The evolution of tropical adaptation: comparing taurine and zebu cattle

Signatures of selection in Angus and Hanwoo beef cattle using imputed whole genome sequence data

In this study, we detected signatures of selection in Hanwoo and Angus beef cattle using allele frequency and haplotype-based methods based on imputed whole genome sequence variants. Our dataset included 13,202 Angus animals with 10,057,633 imputed SNPs and 10,437 Hanwoo animals with 13,241,550 imputed SNPs. The dataset was subset down to 6,873,624 SNPs in common between the two populations to identify within population (runs of homozygosity, extended haplotype homozygosity) and between population signals of selection (allele fixation index, extended haplotype homozygosity). Assuming these selection signals were complementary to each other, they were combined into a decorrelated composite of multiple signals to identify regions under selection for each of the breeds. 27 genomic regions spanning 25.15 Mb and harboring 360 genes were identified in Angus on chromosomes 1,3, 4, 5, 6, 7, 8, 12, 13, 14, 16, 20, 21 and 28. Similarly, in Hanwoo, 59 genes and 17 genomic regions spanning 5.21 Mb on chromosomes 2, 4, 5, 6, 7, 8, 9, 10, 13, 17, 20 and 24 were identified. Apart from a small region on chromosome 13, there was no major overlap of selection signals between the two breeds reflecting their largely different selection histories, environmental challenges, breeding objectives and breed characteristics. Positional candidate genes identified in selected genomic regions in Angus have been previously associated with growth, immunity, reproductive development, feed efficiency and adaptation to environment while the candidate genes identified in Hanwoo included important genes regulating meat quality, fat deposition, cholesterol metabolism, lipid synthesis, neuronal development, and olfactory reception.

Acute death as a result of poisoning tropical (Bos taurus indicus) but not temperate (Bos taurus taurus) cattle after oral dosing with Lupinus leucophyllus (velvet lupine)

Due to climate change and increasing summer temperatures, tropical cattle may graze where temperate cattle have grazed, exposing tropical cattle to toxic plants they may be unfamiliar with. This work compared the toxicity of Lupinus leucophyllus (velvet lupine) in temperate and tropical cattle. Orally dosed velvet lupine in tropical cattle caused death. If producers opt to graze tropical cattle, additional care must be taken on rangelands where toxic lupines like velvet lupine grow.

The genetic secrets of adaptation: decoding the significance of the 30-bp insertion in the KRT77 gene for Chinese cattle

The KRT77 gene is a type II epithelial cell α-keratin gene family member that plays a crucial role in animal epidermal and coat formation. This study aimed to investigate the relationship between the KRT77 gene and the adaptability of Chinese cattle in varying environments by exploring the distribution of an exon insertion of the KRT77 gene in different cattle populations. Our analysis involved amplifying and sequencing DNA samples from 362 individuals from 24 cattle breeds in China. Our findings reveal a gradual increase in the frequency of insertion from the northwest to the southeast population. We conducted an association analysis between the genotypes and climate data, revealing a correlation between the insertion and local annual mean temperature, relative humidity, and temperature humidity index. The study highlights the significance of the newly identified KRT77 gene insertion as a variation associated with environmental adaptation in Chinese cattle.This insertion variation increased insights into the genetic mechanisms that drive adaptation in Chinese cattle, emphasizing the importance of the 30-bp insertion in the KRT77 gene. Our findings facilitate further research to improve cattle breeding strategies for adaptability to changing environments from the northwest to the southeast population. In conclusion, this study provides value.

A missense mutation (rs209302038) of KRT9 gene associated with heat stress in Chinese cattle

Type I keratin 9 encoded by the KRT9 gene serves an important special function either in the mature palmar and plantar skin tissue. The changes in skin conditions and thickening of the outer layer of the skin may be affected by environmental variables. A missense mutation rs209302038 (NC_037346.1: g.41782870 G > A) was detected in KRT9, which changing the isoleucine into valine. This study aimed to identify the frequency of allele in this locus in Chinese indigenous cattle, and analyze the connection with heat stress. Our results indicated that the frequency of allele A gradually decreases from south to north, while the frequency of G allele showed the opposite pattern. Further analysis of the association of the different genotypes with three climate factors, which showed that the genotypes (GG, GA, AA) were significantly related to climatic conditions (p < 0.01). Therefore, we speculated that the mutation of the rs209302038 in Chinese indigenous cattle might be a genetic marker to detect heat stress.

Growth Dynamics on the Skin and the Coat in Normandian and Simmental Cattle During Adaptation to the Farming Technology in Southwestern Part of Bulgaria

The aim of the present study was to identify the adaptability of Normandy cows raised in a loose system to the climatic and technological conditions and to compare their adaptability with already acclimatized Simmental cows in one farm in Southwestern Bulgaria. Total of 20 cows at same age (II – IV lactation) and same body weight (630-660 kg) from both breeds were classified into 2 groups (each having 10 cows) and subjected to skin thickness measurement, fibers total weight determination and fiber categorization during the winter and summer season. The results have shown that during the winter season, the Normandy breed had significantly higher skin thickness at the elbow compared to the Simmental breed, whereas no differences were observed in the skin thickness between both breeds either at the neck or at the middle of the last rib. During the summer season, the differences on the skin thickness compared to the Simmental breed were observed at the neck (p<0.05), whilst at the elbow and at the middle of the last rib no differences were recorded (p>0.05). During the winter seasons, the coat of Normandy cows contained more soft fibers in comparison to the Simmentals cows. Furthermore, the changes in the observed parameters, influenced by climatic conditions showed similar pattern in both breeds. It can be concluded that the two breeds have emphasized their genetic potential and have a good adaptability to the temperate continental climate of the region.

Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation

Climate change is a major influencing factor in beef production. The greenhouse gases produced from livestock production systems contribute to the overall greenhouse gas emissions. The aim of this study was to identify selection signatures within and between Nguni and Bonsmara cattle in relation to production and adaptation. For this purpose, genomic 150 K single nucleotide polymorphism data from Nguni (n = 231) and Bonsmara (n = 252) cattle in South Africa were used. Extended haplotype homozygosity (EHH) based analysis was executed within each population using integrated haplotype score (iHS). The R package rehh was used for detecting selection signatures across the two populations with cross population EHH (XP-EHH). Total of 121 regions of selection signatures were detected (p < 0.0001) in the Bonsmara and Nguni populations. Several genes relating to DNA methylation, heat stress, feed efficiency and nitrogen metabolism were detected within and between each population. These regions also included QTLs associated with residual feed intake, residual gain, carcass weight, stature and body weight in the Bonsmara, while QTLs associated with conception rate, shear force, tenderness score, juiciness, temperament, heat tolerance, feed efficiency and age at puberty were identified in Nguni. Based on the results of the study it is recommended that the Nguni and Bonsmara be utilized in crossbreeding programs as they have beneficial traits that may allow them to perform better in the presence of climate change. Results of this study coincide with Nguni and Bonsmara breed characteristics and performance, and furthermore support informative crossbreeding programs to enhance livestock productivity in South Africa.

Heat Stress: Effects on Rumen Microbes and Host Physiology, and Strategies to Alleviate the Negative Impacts on Lactating Dairy Cows

Heat stress (HS) in dairy cows causes considerable losses in the dairy industry worldwide due to reduced animal performance, increased cases of metabolic disorders, altered rumen microbiome, and other health problems. Cows subjected to HS showed decreased ruminal pH and acetate concentration and an increased concentration of ruminal lactate. Heat-stressed cows have an increased abundance of lactate-producing bacteria such as Streptococcus and unclassified Enterobacteriaceae, and soluble carbohydrate utilizers such as Ruminobacter, Treponema, and unclassified Bacteroidaceae. Cellulolytic bacteria, especially Fibrobacteres, increase during HS due to a high heat resistance. Actinobacteria and Acetobacter, both acetate-producing bacteria, decreased under HS conditions. Rumen fermentation functions, blood parameters, and metabolites are also affected by the physiological responses of the animal during HS. Isoleucine, methionine, myo-inositol, lactate, tryptophan, tyrosine, 1,5-anhydro-D-sorbitol, 3-phenylpropionic acid, urea, and valine decreased under these conditions. These responses affect feed consumption and production efficiency in milk yield, growth rate, and reproduction. At the cellular level, activation of heat shock transcription factor (HSF) (located throughout the nucleus and the cytoplasm) and increased expression of heat shock proteins (HSPs) are the usual responses to cope with homeostasis. HSP70 is the most abundant HSP family responsible for the environmental stress response, while HSF1 is essential for increasing cell temperature. The expression of bovine lymphocyte antigen and histocompatibility complex class II (DRB3) is downregulated during HS, while HSP90 beta I and HSP70 1A are upregulated. HS increases the expression of the cytosolic arginine sensor for mTORC1 subunits 1 and 2, phosphorylation of mammalian target of rapamycin and decreases the phosphorylation of Janus kinase-2 (a signal transducer and activator of transcription factor-5). These changes in physiology, metabolism, and microbiomes in heat-stressed dairy cows require urgent alleviation strategies. Establishing control measures to combat HS can be facilitated by elucidating mechanisms, including proper HS assessment, access to cooling facilities, special feeding and care, efficient water systems, and supplementation with vitamins, minerals, plant extracts, and probiotics. Understanding the relationship between HS and the rumen microbiome could contribute to the development of manipulation strategies to alleviate the influence of HS. This review comprehensively elaborates on the impact of HS in dairy cows and introduces different alleviation strategies to minimize HS.

A novel missense mutation (rs464874590) within BoLA-DOB gene associated with the heat-resistance in Chinese cattle

Bovine leukocyte antigen, class II, DO beta (BoLA-DOB) is related to antigen presentation, which can triggered by multicul factors. And the condition of immune function determines how much cattle load to heat stress. To evaluate the relationship between heat-resistance and single nucleotide polymorphisms (SNPs) in BoLA-DOB gene, our study has taken further analysis in Chinese indigenous cattle for the first time. A missense single nucleotide polymorphism (rs464874590) was detected in BoLA-DOB gene. We directly sequenced rs464874590 (NM_001013600.1 g.7122762 A > G) in BoLA-DOB gene of 522 individuals of 26 cattle breeds. The frequency of allele G gradually decreases from south to north with distinct climatic distribution characteristics. Further association analysis was carried out between different genotypes and environmental parameters, including annual mean temperature (T), relative humidity (RH), and temperature-humidity index (THI). The result showed that three genotypes were significantly correlated with T, H, and THI (P < 0.01), indicating that GG genotype was distributed in areas with hot and moist conditions. Therefore, our results suggested that the rs464874590 could be applied as a genetic marker to detect the heat-resistance of Chinese indigenous cattle.

[Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds]

Changes in the environment force populations of organisms to adapt to new conditions, either through phenotypic plasticity or through genetic or epigenetic changes. Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. Advances in genetics and biotechnology enable a rapid transfer of unique genetic variants that have originated in local cattle breeds in the process of adaptation to local environments into the genomes of cosmopolitan high-performance breeds, in order to preserve their outstanding performance in new environments. It is also possible to use genomic selection approach to increase the frequency of already present adaptive alleles in cosmopolitan breeds. The review examines recent work on the origin and evolution of Turano-Mongolian cattle breeds, adaptation of Turano-Mongolian cattle to extreme environments, and summarizes available information on potential candidate genes for climate adaptation of Turano-Mongolian breeds, including cold resistance genes, immune response genes, and high-altitude adaptation genes. The authors conclude that the current literature data do not provide preference to one of the two possible scenarios of Turano-Mongolian breed origins: as a result of the domestication of a wild aurochs at East Asia or as a result of the migration of taurine proto-population from the Middle East. Turano-Mongolian breeds show a high degree of adaptation to extreme climatic conditions (cold, heat, lack of oxygen in the highlands) and parasites (mosquitoes, ticks, bacterial and viral infections). As a result of high-density genotyping and sequencing of genomes and transcriptomes, prospective candidate genes and genetic variants involved in adaptation to environmental factors have recently been identified.

Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds

Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.

Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids

Background

CNV comprises a large proportion in cattle genome and is associated with various traits. However, there were few population-scale comparison studies on cattle CNV.

Results

Here, autosome-wide CNVs were called by read depth of NGS alignment result and copy number variation regions (CNVRs) defined from 102 Eurasian taurine (EAT) of 14 breeds, 28 Asian indicine (ASI) of 6 breeds, 22 African taurine (AFT) of 2 breeds, and 184 African humped cattle (AFH) of 17 breeds. The copy number of every CNVRs were compared between populations and CNVRs with population differentiated copy numbers were sorted out using the pairwise statistics V_ST and Kruskal-Wallis test. Three hundred sixty-two of CNVRs were significantly differentiated in both statistics and 313 genes were located on the population differentiated CNVRs.

Conclusion

For some of these genes, the averages of copy numbers were also different between populations and these may be candidate genes under selection. These include olfactory receptors, pathogen-resistance, parasite-resistance, heat tolerance and productivity related genes. Furthermore, breed- and individual-level comparison was performed using the presence or copy number of the autosomal CNVRs. Our findings were based on identification of CNVs from short Illumina reads of 336 individuals and 39 breeds, which to our knowledge is the largest dataset for this type of analysis and revealed important CNVs that may play a role in cattle adaption to various environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07808-7.

Genetic Analyses and Genome-Wide Association Studies on Pathogen Resistance of Bos taurus and Bos indicus Cattle Breeds in Cameroon

Autochthonous taurine and later introduced zebu cattle from Cameroon differ considerably in their resistance to endemic pathogens with little to no reports of the underlying genetic make-up. Breed history and habitat variations are reported to contribute significantly to this diversity worldwide, presumably in Cameroon as well, where locations diverge in climate, pasture, and prevalence of infectious agents. In order to investigate the genetic background, the genotypes of 685 individuals of different Cameroonian breeds were analysed by using the BovineSNP50v3 BeadChip. The variance components including heritability were estimated and genome-wide association studies (GWAS) were performed. Phenotypes were obtained by parasitological screening and categorised in Tick-borne pathogens (TBP), gastrointestinal nematodes (GIN), and onchocercosis (ONC). Estimated heritabilities were low for GIN and TBP (0.079 (se = 0.084) and 0.109 (se = 0.103) respectively) and moderate for ONC (0.216 (se = 0.094)). Further than revealing the quantitative nature of the traits, GWAS identified putative trait-associated genomic regions on five chromosomes, including the chromosomes 11 and 18 for GIN, 20 and 24 for TBP, and 12 for ONC. The results imply that breeding for resistant animals in the cattle population from Northern Cameroon might be possible for the studied pathogens; however, further research in this field using larger datasets will be required to improve the resistance towards pathogen infections, propose candidate genes or to infer biological pathways, as well as the genetic structures of African multi-breed populations.

Investigation of ancestral alleles in the Bovinae subfamily

BACKGROUND

In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study.

RESULTS

Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu.

CONCLUSIONS

Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.

Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China

Mongolian cattle (MG, Bos taurus) and Minnan cattle (MN, Bos indicus) are two different breeds of Chinese indigenous cattle, representing North type and South type, respectively. However, their value and potential have not yet been discovered at the genomic level. In this study, 26 individuals of MN and MG were sequenced for the first time at an average of 13.9- and 12.8-fold, respectively. Large numbers of different variations were identified. In addition, the analyses of phylogenetic and population structure showed that these two cattle breeds are distinct from each other, and results of linkage disequilibrium analysis revealed that these two cattle breeds have undergone various degrees of intense natural or artificial selection. Subsequently, 496 and 306 potential selected genes (PSRs) were obtained in MN and MG, containing 1,096 and 529 potential selected genes (PSGs), respectively. These PSGs, together with the analyzed copy number variation (CNV)-related genes, showed potential relations with their phenotypic characteristics, including environmental adaptability (e.g., DVL2, HSPA4, CDHR4), feed efficiency (e.g., R3HDM1, PLAG1, XKR4), and meat/milk production (e.g., PDHB, LEMD3, APOF). The results of this study help to gain new insights into the genetic characteristics of two distinct cattle breeds and will contribute to future cattle breeding.

A novel missense mutation within KRT75 gene strongly affects heat stress in Chinese cattle

The KRT75 gene (Keratin 75) is a member of the type II epithelial α-keratin gene family which plays a key role in hair and nail formation. And the coat conformation affects heat tolarence in mammals. Therefore, the aim of this study was to identify novel single nucleotide polymorphisms (SNPs) of the KRT75 gene and further evaluate its relation to heat stress in Chinese cattle. A missense mutation (NC_037332.1: g.1052 T > C) of the bovine KRT75 was identified using the Bovine Genome Variation Database (BGVD). The g.1052 T > C variant was then genotyped in 519 individuals of 22 cattle breeds. Further analyses showed that the frequency of T allele in Chinese indigenous cattle breeds gradually diminished from northern groups to southern groups, whereas the frequency of C allele displayed a contrary patternl. Simultaneously, the frequency of the CC and CT genotype for southern groups was much greater than that of the TT genotype. Additionally, association analysis showed the genotypes were remarkably associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (P < 0.01). Our results demonstrated that the KRT75 gene might be a candidate gene associated with the heat stress in Chinese cattle.

The distribution of four missense mutations in SPTBN5 gene across native Chinese breeds

Modern cattle belong to two subspecies, Bos taurus and Bos indicus. Since divergence, cattle types have accumulated different genetic variations, which have contributed to highly differentiated phenotypes. The mammalian inner ear possesses functional and morphological innovations that contribute to its unique hearing capacities. The spectrin beta, non-erythrocytic 5 (SPTBN5) gene has been shown to play an important function in the inner ear. Four missense mutations: rs522333459 (c.7232G > C:p.Cys2411Ser), rs718838405 (c.6568A > C:p.Met2190Leu), rs516536785 (c.6283C > T:p.Leu2095Phe) and rs480278206 (c.4201T > C:p.Cys1401Arg) were identified in the bovine SPTBN5 gene by whole genome resequencing (http://animal.nwsuaf.edu.cn/code/index.php/BosVar), which might be candidate mutations related with hearing of both taurine and indicine cattle. In our study, PCR and DNA sequencing were used to explore the allele frequencies of four mutations of 971 individuals belonging to 38 native Chinese cattle breeds. We find that four mutant alleles showing strong geographic distribution, consisting with the ancestry distribution of taurine and indicine in China. In addition, we identified four mutations of SPTBN5 were diverged in taurine and indicine cattle showing signatures of adaptive evolution in two subspecies, which might participate in bovine inner ear development.

Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data

BACKGROUND

The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics.

RESULTS

A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds.

CONCLUSION

The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.

The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.

Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)

Most of the knowledge about genetic variants at the sequence level in cattle is for Bos primigenius taurus populations. Here, we presented a complete genomic characterization of 52 Nellore (Bos primigenius indicus) bulls, revealing specific zebu DNA variants with putative impact in tropical adaptation and productive traits. Single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) mutations were identified using the newest bovine reference genome ARS_UCD1.2, and variant functional consequences were predicted using the Ensembl VEP software. A total of 35,753,707 SNPs and 4,492,636 INDELs were detected and annotated to their functional effects. We identified 400 genes that comprised both, a SNP and an INDEL, of high functional impact on proteins (i.e. variants that cause protein truncation, loss of function or triggering nonsense-mediated decay). Among these, we highlight the following genes: BoLA, associated with cattle immune response to infections and reproduction aspects; HSPA8, DNAJC27, and DNAJC28, involved with thermoregulatory protective mechanisms in mammals; and many olfactory signaling pathway related genes that are important genetic factors in the evolution of mammalian species. All these functional aspects are directly related to cattle adaptability to tropical environments.

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

Background

Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome.

Results

We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region.

Conclusions

Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.

Evaluation of Milk Colostrum Derived Lactoferrin of Sahiwal (Bos indicus) and Karan Fries (Cross-Bred) Cows for Its Anti-Cancerous Potential

Lactoferrin (Lf) is an iron-binding glycoprotein protein known to have immune-modulatory role and recently, its anticancerous effect against different cancer cell types was emphasized. In the present investigation, a comparative evaluation of anticancer potential of colostrum-derived lactoferrin from Indian native zebu cow (Sahiwal, SAC), crossbred (Karan Fries, KFC) and commercially available (C-Lf) lactoferrin from exotic cow using cellular models was made. A protocol was standardized successfully to purify Lf protein from colostrum of both breeds using HPLC and purity was confirmed by LC-MS. A standardized dose of 750 µg/mL Lf was used to treat two cell types MDA-MB-231 and MCF-7 with Lf from three different sources; SAC-Lf, KFC-Lf and C-Lf for 48 h and 72 h. Different cellular parameters including cytotoxicity, viability, apoptosis and cell proliferation were determined. Comparatively, Lf from commercial source (C-Lf) had maximum effect in both cell types followed by SAC-Lf and KFC-Lf. Further, transcriptional changes in genes associated with apoptosis (Bax and Bcl-2), tumor progression (p53, p21, CD44 and NF-κβ) and survival (survivin) were evaluated in Lf treatment. The overall results strongly emphasized to the fact that Lf purified from cow colostrum has the capacity to inhibit the in vitro growth of cancerous cell lines albeit to a varied extent.

Genetic parameters for hair characteristics and core body temperature in a multibreed Brahman-Angus herd1

Thermal stress in hot humid conditions limits cattle production. The objectives for this study were to estimate genetic parameters for hair characteristics and core body temperature under low and high temperature humidity index (THI) conditions. Hair samples were collected and measured for length and diameter. Core body temperature was measured as vaginal temperature every 15 min over a 5-d period using an iButton temperature measuring device implanted in a blank CIDR in 336 heifers from the University of Florida multibreed herd (ranging from 100% Angus to 100% Brahman). Restricted maximum likelihood procedures were used to estimate heritabilities from multiple bivariate animal models using the WOMBAT program. Estimates of heritability for hair diameter, undercoat length, topcoat length, body temperature under low THI conditions, and body temperature under high THI conditions were 0.50, 0.67, 0.42, 0.32, and 0.26, respectively. The genetic parameters estimated in this study indicate a large, exploitable genetic variance which can be selected upon to improve tolerance in cattle. Breed effects for differing compositions of Brahman and Angus were also estimated. As Brahman breed composition increased by 25% undercoat length, topcoat length, body temperature under low THI conditions, and body temperature under high THI conditions decreased by 1.32 mm, 2.94 mm, 0.11 °C, and 0.14 °C, respectively. Under both low and high THI conditions, cattle with 25% Brahman breed composition or greater maintained a significantly lower body temperature than the 100% Angus breed group. The incorporation of Brahman germplasm is recommended for herds that often experience heat stress conditions in order to increase resilience to heat stress.

Copy number variation detection in Chinese indigenous cattle by whole genome sequencing

Copy number variation (CNV) refers to a kind of structural variation, having functional and evolutionary effects on phenotypes. Thus far, further elucidation of the CNVs in different Chinese indigenous cattle breeds by whole genome sequencing have yet not been done. In this study, a comprehensive genomic analysis was performed on 75 cattle individuals including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds. Based on the 11,486 CNVRs discovered, population analysis was performed, showed that all the cattle breeds clustered in to three clades, consistent with their lineages Bos taurus, Bos taurus × Bos indicus and Bos indicus. Importantly, a set of CNVRs related genes were found to be associated with the traits of interest, which include meat production or quality (CAST, ACTC1, etc.), adaption (BLA-DQB, EGLN2, etc.) and coat color (KIT, MITF, etc.). These results provide valuable full genome variation resources for Chinese bovine genome research and would be helpful for cattle breeding and selection programs in the future.

Genome-wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (F_ST ) values across sliding windows were estimated between zebu and reference combined taurine breeds. The most differentiated regions (F_ST  ≥ 0.53), representing the top 1% smoothed F_ST values, were considered to represent regions under diversifying selection. In total, 285 and 317 genes were identified in the comparisons of Ethiopian cattle with taurine and Asian zebu with taurine respectively. Some of these genes are involved in stress responses/thermo-tolerance and DNA damage repair (HSPA4, HSF1, CMPK1 and EIF2AK4), pigmentation (ERBB3 and MYO1A), reproduction/fertility (UBE2D3, ID3 and PSPC1), immune response (PIK3CD and AKIRIN2) and body stature and size (MBP2, LYN and NPM1). Additionally, the candidate genes were associated with functional terms (e.g. cellular response to stress, DNA repair, inflammatory response) important for physiological adaptation to environmental stresses. The results of our study may shed light on the influence of artificial and natural selection in shaping the genomic diversity of modern cattle breeds and also may serve as a basis for further genetic investigation of traits of tropical adaptation in cattle.

Thermal equilibrium of Nellore cattle in tropical conditions: an investigation of circadian pattern

The aim of this work was to evaluate the diurnal patterns of physiological responses and the thermal regulation of adult Nellore bulls. Six 30-mo-old Nellore bulls (669 ± 65 kg BW) were randomly assigned to four 6-h periods in a Latin Square design such that measurements of each animal cover a 24-h cycle. Meteorological variables (air temperature, relative humidity, local solar irradiance, ultraviolet radiation, wind speed and black globe temperature) were recorded at regular one-minute intervals with an automated weather station. Respiratory rate, ventilation rate, oxygen, carbon dioxide, methane, saturation pressure, air temperature of the exhaled air, saturation pressure in the air leaving the ventilated capsule placed over the animal surface, hair coat, skin surface and rectal temperature were assessed. The thermal equilibrium was determined according to the principles of the first law of thermodynamics using biophysical equations. Animals were evaluated in an area which was protected from solar radiation, rain, and had a range of ambient air temperature between 20.57 ± 0.07 and 30.86 ± 0.07 °C. Percentage of O₂ and CO₂ in the exhaled air changed moderately (P < 0.0001) throughout the 24 h, which resulted in an average metabolic heat production of 151.45 ± 13.60 W m^-2. At the largest thermal gradient (T_S - T_A; from 24:00-07:00 h), heat transferred by long wave radiation and surface convection corresponded to near 60% of the metabolism. At 11:00 h the ambient temperature approached 29 °C and latent heat became the main way to cool the body. From this time until 17:00 h, cutaneous evaporation represented approximately 53% of total heat loss. In conclusion, results of the present study seem to be a good indicator of lower energy expenditure for body thermal regulation, high heat tolerance and adaptation of Nellore cattle to the tropical environment.

Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle

Background

Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (F_ROH), genomic relationship matrix approach (F_GRM) and based on the observed versus expected number of homozygous genotypes (F_HOM), and from pedigree-based coefficient (F_PED).

Results

ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH_{1–2 Mb}) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of F_ROH, F_GRM, F_HOM, and F_PED approaches. F_PED estimates ranged from 0.00 to 0.327 and F_ROH from 0.001 to 0.201. Low to moderate correlations were observed between F_PED-F_ROH and F_GRM-F_ROH, with values ranging from −0.11 to 0.51. Low to high correlations were observed between F_ROH-F_HOM and moderate between F_PED-F_HOM and F_GRM-F_HOM. Correlations between F_ROH from different lengths and F_PED gradually increased with ROH length.

Conclusions

Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low F_PED-F_ROH correlations for small segments indicate that F_PED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that F_ROH can be used as an alternative to inbreeding estimates in the absence of pedigree records.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4365-3) contains supplementary material, which is available to authorized users.

Climate Adaptation of Tropical Cattle

There is sustained growth in the number of tropical cattle, which represent more than half of all cattle worldwide. By and large, most research in tropical areas is still focused on breeds of cattle, their particular advantages or disadvantages in tropical areas, and the tropical forages or feeds that could be usefully fed to them. A consistent issue for adaptation to climate is the heat of tropical environments. Changing the external characteristics of the animal, such as color and coat characteristics, is one way to adapt, and there are several major genes for these traits. However, further improvement in heat tolerance and other adaptation traits will need to use the entire genome and all physical and physiological systems. Apart from the response to heat, climate forcing through methane emission identifies dry season weight loss as an important if somewhat neglected trait in climate adaptation of cattle. The use of genome-estimated breeding values in tropical areas is in its infancy and will be difficult to implement, but will be essential for rapid, coordinated genetic improvement. The difficulty of implementation cannot be exaggerated and may require major improvements in methodology.

Species composition and environmental adaptation of indigenous Chinese cattle

Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.

BREEDING AND GENETICS SYMPOSIUM: Breeding for resilience to heat stress effects in dairy ruminants. A comprehensive review

Selection for heat tolerant (HT) animals in dairy production has been so far linked to estimation of declines in production using milk recording and meteorological information on the day of control using reaction norms. Results from these models show that there is a reasonable amount of genetic variability in the individual response to high heat loads, which makes feasible selection of HT animals at low costs. However, the antagonistic relationship between level of production and response to heat stress (HS) implies that selection for HT animals under this approach must be done with caution so that productivity is not damaged. Decomposition of the genetic variability in principal components (PC) can provide selection criteria independent of milk production level although biological interpretation of PC is difficult. Moreover, given that response to heat stress for each animal is estimated with very sparse information collected under different physiological and management circumstances, biased (normally underestimation) and lack of accuracy may be expected. Alternative phenotypic characterization of HT can come from the use of physiological traits, which have also shown moderate heritability. However, costs of a large scale implementation based on physiological characteristics has precluded its use. Another alternative is the use of biomarkers that define heat tolerance. A review of biomarkers of HS from more recent studies is provided. Of particular interest are milk biomarkers, which together with infrared spectra prediction equations can provide useful tools for genetic selection. In the 'omics' era, genomics, transcriptomics, proteomics and metabolomics have been already used to detect genes affecting HT. A review of findings in these areas is also provided. Except for the slick hair gene, there are no other genes for which variants have been clearly associated with HT. However, integration of omics information could help in pointing at knots of the HS control network and, in the end, to a panel of markers to be used in the selection of HT animals. Overall, HT is a complex phenomenon that requires integration of fine phenotypes and omics information to provide accurate tools for selection without damaging productivity. Technological developments to make on-farm implementation feasible and with greater insight into the key biomarkers and genes involved in HT are needed.

Thermotolerance, health profile and cellular expression of HSP90AB1 in Nguni and Boran cows raised on natural pastures under tropical conditions

Boran (n=15) and Nguni (n=15) cows were used in a study to determine the effect of breed, age and coat colour on the concentration of heat shock protein 90 (HSP90AB1), physiological rectal and skin temperature, and markers of health. The cows were exposed to summer heat stress and Boran cows had higher significant (P<0.05) skin temperature (35.1±0.42°C) as compared to the Nguni cows (36.0±0.38°C). Nguni cows had higher body thermal gradients than the Boran cows. Boran cows had thicker skin (P<0.05) and longer hairs (24.3±2.26mm) than their Nguni counterparts (20.2±2.00mm). The HSP90AB1 concentration was increased in Boran cows, although breed had no significant (P>0.05) influence. Significantly (P<0.05) high urea and total cholesterol was recorded in Boran cows. Coat colour had a significant (P<0.05) effect on the weight and rectal temperature of the study animals. Coat colour and age had no significant effect (P>0.05) on the concentration of HSP90AB1, although older cows (≥9 years) had higher concentrations (5.4±1.29ng/ml). Age had a significant (P<0.05) effect on packed cell volume, neutrophil/lymphocyte, urea, total protein and gamma-glutamyl transferase whereas cows with ≥9 years had more concentrations than young ones. Age significantly (P<0.05) influenced hair length, skin temperature and the thermal gradients. Breed was positively correlated (P<0.001) to coat colour, age, body condition score, weight and temperature humidity index while negatively correlated to urea and total cholesterol. It was concluded that Nguni cows were more adaptable to hot environments than the Boran cows as the latter were unable to balance thermal load between their bodies and the environment.

A Meta-Assembly of Selection Signatures in Cattle

Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.

Genome-wide scan for selection signatures in six cattle breeds in South Africa

BACKGROUND

The detection of selection signatures in breeds of livestock species can contribute to the identification of regions of the genome that are, or have been, functionally important and, as a consequence, have been targeted by selection.

METHODS

This study used two approaches to detect signatures of selection within and between six cattle breeds in South Africa, including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31) and Holstein (n = 29). The first approach was based on the detection of genomic regions in which haplotypes have been driven towards complete fixation within breeds. The second approach identified regions of the genome that had very different allele frequencies between populations (F ST).

RESULTS AND DISCUSSION

Forty-seven candidate genomic regions were identified as harbouring putative signatures of selection using both methods. Twelve of these candidate selected regions were shared among the breeds and ten were validated by previous studies. Thirty-three of these regions were successfully annotated and candidate genes were identified. Among these genes the keratin genes (KRT222, KRT24, KRT25, KRT26, and KRT27) and one heat shock protein gene (HSPB9) on chromosome 19 between 42,896,570 and 42,897,840 bp were detected for the Nguni breed. These genes were previously associated with adaptation to tropical environments in Zebu cattle. In addition, a number of candidate genes associated with the nervous system (WNT5B, FMOD, PRELP, and ATP2B), immune response (CYM, CDC6, and CDK10), production (MTPN, IGFBP4, TGFB1, and AJAP1) and reproductive performance (ADIPOR2, OVOS2, and RBBP8) were also detected as being under selection.

CONCLUSIONS

The results presented here provide a foundation for detecting mutations that underlie genetic variation of traits that have economic importance for cattle breeds in South Africa.

Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y₁, Y₂; B. indicus: Y₃), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression.

Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis

The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and four reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following F_ST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics.

Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep

Background

Discerning the traits evolving under neutral conditions from those traits evolving rapidly because of various selection pressures is a great challenge. We propose a new method, composite selection signals (CSS), which unifies the multiple pieces of selection evidence from the rank distribution of its diverse constituent tests. The extreme CSS scores capture highly differentiated loci and underlying common variants hauling excess haplotype homozygosity in the samples of a target population.

Results

The data on high-density genotypes were analyzed for evidence of an association with either polledness or double muscling in various cohorts of cattle and sheep. In cattle, extreme CSS scores were found in the candidate regions on autosome BTA-1 and BTA-2, flanking the POLL locus and MSTN gene, for polledness and double muscling, respectively. In sheep, the regions with extreme scores were localized on autosome OAR-2 harbouring the MSTN gene for double muscling and on OAR-10 harbouring the RXFP2 gene for polledness. In comparison to the constituent tests, there was a partial agreement between the signals at the four candidate loci; however, they consistently identified additional genomic regions harbouring no known genes. Persuasively, our list of all the additional significant CSS regions contains genes that have been successfully implicated to secondary phenotypic diversity among several subpopulations in our data. For example, the method identified a strong selection signature for stature in cattle capturing selective sweeps harbouring UQCC-GDF5 and PLAG1-CHCHD7 gene regions on BTA-13 and BTA-14, respectively. Both gene pairs have been previously associated with height in humans, while PLAG1-CHCHD7 has also been reported for stature in cattle. In the additional analysis, CSS identified significant regions harbouring multiple genes for various traits under selection in European cattle including polledness, adaptation, metabolism, growth rate, stature, immunity, reproduction traits and some other candidate genes for dairy and beef production.

Conclusions

CSS successfully localized the candidate regions in validation datasets as well as identified previously known and novel regions for various traits experiencing selection pressure. Together, the results demonstrate the utility of CSS by its improved power, reduced false positives and high-resolution of selection signals as compared to individual constituent tests.

Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest

Background

Genomic information allows population relatedness to be inferred and selected genes to be identified. Single nucleotide polymorphism microarray (SNP-chip) data, a proxy for genome composition, contains patterns in allele order and proportion. These patterns can be quantified by compression efficiency (CE). In principle, the composition of an entire genome can be represented by a CE number quantifying allele representation and order.

Results

We applied a compression algorithm (DEFLATE) to genome-wide high-density SNP data from 4,155 human, 1,800 cattle, 1,222 sheep, 81 dogs and 49 mice samples. All human ethnic groups can be clustered by CE and the clusters recover phylogeography based on traditional fixation index (F_ST) analyses. CE analysis of other mammals results in segregation by breed or species, and is sensitive to admixture and past effective population size. This clustering is a consequence of individual patterns such as runs of homozygosity. Intriguingly, a related approach can also be used to identify genomic loci that show population-specific CE segregation. A high resolution CE ‘sliding window’ scan across the human genome, organised at the population level, revealed genes known to be under evolutionary pressure. These include SLC24A5 (European and Gujarati Indian skin pigmentation), HERC2 (European eye color), LCT (European and Maasai milk digestion) and EDAR (Asian hair thickness). We also identified a set of previously unidentified loci with high population-specific CE scores including the chromatin remodeler SCMH1 in Africans and EDA2R in Asians. Closer inspection reveals that these prioritised genomic regions do not correspond to simple runs of homozygosity but rather compositionally complex regions that are shared by many individuals of a given population. Unlike F_ST, CE analyses do not require ab initio population comparisons and are amenable to the hemizygous X chromosome.

Conclusions

We conclude with a discussion of the implications of CE for a complex systems science view of genome evolution. CE allows one to clearly visualise the evolution of individual genomes and populations through a formal, mathematically-rigorous information space. Overall, CE makes a set of biological predictions, some of which are unique and await functional validation.

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

BACKGROUND

Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns.

METHODS

By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation.

RESULTS

For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1.

CONCLUSIONS

The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance.

Genome-wide detection of signatures of selection in Korean Hanwoo cattle

The Korean Hanwoo cattle have been intensively selected for production traits, especially high intramuscular fat content. It is believed that ancient crossings between different breeds contributed to forming the Hanwoo, but little is known about the genomic differences and similarities between other cattle breeds and the Hanwoo. In this work, cattle breeds were grouped by origin into four types and used for comparisons: the Europeans (represented by six breeds), zebu (Nelore), African taurine (N'Dama) and Hanwoo. All animals had genotypes for around 680 000 SNPs after quality control of genotypes. Average heterozygosity was lower in Nelore and N'Dama (0.22 and 0.21 respectively) than in Europeans (0.26-0.31, with Shorthorn as outlier at 0.24) and Hanwoo (0.29). Pairwise FST analyses demonstrated that Hanwoo are more related to European cattle than to Nelore, with N'Dama in an intermediate position. This finding was corroborated by principal components and unsupervised hierarchical clustering. Using genome-wide smoothed FST , 55 genomic regions potentially under positive selection in Hanwoo were identified. Among these, 29 were regions also detected in previous studies. Twenty-four regions were exclusive to Hanwoo, and a number of other regions were shared with one or two of the other groups. These regions overlap a number of genes that are related to immune, reproduction and fatty acid metabolism pathways. Further analyses are needed to better characterize the ancestry of the Hanwoo cattle and to define the genes responsible to the identified selection peaks.

Y chromosome diversity and paternal origin of Chinese cattle

To determine the Y chromosome genetic diversity and paternal origin of Chinese cattle, 369 bulls from 17 Chinese native cattle breeds and 30 bulls from Holstein and four bulls from Burma were analyzed using a recently discovered USP9Y marker that could distinguish between taurine and indicine cattle more efficiently. In total, the taurine Y1, Y2 haplogroup and indicine Y3 haplogroup were detected in 7 (1.9 %), 193 (52.3 %) and 169 (45.8 %) individuals of 17 Chinese native breeds, respectively, although these frequencies varied amongst the Chinese native cattle breeds examined. Y2 dominates in northern China (91.4 %), while Y3 dominates in southern China (81.2 %). Central China is an admixture zone with Y2 predominating overall (72.0 %). Our results demonstrate that Chinese cattle have two paternal origins, one from B. taurus (Y2) and the other from B. indicus (Y3). The Y1 haplogroup may originate from the imported beef cattle breeds in western countries. The geographical distributions of the Y2 and Y3 haplogroup frequencies reveal a pattern of male indicine introgression from south to north China, and male taurine introgression from north to south China.

Genetic variation and differentiation of bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies

The genetic relationship of American plains bison (Bison bison bison) and wood bison (Bison bison athabascae) was quantified and compared with that among breeds and subspecies of cattle. Plains bison from 9 herds (N = 136), wood bison from 3 herds (N = 65), taurine cattle (Bos taurus taurus) from 14 breeds (N = 244), and indicine cattle (Bos taurus indicus) from 2 breeds (N = 53) were genotyped for 29 polymorphic microsatellite loci. Bayesian cluster analyses indicate 3 groups, 2 of which are plains bison and 1 of which is wood bison with some admixture, and genetic distances do not show plains bison and wood bison as distinct groups. Differentiation of wood bison and plains bison is also significantly less than that of cattle breeds and subspecies. These and other genetic data and historical interbreeding of bison do not support recognition of extant plains bison and wood bison as phylogenetically distinct subspecies.