The cost-benefit of genomic testing of heifers and using sexed semen in pasture-based dairy herds

Economic benefits of herd genotyping and using sexed semen for pure and beef-on-dairy breeding in dairy herds

The cost benefits of herd genotyping and the benefits of using sexed semen have been affected by recent improvements in sexing technologies, incorporation of direct health traits in the German total merit index for Holstein cattle, deteriorating prices for purebred heifer calves and bull calves, and introduction of herd genotyping programs. Inseminating genetically superior dams with female-sexed Holstein semen increases the mean breeding value of heifer calves and can produce more Holstein heifer calves than are needed for replacement. This provides an opportunity to increase the selection response in health and production traits at the farm level. A deterministic model is introduced that predicts the increase or decrease in net profit when a farmer takes part in a herd genotyping program and follows a certain insemination strategy. The types of semen allocated to cows and heifers may be sexed or unsexed and Holstein or beef breed. Genetically superior heifers and cows are inseminated with female-sexed Holstein semen, intermediate dams with unsexed Holstein semen, and genetically inferior dams with unsexed or male-sexed beef breed semen. In general, participating in a herd genotyping program is beneficial for German Holstein breeders. The optimum proportions of cows and heifers that should be inseminated with a certain type of semen are sensitive to farm-specific peculiarities. A small price difference between crossbred bull calves and crossbred heifer calves often makes the use of male-sexed beef breed semen uneconomic. Under the conditions considered, it was found to be advantageous to inseminate approximately 50% of heifers and 10% of cows with the highest genetic merit with female-sexed Holstein semen. The optimum proportion of cows that should be inseminated with unsexed beef breed semen was found to be approximately 40%. In a herd with a low replacement rate, the selected heifers can exhibit their genetic superiority over a longer period of time, and a larger proportion of cows can be inseminated with beef breed semen. Participation in a herd genotyping program is, therefore, particularly beneficial for herds with low replacement rates.

Developmental Programming of Fertility in Cattle-Is It a Cause for Concern?

Cattle fertility remains sub-optimal despite recent improvements in genetic selection. The extent to which an individual heifer fulfils her genetic potential can be influenced by fetal programming during pregnancy. This paper reviews the evidence that a dam's age, milk yield, health, nutrition and environment during pregnancy may programme permanent structural and physiological modifications in the fetus. These can alter the morphology and body composition of the calf, postnatal growth rates, organ structure, metabolic function, endocrine function and immunity. Potentially important organs which can be affected include the ovaries, liver, pancreas, lungs, spleen and thymus. Insulin/glucose homeostasis, the somatotropic axis and the hypothalamo-pituitary-adrenal axis can all be permanently reprogrammed by the pre-natal environment. These changes may act directly at the level of the ovary to influence fertility, but most actions are indirect. For example, calf health, the timing of puberty, the age and body structure at first calving, and the ability to balance milk production with metabolic health and fertility after calving can all have an impact on reproductive potential. Definitive experiments to quantify the extent to which any of these effects do alter fertility are particularly challenging in cattle, as individual animals and their management are both very variable and lifetime fertility takes many years to assess. Nevertheless, the evidence is compelling that the fertility of some animals is compromised by events happening before they are born. Calf phenotype at birth and their conception data as a nulliparous heifer should therefore both be assessed to avoid such animals being used as herd replacements.

Association between a genetic index for lameness resistance and the incidence of claw horn lesions in Holstein cows

BACKGROUND

This study aimed to determine the association between the lameness advantage genetic index and four outcomes: sole haemorrhage (SH), sole ulcers (SU), white line lesions (WL), and lameness during mobility scoring.

METHODS

We enrolled 2352 Holstein cows from four predominantly housed dairy herds in the UK. Cows were mobility scored and foot lesions recorded at four time points from before calving to late lactation. Cows were genotyped and genetic indexes were assigned to each cow following national genetic evaluations. Lameness records and genetic indexes were matched for 2107 cows. Four separate multivariable logistic regression models, which included farm and parity as covariables, were used to quantify the association between the lameness advantage index and whether animals were affected by SH, SU, WL, or lameness.

RESULTS

The odds ratios (95% confidence intervals) for one-point increases in the lameness advantage index were 0.79 (0.72-0.86), 0.68 (0.59-0.78), 0.94 (0.84-1.04), and 0.82 (0.74-0.91) for SH, SU, WL, and lameness, respectively. The same trends were present when the sire's lameness advantage index was evaluated in place of the animal's own, although the strength of this association was generally weaker.

CONCLUSION

The lameness advantage index is associated with SH, SU, and lameness, therefore selection on the lameness advantage index could be considered in herds aiming to reduce lameness. Where genomic testing of heifers is not conducted, sire lameness advantage index may still be effective to reduce SH and SU incidence.

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.

Genetic consequences of terminal crossbreeding, genomic test, sexed semen, and beef semen in dairy herds

The development of breeding tools, such as genomic selection and sexed semen, has progressed rapidly in dairy cattle breeding during the past decades. In combination with beef semen, these tools are adopted increasingly at herd level. Dairy crossbreeding is emerging, but the economic and genetic consequences of combining it with the other breeding tools are relatively unknown. We investigated 5 different sexed semen schemes where 0, 50, and 90% of the heifers; 50% of the heifers + 25% of the first-parity cows; and 90% of the heifers + 45% of the first-parity cows were bred to sexed semen. The 5 schemes were combined in scenarios managing pure-breeding or terminal crossbreeding, including genomic testing of all newborn heifers or no testing, and keeping Swedish Red or Swedish Holstein as an initial breed. Thus, 40 scenarios were simulated, combining 2 stochastic simulation models: SimHerd Crossbred (operational returns) and ADAM (genetic returns). The sum of operational and genetic returns equaled the total economic return. Beef semen was used in all scenarios to limit the surplus of replacement heifers. Terminal crossbreeding implied having a nucleus of purebred females, where some were inseminated with semen of the opposite breed. The F₁ crossbred females were inseminated with beef semen. The reproductive performance played a role in improving the benefit of any of the tools. The most considerable total economic returns were achieved when all 4 breeding tools were combined. For Swedish Holstein, the highest total economic return compared with a pure-breeding scenario, without sexed semen and genomic test, was achieved when 90% sexed semen was used in heifers and 45% sexed semen was used for first-parity cows combined with genomic test and crossbreeding (+€58, 33% crossbreds in the herd). The highest total economic return for Swedish Red compared with a pure-breeding scenario, without sexed semen and genomic test, was achieved when 90% sexed semen was used in heifers combined with genomic test and crossbreeding (+€94, 46% crossbreds in the herd). Terminal crossbreeding resulted in lower genetic returns across the herd compared with the corresponding pure-breeding scenarios but was compensated by a higher operational return.

Effects of herd fertility on the economics of sexed semen in a high-producing, pasture-based dairy production system

This study used a stochastic simulation model to estimate the potential economic benefit of using sexed semen in heifers only and in heifers and lactating cows in a high-producing, pasture-based system under 3 fertility scenarios. Three breeding strategies were modeled: (1) only heifers inseminated with sexed semen and cows inseminated with conventional unsexed semen (SSH); (2) both heifers and cows inseminated with sexed semen (SSHC); and (3) a reference scenario in which all females were inseminated with conventional, unsexed semen (CONV). Each scenario was evaluated under 3 herd fertility states: high (HF), medium (MF), and low (LF), which, under the reference scenario, corresponded to herd replacement rates of 21, 25, and 31%, respectively. The model estimated the economic profit, including the net present value of the genetic gain from selection intensity. The economic return from adoption of sexed semen strategies declined, with reduced levels of baseline herd fertility turning negative in the LF state. The mean (±SD) sexed semen advantage (SSA) per cow for HF-SSH, MF-SSH, and LF-SSH scenarios were €30.61 ± 8.98, €27.45 ± 7.19, and €14.69 ± 11.06, respectively. However, the SSA per cow for HF-SSHC, MF-SSHC, and LF-SSHC scenarios were €49.14 ± 15.43, €18.46 ± 30.08, and -€19.30 ± 57.11. The range in economic profit for SSA for SSH was most sensitive to calf prices in HF-SSH and the pregnancy rate of sexed semen as a percentage of conventional unsorted semen in MF-SSH and LF-SSH. The range in economic profit for SSA for SSHC scenarios was most sensitive to the pregnancy rate of sexed semen as a percentage of conventional unsorted semen in HF-SSHC, MF-SSHC, and LF-SSHC. This study highlights the effect of baseline herd fertility state on the financial advantage of adopting sexed semen in a pasture-based dairy production system.

Demonstrating the value of herd improvement in the Australian dairy industry

Herd improvement has been occurring since the domestication of livestock, although the tools and technologies that support it have changed dramatically. The Australian dairy industry tracks herd improvement through a range of approaches, including routine monitoring of genetic trends and farmer usage of the various tools and technologies. However, a less structured approach has been taken to valuing the realised and potential impacts of herd improvement. The present paper aims to demonstrate the value of herd improvement, while exploring considerations for undertaking such a valuation. Attractive value propositions differ among and within dairy stakeholder groups. While broad-scale valuations of genetic trends and industry progress are valued by government and industry, such valuations do not resonate with farmers. The cumulative nature of genetic gain and compounding factor of genetic lag means that long timeframes are needed to fully illustrate the value of genetic improvement. However, such propositions do not align with decision-making timeframes of most farming businesses. Value propositions that resonate with farmers and can lead to increased uptake and confidence in herd improvement tools include smaller scale cost–benefit analyses and on-farm case studies developed in consultation with industry, including farmers. Non-monetary assessments of value, such as risk and environmental footprint, are important to some audiences. When additionality, that is, the use of data on multiple occasions, makes quantifying the value of the data hard, qualitative assessments of value can be helpful. This is particularly true for herd recording data. Demonstrating the value of herd improvement to the dairy industry, or any livestock sector, requires a multi-faceted approach that extends beyond monetary worth. No single number can effectively capture the full value of herd improvement in a way that resonates with all farmers, let alone dairy stakeholders. Extending current monitoring of herd improvement to include regular illustrations of the value of the tools that underpin herd improvement is important for fostering uptake of new or improved tools as they are released to industry.

Transfer of a single embryo versus drainage of subordinate follicles to prevent twin pregnancies in dairy cows. Why not both?

In this study, we present two proposed approaches to prevent twin pregnancies in dairy cattle: 1) single, in vitro-produced embryonic transfer into a recipient cow or 2) subordinate follicle drainage at the time of insemination. Both procedures lead to improved embryonic survival. As the use of sexed semen generates herd replacements and additional heifers, we propose the transfer of a single female cattle embryo into cows that are not suitable for producing replacements, and follicular drainage in lactating cows with genetic merit. This should eliminate economic losses associated with twin pregnancies and increase cattle output of the herd.

On-farm net benefit of genotyping candidate female replacement cattle and sheep

The net benefit from investing in any technology is a function of the cost of implementation and the expected return in revenue. The objective of the present study was to quantify, using deterministic equations, the net monetary benefit from investing in genotyping of commercial females. Three case studies were presented reflecting dairy cows, beef cows and ewes based on Irish population parameters; sensitivity analyses were also performed. Parameters considered in the sensitivity analyses included the accuracy of genomic evaluations, replacement rate, proportion of female selection candidates retained as replacements, the cost of genotyping, the sire parentage error rate and the age of the female when it first gave birth. Results were presented as an annualised monetary net benefit over the lifetime of an individual, after discounting for the timing of expressions. In the base scenarios, the net benefit was greatest for dairy, followed by beef and then sheep. The net benefit improved as the reliability of the genomic evaluations improved and, in fact, a negative net benefit of genotyping was less frequent when the reliability of the genomic evaluations was high. The impact of a 10% point increase in genomic reliability was, however, greatest in sheep, followed by beef and then dairy. The net benefit of genotyping female selection candidates reduced as replacement rate increased. As genotyping costs increased, the net benefit reduced irrespective of the percentage of selection candidates kept, the replacement rate or even the population considered. Nonetheless, the association between the genotyping cost and the net benefit of genotyping differed by the percentage of selection candidates kept. Across all replacement rates evaluated, retaining 25% of the selection candidates resulted in the greatest net benefit when genotyping cost was low but the lowest net benefit when genotyping cost was high. Genotyping breakeven cost was non-linearly associated with the percentage of selection candidates retained, reaching a maximum when 50% of selection candidates were retained, irrespective of replacement rate, genomic reliability or the population. The genotyping breakeven cost was also non-linearly associated with replacement rate. The approaches outlined within provide the back-end framework for a decision support tool to quantify the net benefit of genotyping, once parameterised by the relevant population metrics.

Use of sexed semen and female genotyping affects genetic and economic outcomes of Montbéliarde dairy herds depending on the farming system considered

Genomic evaluation of cows and the use of sexed semen have recently provided opportunities for commercial dairy farmers to accelerate genetic progress at the herd level by increasing both selection accuracy and selection intensity. Because implementing genomic tests or using sexed semen generate extra costs, a higher investment capacity of the farm is required. In this study, we compared the effect of female genotyping alone or combined with the use of sexed semen on genetic and economic performance of the herds. Three typical Montbéliarde herds with different farming systems were considered: a 77-cow herd producing milk at a high price sold to make cheese with a protected designation of origin, a 60-cow herd producing organic milk at a medium price sold for dairy, and a 120-cow herd producing standard milk at a lower price sold for dairy. Eight alternative scenarios were simulated over a 10-yr period for each herd, with combinations of the following: use (or not) of dairy sexed semen, use (or not) of beef breed semen, use (or not) of female genotyping at 15 d of age. A mechanistic, stochastic, and dynamic model was used to mimic the farmer's daily decisions and the individual cow's biology. Heifers (80%) and first-lactation cows (30%) that ranked highest on the French total merit index (France's national dairy index) were inseminated with sexed semen to ensure replacement and to maximize genetic gain, when sexed semen was used. During the 10 yr of simulation, scenarios that included sexed semen (whether female genotyping was used or not) gained, on average, one extra year of overall genetic gain over scenarios that did not include sexed semen. During the same period, scenarios that used female genotyping (whether sexed semen was used or not) gained, on average, 5 mo of overall genetic gain over scenarios using parent average only. The highest gains in net margin were always obtained when combining use of sexed semen with terminal crossbreeding. Maximum genotyping prices under which routine female genotyping is economically valuable (breakeven prices of genotyping) were under €37. Maximum genotyping prices, such that the female genotyping costs are refunded within 10 yr of investment (investor genotyping price), were under €26. However, they would be higher over a longer period of use because genetic gain is cumulative. Because genotyping price is expected to decrease in the future, female genotyping will be worthwhile if combined with the use of sexed semen and beef breed semen.

Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories "Science to Practice," "Discovery Science," and "Infrastructure." New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The updated blueprint that follows describes the vision, current state of the art, the research needed to advance the field, expected deliverables, and partnerships needed for each animal genomics research topic. Accomplishment of the goals described in the blueprint will significantly increase the ability to meet the demands for animal products by an increasing world population within the next decade.