, -0.02), 600 days (-0.05, -0.01), mature cow live weight (-0.08, -0.02), and carcass weight (-0.19, -0.05). In conclusion, although there is some evidence that historical selection for polled breeding animals may have reduced productivity, there is strong evidence that more recent selection for polled genotypes in the breeds studied has not resulted in any adverse effects on genetic merit.

Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle

Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10⁻⁸) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10⁻⁶) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10⁻⁸). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.

Symposium review: Exploiting homozygosity in the era of genomics-Selection, inbreeding, and mating programs

The advent of genomic selection paved the way for an unprecedented acceleration in genetic progress. The increased ability to select superior individuals has been coupled with a drastic reduction in the generation interval for most dairy populations, representing both an opportunity and a challenge. Homozygosity is now rapidly accumulating in dairy populations. Currently, inbreeding depression is managed mostly by culling at the farm level and by controlling the overall accumulation of homozygosity at the population level. A better understanding of how homozygosity and recessive load are related will guarantee continued genetic improvement while curtailing the accumulation of harmful recessives and maintaining enough genetic variability to ensure the possibility of selection in the face of changing environmental conditions. In this review, we present a snapshot of the current dairy selection structure as it relates to response to selection and accumulation of homozygosity, briefly outline the main approaches currently used to manage inbreeding and overall variability, and present some approaches that can be used in the short term to control accumulation of harmful recessives while maintaining sustained selection pressure.