Genomic selection (GS) and genome-wide association studies (GWAS) have not been investigated in Vietnamese dairy cattle, even for basic milk production traits, largely due to the scarcity of individual phenotype recording in smallholder dairy farms (SDFs). This study aimed to estimate heritability (h 2) and test the applicability of GS and GWAS for milk production, body conformation and novel heat tolerance traits using single test day phenotypic data. Thirty-two SDFs located in either the north (a lowland vs. a highland) or the south (a lowland vs. a highland) of Vietnam were each visited for an afternoon and the next morning to collect phenotype data of all lactating cows (n = 345). Tail hair from each cow was sampled for subsequent genotyping with a 50K SNP chip at that same visit. Milk production traits (single-test day) were milk yield (MILK, kg/cow/day), energy corrected milk yield adjusted for body weight (ECMbw, kg/100 kg BW/day), fat (mFA, %), protein (mPR, %) and dry matter (mDM, %). Conformation traits were body weight (BW, kg) and body condition score (BCS, 1 = thin to 5 = obese). Heat tolerance traits were panting score (PS, 0 = normal to 4.5 = extremely heat-stressed) and infrared temperatures (IRTs, °C) at 11 areas on the external body surface of the cow (inner vulval lip, outer vulval surface, inner tail base surface, ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, forehoof and hind hoof), assessed by an Infrared Camera. Univariate linear mixed models and a 10-fold cross-validation approach were applied for GS. Univariate single SNP mixed linear models were applied for the GWAS. Estimated h 2 (using the genotype information to build relationships among animals) were moderate (0.20-0.37) for ECMbw, mFA, mPR, mRE, BW, BCS and IRT at rear udder; low (0.08-0.19) for PS and other IRTs; and very low (≤ 0.07) for MILK, ECM and mDM. Accuracy of genomic estimated breeding values (GEBVs) was low (≤ 0.12) for MILK, ECM, mDM and IRT at hind hoof; and moderate to high (0.32-0.46) for all other traits. The most significant regions on chromosomes (BTA) associated with milk production traits were 0.47-1.18 Mb on BTA14. Moderate to high h 2 and moderate accuracies of GEBVs for mFA, mPR, ECMbw, BCS, BW, PS and IRTs at rear udder and outer vulval surface suggested that GS using single test day phenotypic data could be applied for these traits. However, a greater sample size is required to decrease the bias of GEBVs by GS and increase the power of detecting significant quantitative trait loci (QTLs) by GWAS.

Fertility and temperament are important drivers of productivity in the beef industry of northern Australia. The purpose of this study was to determine the heritability of temperament and fertility traits and to estimate the genetic correlation between these traits using a gBLUP analysis. Fertility phenotypes, Post-partum anoestrus interval (PPAI) and age at puberty (AGECL, Tscore) were recorded in Brahman (n=936), Tropical composite (n=1,097) and Smart Futures Heifers (n=3,696). Flighttime records totalled 4,645. The genotype data was imputed from 35k to 800k SNP. Heritability was 0.56(0.08), 0.37(0.08), 0.44(0.11), 0.24(0.08), 0.19(0.03) and 0.33(0.03) for AGECL(Brahman), AGECL (Tropical composite), PPAI (Brahman), PPAI (Tropical composite), Tscore (Smart Futures Heifers) and Flighttime respectively. Genetic correlation was -0.01(0.10), -0.06(0.11), -0.03(0.07) and 0.32(0.09) between AGECL and Flighttime, PPAI and Flighttime, Tscore and Flighttime and PPAI and AGECL respectively. The result suggests that selecting for improved temperament would not improve fertility.

This study aimed to rank potential drivers of cow productivity and welfare in tropical smallholder dairy farms (SDFs) in Vietnam. Forty-one variables were collected from 32 SDFs located in four geographically diverse dairy regions, with eight SDFs per region. Twelve variables, including milk yield (MILK), percentages of milk fat (mFA), protein (mPR), dry matter (mDM), energy-corrected milk yield (ECM), heart girth (HG), body weight (BW), ECM per 100 kg BW (ECMbw), body condition score (BCS), panting score (PS), inseminations per conception (tAI), and milk electrical resistance (mRE) of cows, were fitted as outcome variables in the models. Twenty-one other variables describing farm altitude, housing condition, and diet for the cows, cow genotypes, and cow physiological stage were fitted as explanatory variables. Increased farm altitude was associated with increases in ECM and mRE and with decreases in PS and tAI ( P < 0.05). Increases in roof heights and percentage of shed side open were associated with increases in ECM, mFA, and mDM ( P < 0.05). Increased dry matter intake and dietary densities of dry matter and fat were associated with increased MILK, ECM, and ECMbw and decreased tAI ( P < 0.05). Increased dietary lignin density was associated with increased PS. Increased genetic proportion of Brown Swiss in the herd was associated with increased MILK, ECM, and ECMbw ( P < 0.05). Thus, to improve cow productivity and welfare in Vietnamese SDFs, the following interventions were identified for testing in future cause-effect experiments: increasing floor area per cow, roof heights, shed sides open, dry matter intake, dietary fat density, and the genetic proportion of Brown Swiss and decreasing dietary lignin density.

Parasitic worms are serious pests of humans, livestock, and crops worldwide. Multiple management strategies are employed in order to reduce their impact, and some of these may affect their genome and population allelic frequency distribution. The evolution of chemical resistance, ecological changes, and pest dispersal has allowed an increasing number of pests to become difficult to control with current management methods. Their lifestyle limits the use of ecological and individual-based management of populations. There is a need to develop rapid, affordable, and simple diagnostics to assess the efficacy of management strategies and delay the evolution of resistance to these strategies. This study presents a multilocus, equal-representation, whole-genome pooled single nucleotide polymorphisms (SNPs) selection approach as a monitoring tool for the ovine nematode parasite Haemonchus contortus. The SNP selection method used two reference genomes of different quality, then validated these SNPs against a high-quality recent genome assembly. From over 11 million high-quality SNPs identified, 334 SNPs were selected, of which 262 were species-specific, yielded similar allele frequencies when assessed as multiple individuals or as pools of individuals, and suitable to distinguish mixed nematode isolate pools from single isolate pools. As a proof-of-concept, 21 Australian H. contortus populations with various phenotypes and genotypes were screened. This analysis confirmed the overall low level of genetic differentiation between populations collected from the field, but clearly identifying highly inbred populations, and populations showing genetic signatures associated with chemical resistance. The analysis showed that 66% of the SNPs were necessary for stability in assessing population genetic patterns, and SNP pairs did not show linkage according to allelic frequencies across the 21 populations. This method demonstrates that ongoing monitoring of parasite allelic frequencies and genetic changes can be achieved as a management assessment tool to identify drug-treatment failure, population incursions, and inbreeding signatures due to selection. The SNP selection method could also be applied to other parasite species.

Panting score (PS) is a common research tool used to assess the physiological state of cows exposed to heat stress, but it is subjective. Infrared temperature (IRT), measured by either infrared thermometers or cameras, may be a more objective and reliable alternative. Very few studies thus far have evaluated the associations between PS, IRT, and milk production. We investigated the applicability of IRT compared with PS as a means of assessing heat stress and milk yield reduction in dairy cows in tropical smallholder dairy farms (SDF). In autumn 2017, SDF located across 4 typical dairy regions of Vietnam were each visited once to collect farm (n = 32) and individual cow data (n = 344). For each SDF, heat load index (HLI) inside the cowsheds, an indicator of environmental heat load calculated from ambient temperature, humidity, and wind speed, was measured. For each cow, PS (0 indicates a cow breathing normally, not panting; 4.5 indicates an extremely heat-stressed cow with excessive panting, tongue fully extended, and excessive drooling), IRT of the cow's body, single-day energy-corrected milk yield (ECM), body weight, and body condition score were measured. Cow genotype, age, lactation number, and days in milk were recorded. The IRT of the cows' inner vulval lip (IVuT) were measured with an infrared thermometer; and the IRT of the cows' vulval surface (OVuT), inner tail base surface (ITBT), ocular area, muzzle, armpit area, paralumbar fossa area, fore udder, rear udder, fore hoof, and hind hoof were also measured with an infrared camera. Multivariate mixed-effects models were used to assess the associations between HLI with PS and IRT, and associations between PS and IRT with ECM while accounting for the effects of other cow variables. All IRT correlated positively with PS (Pearson correlation, r = 0.23-0.50). Each unit increase in HLI was associated with increases of 0.07 units in PS and 0.09 to 0.23°C in IRT. Each degree (°C) increase in IVuT, OVuT, and ITBT was associated with decreases of 0.75, 0.87, and 0.70 kg/cow per day in ECM, respectively, whereas PS and other IRT were not significantly associated with ECM. Thus, all IRT showed potential to assess the heat stress level of cows; and IVuT, OVuT, and ITBT, but not PS and other IRT, showed potential to predict ECM reduction in cows during heat stress. First cross (F1) Holstein Brown Swiss and F1 Holstein Jersey showed lower PS and yielded higher ECM than the third backcross (B3) Holstein Zebu (7/8 Holstein + 1/8 Zebu) and pure Holstein. Thus, F1 Holstein Brown Swiss and F1 Holstein Jersey could be more suitable for tropical SDF than B3 Holstein Zebu and pure Holstein.

A limited literature suggests relatively simple feeding regimes and diet formulation strategies for dairy cows in Vietnamese smallholder dairy farms (SDFs). This study aimed to classify and compare feeding regimes and nutrient balance for lactating cows between four typical dairy regions (south lowland, south highland, north lowland, and north highland) in Vietnam and evaluate the possibility of systematic dietary imbalance. Eight SDFs from each of the four regions were visited for two adjacent milking periods per farm. For each visit, frequency and methods of feed and water supply to the lactating cows were recorded, and individual fat corrected milk yield (ECM) of lactating cows were calculated from milk yield and fat concentration. The amount of each diet ingredient offered and refused by each lactating group was weighed and sampled for calculation of dry matter intake per cow (DMI) and analysis of nutrient composition in the component offered. PCDairy, a diet formulation computer model, was used to calculate actual and recommended dietary nutrient concentrations and predict potential milk production. Factor analysis, cluster analysis, and ANOVA were applied to determine grouping effects across as well as between regions. Feeding regimes and diets were grouped into three and nine clusters, respectively. Farmers in the same region tended to apply similar diets and feeding regimes. Across regions, only 47% of all SDFs supplied water ad libitum to the cows. The most used roughages including Napier grass, corn silage, fresh corn with cob, and rice straw were all relatively high in neutral detergent fibre (NDF), acid detergent fibre (ADF), and acid detergent lignin (ADL). The diets in all regions were excessive in crude protein, NDF, ADF, ADL, and most minerals (Ca, P, Mg, K, Na, S, Fe, Zn, Cu, and Mn) but insufficient in net energy and non-fibre carbohydrate. Feed efficiency (1.06 kg FCM/kg DMI) of the diets were sub-optimal. Feeding regimes and dietary nutrient balance of the south lowland SDFs were most problematic. Increasing dietary net energy concentration by increasing the use of starch and fat and decreasing dietary fibre concentration by decreasing the use of Napier grass or rice straw to balance the diets might help improve the milk production and thereby increase feed efficiency.

The Wagyu breed of taurine cattle possess favourable genetics for intramuscular fat (IMF) but genomic loci associated with the trait remain under characterised. Here, we report the identification of a previously unidentified genomic region possessing a particular haplotype structure in Wagyu. Through deployment of a genome-wide haplotype detection analysis that captures regions conserved in a target population but not other populations we screened 100 individual Wagyu and contrasted them with 100 individuals from two independent comparison breeds, Charolais and Angus, using high-density SNPs. An extreme level of Wagyu conservation was assigned to a single genomic window (spanning genomic coordinates BTA28:41 088-300 265 bp). In fact, a five-SNP region spanning 27 096 bp is almost perfectly conserved among the 100 Wagyu individuals assayed and partially overlaps RAB4A. Focussing in, two consecutive SNPs (genomic coordinates 236 949 and 239 950) are apparently fixed within the Wagyu (BB and AA respectively), but at mixed frequencies in the other two breeds. These SNPs are located in the two introns straddling exon 7. In a separate analysis using the 1000 Bulls database, we found that, coincident with exon 7 of RAB4A first allele frequencies were highest in the high IMF Japanese Native (Wagyu) breeds (0.78) and lowest in the low IMF indicine breeds (Nelore and Brahman), with intermediate marbling breeds (Angus and Charolais) assigned intermediate rankings (0.42). RAB4A is known to encode a protein that regulates intracellular trafficking of the insulin-regulated glucose transporter GLUT4. RAB4A can be considered an attractive new positional candidate for IMF development.

In smallholder dairy farms (SDFs), farmers often build cowsheds using local materials and based on self-accumulated experience without due consideration to reducing the risk of heat stress. This study aimed to characterise the heat stress abatement strategies and microclimate within SDF cowsheds from four typical dairy regions of Vietnam (south lowland, south highland, north lowland and north highland) and identify the housing parameters most associated with the microclimate. The study was conducted on 32 SDFs (eight SDFs per region) in autumn 2017. Twelve housing management variables, illustrating cowshed design and heat stress abatement methods of each SDF, were collected. Six microclimate parameters, collected within the cowshed, were temperature (AT), humidity, air speed (AS), heat load index (HLI), Temperature-humidity index (THI) and accumulated heat load units (AHLU) during a day (06:00 h to 18:00 h). Factor analysis and cluster analysis was applied to group cowsheds of SDFs into clusters where SDFs in the cluster had the same cowshed characteristics. Multivariable linear models were applied to define the parameters most likely to inform future research into heat stress mitigation on SDF. Averaged from 08:00 h to 18:00 h, microclimate inside the cowsheds was considered hot (HLI > 79) in the highland and very hot (HLI > 86) in the lowland regions. Cows in the lowland regions accumulated high heat load (AHLU > 50) by 18:00 h. Cowsheds of SDFs varied widely and grouped into seven cowshed types, but no type was more effective than others in reducing heat stress conditions within cowsheds. Using roof soakers together with fans decreased AT and HLI by 1.3 °C and 3.2 units, respectively, at 14:00 h compared to 11:00 h. Each 100 m increase in altitude was associated with decreases of 0.4 °C in AT, 1.3 units in HLI and 0.8 units in THI (p < 0.001). Each meter increase in the eave height of the cowshed roof was associated with decreases of 0.87 °C in AT, 3.31 units in HLI and 1.42 units in THI, and an increase of 0.14 m/s in AS (p < 0.05). The cowshed parameters that should be prioritised for future research into the amelioration of heat stress in SDF cows include using the roof soakers together with fans, increasing altitude, eave roof height and floor area per cow.

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.

Vietnamese smallholder dairy cows (VDC) are the result of crossbreeding between different zebu (ZEB) and taurine dairy breeds through many undefined generations. Thus, the predominant breed composition of VDC is currently unknown. This study aimed to evaluate the level of genetic diversity and breed composition of VDC. The SNP data of 344 animals from 32 farms located across four dairy regions of Vietnam were collected and merged with genomic reference data, which included three ZEB breeds: Red Sindhi, Sahiwal and Brahman, three taurine breeds: Holstein (HOL), Jersey (JER) and Brown Swiss (BSW), and a composite breed: Chinese Yellow cattle. Diversity and admixture analyses were applied to the merged data set. The VDC were not excessively inbred, as indicated by very low inbreeding coefficients (Wright's FIS ranged from -0.017 to 0.003). The genetic fractions in the test herds suggested that the VDC are primarily composed of HOL (85.0%); however, JER (6.0%), BSW 5.3%) and ZEB (4.5%) had also contributed. Furthermore, major genotype groupings in the test herds were pure HOL (48%), B3:15/16HOL_1/16ZEB (22%) and B2:7/8HOL_1/8ZEB (12%). The genetic makeup of the VDC is mainly components of various dairy breeds but also has a small percentage of ZEB; thus, the VDC could be a good genetic base for selecting high milk-producing cows with some degree of adaptation to tropical conditions.

Smallholder dairy farms (SDFs) are distributed widely across lowland and highland regions in Vietnam, but data on the productivity and welfare status of these cows remains limited. This cross-sectional study was conducted to describe and compare the productivity and welfare status of SDF cows across contrasting regions. It was conducted in autumn 2017 on 32 SDFs randomly selected from four typical but contrasting dairy regions (eight SDFs per region); a south lowland, a south highland, a north lowland, and a north highland region. Each farm was visited over a 24-h period (an afternoon followed by a morning milking and adjacent husbandry activities) to collect data of individual lactating cows (n = 345) and dry cows (n = 123), which included: milk yield and concentrations, body weight (BW), body condition score (BCS, 5-point scale, 5 = very fat), inseminations per conception, and level of heat stress experienced (panting score, 4.5-point scale, 0 = no stress). The high level of heat stress (96% of lactating cows were moderate to highly heat-stressed in the afternoon), low energy corrected milk yield (15.7 kg/cow/d), low percentage of lactating cows (37.3% herd), low BW (498 and 521 kg in lactating and dry cows, respectively), and low BCS of lactating cows (2.8) were the most important productivity and welfare concerns determined and these were most serious in the south lowland. By contrast, cows in the north lowland, a relatively hot but new dairying region, performed similarly to those in the south highland; a region historically considered to be one of the most suitable for dairy cows in Vietnam due to its cool environment. This indicates the potential to mitigate heat stress through new husbandry strategies. Cows in the north highland had the highest BW (535 and 569 kg in lactating and dry cows, respectively) and the highest energy corrected milk yield (19.2 kg/cow/d). Cows in all regions were heat-stressed during the daytime, although less so in the highlands compared to the lowlands. Opportunities for research into improving the productivity and welfare of Vietnamese SDF cows are discussed.

Background In tropically-adapted beef heifers, application of genomic prediction for age at puberty has been limited due to low prediction accuracies. Our aim was to investigate novel methods of pre-selecting whole-genome sequence (WGS) variants and alternative analysis methodologies; including genomic best linear unbiased prediction (GBLUP) with multiple genomic relationship matrices (MGRM) and Bayesian (BayesR) analyses, to determine if prediction accuracy for age at puberty can be improved. Methods Genotypes and phenotypes were obtained from two research herds. In total, 868 Brahman and 960 Tropical Composite heifers were recorded in the first population and 3695 Brahman, Santa Gertrudis and Droughtmaster heifers were recorded in the second population. Genotypes were imputed to 23 million whole-genome sequence variants. Eight strategies were used to pre-select variants from genome-wide association study (GWAS) results using conditional or joint (COJO) analyses. Pre-selected variants were included in three models, GBLUP with a single genomic relationship matrix (SGRM), GBLUP MGRM and BayesR. Five-way cross-validation was used to test the effect of marker panel density (6 K, 50 K and 800 K), analysis model, and inclusion of pre-selected WGS variants on prediction accuracy. Results In all tested scenarios, prediction accuracies for age at puberty were highest in BayesR analyses. The addition of pre-selected WGS variants had little effect on the accuracy of prediction when BayesR was used. The inclusion of WGS variants that were pre-selected using a meta-analysis with COJO analyses by chromosome, fitted in a MGRM model, had the highest prediction accuracies in the GBLUP analyses, regardless of marker density. When the low-density (6 K) panel was used, the prediction accuracy of GBLUP was equal (0.42) to that with the high-density panel when only six additional sequence variants (identified using meta-analysis COJO by chromosome) were included. Conclusions While BayesR consistently outperforms other methods in terms of prediction accuracies, reasonable improvements in accuracy can be achieved when using GBLUP and low-density panels with the inclusion of a relatively small number of highly relevant WGS variants.

Brahman cattle (Bos indicus) are well adapted to thrive in tropical environments. Since their introduction to Australia in 1933, Brahman's ability to grow and reproduce on marginal lands has proven their value in the tropical beef industry. The poll phenotype, which describes the absence of horns, has become desirable in the cattle industry for animal welfare and handler safety concerns. The poll locus has been mapped to chromosome one. Four alleles, each a copy number variant, have been reported across this locus in B. indicus and Bos taurus. However, the causative mutation in Brahman cattle has not been fully characterized. Oxford Nanopore Technologies' minION sequencer was used to sequence four homozygous poll (PcPc), four homozygous horned (pp), and three heterozygous (P(c)p) Brahmans to characterize the poll allele in Brahman cattle. A total of 98 Gb were sequenced and an average coverage of 3.33X was achieved. Read N50 scores ranged from 9.9 to 19 kb. Examination of the mapped reads across the poll locus revealed insertions approximately 200 bp in length in the poll animals that were absent in the horned animals. These results are consistent with the Celtic poll allele, a 212-bp duplication that replaces 10 bp. This provides direct evidence that the Celtic poll allele is segregating in the Australian Brahman population.

In beef cattle, horn management is practiced to physically or surgically remove horns for the safety of animals and workers. However, invasive practices of dehorning and disbudding are a great threat to animal welfare, health, production and human safety, as well as labour intensive and costly. The most effective way to limit the impacts and costs of horns is to prevent their occurrences by breeding naturally polled (hornless) herds. Horn development is complex, although two mutually exclusive genetic variants (Celtic and Friesian) have been found prevalent on each copy of chromosome 1 in most polled cattle. Predicting genotypes in an animal is challenging. Available genetic testing assays were often limited in tropically adapted beef cattle. In this study we present a new optimized poll testing (OPT) assay, which has been bundled with SNP genotyping arrays being used for genomic evaluation in cattle. Breeding schemes can profile future parents for pure-polled stock based on the OPT results. We also evaluated the factors causing complexity in horn conditions. Thus, we coupled OPT predictions with head-status and sex distributions, by modelling genetic and non-genetic impacts, revealing that genetics, sex and sex hormones control horn ontology. Finally, concerns of polledness adversely affecting production and reproduction were investigated by using estimated breeding values of several beef traits. We found no detrimental effects of polledness on production or reproduction. Overall, this research concludes that genetically polled cattle will minimize issues about animal welfare and management costs without reducing production potentials in the tropically adapted beef 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.

Management of horns in beef cattle has major economic and welfare impacts, and therefore, breeding for naturally hornless (polled) cattle is widely practiced. Poll breeding can be significantly accelerated by using DNA diagnostic tools (Prayaga 2007), and the Australian beef cattle industry has adopted the available DNA poll testing assays, which are generally successful. However, issues of applicability in Bos indicus cattle has arisen due to a more complex mode of inheritance of the horn phenotype. This study has investigated these limitations and further optimized the poll gene testing to increase accuracy and informativeness across all breeds. We also investigated if polled genetics were different than horned animals for beef production.

Heifers that have an earlier age at puberty often have greater lifetime productivity. Age at puberty is moderately heritable so selection should effectively reduce the number of days to puberty, and improve heifer productivity and profitability as a result. However, recording age at puberty is intensive, requiring repeat ovarian scanning to determine age at first corpus luteum (AGECL). Genomic selection has been proposed as a strategy to select for earlier age at puberty; however, large reference populations of cows with AGECL records and genotypes would be required to generate accurate GEBV for this trait. Reproductive maturity score (RMS) is a proxy trait for age at puberty for implementation in northern Australia beef herds, where large scale recording of AGECL is not feasible. RMS assigns a score of 0 to 5 from a single ovarian scan to describe ovarian maturity at ~600 d. Here we use multivariate genomic prediction to evaluate the value of a large RMS data set to improve accuracy of GEBV for age at puberty (AGECL). There were 882 Brahman and 990 Tropical Composite heifers with AGECL phenotypes, and an independent set of 974 Brahman, 1,798 Santa Gertrudis, and 910 Droughtmaster heifers with RMS phenotypes. All animals had 728,785 real or imputed SNP genotypes. The correlation of AGECL and RMS (h2 = 0.23) was estimated as -0.83 using the genomic information. This result also demonstrates that using genomic information it is possible to estimate genetic correlations between traits collected on different animals in different herds, with minimal or unknown pedigree linkage between them. Inclusion of heifers with RMS in the multi-trait model improved the accuracy of genomic evaluations for AGECL. Accuracy of RMS GEBV generally did not improve by adding heifers with AGECL phenotypes into the reference population. These results suggest that RMS and AGECL may be used together in a multi-trait prediction model to increase the accuracy of prediction for age at puberty in tropically adapted beef cattle.