D. J. Johnston

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.

Days to calving in Angus cattle: Genetic and environmental effects, and covariances with other traits

Abstract Field data from Angus herds in Australia were used to examine systematic effects influencing days to calving (DC) and to estimate genetic correlations between DC and other traits. Days to calving was computed as the interval in days between the first joining date each year for a cow under paddock mating and subsequent calving. Non-calvers received a predicted DC record. Herd, year-month of joining, service sire, previous joining season and age at joining significantly influenced DC. Lactation status of older cows did not affect DC. Calving difficulty in first calf heifers had no observed effect on their subsequent DC record. Alternative methods for allocating a predicted or ‘penalty’ DC record for non-calvers were investigated. Estimates of covariances among DC records from different parities, and between DC and calving success and weight traits were obtained by Restricted Maximum Likelihood, using a derivative-free algorithm. Very high genetic correlations among repeat DC records ( r g = 0.85) and between DC and calving success ( r g = −0.97) were observed. Genetic correlations between early weight traits and DC were positive and low, but not significantly different from zero.

Genetics of heifer puberty in two tropical beef genotypes in northern Australia and associations with heifer- and steer-production traits

A total of 2115 heifers from two tropical genotypes (1007 Brahman and 1108 Tropical Composite) raised in four locations in northern Australia were ovarian-scanned every 4–6 weeks to determine the age at the first-observed corpus luteum (CL) and this was used to define the age at puberty for each heifer. Other traits recorded at each time of ovarian scanning were liveweight, fat depths and body condition score. Reproductive tract size was measured close to the start of the first joining period. Results showed significant effects of location and birth month on the age at first CL and associated puberty traits. Genotypes did not differ significantly for the age or weight at first CL; however, Brahman were fatter at first CL and had a small reproductive tract size compared with that of Tropical Composite. Genetic analyses estimated the age at first CL to be moderately to highly heritable for Brahman (0.57) and Tropical Composite (0.52). The associated traits were also moderately heritable, except for reproductive tract size in Brahmans (0.03) and for Tropical Composite, the presence of an observed CL on the scanning day closest to the start of joining (0.07). Genetic correlations among puberty traits were mostly moderate to high and generally larger in magnitude for Brahman than for Tropical Composite. Genetic correlations between the age at CL and heifer- and steer-production traits showed important genotype differences. For Tropical Composite, the age at CL was negatively correlated with the heifer growth rate in their first postweaning wet season (–0.40) and carcass marbling score (–0.49), but was positively correlated with carcass P8 fat depth (0.43). For Brahman, the age at CL was moderately negatively genetically correlated with heifer measures of bodyweight, fatness, body condition score and IGF-I, in both their first postweaning wet and second dry seasons, but was positively correlated with the dry-season growth rate. For Brahman, genetic correlations between the age at CL and steer traits showed possible antagonisms with feedlot residual feed intake (–0.60) and meat colour (0.73). Selection can be used to change the heifer age at puberty in both genotypes, with few major antagonisms with steer- and heifer-production traits.

Genetic evaluation for the beef industry in Australia

Genetic evaluation for beef cattle in Australia has been performed using an animal model with best linear unbiased prediction since 1984. The evaluation procedures have evolved from simple to more complex models and from few to a large number of traits, including traits for reproduction, growth and carcass characteristics. This paper describes in detail the current beef cattle genetic evaluation system ‘BREEDPLAN’ used for the Australian beef cattle industry, the traits analysed and underlying models, and presents a short overview of the challenges and planned developments of coming years.

Genetic and phenotypic relationships between insulin-like growth factor-I (IGF-I) and net feed intake, fat, and growth traits in Angus beef cattle

Insulin-like growth factor-I (IGF-I) concentration measured in the blood plasma of 6520 seedstock Angus beef cattle (3622 bulls and 2898 heifers) from eastern Australia between 2002 and 2004 was used to estimate the heritability of IGF-I and phenotypic and genetic correlations with net feed intake (NFI) and other production traits. The average concentration of IGF-I was 314 ng/mL measured at the average age of 242 days. A moderate heritability of 0.35 was estimated for IGF-I. IGF-I was further defined as being measured either at, or prior to, weaning (average age of 201 days) or post-weaning (average age 310 days). The genetic correlation between IGF-I recorded at the different ages was 1.0 ± 0.04. IGF-I and NFI were found to have a genetic correlation of 0.41 ± 0.21. IGF-I had positive genetic correlations of 0.22 ± 0.14, 0.19 ± 0.14, and 0.26 ± 0.15 with ultrasound-scanned subcutaneous fat depth at the rump (P8) and 12/13th rib (RIB) sites and intramuscular fat % (IMF), respectively. Corresponding phenotypic correlations were 0.14, 0.13, and 0.12, respectively, for P8, RIB, and IMF. IGF-I had low to moderate negative genetic correlations with growth traits. Direct genetic correlations for IGF-I of –0.22 ± 0.08, –0.17 ± 0.09 and –0.10 ± 0.14 were estimated with birth (BWT), 200-day (WT200), and 400-day (WT400) weights, respectively. Genetic correlations between the direct component of IGF-I and maternal components of BWT and WT200 were 0.15 ± 0.13 and 0.31 ± 0.11, respectively. Phenotypic correlations of the direct component of IGF-I with the direct components of BWT, WT200, and WT400 were –0.10, 0.06, and 0.16, respectively. Ultrasound-scanned eye muscle area (EMA) and IGF-I had genetic and phenotypic correlations of –0.22 ± 0.15 and 0.13, respectively. This study showed that IGF-I is heritable and genetically correlated with important production traits. The genetic correlations indicate that selection for lower IGF-I concentrations would result in cattle that have lower NFI (i.e. more feed efficient), are leaner, with increased growth, and possibly decreased maternal weaning weight.

Quantitative and molecular genetic influences on properties of beef : a review

The scientific literature is reviewed to identify quantitative and molecular genetic influences on quantity and quality of beef. Genetic variation between breeds is of similar magnitude to genetic variation within breeds for many economically important traits. Differences between breeds are significant and large for most carcass and beef quality attributes, including beef tenderness, although differences for sensory juiciness and flavour are of little practical importance. For traits such as beef tenderness, between-breed differences may be more easily exploited than within-breed differences, because exceptional breeds are easier to identify than exceptional animals. Effects of heterosis on carcass and beef quality attributes are relatively small (3% or less), with most effects mediated through heterotic effects on weight. Carcass composition traits (e.g. carcass weight, fat thickness and marbling) are moderately to highly heritable. Most estimates of retail beef yield percentage are highly heritable, offering good potential for within-breed selection for the trait, although a moderate to strong antagonistic relationship exists between yield and marbling. This relationship needs to be considered in within-breed selection programs for yield percentage. Early estimates of heritability of objective measures of beef tenderness (Warner Bratzler shear force values) indicated tenderness was moderately to highly heritable. Recent estimates using larger numbers of carcasses and more discriminatory methods of analysis indicate that beef tenderness is lowly heritable in Bos taurus breeds and moderately heritable inBos indicus and Bos indicus-derived breeds. Within breeds, measures of 24-h calpastatin activity are genetically strongly correlated with shear force values but are more heritable. However, phenotypic correlations between shear force values and 24-h calpastatin activities are low. There are also inconsistencies in relationships between these measurements across breeds. Low correlations between tenderness in different muscles, low to moderate heritabilities and inconsistent variation within- and between-breeds for traits such as 24-h calpastatin activity suggest that genetic improvement in beef tenderness may be difficult. The possibility exists that significant mitochondrial genetic effects occur for some carcass and beef quality attributes. A major gene for muscular hypertrophy in cattle significantly affects carcass and beef quality characteristics. Genome-wide screening of DNA markers indicates a number of putative Quantitative Trait Loci (QTL) associated with carcass and meat quality characteristics. Published data for these QTL are summarised. Strategies to combine quantitative and molecular genetic information to maximise genetic progress are discussed.

Genetics of adaptive traits in heifers and their relationship to growth, pubertal and carcass traits in two tropical beef cattle genotypes.

Genetic analyses of tropical adaptive traits were conducted for two tropically adapted genotypes, Brahman (BRAH) and Tropical Composite (TCOMP). Traits included tick scores (TICK), faecal egg counts (EPG), buffalo fly-lesion scores (FLY), rectal temperatures under hot conditions (TEMP), coat scores (COAT), coat colour on a light to dark scale (COLOUR), navel scores (NAVEL) and temperament measured as flight time (FT). The data comprised adaptive measures recorded at specific times on 2071 heifers comprising 966 BRAH and 1105 TCOMP. The genetic correlations of these adaptive traits with heifer growth, scanned carcass, pubertal measures and steer growth and carcass traits were estimated. BRAH recorded significantly (P 50%). In general, phenotypic correlations between these adaptive traits were low and genetic correlations were non-significant, implying trait independence. Genetic correlations between EPG and weight traits (0.29 to 0.44) indicated a positive relationship, implying no deleterious effect of worms on the growth at a genetic level, especially in TCOMP. The negative genetic correlations between COAT and body-condition score across genotypes (–0.33 to –0.48) indicated genetic advantage of sleek coats in tropics. A positive genetic correlation between COAT and the age at the first-observed corpus luteum (0.73) in BRAH indicated that BRAH with sleeker coats were genetically early maturing. Further, sleeker coats were genetically indicative of lower weights and lower fat cover at puberty in BRAH. The scanned fat measures at rump and rib sites for feedlot steers showed strong genetic correlation (0.50–0.58) with heifer TEMP, indicating genetically fatter animals had genetically lower heat tolerance. In BRAH, a positive genetic association between heifer COLOUR and scanned fat measures in steers (0.50–0.54) implied increased fatness in genetically darker animals. Further, in BRAH, a strong negative genetic correlation (–0.97) was observed between steer retail beef yield and heifer TEMP, indicating a favourable genetic association. In general, genetic correlations between adaptive traits and other economic traits were genotype specific. Further, it can be concluded that selection for productive and pubertal traits in tropical beef cattle genotypes would not adversely affect their tropical adaptability.

Genetics of steer daily and residual feed intake in two tropical beef genotypes, and relationships among intake, body composition, growth and other post-weaning measures

Genetic parameters for Brahman (BRAH) and Tropical Composite (TCOMP) cattle were estimated for steer production traits recorded at weaning (WEAN), 80 days post-weaning (POSTW), feedlot entry (ENTRY) and after ∼120 days feedlot finishing (EXIT). The TCOMP was 50% Bos indicus, African Sanga or other tropically adapted Bos taurus, and 50% non-tropically adapted Bos taurus. Data involved 2216 steers, comprising 1007 BRAH by 53 sires and 1209 TCOMP by 50 sires. Individual daily feed intake (DFI) and residual feed intake (RFI) were assessed on 680 BRAH and 783 TCOMP steers over an ~70-day feedlot test. Other traits were liveweight (LWT), average daily gain (ADG), ultrasonically scanned rump (SP8) fat depth, rib (SRIB) fat depth, M. longissimus area (SEMA) and intra-muscular fat % (SIMF), body condition score (CS), hip height (HH), flight time (FT) and serum insulin-like growth factor-I concentration (IGF-I). BRAH were significantly (P < 0.05) lighter at ENTRY and EXIT, and had lower DFI (10.8 v. 13.2 kg/day) and RFI (–0.30 v. 0.17 kg/day), greater SP8 (5.8 v. 5.1 mm) but similar SRIB at ENTRY, lower SRIB (8.2 v. 8.9 mm) but similar SP8 at EXIT, and greater HH than TCOMP. Heritabilities for DFI, RFI, LWT, ADG, scanned body composition, HH and IGF-I measures, across measurement times, were generally in the 20 to 60% range for both genotypes. Genetic variance for RFI was 0.19 (kg/day)2 in BRAH and 0.41 (kg/day)2 in TCOMP, suggesting a clear potential to genetically change RFI in both genotypes. Trait variances and genetic correlations often differed between the genotypes, supporting the use of genotype-specific parameters in genetic evaluation. The genotype differences may be associated with evolutionary changes that have occurred in B. indicus as a part of their adaptation to tropical environments. Measures with potential to be used as genetic indicators of DFI were LWT measures in BRAH and TCOMP, ADG at ENTRY in TCOMP, and SP8 and SIMF at ENTRY in BRAH. Measures with potential to be genetic indicators of RFI were HH and ADG at ENTRY in BRAH, and IGF-I in both genotypes. Taller and faster-growing BRAH steers at ENTRY had genetically lower RFI. IGF-I was negatively genetically correlated with RFI whether IGF-I was measured at POSTW, ENTRY or EXIT. SRIB fatness at EXIT was strongly positively genetically correlated with RFI in TCOMP but only lowly correlated in BRAH. Fatness at ENTRY was lowly and negatively genetically correlated with RFI. The results emphasise the need for a population-specific understanding of trait relationships and of trait differences between measurement times if genetic indicator traits are to be utilised in genetic evaluation of RFI.

Estimated gene frequencies of GeneSTAR markers and their size of effects on meat tenderness, marbling, and feed efficiency in temperate and tropical beef cattle breeds across a range of production systems.

The objectives of this study were to use genotypes for 12 commercially available GeneSTAR gene markers on 12,330 animals to estimate gene frequencies of the markers across a range of beef cattle breeds and to determine the effects of these markers on target traits using a subset of animals with both genotypic and phenotypic data (n = 9,414) for at least one trait. Tenderness markers (T1, T2, T3, T4) were assessed against shear force of 2 muscles, marbling markers (M1, M2, M3, M4) were assessed against intramuscular fat percent and marbling score, and the feed-efficiency markers (N1, N2, N3, N4) were assessed on daily feed intake and residual feed intake. Animals used were from 5 beef cattle research populations: Beef Cooperative Research Centre 1 (CRC1) temperate breeds (Angus, Hereford, Murray Grey, Shorthorn; n = 3,721), Beef CRC1 tropical breeds (Brahman, Santa Gertrudis, Belmont Red; n = 3,899), Beef CRC2 tropically adapted genotypes (Brahman and Tropical Composite; n = 4,446), and progeny test programs in Angus (n = 742) and Shorthorn (n = 347). Gene frequencies varied significantly across breeds and markers, with 86% of the markers estimated to be in Hardy-Weinberg equilibrium. Tenderness markers T1 and T2 had significant effects (P < 0.0001) on shear force, with the size and direction of effects consistent across the range of breeds for the 3 populations with phenotypes. However, sizes of marker effects differed across muscles and reduced upon tenderstretch hanging. Marker T3 was not significant (P > 0.05) in CRC1 temperate breeds but was significant (P < 0.0001) in tropically adapted breeds, with a large effect in Brahman. Marker T4 was significant for shear force in 2 CRC1 tropical breeds but with a different favorable allele. The 4 marbling markers were generally not significantly associated with intramuscular fat percent or marbling score across the 5 populations studied. Feed-efficiency markers N3 and N4 were significantly associated with residual feed intake and daily feed intake in the CRC1 temperate data set, in which a subset of the CRC1 data was used in their discovery, but were not significant in the other 4 populations. Markers N1 and N2 were generally not significant, but when they were significant, their direction of effects differed. The 12 GeneSTAR markers were studied in populations consisting of different breeds and genetic variability and showed gene frequencies and estimated effects that varied greatly across traits, suggesting large differences between the markers for their utility as selection tools in these populations.

The Genetic Architecture of Climatic Adaptation of Tropical Cattle

Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.