Genomic Selection and Use of Molecular Tools in Breeding Programs for Indigenous and Crossbred Cattle in Developing Countries: Current Status and Future Prospects

Genomic Prediction and Genome-Wide Association Studies for Productivity, Conformation and Heat Tolerance Traits in Tropical Smallholder Dairy Cows

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.

Genetic estimates and genome-wide association studies of antibody response in Tanzanian dairy cattle

Identifying the genetic determinants of host defence against infectious pathogens is central to enhancing disease resilience and therapeutic efficacy in livestock. Here, we investigated immune response heritability to important infectious diseases affecting smallholder dairy cattle using variance component analysis. We also conducted genome-wide association studies (GWAS) to identify genetic variants that may help understand the underlying biology of these health traits. By assessing 668,911 single-nucleotide polymorphisms (SNPs) genotyped in 2,045 crossbred cattle sampled from six regions of Tanzania, we identified high levels of interregional admixture and European introgression, which may increase infectious disease susceptibility relative to indigenous breeds. Heritability estimates were low to moderate, ranging from 0.03 (SE ± 0.06) to 0.44 (SE ± 0.07), depending on the health trait. GWAS results revealed several loci associated with seropositivity to the viral diseases Rift Valley fever and bovine viral diarrhoea, the protozoan parasites Neospora caninum and Toxoplasma gondii, and the bacterial pathogens Brucella sp, Leptospira hardjo, and Coxiella burnetii. The identified quantitative trait loci mapped to genes involved in immune defence, tumour suppression, neurological processes, and cell exocytosis. We propose that our results provide a basis for future understanding of the cellular pathways contributing to general and taxon-specific infection responses, and for advancing selective breeding and therapeutic target design.

Genomic Prediction of Milk Fat Percentage Among Crossbred Cattle in the Indian Subcontinent

This study focused on improving the milk fat percentage for crossbred dairy cows in smallholder systems, using GEBV. The data were collected from 2507 animals between 2016 and 2023 under BAIF's Enhanced Genetic Gains program in Pune, India. After refining the dataset, 33,845 records from 1896 animals were analyzed. The result showed that 75.54% of farms had either one or two animals. Prior to quality control, the mean milk fat percentage was 3.94%, but it decreased to 3.83% after data pruning, which necessitated removing the outliers. Genetic analysis involved 1478 animals genotyped for 49,911 SNPs after applying a rigorous quality control process, and imputation improved the accuracy of genomic data, boosting allele frequency correlation from 0.594 to 0.882. The study revealed that the additive genetic variance, phenotypic variance, and error variance were calculated as 0.012, 0.118, and 0.106, respectively. The heritability was estimated at 0.10, suggesting cautious use for breeding improvements. The GEBV ranged from 0.096 to 3.10%, which offers breeders a practical tool for selecting high-fat-producing cows. This research provides valuable insights into optimizing milk quality and advancing genetic improvement strategies in smallholder dairy systems.

The African Animal Breeding Network as a pathway towards genetic improvement of livestock

Transforming Africa's agricultural production and food systems is an imperative to achieve the United Nations Sustainable Development Goals and deliver on the Africa Union's 2063 vision, 'the Africa we want'. Transforming livestock systems through genetic improvement will sustainably increase productivity and proffer an inclusive socioeconomic development of farming communities. The African Animal Breeding Network (AABNet) is a platform of highly knowledgeable geneticists, animal breeders and professionals willing to provide information, training, advice and support across the continent. It will leverage available human resources among its members, facilitate partnerships and investment and develop infrastructure for innovative livestock genetic improvement in Africa.

Evaluation of crossbreeding strategies for improved adaptation and productivity in African smallholder cattle farms

BACKGROUND

Crossbreeding is successfully implemented worldwide to improve animal productivity and adaptability. However, recurrent failures of crossbreeding programmes in African countries imply the need to design effective strategies for the predominant smallholder production systems.

METHODS

A comprehensive simulation procedure mimicked body weight (BWL) and tick count (TCL) incidence in a local taurine cattle breed and in an exotic indicine beef cattle breed (BWE and TCE, respectively). The two breeds were crossed to produce F1 and rotational animals. Additionally, synthetic breeds were created by applying four schemes defined as farm bull (FB), intra-village bull (IVB), exchanged-village bull (EVB), and population-wide bull (PWB) scheme. These schemes reflect different strategies to select and allocate bulls to smallholder farms. The different crosses were compared with the local breed over 20 generations by varying the genetic correlation between the traits ( r g = - 0.4, 0, 0.4), genotype-by-environment effects (GxE) between local and exotic environment ( r g × e = 0.4, 0.6, 0.8), and the relative emphasis of TCL compared to BWL in a selection index (SI_TCL10%, SI_TCL30%, SI_TCL50%).

RESULTS

Regardless of r g and r g × e , EVB achieved the highest phenotypic and genetic gains for BWL and TCL over the 20 generations with SI_TCL50%. However, EVB displayed lower phenotypic means than F1 crosses in the first seven generations due to the loss of heterosis. Additive genetic variances were generally larger in synthetic crosses than in F1 and local animals, explaining the larger responses to selection. In addition, the EVB was the most effective strategy to stabilize inbreeding and retain heterosis in the advanced generations of synthetic animals. Low emphasis on TCL (SI_TCL30%, SI_TCL10%) resulted in negative phenotypic gain for TCL in synthetic animals when rg = - 0.4. In contrast to F1 and rotational crosses, GxE effects did not affect phenotypic gain in synthetic crosses.

CONCLUSIONS

The study demonstrates opportunities for long-term genetic improvement of adaptive and productive performances in smallholder cattle farms using synthetic breeding. Extensive exchange of semen between villages or regions controls inbreeding and additionally contributes to increasing genetic gain. Furthermore, the definition of a suitable selection index prevents antagonistic selection responses caused by negative correlations between traits and GxE effects.

Performance of weighted genomic BLUP and Bayesian methods for Hanwoo carcass traits

To improve the quality and yield of the Korean beef industry, selection criteria often focus on estimated breeding values for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS). This study estimated genetic parameters and assessed the accuracy of genomic estimated breeding values (GEBVs) using SNP weighting methods. We compared the accuracy of these methods with the genomic best linear unbiased prediction (GBLUP) and various Bayesian approaches (BayesA, BayesB, BayesC, and BayesCPi) for the specified traits. The study used single-trait animal models, including GBLUP, weighted GBLUP (WGBLUP), and the Bayesian methods to predict genomic breeding values in a population of Hanwoo steers. A total of 19154 phenotypes were collected with all animals genotyped using the Illumina Bovine 50 K SNP chip. The average heritability for the carcass traits was 0.33 (GBLUP) and 0.35 (Bayesian), with Bayesian methods yielding heritability estimates that were on average 0.02 points (6.1%) higher than GBLUP. The accuracy of genomic predictions ranged from 0.7-0.83 (GBLUP), 0.83-0.87 (WGBLUP), and 0.81-0.87 across the Bayesian methods. WGBLUP accuracies for the carcass traits were, on average 8.97% higher than the GBLUP accuracies and 1.80% higher than the Bayesian alphabets. The Bayesian alphabet's accuracy is also, on average 6.00% higher than the GBLUP accuracy. According to these findings, the weighting GBLUP approach provides higher prediction accuracy for Hanwoo carcass traits than the Bayesian alphabet. Therefore, WGBLUP can be used for genomic selection in the Hanwoo evaluation program.

Parent of origin genetic effects on milk production traits in a population of Iranian Holstein cows

The aim was to estimate the relative contribution of imprinting effects from both paternal and maternal sides to phenotypic variation in milk production traits including 305 days milk yield (MY), average daily milk production (ADM), fat percentage (F%), protein percentage (P%), 305 days fat yield (FY), 305 days protein yield (PY), ratio of fat percentage to protein percentage (F:P) and somatic cell score (SCS) in Iranian Holstein cows. To do this, each trait was analysed with a series of four animal models, which were identical for fixed and additive genetic effects but differed for combinations of paternal and maternal imprinting effects. The log-likelihood ratio test (LRT) and Akaike's information criteria (AIC) were used to select the best model for each trait. Correlations between traits due to additive and imprinting effects were estimated by bivariate analyses. For all traits studied, fitting the imprinting effect led to a better data fit. Also, it resulted in a noticeable decrease in additive genetic variance from 8% (SCS) to 28% (F:P). A significant maternal imprinting effect was detected on all traits studied. Estimates of maternal imprinting heritability (h mi 2 ) were 0.07 ± 0.02, 0.04 ± 0.01, 0.06 ± 0.01, 0.05 ± 0.01, 0.5 ± 0.01, 0.09 ± 0.02, 0.07 ± 0.02 and 0.06 ± 0.01 for MY, ADM, F%, P%, FY, PY, F:P and SCS, respectively. For F:P, in addition to the maternal imprinting effect, a significant paternal imprinting component was also detected with a 7% contribution to phenotypic variance of F:P. Estimates of direct heritability (h a 2 ) were 0.29 ± 0.02, 0.17 ± 0.01, 0.22 ± 0.02, 0.11 ± 0.01, 0.18 ± 0.02, 0.22 ± 0.02, 0.15 ± 0.04 and 0.06 ± 0.01 for MY, ADM, F%, P%, FY, PY, F:P and SCS, respectively. Maternal imprinting correlations (rmi) were in a wide range between -0.75 ± 0.15 (P%-SCS) and 0.95 ± 0.11 (MY-ADM). Additive genetic correlations (ra) ranged between -0.54 ± 0.05 (MY-P%) and 0.99 ± 0.01 (MY-ADM) and phenotypic correlations (rp) ranged from -0.30 ± 0.01 (MY-F%) to 0.93 ± 0.01 (MY-ADM). The Spearman's correlation between additive breeding values including and excluding imprinting effects deviated from unity especially for top-ranked animals implying re-ranking of top animals following the inclusion of imprinting effects in the model. Since including imprinting effects in the model resulted in better data fit and re-ranking of top animals, including these effects in the genetic evaluation models for milk production traits was recommended.

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex tapestry of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White breeds. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African and residually admixed Southern European cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, and Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa.

Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis

Days open (DO) is a critical economic and reproductive trait that is commonly employed in genetic selection. Making improvements using conventional genetic techniques is exceedingly challenging. Therefore, new techniques are required to improve the accuracy of genetic selection using genomic data. This study examined the genetic approaches of traditional AIREML and single-step genomic AIREML (ssGAIREML) to assess genetic parameters and the accuracy of estimated breeding values while also investigating SNP regions associated with DO and identifying candidate genes through a genome-wide association study (GWAS). The dataset included 59415 DO records from 36368 Thai-Holstein crossbred cows and 882 genotyped animals. The cows were classified according to their Holstein genetic proportion (breed group, BG) as follows: BG1 (>93.7% Holstein genetics), BG2 (87.5% to 93.6% Holstein genetics), and BG3 (<87.5% Holstein genetics). AIREML was utilized to estimate genetic parameters and variance components. The results of this study reveal that the average DO values for BG1, BG2, and BG3 were 97.64, 97.25, and 96.23 days, respectively. The heritability values were estimated to be 0.02 and 0.03 for the traditional AIREML and ssGAIREML approaches, respectively. Depending on the dataset, the ssGAIREML method produced more accurate estimated breeding values than the traditional AIREML method, ranging from 40.5 to 45.6%. The highest values were found in the top 20% of the dam dataset. For the GWAS, we found 12 potential candidate genes (DYRK1A, CALCR, MIR489, MIR653, SLC36A1, GNA14, GNAQ, TRNAC-GCA, XYLB, ACVR2B, SLC22A14, and EXOC2) that are believed to have a significant influence on days open. In summary, the ssGAIREML method has the potential to enhance the accuracy and heritability of reproductive values compared to those obtained using conventional AIREML. Consequently, it is a viable alternative for transitioning from conventional methodologies to the ssGAIREML method in the breeding program for dairy cattle in Thailand. Moreover, the 12 identified potential candidate genes can be utilized in future studies to select markers for days open in regard to dairy cattle.

Genotype-by-environment interactions in beef and dairy cattle populations: A review of methodologies and perspectives on research and applications

Modern livestock production systems are characterized by a greater focus on intensification, involving managing larger numbers of animals to achieve higher productive efficiency and animal health and welfare within herds. Therefore, animal breeding programs need to be strategically designed to select animals that can effectively enhance production performance and animal welfare across a range of environmental conditions. Thus, this review summarizes the main methodologies used for assessing the levels of genotype-by-environment interaction (G × E) in cattle populations. In addition, we explored the importance of integrating genomic and phenotypic information to quantify and account for G × E in breeding programs. An overview of the structure of cattle breeding programs is provided to give insights into the potential outcomes and challenges faced when considering G × E to optimize genetic gains in breeding programs. The role of nutrigenomics and its impact on gene expression related to metabolism in cattle are also discussed, along with an examination of current research findings and their potential implications for future research and practical applications. Out of the 116 studies examined, 60 and 56 focused on beef and dairy cattle, respectively. A total of 83.62% of these studies reported genetic correlations across environmental gradients below 0.80, indicating the presence of G × E. For beef cattle, 69.33%, 24%, 2.67%, 2.67%, and 1.33% of the studies evaluated growth, reproduction, carcass and meat quality, survival, and feed efficiency traits, respectively. By contrast, G × E research in dairy cattle populations predominantly focused on milk yield and milk composition (79.36% of the studies), followed by reproduction and fertility (19.05%), and survival (1.59%) traits. The importance of G × E becomes particularly evident when considering complex traits such as heat tolerance, disease resistance, reproductive performance, and feed efficiency, as highlighted in this review. Genomic models provide a valuable avenue for studying these traits in greater depth, allowing for the identification of candidate genes and metabolic pathways associated with animal fitness, adaptation, and environmental efficiency. Nutrigenetics and nutrigenomics are emerging fields that require extensive investigation to maximize our understanding of gene-nutrient interactions. By studying various transcription factors, we can potentially improve animal metabolism, improving performance, health, and quality of products such as meat and milk.

Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle

Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the future profitability of the dairy sector. Registered body conformation traits are reliable and cost-effective tools for use in national cattle breeding selection programs. These traits are significantly related to the production, longevity, mobility, health, fertility, and environmental adaptation of dairy cows. Therefore, they can be considered indirect indicators of economically important traits in dairy cows. Utilizing efficacious genetic methods, such as genome-wide association studies (GWASs), allows for a deeper understanding of the genetic architecture of complex traits through the identification and application of genetic markers. In the current review, we summarize information on candidate genes and genomic regions associated with body conformation traits in dairy cattle worldwide. The manuscript also reviews the importance of body conformation, the relationship between body conformation traits and other traits, heritability, influencing factors, and the genetics of body conformation traits. The information on candidate genes related to body conformation traits provided in this review may be helpful in selecting potential genetic markers for the genetic improvement of body conformation traits in dairy cattle.

Whole genome sequences of 70 indigenous Ethiopian cattle

Indigenous animal genetic resources play a crucial role in preserving global genetic diversity and supporting the livelihoods of millions of people. In Ethiopia, the majority of the cattle population consists of indigenous breeds. Understanding the genetic architecture of these cattle breeds is essential for effective management and conservation efforts. In this study, we sequenced DNA samples from 70 animals from seven indigenous cattle breeds, generating about two terabytes of pair-end reads with an average coverage of 14X. The sequencing data were pre-processed and mapped to the cattle reference genome (ARS-UCD1.2) with an alignment rate of 99.2%. Finally, the variant calling process produced approximately 35 million high-quality SNPs. These data provide a deeper understanding of the genetic landscape, facilitate the identification of causal mutations, and enable the exploration of evolutionary patterns to assist cattle improvement and sustainable utilization, particularly in the face of unpredictable climate changes.

Genome-Wide Association Study Reveals Quantitative Trait Loci and Candidate Genes Associated with High Interferon-gamma Production in Holstein Cattle Naturally Infected with Mycobacterium Bovis

Mycobacterium bovis (Mb) is the causative agent of bovine tuberculosis (bTb). Genetic selection aiming to identify less susceptible animals has been proposed as a complementary measure in ongoing programs toward controlling Mb infection. However, individual animal phenotypes for bTb based on interferon-gamma (IFNɣ) and its use in bovine selective breeding programs have not been explored. In the current study, IFNɣ production was measured using a specific IFNɣ ELISA kit in bovine purified protein derivative (bPPD)-stimulated blood samples collected from Holstein cattle. DNA isolated from the peripheral blood samples collected from the animals included in the study was genotyped with the EuroG Medium Density bead Chip, and the genotypes were imputed to whole-genome sequences. A genome-wide association analysis (GWAS) revealed that the IFNɣ in response to bPPD was associated with a specific genetic profile (heritability = 0.23) and allowed the identification of 163 SNPs, 72 quantitative trait loci (QTLs), 197 candidate genes, and 8 microRNAs (miRNAs) associated with this phenotype. No negative correlations between this phenotype and other phenotypes and traits included in the Spanish breeding program were observed. Taken together, our results define a heritable and distinct immunogenetic profile associated with strong production of IFNɣ in response to Mb.

Community-based breeding programs can realize sustainable genetic gain and economic benefits in tropical dairy cattle systems

Implementing an appropriate breeding program is crucial to control fluctuation in performance, enhance adaptation, and further improve the crossbred population of dairy cattle. Five alternative breeding programs (BPs) were modeled considering available breeding units in the study area, the existing crossbreeding practices, and the future prospects of dairy research and development in Ethiopia. The study targeted 143,576 crossbred cows of 54,822 smallholder households in the Arsi, West Shewa, and North Shewa zones of the Oromia Region, as well as the North Shewa zone of the Amhara Region. The alternative BPs include conventional on-station progeny testing (SPT), conventional on-farm progeny testing (FPT), conventional on-station and on-farm progeny testing (SFPT), genomic selection (GS), and genomic progeny testing (GPT). Input parameters for modeling the BPs were taken from the analysis of long-term data obtained from the Holetta Agricultural Research Center and a survey conducted in the study area. ZPLAN+ software was used to predict estimates of genetic gain (GG) and discounted profit for goal traits. The predicted genetic gains (GGs) for milk yield (MY) per year were 34.52 kg, 49.63 kg, 29.35 kg, 76.16 kg, and 77.51 kg for SPT, FPT, SFPT, GS, and GPT, respectively. The GGs of the other goal traits range from 0.69 to 1.19 days per year for age at first calving, from 1.20 to 2.35 days per year for calving interval, and from 0.06 to 0.12 days per year for herd life. Compared to conventional BPs, genomic systems (GPT and GS) enhanced the GG of MY by 53%-164%, reduced generation interval by up to 21%, and improved the accuracy of test bull selection from 0.33 to 0.43. The discounted profit of the BPs varied from 249.58 Ethiopian Birr (ETB, 1 USD = 39.55696 ETB) per year in SPT to 689.79 ETB per year in GS. Genomic selection outperforms SPT, SFPT, and FPT by 266, 227%, and 138% of discounted profit, respectively. Community-based crossbreeding accompanied by GS and gradual support with progeny testing (GPT) is recommended as the main way forward to attain better genetic progress in dairy farms in Ethiopia and similar scenarios in other tropical countries.

Genetic analysis of phenotypic indicators for heat tolerance in crossbred dairy cattle

Climate change-induced rise in global temperatures has intensified heat stress on dairy cattle and is contributing to the generally observed low milk productivity. Selective breeding aimed at enhancing animals' ability to withstand rising temperatures while maintaining optimal performance is crucial for ensuring future access to dairy products. However, phenotypic indicators of heat tolerance are yet to be effectively factored into the objectives of most selective breeding programs. This study investigated the response of milk production to changing heat load as an indication of heat tolerance and the influence of calving season on this response in multibreed dairy cattle performing in three agroecological zones Kenya. First-parity 7-day average milk yield (65 261 milk records) of 1 739 cows were analyzed. Based on routinely recorded weather data that were accessible online, the Temperature-Humidity Index (THI) was calculated and used as a measure of heat load. THI measurements used represented averages of the same 7-day periods corresponding to each 7-day average milk record. Random regression models, including reaction norm functions, were fitted to derive two resilience indicators: slope of the reaction norm (Slope) and its absolute value (Absolute), reflecting changes in milk yield in response to the varying heat loads (THI 50 and THI 80). The genetic parameters of these indicators were estimated, and their associations with average test-day milk yield were examined. There were no substantial differences in the pattern of milk yield response to heat load between cows calving in dry and wet seasons. Animals with ≤50% Bos taurus genes were the most thermotolerant at extremely high heat load levels. Animals performing in semi-arid environments exhibited the highest heat tolerance capacity. Heritability estimates for these indicators ranged from 0.06 to 0.33 and were mostly significantly different from zero (P < 0.05). Slope at THI 80 had high (0.64-0.71) negative correlations with average daily milk yield, revealing that high-producing cows are more vulnerable to heat stress and vice versa. A high (0.63-0.74) positive correlation was observed between Absolute and average milk yield at THI 80. This implied that low milk-producing cows have a more stable milk production under heat-stress conditions and vice versa. The study demonstrated that the slope of the reaction norms and its absolute value can effectively measure the resilience of crossbred dairy cattle to varying heat load conditions. The implications of these findings are valuable in improving the heat tolerance of livestock species through genetic selection.

A Genome-Wide Association Study for Resistance to Tropical Theileriosis in Two Bovine Portuguese Autochthonous Breeds

The control of Tropical Theileriosis, a tick-borne disease with a strong impact on cattle breeding, can be facilitated using marker-assisted selection in breeding programs. Genome-wide association studies (GWAS) using high-density arrays are extremely important for the ongoing process of identifying genomic variants associated with resistance to Theileria annulata infection. In this work, single-nucleotide polymorphisms (SNPs) were analyzed in the Portuguese autochthonous cattle breeds Alentejana and Mertolenga. In total, 24 SNPs suggestive of significance (p ≤ 10-4) were identified for Alentejana cattle and 20 SNPs were identified for Mertolenga cattle. The genomic regions around these SNPs were further investigated for annotated genes and quantitative trait loci (QTLs) previously described by other authors. Regarding the Alentejana breed, the MAP3K1, CMTM7, SSFA2, and ATG13 genes are located near suggestive SNPs and appear as candidate genes for resistance to Tropical Theileriosis, considering its action in the immune response and resistance to other diseases. On the other hand, in the Mertolenga breed, the UOX gene is also a candidate gene due to its apparent link to the pathogenesis of the disease. These results may represent a first step toward the possibility of including genetic markers for resistance to Tropical Theileriosis in current breed selection programs.

Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale

Linkage disequilibrium (LD) affects genomic studies accuracy. High-density genotyping platforms identify SNPs across animal genomes, increasing LD evaluation resolution for accurate analysis. This study aimed to evaluate the decay and magnitude of LD in a cohort of 81 crossbred dairy cattle using the GGP_HDv3_C Bead Chip. After quality control, 116,710 Single Nucleotide Polymorphisms (SNPs) across 2520.241 Mb of autosomes were retained. LD extent was assessed between autosomal SNPs within a 10 Mb range using the r2 statistics. LD value declined as inter-marker distance increased. The average r2 value was 0.24 for SNP pairs < 10 kb apart, decreasing to 0.13 for 50-100 kb distances. Minor allele frequency (MAF) and sample size significantly impact LD. Lower MAF thresholds result in smaller r2 values, while higher thresholds show increased r2 values. Additionally, smaller sample sizes exhibit higher average r2 values, especially for larger physical distance intervals (> 50 kb) between SNP pairs. Effective population size and inbreeding coefficient were 150 and 0.028 for the present generation, indicating a decrease in genetic diversity over time. These findings imply that the utilization of high-density SNP panels and customized/breed-specific SNP panels represent a highly favorable approach for conducting genome-wide association studies (GWAS) and implementing genomic selection (GS) in the Bos indicus cattle breeds, whose genomes are still largely unexplored. Furthermore, it is imperative to devise a meticulous breeding strategy tailored to each herd, aiming to enhance desired traits while simultaneously preserving genetic diversity.

Progress and future perspectives of livestock genomics in India: a mini review

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India.

Early Weaning Possibly Increases the Activity of Lipogenic and Adipogenic Pathways in Intramuscular Adipose Tissue of Nellore Calves

This study aimed to evaluate by wide-expression profile analysis how early weaning at 120 days can alter the skeletal muscle metabolism of calves supplemented with a concentrated diet until the growth phase. Longissimus thoracis muscle samples were obtained by biopsy from two groups of calves, early weaned (EW; n = 8) and conventionally weaned (CW; n = 8) at two different times (120 days of age-T1 [EW] and 205 days of age-T2 [CW]). Next, differential gene expression analysis and functional enrichment of metabolic pathways and biological processes were performed. The results showed respectively 658 and 165 differentially expressed genes when T1 and T2 were contrasted in the early weaning group and when early and conventionally weaned groups were compared at T2. The FABP4, SCD1, FASN, LDLR, ADIPOQ, ACACA, PPARD, and ACOX3 genes were prospected in both comparisons described above. Given the key role of these differentially expressed genes in lipid and fatty acid metabolism, the results demonstrate the effect of diet on the modulation of energy metabolism, particularly favoring postnatal adipogenesis and lipogenesis, as well as a consequent trend in obtaining better quality cuts, as long as an environment for the maintenance of these alterations until adulthood is provided.

A review of machine learning models applied to genomic prediction in animal breeding

The advent of modern genotyping technologies has revolutionized genomic selection in animal breeding. Large marker datasets have shown several drawbacks for traditional genomic prediction methods in terms of flexibility, accuracy, and computational power. Recently, the application of machine learning models in animal breeding has gained a lot of interest due to their tremendous flexibility and their ability to capture patterns in large noisy datasets. Here, we present a general overview of a handful of machine learning algorithms and their application in genomic prediction to provide a meta-picture of their performance in genomic estimated breeding values estimation, genotype imputation, and feature selection. Finally, we discuss a potential adoption of machine learning models in genomic prediction in developing countries. The results of the reviewed studies showed that machine learning models have indeed performed well in fitting large noisy data sets and modeling minor nonadditive effects in some of the studies. However, sometimes conventional methods outperformed machine learning models, which confirms that there's no universal method for genomic prediction. In summary, machine learning models have great potential for extracting patterns from single nucleotide polymorphism datasets. Nonetheless, the level of their adoption in animal breeding is still low due to data limitations, complex genetic interactions, a lack of standardization and reproducibility, and the lack of interpretability of machine learning models when trained with biological data. Consequently, there is no remarkable outperformance of machine learning methods compared to traditional methods in genomic prediction. Therefore, more research should be conducted to discover new insights that could enhance livestock breeding programs.

(Quasi) multitask support vector regression with heuristic hyperparameter optimization for whole-genome prediction of complex traits: a case study with carcass traits in broilers

This study investigates nonlinear kernels for multitrait (MT) genomic prediction using support vector regression (SVR) models. We assessed the predictive ability delivered by single-trait (ST) and MT models for 2 carcass traits (CT1 and CT2) measured in purebred broiler chickens. The MT models also included information on indicator traits measured in vivo [Growth and feed efficiency trait (FE)]. We proposed an approach termed (quasi) multitask SVR (QMTSVR), with hyperparameter optimization performed via genetic algorithm. ST and MT Bayesian shrinkage and variable selection models [genomic best linear unbiased predictor (GBLUP), BayesC (BC), and reproducing kernel Hilbert space (RKHS) regression] were employed as benchmarks. MT models were trained using 2 validation designs (CV1 and CV2), which differ if the information on secondary traits is available in the testing set. Models' predictive ability was assessed with prediction accuracy (ACC; i.e. the correlation between predicted and observed values, divided by the square root of phenotype accuracy), standardized root-mean-squared error (RMSE*), and inflation factor (b). To account for potential bias in CV2-style predictions, we also computed a parametric estimate of accuracy (ACCpar). Predictive ability metrics varied according to trait, model, and validation design (CV1 or CV2), ranging from 0.71 to 0.84 for ACC, 0.78 to 0.92 for RMSE*, and between 0.82 and 1.34 for b. The highest ACC and smallest RMSE* were achieved with QMTSVR-CV2 in both traits. We observed that for CT1, model/validation design selection was sensitive to the choice of accuracy metric (ACC or ACCpar). Nonetheless, the higher predictive accuracy of QMTSVR over MTGBLUP and MTBC was replicated across accuracy metrics, besides the similar performance between the proposed method and the MTRKHS model. Results showed that the proposed approach is competitive with conventional MT Bayesian regression models using either Gaussian or spike-slab multivariate priors.

A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan

Domestic buffaloes (Bubalus bubalis), known as water buffaloes, play a key role as versatile multipurpose agricultural animals in the Asiatic region. Pakistan, with the second-largest buffalo population in the world, holds a rich domestication history of buffaloes. The overall trends in buffalo production demand the genomic characterization of Pakistani buffalo breeds. To this end, the resequencing data of Pakistani breeds, along with buffalo breeds from 13 other countries, were retrieved from our previous study. This dataset, which contained 34,671,886 single-nucleotide polymorphisms (SNPs), was analyzed through a pipeline that was developed to compare possible allele differences among breeds at each SNP position. In contrast, other available tools only check for positional SNP differences for breed-specific markers. In total, 1918, 1549, 404, and 341 breed-specific markers were identified to characterize the Nili, Nili-Ravi, Azakheli, and Kundi breeds of Pakistani buffalo, respectively. Sufficient evidence in the form of phenotypic data, principal component analysis, admixture analysis, and linkage analysis showed that the Nili breed has maintained its distinct breed status despite sharing a close evolutionary relationship with the Nili-Ravi breed of buffalo. In this era of genome science, the conservation of these breeds and the further validation of the given selection markers in larger populations is a pressing need.

Selective genotyping to implement genomic selection in beef cattle breeding

Genomic selection (GS) plays an essential role in livestock genetic improvement programs. In dairy cattle, the method is already a recognized tool to estimate the breeding values of young animals and reduce generation intervals. Due to the different breeding structures of beef cattle, the implementation of GS is still a challenge and has been adopted to a much lesser extent than dairy cattle. This study aimed to evaluate genotyping strategies in terms of prediction accuracy as the first step in the implementation of GS in beef while some restrictions were assumed for the availability of phenotypic and genomic information. For this purpose, a multi-breed population of beef cattle was simulated by imitating the practical system of beef cattle genetic evaluation. Four genotyping scenarios were compared to traditional pedigree-based evaluation. Results showed an improvement in prediction accuracy, albeit a limited number of animals being genotyped (i.e., 3% of total animals in genetic evaluation). The comparison of genotyping scenarios revealed that selective genotyping should be on animals from both ancestral and younger generations. In addition, as genetic evaluation in practice covers traits that are expressed in either sex, it is recommended that genotyping covers animals from both sexes.

Detection of Candidate Genes Associated with Fecundity through Genome-Wide Selection Signatures of Katahdin Ewes

One of the strategies to genetically improve reproductive traits, despite their low inheritability, has been the identification of candidate genes. Therefore, the objective of this study was to detect candidate genes associated with fecundity through the fixation index (F_ST) and runs of homozygosity (ROH) of selection signatures in Katahdin ewes. Productive and reproductive records from three years were used and the genotypes (OvineSNP50K) of 48 Katahdin ewes. Two groups of ewes were identified to carry out the genetic comparison: with high fecundity (1.3 ± 0.03) and with low fecundity (1.1 ± 0.06). This study shows for the first time evidence of the influence of the CNOT11, GLUD1, GRID1, MAPK8, and CCL28 genes in the fecundity of Katahdin ewes; in addition, new candidate genes were detected for fecundity that were not reported previously in ewes but that were detected for other species: ANK2 (sow), ARHGAP22 (cow and buffalo cow), GHITM (cow), HERC6 (cow), DPF2 (cow), and TRNAC-GCA (buffalo cow, bull). These new candidate genes in ewes seem to have a high expression in reproduction. Therefore, future studies are needed focused on describing the physiological basis of changes in the reproductive behavior influenced by these genes.

Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle

Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China. It is a small to medium-sized breed with slower growth, but with good meat quality and fat deposition. Genetic markers could be used for the estimation of population genetic structure and genetic parameters. In this work, we genotyped the DBSC breeding population (n = 235) with the GeneSeek Genomic Profiler (GGP) 100 k density genomic chip. Genotype data of 222 individuals and 81,579 SNPs were retained after quality control. The average minor allele frequency (MAF) was 0.20 and the average linkage disequilibrium (LD) level (r²) was 0.67 at a distance of 0-50 Kb. The estimated relationship coefficient and effective population size (Ne) were 0.023 and 86 for the current generation. In addition, we used genotype data to estimate the genetic parameters of the population's phenotypic traits. Among them, height at hip cross (HHC) and shin circumference (SC) were rather high heritability traits, with heritability of 0.41 and 0.54, respectively. The results reflected the current cattle population's extent of inbreeding and history. Through the principal breeding parameters, genomic breeding would significantly improve the genetic progress of breeding.

Genomic selection in tropical perennial crops and plantation trees: a review

To overcome the multiple challenges currently faced by agriculture, such as climate change and soil deterioration, more efficient plant breeding strategies are required. Genomic selection (GS) is crucial for the genetic improvement of quantitative traits, as it can increase selection intensity, shorten the generation interval, and improve selection accuracy for traits that are difficult to phenotype. Tropical perennial crops and plantation trees are of major economic importance and have consequently been the subject of many GS articles. In this review, we discuss the factors that affect GS accuracy (statistical models, linkage disequilibrium, information concerning markers, relatedness between training and target populations, the size of the training population, and trait heritability) and the genetic gain expected in these species. The impact of GS will be particularly strong in tropical perennial crops and plantation trees as they have long breeding cycles and constrained selection intensity. Future GS prospects are also discussed. High-throughput phenotyping will allow constructing of large training populations and implementing of phenomic selection. Optimized modeling is needed for longitudinal traits and multi-environment trials. The use of multi-omics, haploblocks, and structural variants will enable going beyond single-locus genotype data. Innovative statistical approaches, like artificial neural networks, are expected to efficiently handle the increasing amounts of heterogeneous multi-scale data. Targeted recombinations on sites identified from profiles of marker effects have the potential to further increase genetic gain. GS can also aid re-domestication and introgression breeding. Finally, GS consortia will play an important role in making the best of these opportunities.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01326-4.

Trajectory of livestock genomics in South Asia: A comprehensive review

Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus)

The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.

Genetic diversity in reproductive traits of Braunvieh cattle determined with SNP markers

Braunvieh is an important dual‐purpose breed in the Mexican tropics. The study of its genetic diversity is key to implementing genetic improvement programs. This study was conducted to determine genetic diversity of reproductive traits in a Mexican Braunvieh beef cattle population using single nucleotide polymorphisms in candidate genes. Information from 24 genes with 52 intra‐genic loci reported in literature to be associated with productive life, pregnancy rate and cow and heifer conception rate of 150 Braunvieh males and females was considered. Observed heterozygosity (Ho) revealed high genetic diversity for the studied traits, Ho = 0.42 ± 0.087, relative to that of other populations of the same breed. Cluster analyses were carried out using the Ward and K‐means algorithms. These analyses revealed high genetic diversity that was observed in the biplot of non‐metric multi‐dimensional scaling. It was found that clustering strategy allowed visualisation of distant groups by genotype but not by favourable alleles in all the loci. We found that the genes CSNK1E, DNAH11, DSC2, IBSP and OCLN affected most of the traits in our study and they were highly informative. Therefore, they represent a potential resource for selection and crossbreeding programs of the traits studied in Braunvieh. The analyses showed that the Mexican Braunvieh population has a high level of genetic diversity, arguably due to decades‐long adaptation to the Mexican tropics.

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals' life, a potentially important aspect in the study of the traits' genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50-60 Mb), while the hotspot associated with CF and DP was on BTA18 (55-62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.

Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle

Mastitis is a disease that causes significant economic losses, since resistance to mastitis is a difficult trait to be improved due to its multifactorial occurrence. Therefore, our objective was to characterize a Mexican Braunvieh cattle population for genetic resistance and susceptibility to mastitis. We used 66 SNP markers for 45 candidate genes in 150 animals. The average heterozygosity was 0.445 ± 0.076, a value higher than those reported for some European breeds. The inbreeding coefficient was slightly negative for resistance to subclinical (−0.058 ± 0.055) and clinical (−0.034 ± 0.076) mastitis, possibly due to low selection for the immunological candidate genes that influence these traits. The genotypic profiles for the candidate loci per K-means group were obtained, as well as the group distribution through the graphics of the principal component analysis. The genotypic profiles showed high genetic diversity among groups. Resistance to clinical mastitis had the lowest presence of the heterozygous genotypes. Although the percentage of highly inbred animals (>50%) is up to 13.3%, there are highly heterozygous groups in terms of the studied traits, a favorable indicator of the presence of genetic diversity. The results of this study constitute evidence of the genetic potential of the Mexican Braunvieh population to improve mastitis-related traits.

FMixFN: A Fast Big Data-Oriented Genomic Selection Model Based on an Iterative Conditional Expectation algorithm

Genomic selection is an approach to select elite breeding stock based on the use of dense genetic markers and that has led to the development of various models to derive a predictive equation. However, the current genomic selection software faces several issues such as low prediction accuracy, low computational efficiency, or an inability to handle large-scale sample data. We report the development of a genomic prediction model named FMixFN with four zero-mean normal distributions as the prior distributions to optimize the predictive ability and computing efficiency. The variance of the prior distributions in our model is precisely determined based on an F2 population, and genomic estimated breeding values (GEBV) can be obtained accurately and quickly in combination with an iterative conditional expectation algorithm. We demonstrated that FMixFN improves computational efficiency and predictive ability compared to other methods, such as GBLUP, SSgblup, MIX, BayesR, BayesA, and BayesB. Most importantly, FMixFN may handle large-scale sample data, and thus should be able to meet the needs of large breeding companies or combined breeding schedules. Our study developed a Bayes genomic selection model called FMixFN, which combines stable predictive ability and high computational efficiency, and is a big data-oriented genomic selection model that has potential in the future. The FMixFN method can be freely accessed at https://zenodo.org/record/5560913 (DOI: 10.5281/zenodo.5560913).

Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data

Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.

Genome-wide association study on milk production and somatic cell score for Thai dairy cattle using weighted single-step approach with random regression test-day model

Genome-wide association studies are a powerful tool to identify genomic regions and variants associated with phenotypes. However, only limited mutual confirmation from different studies is available. The objectives of this study were to identify genomic regions as well as genes and pathways associated with the first-lactation milk, fat, protein, and total solid yields; fat, protein, and total solid percentage; and somatic cell score (SCS) in a Thai dairy cattle population. Effects of SNPs were estimated by a weighted single-step GWAS, which back-solved the genomic breeding values predicted using single-step genomic BLUP (ssGBLUP) fitting a single-trait random regression test-day model. Genomic regions that explained at least 0.5% of the total genetic variance were selected for further analyses of candidate genes. Despite the small number of genotyped animals, genomic predictions led to an improvement in the accuracy over the traditional BLUP. Genomic predictions using weighted ssGBLUP were slightly better than the ssGBLUP. The genomic regions associated with milk production traits contained 210 candidate genes on 19 chromosomes [Bos taurus autosome (BTA) 1 to 7, 9, 11 to 16, 20 to 21, 26 to 27 and 29], whereas 21 candidate genes on 3 chromosomes (BTA 11, 16, and 21) were associated with SCS. Many genomic regions explained a small fraction of the genetic variance, indicating polygenic inheritance of the studied traits. Several candidate genes coincided with previous reports for milk production traits in Holstein cattle, especially a large region of genes on BTA14. We identified 141 and 5 novel genes related to milk production and SCS, respectively. These novel genes were also found to be functionally related to heat tolerance (e.g., SLC45A2, IRAG1, and LOC101902172), longevity (e.g., SYT10 and LOC101903327), and fertility (e.g., PAG1). These findings may be attributed to indirect selection in our population. Identified biological networks including intracellular cell transportation and protein catabolism implicate milk production, whereas the immunological pathways such as lymphocyte activation are closely related to SCS. Further studies are required to validate our findings before exploiting them in genomic selection.

Genomic prediction of milk-production traits and somatic cell score using single-step genomic best linear unbiased predictor with random regression test-day model in Thai dairy cattle

Cow genotypes are expected to improve the accuracy of genomic estimated breeding values (GEBV) for young bulls in relatively small populations such as Thai Holstein-Friesian crossbred dairy cattle in Thailand. The objective of this study was to investigate the effect of cow genotypes on the predictive ability and individual accuracies of GEBV for young dairy bulls in Thailand. Test-day data included milk yield (n = 170,666), milk component traits (fat yield, protein yield, total solids yield, fat percentage, protein percentage, and total solids percentage; n = 160,526), and somatic cell score (n = 82,378) from 23,201, 82,378, and 13,737 (for milk yield, milk component traits, and SCS, respectively) cows calving between 1993 and 2017, respectively. Pedigree information included 51,128; 48,834; and 32,743 animals for milk yield, milk component traits, and somatic cell score, respectively. Additionally, 876, 868, and 632 pedigreed animals (for milk yield, milk component traits, and SCS, respectively) were genotyped (152 bulls and 724 cows), respectively, using Illumina Bovine SNP50 BeadChip. We cut off the data in the last 6 yr, and the validation animals were defined as genotyped bulls with no daughters in the truncated set. We calculated GEBV using a single-step random regression test-day model (SS-RR-TDM), in comparison with estimated breed value (EBV) based on the pedigree-based model used as the official method in Thailand (RR-TDM). Individual accuracies of GEBV were obtained by inverting the coefficient matrix of the mixed model equations, whereas validation accuracies were measured by the Pearson correlation between deregressed EBV from the full data set and (G)EBV predicted with the reduced data set. When only bull genotypes were used, on average, SS-RR-TDM increased individual accuracies by 0.22 and validation accuracies by 0.07, compared with RR-TDM. With cow genotypes, the additional increase was 0.02 for individual accuracies and 0.06 for validation accuracies. The inflation of GEBV tended to be reduced using cow genotypes. Genomic evaluation by SS-RR-TDM is feasible to select young bulls for the longitudinal traits in Thai dairy cattle, and the accuracy of selection is expected to be increased with more genotypes. Genomic selection using the SS-RR-TDM should be implemented in the routine genetic evaluation of the Thai dairy cattle population. The genetic evaluation should consider including genotypes of both sires and cows.

Imaging diagnosis of canine hip dysplasia with and without human exposure to ionizing radiation

Hip dysplasia (HD) is one of the most common hereditary orthopaedic diseases in dogs, with serious implications for the quality of life of the affected animals. Radiographic screening is essential for the selection of breeding stock in some at-risk breeds, and radiography is also used in the diagnosis of clinical HD cases. A definitive diagnosis of HD is based on radiographic examination, and the most commonly used view is the ventrodorsal hip extended projection, sometimes in combination with various hip stress-based techniques. Radiographic images require high quality positioning and dogs are usually anesthetized and often manually restrained to facilitate optimal positioning. The 'as low as reasonably achievable' (ALARA) principle used in human radioprotection is not always fulfilled in veterinary practice, except in the UK, where human exposure to ionizing radiation in veterinary medicine is strictly regulated. While each dose of ionizing radiation is small, doses accumulate over a lifetime, which can eventually result in substantial radiation exposure. Therefore, manual restraint should be avoided and mechanical immobilization, sedation or general anaesthesia should be used. This review examines the biological effects of human exposure to ionizing radiation and common sources of veterinary exposure. The diagnostic quality of imaging methods for the diagnosis of canine HD is compared between manually restrained and hands-free dog positioning. Hands-free radiographic techniques are available to assess hip laxity, degenerative joint changes and hip osseous structure while preserving image quality, and can be used to select animals for breeding or for the diagnosis of HD.

Genomic prediction of crossbred dairy cattle in Tanzania: A route to productivity gains in smallholder dairy systems

Selection based on genomic predictions has become the method of choice for genetic improvement in dairy cattle. This offers huge opportunity for developing countries with little or no pedigree data, and preliminary studies have shown promising results. The African Dairy Genetic Gains (ADGG) project initiated a digital system of dairy performance data collection, accompanied by genotyping in Tanzania in 2016. Currently, ADGG has the largest body of dairy performance data generated in East Africa from a smallholder dairy system. This study examines the use of genomic best linear unbiased prediction (GBLUP) and single-step (ss)GBLUP for the estimation of genetic parameters and accuracy of genomic prediction for daily milk yield and body weight in Tanzania. The estimates of heritability for daily milk yield from GBLUP and ssGBLUP were essentially the same, at 0.12 ± 0.03. The heritability estimates for daily milk yield averaged over the whole lactation from random regression model (RRM) GBLUP or ssGBLUP were 0.22 and 0.24, respectively. The heritability of body weight from GBLUP was 0.24 ± 04 but was 0.22 ± 04 from the ssGBLUP analysis. Accuracy of genomic prediction for milk yield from a forward validation was 0.57 for GBLUP based on fixed regression model or 0.55 from an RRM. Corresponding estimates from ssGBLUP were 0.59 and 0.53, respectively. Accuracy for body weight, however, was much higher at 0.83 from GBLUP and 0.77 for ssGBLUP. The moderate to high levels of accuracy of genomic prediction (0.53-0.83) obtained for milk yield and body weight indicate that selection on the basis of genomic prediction is feasible in smallholder dairy systems and most probably the only initial possible pathway to implementing sustained genetic improvement programs in such systems.

Genomic selection in Gir cattle using female reference population

When a sizeable reference population of proven bulls is not available for implementing Genomic selection for a particular trait, and when a recording of certain traits on large scale is difficult, the use of a female reference population is recommended. Gir, one of the important milk purpose cattle breeds of India falls under this category. There is no large scale Progeny Testing (PT) programme in Gir, so proven bulls based on daughter performance in large numbers are not available. Considering the constraints, a genomic BLUP (GBLUP) model was implemented based on recorded cow reference population in Gir breed. Cows (3491) and 23 bulls were genotyped using INDUSCHIP for this purpose. Due to non-availability of pedigreed data, conventional breeding values (BV) of bulls and their reliabilities were not known. For comparison, assumed theoretical reliability of BV of a bull selected based on its dam's yield was compared with reliability obtained for genomic breeding value (GBV) using a GBLUP model. The reliability estimates for GBVs were 4 times higher than that for BVs. The predictive ability of the model was demonstrated by measuring the correlation between corrected phenotypes and GBVs for animals whose records were masked in a five-fold cross-validation study. The correlation was around 0.45 showing reasonable predictability of the GBLUP model. The GBVs were not biased. The regression coefficient between the corrected phenotype and GBV was 1.045. The present study demonstrates that it is feasible to implement genomic selection in Gir cattle in Indian conditions using a female reference population. It is expected that the bulls can be selected with around 4 fold more accuracy than the current method of selecting based on their dams' yield accelerating expected genetic growth in Gir cattle.

Genomic Prediction in Local Breeds: The Rendena Cattle as a Case Study

Simple Summary

Although genomic selection is being used in many livestock species, it has not yet been considered in local breeds due to the lower population size and the potential less effective impact on the genetic evaluation of these breeds. The current research aims to investigate how genomic data can impact the accuracy of genetic predictions for beef traits in Rendena, a small local cattle breed of the North-East of Italy selected for a dual purpose. Classical animal models using only phenotypic information were compared with two models that integrated genomic data with pedigree information. The genomic models presented better accuracy in estimated breeding values of the animals than the ‘classical’ animal model, especially the ‘simpler’ one assuming homogeneous variances of single nucleotide polymorphisms. Our results show that the inclusion of genomic information can be successfully applied to breeding selection scenarios even in small local cattle breeds such as Rendena.

Abstract

The maintenance of local cattle breeds is key to selecting for efficient food production, landscape protection, and conservation of biodiversity and local cultural heritage. Rendena is an indigenous cattle breed from the alpine North-East of Italy, selected for dual purpose, but with lesser emphasis given to beef traits. In this situation, increasing accuracy for beef traits could prevent detrimental effects due to the antagonism with milk production. Our study assessed the impact of genomic information on estimated breeding values (EBVs) in Rendena performance-tested bulls. Traits considered were average daily gain, in vivo EUROP score, and in vivo estimate of dressing percentage. The final dataset contained 1691 individuals with phenotypes and 8372 animals in pedigree, 1743 of which were genotyped. Using the cross-validation method, three models were compared: (i) Pedigree-BLUP (PBLUP); (ii) single-step GBLUP (ssGBLUP), and (iii) weighted single-step GBLUP (WssGBLUP). Models including genomic information presented higher accuracy, especially WssGBLUP. However, the model with the best overall properties was the ssGBLUP, showing higher accuracy than PBLUP and optimal values of bias and dispersion parameters. Our study demonstrated that integrating phenotypes for beef traits with genomic data can be helpful to estimate EBVs, even in a small local breed.

Genomic Prediction of Average Daily Gain, Back-Fat Thickness, and Loin Muscle Depth Using Different Genomic Tools in Canadian Swine Populations

Improvement of prediction accuracy of estimated breeding values (EBVs) can lead to increased profitability for swine breeding companies. This study was performed to compare the accuracy of different popular genomic prediction methods and traditional best linear unbiased prediction (BLUP) for future performance of back-fat thickness (BFT), average daily gain (ADG), and loin muscle depth (LMD) in Canadian Duroc, Landrace, and Yorkshire swine breeds. In this study, 17,019 pigs were genotyped using Illumina 60K and Affymetrix 50K panels. After quality control and imputation steps, a total of 41,304, 48,580, and 49,102 single-nucleotide polymorphisms remained for Duroc (n = 6,649), Landrace (n = 5,362), and Yorkshire (n = 5,008) breeds, respectively. The breeding values of animals in the validation groups (n = 392–774) were predicted before performance test using BLUP, BayesC, BayesCπ, genomic BLUP (GBLUP), and single-step GBLUP (ssGBLUP) methods. The prediction accuracies were obtained using the correlation between the predicted breeding values and their deregressed EBVs (dEBVs) after performance test. The genomic prediction methods showed higher prediction accuracies than traditional BLUP for all scenarios. Although the accuracies of genomic prediction methods were not significantly (P > 0.05) different, ssGBLUP was the most accurate method for Duroc-ADG, Duroc-LMD, Landrace-BFT, Landrace-ADG, and Yorkshire-BFT scenarios, and BayesCπ was the most accurate method for Duroc-BFT, Landrace-LMD, and Yorkshire-ADG scenarios. Furthermore, BayesCπ method was the least biased method for Duroc-LMD, Landrace-BFT, Landrace-ADG, Yorkshire-BFT, and Yorkshire-ADG scenarios. Our findings can be beneficial for accelerating the genetic progress of BFT, ADG, and LMD in Canadian swine populations by selecting more accurate and unbiased genomic prediction methods.

Evaluating efficiency of customized medium density INDUSCHIP for genotyping of Indicine cattle breeds

To initiate genomic selection programme for indicine cattle breeds and their crosses in India, National Dairy Development Board designed a medium-density (52K) customized chip on Illumina platform named as “INDUSCHIP”. The present study was conducted to examine the efficiency of INDUSCHIP SNP panel for genotyping indicine cattle breeds. Total of 500 animals belonging to 14 different indicine breeds were genotyped with Illumina Bovine HD chip. A subset of SNPs was taken for evaluating the performance of selected SNPs in different indicine breeds. The average minor allele frequency (MAF) was found to vary between 0.20–0.29 for different indicine breeds. However, for important milk breeds like Sahiwal, Gir, Red Sindhi and Kankrej the average MAF was found to be 0.27 and above. Mean Linkage Disequilibrium (LD) at 50–60 kbp distance was found to be around 0.21. There was considerable LD decay with increasing distance between SNPs. Around 0.06% SNPs were found to be significantly deviating from Hardy-Weinberg equilibrium. From the Principal component analysis (PCA) it was found that the first three Principal Components i.e. PC1, PC2 and PC3) could separate different indicine breeds. The present study indicated that due to the presence of highly polymorphic SNPs for the breeds of indicine origin, INDUSCHIP panel was found to be effective and informative in genotyping indicine breeds.

Genomic Selection for Any Dairy Breeding Program via Optimized Investment in Phenotyping and Genotyping

This paper evaluates the potential of maximizing genetic gain in dairy cattle breeding by optimizing investment into phenotyping and genotyping. Conventional breeding focuses on phenotyping selection candidates or their close relatives to maximize selection accuracy for breeders and quality assurance for producers. Genomic selection decoupled phenotyping and selection and through this increased genetic gain per year compared to the conventional selection. Although genomic selection is established in well-resourced breeding programs, small populations and developing countries still struggle with the implementation. The main issues include the lack of training animals and lack of financial resources. To address this, we simulated a case-study of a small dairy population with a number of scenarios with equal available resources yet varied use of resources for phenotyping and genotyping. The conventional progeny testing scenario collected 11 phenotypic records per lactation. In genomic selection scenarios, we reduced phenotyping to between 10 and 1 phenotypic records per lactation and invested the saved resources into genotyping. We tested these scenarios at different relative prices of phenotyping to genotyping and with or without an initial training population for genomic selection. Reallocating a part of phenotyping resources for repeated milk records to genotyping increased genetic gain compared to the conventional selection scenario regardless of the amount and relative cost of phenotyping, and the availability of an initial training population. Genetic gain increased by increasing genotyping, despite reduced phenotyping. High-genotyping scenarios even saved resources. Genomic selection scenarios expectedly increased accuracy for young non-phenotyped candidate males and females, but also proven females. This study shows that breeding programs should optimize investment into phenotyping and genotyping to maximize return on investment. Our results suggest that any dairy breeding program using conventional progeny testing with repeated milk records can implement genomic selection without increasing the level of investment.

Genome-wide association study of economically important traits in Charolais and Limousin beef cows

Genomic selection has proven effective for advancing genetic gain for key profit traits in dairy cattle production systems. However, its impact to-date on genetic improvement programs for beef cattle has been less effective. Despite this, the technology is thought to be particularly useful for low heritability traits such as those associated with reproductive efficiency. The objective of this study was to identify genetic variants associated with key determinants of reproductive and overall productive efficiency in beef cows. The analysis employed a large dataset derived from the national genetic evaluation program in Ireland for two of the most predominant beef breeds, viz. Charolais (n = 5 244 cows) and Limousin (n = 7 304 cows). Single nucleotide polymorphisms (SNPs) were identified as being statistically significantly associated (adj. P < 0.05) with both reproductive and productive traits for both breed types. However, there was little across breed commonality, with only two SNPs (rs110240246 and rs110344317; adj. P < 0.05) located within the genomic regions of the LCORL and MSTN genes respectively, identified in both Charolais and Limousin populations, associated with traits including carcass weight, cull-cow weight and live-weight. Significant SNPs within the MSTN gene were also associated with both reproduction and production related traits within each breed. Finally, traits including calving difficulty, calf mortality and calving interval were associated with SNPs within genomic regions comprising genes involved in cellular growth and lipid metabolism. Genetic variants identified as associated with both important reproductive efficiency and production related traits from this study warrant further analyses for their potential incorporation into breeding programmes to support the sustainability of beef cattle production.

Marker-assisted selection vis-à-vis bull fertility: coming full circle-a review

Bull fertility is considered an indispensable trait, as far as farm economics is concerned since it is the successful conception in a cow that provides calf crop, along with the ensuing lactation. This ensures sustainability of a dairy farm. Traditionally, bull fertility did not receive much attention by the farm managers and breeding animals were solely evaluated based on phenotypic predictors, namely, sire conception rate and seminal parameters in bull. With the advent of the molecular era in animal breeding, attempts were made to unravel the genetic complexity of bull fertility by the identification of genetic markers related to the trait. Marker-Assisted Selection (MAS) is a methodology that aims at utilizing the genetic information at markers and selecting improved populations for important traits. Traditionally, MAS was pursued using a candidate gene approach for identifying markers related to genes that are already known to have a physiological function related to the trait but this approach had certain shortcomings like stringent criteria for significance testing. Now, with the availability of genome-wide data, the number of markers identified and variance explained in relation to bull fertility has gone up. So, this presents a unique opportunity to revisit MAS by selection based on the information of a large number of genome-wide markers and thus, improving the accuracy of selection.

Accuracies of direct genomic breeding values for birth and weaning weights of registered Charolais cattle in Mexico

Context Genomic prediction is now routinely used in many livestock species to rank individuals based on genomic breeding values (GEBV). Aims This study reports the first assessment aimed to evaluate the accuracy of direct GEBV for birth (BW) and weaning (WW) weights of registered Charolais cattle in Mexico. Methods The population assessed included 823 animals genotyped with an array of 77000 single nucleotide polymorphisms. Genomic prediction used genomic best linear unbiased prediction (GBLUP), Bayes C (BC), and single-step Bayesian regression (SSBR) methods in comparison with a pedigree-based BLUP method. Key results Our results show that the genomic prediction methods provided low and similar accuracies to BLUP. The prediction accuracy of GBLUP and BC were identical at 0.31 for BW and 0.29 for WW, similar to BLUP. Prediction accuracies of SSBR for BW and WW were up to 4% higher than those by BLUP. Conclusions Genomic prediction is feasible under current conditions, and provides a slight improvement using SSBR. Implications Some limitations on reference population size and structure were identified and need to be addressed to obtain more accurate predictions in liveweight traits under the prevalent cattle breeding conditions of Mexico.