Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits

Unexpected recombination at the polled locus in a horned Holstein calf from the mating of a homozygous polled sire and a heterozygous polled cow

In this study, I report an unexpected case of a Holstein calf that developed horns even though the sire was homozygous and the dam was heterozygous for polledness. After verifying and confirming the correct parentage, the parents and offspring were genotyped with the Illumina EuroG_MD BeadChip and the SNPs in the polled region on chromosome 1 were evaluated. In addition, the father was sequenced with next generation sequencing to identify possible, previously unknown variants. The deletion of two base pairs within the causative 80-kb duplication described for the Friesian polled variant was verified by melting curve analysis and the 80-kb duplication by droplet digital PCR. Analysis of all data showed that, as expected, the calf was heterozygous for all SNP positions flanking the 80-kb duplication but was homozygous wild type in the 80-kb duplication region and therefore carried horns. This is certainly a very rare case of a recombination within the highly conserved polled region, which on the one hand confirms that only the 80-kb duplication is responsible for the expression of the Friesian polled variant, but on the other hand also shows that caution is required when interpreting the usual routine genotyping of the horn status based on linked single nucleotide polymorphisms in the polled region on chromosome 1. Based on the present case, it is recommended that, in addition to the evaluation of the SNP data of the BeadChip, an extended diagnosis with direct detection of the 2-bp deletion (1:g.2629156_2629158delGT) should be carried out in any case when detecting the Friesian polled variant.

Behavioral changes in the first 3 weeks after disbudding in dairy calves

Hot-iron disbudding, the practice of cauterizing horn bud tissue to prevent horn growth in dairy calves, results in behavioral changes indicative of pain in the first few days after the procedure. However, few studies have quantified behavioral changes in the following weeks, while the burn wounds are still healing. Female Holstein calves were disbudded with a heated iron and pain relief (5.5 mL lidocaine cornual nerve block and 1 mg/kg oral meloxicam) at 4 to 10 d of age (n = 19) or not disbudded (n = 19). Calves wore ear tag accelerometers that reported the dominant behavior being performed at 1-min intervals from 3 to 21 d after disbudding. Compared with age-matched controls, disbudded calves tended to spend more time inactive throughout the observation period, ruminated less in the first 3 to 11 d after disbudding, and sucked more from a milk bottle beginning 5 d after disbudding until the end of the 21-d observation period. In addition to the accelerometer data, live observations of sleeping (using a behavioral proxy), lying, and ruminating were collected using instantaneous sampling at 5-min intervals for 24-h periods 3, 10, and 17 d after disbudding. Disbudded calves slept with their head down more on all live observation days and spent more time lying on the 17th d after disbudding, but ruminating did not differ compared with controls, in contrast to the accelerometer results. More time spent inactive, sleeping, and lying, and less time spent ruminating (as indicated by the accelerometer) can be interpreted as attempts to reduce painful stimulation of the disbudding wounds and allocate energy to healing. It is unclear whether the greater amount of sucking in the disbudded calves is nutritive (milk present) or non-nutritive (milk absent), as the algorithm did not distinguish the type of sucking, and further research is needed to explore the factors underlying this effect. We conclude that disbudding alters daily behavior patterns for at least 3 wk, far beyond the duration of recommended pain medication, raising additional welfare concerns about the procedure.

Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level

In this study, we explored mating allocation in Holstein using genomic information for 24,333 Holstein females born in Denmark, Finland, and Sweden. We used 2 data sets of bulls: the top 50 genotyped bulls and the top 25 polled genotyped bulls on the Nordic total merit scale. We used linear programming to optimize economic scores within each herd, considering genetic level, genetic relationship, semen cost, the economic impact of genetic defects, polledness, and β-casein. We found that it was possible to reduce genetic relationships and eliminate expression of genetic defects with minimal effect on the genetic level in total merit index. Compared with maximizing only Nordic total merit index, the relative frequency of polled offspring increased from 13.5 to 22.5%, and that of offspring homozygous for β-casein (A2A2) from 66.7 to 75.0% in one generation, without any substantial negative impact on other comparison criteria. Using only semen from polled bulls, which might become necessary if dehorning is banned, considerably reduced the genetic level. We also found that animals carrying the polled allele were less likely to be homozygous for β-casein (A2A2) and more likely to be carriers of the genetic defect HH1. Hence, adding economic value to a monogenic trait in the economic score used for mating allocation sometimes negatively affected another monogenetic trait. We recommend that the comparison criteria used in this study be monitored in a modern genomic mating program.

Early Life Painful Procedures: Long-Term Consequences and Implications for Farm Animal Welfare

Farm animals routinely undergo painful husbandry procedures early in life, including disbudding and castration in calves and goat kids, tail docking and castration in piglets and lambs, and beak trimming in chicks. In rodents, inflammatory events soon after birth, when physiological systems are developing and sensitive to perturbation, can profoundly alter phenotypic outcomes later in life. This review summarizes the current state of research on long-term phenotypic consequences of neonatal painful procedures in rodents and farm animals, and discusses the implications for farm animal welfare. Rodents exposed to early life inflammation show a hypo-/hyper-responsive profile to pain-, fear-, and anxiety-inducing stimuli, manifesting as an initial attenuation in responses that transitions into hyperresponsivity with increasing age or cumulative stress. Neonatal inflammation also predisposes rodents to cognitive, social, and reproductive deficits, and there is some evidence that adverse effects may be passed to offspring. The outcomes of neonatal inflammation are modulated by injury etiology, age at the time of injury and time of testing, sex, pain management, and rearing environment. Equivalent research examining long-term phenotypic consequences of early life painful procedures in farm animals is greatly lacking, despite obvious implications for welfare and performance. Improved understanding of how these procedures shape phenotypes will inform efforts to mitigate negative outcomes through reduction, replacement, and refinement of current practices.

Boosting the potential of cattle breeding using molecular biology, genetics, and bioinformatics approaches – a review

Cattle are among the most important farm animals that underwent an intense selection with the aim to increase milk production and to improve growth and meat properties, meanwhile reducing the generation interval allowing for a faster herd turnover. Recently, a shift from traditional breeding methods to breeding based on genetic testing has been observed. In this perspective, we review the techniques of molecular biology, genetics, and bioinformatics that are expected to further boost the agricultural potential of cattle. We discuss embryo selection based on next-generation and Nanopore sequencing and in vitro embryo production, boosting the potential of genetically superior animals. Gene editing of embryos could further speed up the selection process, essentially introducing a change in a single generation. Lastly, we discuss the host-microbiome co-evolution and adaptation. For example, cattle already adapted to low-quality low-cost fodder could be bred to achieve desired properties for the beef and dairy industry. The challenge of breeding and genetic editing is to accompany the selection on desired consumer-oriented traits with the push for sustainability and the adaptation to a changing climate while remaining economically viable. We propose that we are yet to see the limits of what is possible to achieve with modern technology for the cattle of the future; the ultimate goal will be to produce and maintain genetically elite individuals that can sustain the growing demands on the production.

A variance component estimation approach to infer associations between Mendelian polledness and quantitative production and female fertility traits in German Simmental cattle

BACKGROUND

Managing beneficial Mendelian characteristics in dairy cattle breeding programs implies that the correlated genetic effects are considered to avoid possible adverse effects in selection processes. The Mendelian trait polledness in cattle is traditionally associated with the belief that the polled locus has unfavorable effects on breeding goal traits. This may be due to the inferior breeding values of former polled bulls and cows in cattle breeds, such as German Simmental, or to pleiotropic or linkage effects of the polled locus.

METHODS

We focused on a variance component estimation approach that uses a marker-based numerator relationship matrix reflecting gametic relationships at the polled locus to test for direct pleiotropic or linked quantitative trait loci (QTL) effects of the polled locus on relevant traits. We applied the approach to performance, health, and female fertility traits in German Simmental cattle.

RESULTS

Our results showed no evidence for any pleiotropic QTL effects of the polled locus on test-day production traits milk yield and fat percentage, on the mastitis indicator 'somatic cell score', and on several female fertility traits, i.e. 56 days non return rate, days open and days to first service. We detected a significant and unfavorable QTL effect accounting for 6.6% of the genetic variance for protein percentage only.

CONCLUSIONS

Pleiotropy does not explain the lower breeding values and phenotypic inferiority of polled German Simmental sires and cows relative to the horned population in the breed. Thus, intensified selection in the polled population will contribute to increased selection response in breeding goal traits and genetic merit and will narrow the deficit in breeding values for production traits.

Injury alters motivational trade-offs in calves during the healing period

Injury can produce long-lasting motivational changes that may alter decisions made under risk. Our objective was to determine whether a routine painful husbandry procedure, hot-iron disbudding, affects how calves trade off risk avoidance against a competing motivation (i.e., feeding), and whether this response depends on time since injury. We used a startle test to evaluate this trade-off in calves disbudded 0 or 21 days previously and non-injured control calves. For 3 days, calves were individually habituated to the testing arena in which they received a 0.5 L milk meal via a rubber teat. On the 4^th day, upon approaching the milk reward, the calf was startled by a sudden noise. We assessed the duration and magnitude of the calf’s startle response, their latency to return to the milk bottle, and duration spent suckling after startling. No treatment differences were observed in the duration and magnitude of the startle response or in the probability of returning to the bottle after startling. However, among those who did return, disbudded calves spent longer suckling, indicating they accepted more risk in order to feed compared to controls. In addition, calves with 21-day-old injuries tended to return to the bottle faster compared to newly disbudded calves and controls. We suggest that hot-iron disbudding increases calves’ motivation to suckle, as they were more likely to prioritize this behaviour over risk avoidance compared to control calves. This effect was most evident 21 days after disbudding, indicating that injury can produce long-term changes in motivational state.

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.

Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future.

Comparison of Gene Editing Versus Conventional Breeding to Introgress the POLLED Allele Into the Tropically Adapted Australian Beef Cattle Population

Dehorning is the process of physically removing horns to protect animals and humans from injury, but the process is costly, unpleasant, and faces increasing public scrutiny. Genetic selection for polled (hornless), which is genetically dominant to horned, is a long-term solution to eliminate the need for dehorning. However, due to the limited number of polled Australian Brahman bulls, the northern Australian beef cattle population remains predominantly horned. The potential to use gene editing to produce high-genetic-merit polled cattle was recently demonstrated. To further explore the concept, this study simulated introgression of the POLLED allele into a tropically adapted Australian beef cattle population via conventional breeding or gene editing (top 1% or 10% of seedstock bulls/year) for 3 polled mating schemes and compared results to baseline selection on genetic merit (Japan Ox selection index, $JapOx) alone, over the course of 20 years. The baseline scenario did not significantly decrease the 20-year HORNED allele frequency (80%), but resulted in one of the fastest rates of genetic gain ($8.00/year). Compared to the baseline, the conventional breeding scenarios where polled bulls were preferentially used for breeding, regardless of their genetic merit, significantly decreased the 20-year HORNED allele frequency (30%), but resulted in a significantly slower rate of genetic gain ($6.70/year, P ≤ 0.05). The mating scheme that required the exclusive use of homozygous polled bulls, resulted in the lowest 20-year HORNED allele frequency (8%), but this conventional breeding scenario resulted in the slowest rate of genetic gain ($5.50/year). The addition of gene editing the top 1% or 10% of seedstock bull calves/year to each conventional breeding scenario resulted in significantly faster rates of genetic gain (up to $8.10/year, P ≤ 0.05). Overall, our study demonstrates that, due to the limited number of polled Australian Brahman bulls, strong selection pressure on polled will be necessary to meaningfully increase the number of polled animals in this population. Moreover, these scenarios illustrate how gene editing could be a tool for accelerating the development of high-genetic-merit homozygous polled sires to mitigate the current trade-off of slower genetic gain associated with decreasing HORNED allele frequency in the Australian Brahman population.

A unifying concept of animal breeding programmes

Modern animal breeding programmes are constantly evolving with advances in breeding theory, biotechnology and genetics. Surprisingly, there seems to be no generally accepted succinct definition of what exactly a breeding programme is, neither is there a unified language to describe breeding programmes in a comprehensive, unambiguous and reproducible way. In this work, we try to fill this gap by suggesting a general definition of breeding programmes that also pertains to cases where genetic progress is not achieved through selection, but, for example, through transgenic technologies, or the aim is not to generate genetic progress, but, for example, to maintain genetic diversity. The key idea of the underlying concept is to represent a breeding programme in modular form as a directed graph that is composed of nodes and edges, where nodes represent cohorts of breeding units, usually individuals, and edges represent breeding activities, like "selection" or "reproduction." We claim, that by defining a comprehensive set of nodes and edges, it is possible to represent any breeding programme of arbitrary complexity by such a graph, which thus comprises a full description of the breeding programme. This concept is implemented in a web-based tool (MoBPSweb, available at www.mobps.de) and has a link to the R-package MoBPS (Modular Breeding Program Simulator) to simulate the described breeding programmes. The approach is illustrated by showcasing three different breeding programmes of increasing complexity. The concept allows a formal description of breeding programmes, which is requested, for example, in legal regulations of the European Union, but so far cannot be provided in a standardized format. In the discussion, we point out potential limitations of the concept and argue that the general approach can be easily extended to account for novel breeding technologies, to breeding of crops or experimental species, but also to modelling diversity dynamics in natural populations.

CRISPR/Cas12a mediated knock-in of the Polled Celtic variant to produce a polled genotype in dairy cattle

In modern livestock farming horned cattle pose an increased risk of injury for each other as well as for the farmers. Dehorning without anesthesia is associated with stress and pain for the calves and raises concerns regarding animal welfare. Naturally occurring structural variants causing polledness are known for most beef cattle but are rare within the dairy cattle population. The most common structural variant in beef cattle consists of a 202 base pair insertion-deletion (Polled Celtic variant). For the generation of polled offspring from a horned Holstein-Friesian bull, we isolated the Polled Celtic variant from the genome of an Angus cow and integrated it into the genome of fibroblasts taken from the horned bull using the CRISPR/Cas12a system (formerly Cpf1). Modified fibroblasts served as donor cells for somatic cell nuclear transfer and reconstructed embryos were transferred into synchronized recipients. One resulting pregnancy was terminated on day 90 of gestation for the examination of the fetus. Macroscopic and histological analyses proved a polled phenotype. The remaining pregnancy was carried to term and delivered one calf with a polled phenotype which died shortly after birth. In conclusion, we successfully demonstrated the practical application of CRISPR/Cas12a in farm animal breeding and husbandry.

Optimized Genetic Testing for Polledness in Multiple Breeds of Cattle

Many breeds of modern cattle are naturally horned, and for sound husbandry management reasons the calves frequently undergo procedures to physically remove the horns by disbudding or dehorning. These procedures are however a welfare concern. Selective breeding for polledness - absence of horns - has been effective in some cattle breeds but not in others (Bos indicus genotypes) due in part to the complex genetics of horn phenotype. To address this problem different approaches to genetic testing which provide accurate early-in-life prediction of horn phenotype have been evaluated, initially using microsatellites (MSAT) and more recently single nucleotide polymorphism (SNP). A direct gene test is not effective given the genetic heterogeneity and large-sized sequence variants associated with polledness in different breeds. The current study investigated 39,943 animals of multiple breeds to assess the accuracy of available poll testing assays. While the standard SNP-based test was an improvement on the earlier MSAT haplotyping method, 1999 (9.69%) out of 20,636 animals tested with this SNP-based assay did not predict a genotype, most commonly associated with the Indicus-influenced breeds. The current study has developed an optimized poll gene test that resolved the vast majority of these 1999 unresolved animals, while the predicted genotypes of those previously resolved remained unchanged. Hence the optimized poll test successfully predicted a genotype in 99.96% of samples assessed. We demonstrated that a robust set of 5 SNPs can effectively determine P_C and P_F alleles and eliminate the ambiguous and undetermined results of poll gene testing previously identified as an issue in cattle.

The importance of controlled mating in honeybee breeding

BACKGROUND

Controlled mating procedures are widely accepted as a key aspect of successful breeding in almost all animal species. In honeybees, however, controlled mating is hard to achieve. Therefore, there have been several attempts to breed honeybees using free-mated queens. In such breeding schemes, selection occurs only on the maternal path since the drone sires are random samples of the population. The success rates of breeding approaches without controlled mating have so far not been investigated on a theoretical or simulation-based level.

METHODS

Stochastic simulation studies were carried out to examine the chances of success in honeybee breeding with and without controlled mating. We investigated the influence of different sizes of breeding populations (500, 1000, 2000 colonies per year) and unselected passive populations (0, 500, 1000, 2000, infinitely many colonies per year) on selection for a maternally (queen) and directly (worker group) influenced trait with moderate ([Formula: see text]) or strong ([Formula: see text]) negative correlation between the two effects. The simulations described 20 years of selection.

RESULTS

Our simulations showed a reduction of breeding success between 47 and 99% if mating was not controlled. In the most drastic cases, practically no genetic gain could be generated without controlled mating. We observed that in the trade-off between selection for direct or maternal effects, the absence of mating control leads to a shift in favor of maternal effects. Moreover, we describe the implications of different breeding strategies on the unselected passive population that benefits only indirectly via the transfer of queens or drones from the breeding population. We show that genetic gain in the passive population develops parallel to that of the breeding population. However, we found a genetic lag that became significantly smaller as more breeding queens served as dams of queens in the passive population.

CONCLUSIONS

We conclude that even when unwanted admixture of subspecies can be excluded in natural matings, controlled mating is imperative for successful breeding efforts. This is especially highlighted by the strong positive impact that controlled mating in the breeding population has on the unselected passive population.

Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the US dairy cattle population

Disbudding and dehorning are commonly used cattle management practices to protect animals and humans from injury. They are unpleasant, costly processes subject to increased public scrutiny as an animal welfare issue. Horns are a recessively inherited trait, so one option to eliminate dehorning is to breed for polled (hornlessness). However, due to the low genetic merit and scarcity of polled dairy sires, this approach has not been widely adopted. In March 2018, only 3 Holstein and 0 Jersey active homozygous polled sires were registered with the National Association of Animal Breeders. Alternatively, gene editing to produce high-genetic-merit polled sires has been proposed. To further explore this concept, introgression of the POLLED allele into both the US Holstein and Jersey cattle populations via conventional breeding or gene editing (top 1% of bulls/year) was simulated for 3 polled mating schemes and compared with baseline selection on lifetime net merit (NM$) alone, over the course of 20 yr. Scenarios were replicated 10 times and the changes in HORNED allele frequency, inbreeding, genetic gain (NM$), and number of unique sires used were calculated. Gene editing decreased the frequency of the HORNED allele to <0.1 after 20 yr, which was as fast or faster than conventional breeding for both breeds. In the mating scheme that required the use of only existing homozygous polled sires, inbreeding reached 17% (Holstein) and 14% (Jersey), compared with less than 7% in the baseline scenarios. However, gene editing in the same mating scheme resulted in significantly less inbreeding, 9% (Holstein) and 8% (Jersey). Also, gene editing resulted in significantly higher NM$ after 20 yr compared with conventional breeding for both breeds. Additionally, the gene editing scenarios of both breeds used a significantly greater number of unique sires compared with either the conventional breeding or baseline scenarios. Overall, our simulations show that, given the current genetic merit of horned and polled dairy sires, the use of conventional breeding methods to decrease the frequency of the HORNED allele will increase inbreeding and slow genetic improvement. Furthermore, this study demonstrates how gene editing could be used to rapidly decrease the frequency of the HORNED allele in US dairy cattle populations while maintaining the rate of genetic gain, constraining inbreeding to acceptable levels, and simultaneously addressing an emerging animal welfare concern.

Comparison of infinitesimal and finite locus models for long-term breeding simulations with direct and maternal effects at the example of honeybees

Stochastic simulation studies of animal breeding have mostly relied on either the infinitesimal genetic model or finite polygenic models. In this study, we investigated the long-term effects of the chosen model on honeybee breeding schemes. We implemented the infinitesimal model, as well as finite locus models, with 200 and 400 gene loci and simulated populations of 300 and 1000 colonies per year over the course of 100 years. The selection was of a directly and maternally influenced trait with maternal heritability of [Formula: see text], direct heritability of [Formula: see text], and a negative correlation between the effects of rmd = - 0.18. Another set of simulations was run with parameters [Formula: see text], [Formula: see text], and rmd = - 0.53. All models showed similar behavior for the first 20 years. Throughout the study, we observed a higher genetic gain in the direct than in the maternal effects and a smaller gain with a stronger negative covariance. In the long-term, however, only the infinitesimal model predicted sustainable linear genetic progress, while the finite locus models showed sublinear behavior and, after 100 years, only reached between 58% and 62% of the mean breeding values in the infinitesimal model. While the infinitesimal model suggested a reduction of genetic variance by 33% to 49% after 100 years, the finite locus models saw a more drastic loss of 76% to 92%. When designing sustainable breeding strategies, one should, therefore, not blindly trust the infinitesimal model as the predictions may be overly optimistic. Instead, the more conservative choice of the finite locus model should be favored.

The impact of genome editing on the introduction of monogenic traits in livestock

Background

Genome editing technologies provide new tools for genetic improvement and have the potential to become the next game changer in animal and plant breeding. The aim of this study was to investigate how genome editing in combination with genomic selection can accelerate the introduction of a monogenic trait in a livestock population as compared to genomic selection alone.

Methods

A breeding population was simulated under genomic selection for a polygenic trait. After reaching Bulmer equilibrium, the selection objective was to increase the allele frequency of a monogenic trait, with or without genome editing, in addition to improving the polygenic trait. Scenarios were compared for time to fixation of the desired allele, selection response for the polygenic trait, and level of inbreeding. The costs, in terms of number of editing procedures, were compared to the benefits of having more animals with the desired phenotype of the monogenic trait. Effects of reduced editing efficiency were investigated.

Results

In a population of 20,000 selection candidates per generation, the total number of edited zygotes needed to reach fixation of the desired allele was 22,118, 7072, or 3912 with, no, moderate, or high selection emphasis on the monogenic trait, respectively. Genome editing resulted in up to four-fold faster fixation of the desired allele when efficiency was 100%, while the loss in long-term selection response for the polygenic trait was up to seven-fold less compared to genomic selection alone. With moderate selection emphasis on the monogenic trait, introduction of genome editing led to a four-fold reduction in the total number of animals showing the undesired phenotype before fixation. However, with a currently realistic editing efficiency of 4%, the number of required editing procedures increased by 72% and loss in selection response increased eight-fold compared to 100% efficiency. With low efficiency, loss in selection response was 29% more compared to genomic selection alone.

Conclusions

Genome editing strongly decreased the time to fixation for a desired allele compared to genomic selection alone. Reduced editing efficiency had a major impact on the number of editing procedures and on the loss in selection response. In addition to ethical and welfare considerations of genome editing, a careful assessment of its technical costs and benefits is required.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0389-7) contains supplementary material, which is available to authorized users.

Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement

Improving breeding has been widely utilized in crop breeding and contributed to yield and quality improvement, yet few researches have been done to analyze genetic architecture underlying breeding improvement comprehensively. Here, we collected genotype and phenotype data of 99 cultivars from the complete pedigree including Huanghuazhan, an elite, high-quality, conventional indica rice that has been grown over 4.5 million hectares in southern China and from which more than 20 excellent cultivars have been derived. We identified 1,313 selective sweeps (SSWs) revealing four stage-specific selection patterns corresponding to improvement preference during 65 years, and 1113 conserved Huanghuazhan traceable blocks (cHTBs) introduced from different donors and conserved in >3 breeding generations were the core genomic regions for superior performance of Huanghuazhan. Based on 151 quantitative trait loci (QTLs) identified for 13 improved traits in the pedigree, we reproduced their improvement process in silico, highlighting improving breeding works well for traits controlled by major/major + minor effect QTLs, but was inefficient for traits controlled by QTLs with complex interactions or explaining low levels of phenotypic variation. These results indicate long-term breeding improvement is efficient to construct superior genetic architecture for elite performance, yet molecular breeding with designed genotype of QTLs can facilitate complex traits improvement.

Economic considerations of breeding for polled dairy cows versus dehorning in the United States

This paper examines the costs and benefits of selecting for polled dairy heifers versus traditional dehorning practices. Stochastic budgets were developed to analyze the expected costs (EC) associated with polled dairy genetics. The economic assessment was expanded beyond on-farm cash costs by incorporating cost and benefit estimates to generate industry-wide discussion, and preliminary economic evaluations, surrounding the public acceptance and attitude toward polled genetics versus dehorning calves. Triangular distributions, commonly used to represent distributions with limited data, were used to represent labor costs for dehorning, the likelihood of treatment of calf, and the cost of veterinary treatment. In total, 10,000 iterations were run using @Risk v 6.0 (Palisade Corp., Newfield, NY). The EC of the 4 traditional dehorning methods evaluated in this study ranged from $6 to $25/head, with a mean EC around $12 to $13/head. The EC of incorporating polled genetics into a breeding program ranged from $0 to $26/head depending on the additional cost, or premium, associated with polled relative to horned genetics. Estimated breakeven premiums associated with polled genetics indicate that, on average, producers could spend up to $5.95/head and $11.90/head more for heterozygous and homozygous polled genetics, respectively, compared with conventional horned genetics (or $2.08 and $4.17/straw of semen at an assumed average conception rate of 35%). Given the parameters outlined, sensitivity to individual farm semen and dehorning costs are likely to swamp these differences. Beyond on-farm costs, industry-wide discussion may be warranted surrounding the public's acceptance and attitude toward polled genetics versus dehorning or disbudding of calves. The value of avoiding dehorning may be larger for the industry, and perhaps some individual farms, than initially suggested if additional value is put on calf comfort and possible worker aversion to dehorning. If public perception of dehorning influences market access, the EC of dehorning may be large but that cost is unknown at present.