Genomic selection in beef cattle creates additional opportunities for embryo technologies to meet industry needs
The use of genotype information to improve the predictability of Expected Progeny Difference was first implemented in American Angus cattle in 2009 and has now grown to where over 50% of all registered calves are genotyped. Animals with only a genotype now have genetic prediction accuracy equivalent to eight or more progeny records across all traits. Reproductive technologies have also been widely adopted with approximately 50% of all calves born being the result of artificial insemination. Non-surgical embryo transfer started increasing in the mid 1990s with just over 10% of calves born being the result of embryo transfer since 2005. The number of embryos created with in vitro technologies has risen sharply since 2015 and now accounts for close to 30% of all ET calves. Genomics has enabled embryo technologies to be more impactful, as females can be selected with greater accuracy and sires can be used at earlier ages with moderate accuracy. Large numbers of females genotyped each year also increases the number of selection candidates, increasing the selection intensity. Genomics, combined with increased recording, also provides more information on females. This increases the spread in the estimated index values of current dams, identifying more elite dams for selection as embryo donors. The greater scope of female selection also contributes to better inbreeding management. Commercial animals genotyped could be targeted for oocyte harvesting at slaughter, creating opportunities for low cost high value beef embryos to be used in the beef on dairy segment of the industry.
Remodelling the genetic evaluation of NFI in beef cattle - Part 1: Developing an equivalent genetic model
Net feed intake (NFI) is the residual portion of daily feed intake (DFI) not explained by growth or maintenance requirements. The NFI phenotype (NFIp) is based on a 70-day test period where DFI and fortnightly weights (to calculate average daily gain (ADG) and maintenance as metabolic mid-weight (MMWT)) are measured. Recording NFIp is costly, and shortening the test length would be advantageous. However, research has shown that ADG cannot be accurately measured from a shortened test. Genetic NFI EBVs (NFIg) were calculated using DFI EBV adjusted for ADG and MMWT EBV and were shown to have a Pearson correlation of 0.99 with the NFIp EBV from 3,088 Angus steers. The regression slope between NFIg and NFIp EBVs was 1.14. Alternative NFIg models where growth and maintenance requirements were obtained from BREEDPLAN live weight traits instead of live weights recorded in the test period, demonstrated high Pearson correlations (r=0.87 to 0.93) and regression slopes between 0.63 and 0.97 with NFIp EBVs. Results suggest that genetic NFI EBVs can be obtained, with growth and maintenance requirements being determined from BREEDPLAN live weight traits. This provides the opportunity to determine if the length of the test to measure DFI can be shortened, reducing the cost of recording NFI per animal.
Assessing the value of metafounders for genomic prediction in Australian Simmental beef cattle
The “metafounders” framework is used to augment relationship matrixes to accommodate genetic structure in founder populations, and can be estimated from genotypes, making it useful to align pedigree and genomic relationships in single-step genomic analyses. This paper aimed to assess the value of metafounders in the genomic evaluation of beef traits in Australian Simmental cattle, and in particular the possibility of collapsing genetic groupings based on metafounder similarity. Estimated breeding values from metafounder models with different groupings had similar predictive ability across 12 beef traits, while models with higher weighting on genomic relative to pedigree information tended to perform better.
Breeding for future social license for beef production
Examples from Angus cattle provide evidence of positive genetic trends for production traits and, with increasing frequency, for traits more directly related to welfare outcomes. Genetic improvement programs are optimized when clear market signals linked to the commercial sector are in place. When welfare related traits like foot structure were added to profit driven selection indexes, recording levels increased and the accuracy of the evaluation for these traits improved. It is postulated that effective recording and genetic selection for improved welfare should be of interest to consumers. When faced with an informed choice, consumers should be more attracted to beef products which are sourced from production systems where through selection, welfare issues such as dystocia, lameness and reduced longevity are actively minimized. Beef breeders should be making efforts now to ensure a future 'social license' for their products by preparing for such economic feedback in the future.
Remodelling the genetic evaluation of NFI in beef cattle - Part 2: Shortening the length of the feed intake test
BREEDPLAN net feed intake (NFI) EBV is derived from a phenotypic regression based on a 70-day feed intake test. Genetic NFI (NFIg) EBVs have been proposed as an alternative EBV and this recent development may also allow for a shortened feed intake test period. This study used feed intake records of 3,088 Angus steers from the full 70-day test and compared them to daily feed intake (DFI) from shortened test periods. Results showed DFI from shortened test periods had similar means but increased phenotypic variation. Phenotypic correlation with DFI from the full test period decreased as the test period decreased in weekly intervals and ranged between 0.75 and 0.99. NFIg EBVs were predicted using DFI from different length tests. The mean of all NFIg EBVs was close to zero, but the EBV standard deviation increased as the test period decreased. Pearson correlations between NFIg EBVs from a full test period and reduced test periods ranged between 0.73 and 0.99, the regression slope of NFIg from reduced test periods on NFIg from the full test period ranged between 0.73 and 0.95, and the bias ranged between 0.00 and 0.02. These results indicate that as the test period decreases, the spread of EBVs increases, resulting in extreme animals having overestimated NFIg EBVs. A shortened DFI test period could be used to estimate NFIg EBVs.
Opportunities for utilising DNA-based technologies to enhance traceability and profitability in the Australian Red Meat Industry
The potential role of genomics to further improve traceability levels in the red meat industry was investigated, as DNA-based technologies offer unambiguous identification with a range of auxiliary benefits. Modelling indicated that genotyping the entire national beef herd for traceability is unlikely to compensate for the additional costs involved. However, potential additional benefits (faster genetic gain and better management decisions) make several implementation models appear to be highly attractive. Genotyping the national sheep flock is impractical, but the cost of using DNA judiciously to augment NLIS could be quite cost effective.
Perceptions, concerns and experiences around traceability, DNA technologies, costs and willingness to pay were explored through industry consultations. Application of genomic technology for traceability alone was not generally seen as attractive, but the ancillary benefits that accompany lifetime traceability would make the value proposition more attractive.
There are instances of DNA already being used to augment traceability and there is a strong argument for taking a proactive approach to coordinating its wider use. The longer the delay, the greater the costs and difficulties arising from fragmentation. A program of work with a series of stop/go decision points is proposed, to be coordinated and overseen by an appropriately-qualified steering group.
Live weight and body condition score of mixed-aged beef breeding cows on commercial hill country farms in New Zealand
Extensive farming systems require beef cows to cope with varying environmental conditions while repeatedly producing calves. Cows use body energy reserves as a buffer in times of feed shortage and replenish reserves under a feed surplus. The aims of the research were to (1) quantify live weight (LW) and body condition score (BCS) fluctuations among farms, years and over the production cycle (mating, weaning and calving) and to (2) quantify the relationship between LW and BCS at mating, weaning and calving, for cows of different hip heights. A total of 7,649 individual cow records from nine commercial New Zealand farms with information on LW and BCS (1–10 scale, 1 = emaciated and 10 = obese) were analysed. Analyses revealed significant (P < 0.001) within-year variation in mean LW (32.4–77.2 kg) and BCS (0.4–1.8 scores) profiles among farms, but profiles were not consistent from year to year. There was a quadratic relationship (P < 0.001) between LW and BCS, such that one unit change in BCS corresponded to 15.1 kg LW increase at BCS 4–5 compared to 41.1 kg LW increase at BCS 8–9 at mating. This relationship was similar, irrespective of hip height.
A new tool to select Angus bulls to breed to dairy cows
Widespread use of sexed semen among other factors has resulted in a dramatic increase in dairy cows being mated to beef bulls. Economic selection indexes were developed to identify the best Angus bulls, a predominant breed in this market, to use on Holstein and Jersey cows. Through interviews and site visits with key participants in the dairy beef supply chain, production and economic parameters were sourced to inform the modification of the standard American Angus terminal sire index $Beef. $Angus-on-Holstein Value ($AxH) and $Angus-on-Jersey Value ($AxJ) were developed and although highly correlated to each other (0.96), were considered to rank bulls different enough, especially at the top end, that both were needed. Generally, the dairy indexes identify bulls with the best $Beef but avoid three particular traits that are problematic in the dairy industry, with non-linear emphasis. Calving ease had relatively lower emphasis with a similar penalty in both the $AxH and $AxJ indexes , where muscling was heavily weighted with greatest emphasis in $AxJ and a penalty for excessive yearling height EPD was implemented in $AxH in an effort to reduce excessively long carcasses in that cross. These new indexes provide dairy farmers and players in the supply chain through to slaughter a tool to select Angus bulls to produce calves that are better suited to the requirements of this unique sector.