Accounting for selective slaughter over time when estimating breeding values for carcase traits?: A simulation study
Progeny test data used to estimate breeding values (EBVs) of sires for carcase traits may come from measurements taken on animals that have been slaughtered over time based on individual animal market suitability. Confounding between genetic effects and age can result. However, in the current study appropriate adjustment for growth rate resulted in highly accurate sire EBVs for both the slaughtering criteria, namely liveweight, and for a second trait (e.g. a carcase trait) regardless of the genetic correlation between the two traits.
Beef cattle breeding in Australia with genomics: opportunities and needs
Opportunities exist in beef cattle breeding to significantly increase the rates of genetic gain by increasing the accuracy of selection at earlier ages. Currently, selection of young beef bulls incorporates several economically important traits but estimated breeding values for these traits have a large range in accuracies. While there is potential to increase accuracy through increased levels of performance recording, several traits cannot be recorded on the young bull. Increasing the accuracy of these traits is where genomic selection can offer substantial improvements in current rates of genetic gain for beef. The immediate challenge for beef is to increase the genetic variation explained by the genomic predictions for those traits of high economic value that have low accuracies at the time of selection. Currently, the accuracies of genomic predictions are low in beef, compared with those in dairy cattle. This is likely to be due to the relatively low number of animals with genotypes and phenotypes that have been used in developing genomic prediction equations. Improving the accuracy of genomic predictions will require the collection of genotypes and phenotypes on many more animals, with even greater numbers needed for lowly heritable traits, such as female reproduction and other fitness traits. Further challenges exist in beef to have genomic predictions for the large number of important breeds and also for multi-breed populations. Results suggest that single-nucleotide polymorphism (SNP) chips that are denser than 50 000 SNPs in the current use will be required to achieve this goal. For genomic selection to contribute to genetic progress, the information needs to be correctly combined with traditional pedigree and performance data. Several methods have emerged for combining the two sources of data into current genetic evaluation systems; however, challenges exist for the beef industry to implement these effectively. Changes will also be needed to the structure of the breeding sector to allow optimal use of genomic information for the benefit of the industry. Genomic information will need to be cost effective and a major driver of this will be increasing the accuracy of the predictions, which requires the collection of much more phenotypic data than are currently available.
Genetic variation in adaptive traits of cattle in north Australia
Adaptation to environmental stressors is of particular importance for cattle breeders in tropical regions of northern Australia. Various studies have estimated the genetic parameters for adaptive traits measured in northern Australian cattle herds, but most were specific to regions and breeds. The current study assesses adaptability measures of both Brahman and Composite cattle (n=2071) raised in four distinct environments of northern Australia. Heritabilities for tick score, worm egg count, buffalo-fly lesion score, rectal temperature, coat score, flight time, navel score and colour score ranged from 0.12 to 0.70. The heritability of most traits indicated potential to genetically improve these traits in both Composite and Brahman populations.
The effect of age slicing interval on the variance components and data effectiveness for birth and 200 day weights in Angus cattle
In BREEDPLAN analyses, contemporary groups for birth weight and 200d weight are sliced at 45 day intervals to avoid possible inaccuracies in age adjustment, rapid changes in environmental conditions and confounding of sires and seasons biasing the estimated breeding values. However age slicing can have a significant impact on data structure and effectiveness of records. The aim of this study was to re-estimate the variance components and examine the effectiveness of the data for birth and 200day weights from Angus cattle with different contemporary group slicing intervals. The result showed that altering the slicing interval from 15 to 60 days did not have a significant impact on the variance components for birth or 200day weight. However increasing slice interval significantly improved the average effectiveness of the data for both traits. On average the animal record effectiveness increased by 10% and the average total effective progeny records per sire more than doubled. The results suggest that the age slicing interval could be altered from 45 to 60 days to increase the effectiveness of the data available without impacting on the genetic parameters. However altering the contemporary group structure will cause changes to the existing estimated breeding values.
Genome-wide association studies of female reproduction in tropically adapted beef cattle
The genetics of reproduction is poorly understood because the heritabilities of traits currently recorded are low. To elucidate the genetics underlying reproduction in beef cattle, we performed a genome-wide association study using the bovine SNP50 chip in 2 tropically adapted beef cattle breeds, Brahman and Tropical Composite. Here we present the results for 3 female reproduction traits: 1) age at puberty, defined as age in days at first observed corpus luteum (CL) after frequent ovarian ultrasound scans (AGECL); 2) the postpartum anestrous interval, measured as the number of days from calving to first ovulation postpartum (first rebreeding interval, PPAI); and 3) the occurrence of the first postpartum ovulation before weaning in the first rebreeding period (PW), defined from PPAI. In addition, correlated traits such as BW, height, serum IGF1 concentration, condition score, and fatness were also examined. In the Brahman and Tropical Composite cattle, 169 [false positive rate (FPR) = 0.262] and 84 (FPR = 0.581) SNP, respectively, were significant (P < 0.001) for AGECL. In Brahman, 41% of these significant markers mapped to a single chromosomal region on BTA14. In Tropical Composites, 16% of these significant markers were located on BTA5. For PPAI, 66 (FPR = 0.67) and 113 (FPR = 0.432) SNP were significant (P < 0.001) in Brahman and Tropical Composite, respectively, whereas for PW, 68 (FPR = 0.64) and 113 (FPR = 0.432) SNP were significant (P < 0.01). In Tropical Composites, the largest concentration of PPAI markers were located on BTA5 [19% (PPAI) and 23% (PW)], and BTA16 [17% (PPAI) and 18% (PW)]. In Brahman cattle, the largest concentration of markers for postpartum anestrus was located on BTA3 (14% for PPAI and PW) and BTA14 (17% PPAI). Very few of the significant markers for female reproduction traits for the Brahman and Tropical Composite breeds were located in the same chromosomal regions. However, fatness and BW traits as well as serum IGF1 concentration were found to be associated with similar genome regions within and between breeds. Clusters of SNP associated with multiple traits were located on BTA14 in Brahman and BTA5 in Tropical Composites.
Opportunities for selection to improve steer and cow productivity in northern Australia
This thesis analysed carcass records from 2180 tropically adapted, steers (986 Brahman (BRAH) and 1194 Tropical Composite (TCOMP)) describing weight, eye muscle area, P8 and 12/13th rib fat depth, percent intramuscular fat and retail beef yield, with tenderness assessed as shear force. All steers were feedlot finished with a subset (680 BRAH and 783 TCOMP) recorded for individual feed intake. Female reproductive performance in the half-sib sisters of these steers (1007 BRAH and 1108 TCOMP) was evaluated as outcomes of their first (Mating 1: when females averaged 27 months of age) and second (Mating 2) annual matings, and averaged over up to 6 matings (termed 'lifetime' reproduction traits). Heifer and cow weight, eye muscle area, P8 and 12/13th rib fat depth, body condition score and hip height were recorded at 18 months of age, immediately prior to first calving and at Mating 2. The maternal genetic component of weaning weight (Maternal WWT) was estimated based on weaning weight records available for these steers and females and the progeny of females (N = 12528).
Genetic analysis of feet and leg traits of Australian Angus cattle using linear and threshold models
The advantages of using a univariate threshold animal model (TAM) over the conventional linear animal model (AM) in the development of a genetic evaluation system for feet and leg traits of Angus cattle were explored. The traits were scored on a scale of 1-9 with scores 5 and 6 being the most desirable. The genetic parameters and estimated breeding values for front feet angle (FA), rear feet angle (RA), front feet claw set (FC), rear feet claw set (RC), rear leg hind view (RH) and rear leg side view (RS) were compared from AM and TAM. In order to predict breeding values to identify the animals with intermediate optimum, the scores were categorised to form three groups to differentiate the desirable group (5-6) from the other two groups with less desirable feet and leg appearances (1-4 and 7-9). The AM and TAM were used to estimate genetic parameters for the grouped data as well as the original score data. A TAM using the group data was used to predict the probability and breeding value for the desirable intermediate group. For the original score data, estimated heritabilities on the underlying scale, using TAM, were 0.50, 0.46, 0.35, 0.44, 0.32 and 0.22 for FA, FC, RA, RC, RH and RS, respectively, and were 0.01-0.18 higher than the heritabilities estimated using AM. Genetic correlation between the six traits using a bivariate TAM with all scores ranged from 0.02 to 0.50 with front and rear angles had the highest genetic correlation at 0.50. For all six traits, proportion in the intermediate desirable group was higher than the other two groups combined. The low annual genetic change observed for all six traits over the 10 years of data recording reflected the lack of directional selection to improve the traits in Angus cattle. For genetic evaluation of feet and leg traits with an intermediate optimum, TAM is a preferred method for estimating genetic parameters and predicting breeding values for the desirable category. The TAM has now been implemented for regular estimated breeding value analysis of feet and leg traits of Angus cattle.
Genetic trends in Australian beef cattle: Making real progress
Significant genetic change has occurred in many domestic livestock species and is evident in most Australian beef breeds across a range of economically important traits and selection indexes. Large variation in rates of gain is apparent across breeds, and even larger differences between herds within breeds. Reasons for these differences are examined and results show the selection differential of sires was the key factor explaining the across herd differences in genetic progress for all breeds. Validating genetic trends is important to ensure change is reported accurately. Evidence is presented that show the estimated genetic trends are real and key assumptions used in genetic evaluations are examined, in particular the accuracy of the assumed genetic parameters. The paper identifies opportunities which exist to increase rates of gain across the beef industry, including improvements to the genetic evaluation system, increased levels of performance recording, clearer breeding objectives, and adoption of new technologies.
Selection to reduce residual feed intake in pigs produces a correlated response in juvenile insulin-like growth factor-I concentration
Data from a selection experiment for residual feed intake (RFI) were used to estimate genetic correlations between measures of efficiency and performance traits with juvenile IGF-I, and to demonstrate direct and correlated responses to selection. The heritability of IGF-I was 0.28 ± 0.06 and genetic correlations of IGF-I with feed intake (0.26 ± 0.17), backfat (0.52 ± 0.11), and feed conversion ratio (0.78 ± 0.14) were moderate to large. The estimated and realized genetic correlations between RFI and IGF-I were 0.63 ± 0.15 and 0.84. In contrast, genetic correlations between IGF-I and lifetime or test period growth did not differ (P > 0.05) significantly from zero (0.06 ± 0.14 and –0.19 ± 0.14). Selection for decreased RFI produced a direct response in RFI, as expected, and was accompanied by downward correlated responses in ADFI, juvenile IGF-I, backfat, and growth traits, listed in order of decreasing relative magnitude, and an increased loin muscle area. The correlated response in IGF-I to selection on RFI demonstrates that this physiological measure is genetically associated with efficiency, and is thus useful as an early information source to estimate genetic merit for efficiency before performance testing. Decreased juvenile IGF-I is associated with leaner, more efficient animals.
Development of a genetic evaluation system for structural soundness traits in Angus cattle
Three options comprising a generalized threshold model and two linear animal models were explored to predict and express breeding values for structural soundness traits in Angus cattle, using front feet angle as an example trait. Front feet angle scores (scored on a 1 to 9 scale, with 5 being the most desirable score) from 2926 Angus cattle under three years of age were used. Estimated breeding values (EBVs) predicted from a generalized threshold model by grouping animals with scores 1 to 4 as category 1, representing steep foot angle (%STE), category 2 with score of 5, representing desirable score (%DESI) and category 3 with scores 6 to 9, representing shallow foot angle (%SHA). These were compared with EBVs from a conventional linear animal model with the original scores of 1 to 9 or after assigning scores according to Snell's procedure to differentiate desirable scores. EBVs obtained as %DESI was identified as an appropriate way to express EBVs in a manner that would allow breeders to identify differences in Angus cattle for expected progeny structural soundness.