A bubaline-derived satellite DNA probe uncovers generic affinities of gaur with other bovids

DNA typing using genome derived cloned probes may be conducted for ascertaining genetic affinities of closely related species. We analysed gaurBos gaurus, cattleBos indicus, buffaloBubalus bubalis, sheepOvis aries and goatCapra hircus DNA using buffalo derived cloned probe pDS5 carrying an array ofBamHI satellite fraction of 1378 base residues to uncover its genomic organization. Zoo-blot analysis showed that pDS5 does not cross hybridize with non-bovid animals and surprisingly with female gaur genomic DNA. The presence of pDS5 sequences in the gaur males suggests their possible location on the Y chromosome. Genotyping of pDS5 withBamHI enzyme detected mostly monomorphic bands in the bubaline samples and polymorphic ones in cattle and gaur giving rise to clad specific pattern. Similar typing withRsaI enzyme also revealed clad specific band pattern detecting more number of bands in buffalo and fewer in sheep, goat and gaur samples. Copy number variation was found to be prominent in cattle and gaur withRsaI typing. Our data based on matched band profiles (MBP) suggest that gaur is genetically closer to cattle than buffalo contradicting the age-old notion held by some that gaur is a wild buffalo. The pDS5 clone has a potential for estimating the generic and genetic relationship amongst closely related bovid species.     

The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers

Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.     

Estrous synchronization in the gaur (Bos gaurus): Behavior and fertility to artificial insemination after prostaglandin treatment

The gaur (Bos guarus) is an endangered species that is a wild ancestor of domestic cattle. This study was conducted to evaluate 1) the efficacy of prostaglandin F_2α (PG) to synchronize estrus in gaur, 2) behavior of male and female gaur around estrus, and 3) fertility after artificial insemination (AI) at the PG-induced estrus. Six female gaur were utilized, along with a vasectomized gaur bull used to aid in detecting estrus. All females were given two i.m. injections of PG (25 mg/injection) 11 days apart, and monitored for estrus for 120 hr (48 hr via chinball marks, followed by 72 hr continuous observation) after the second PG injection. Three of the six females were in estrus during the 120-hr evaluation period. One female was in estrus prior to 48 hr after the second PG injection, and two females were observed in estrus during the 72-hr continuous observation period. When a female was observed in estrus (standing to be mounted by the vasectomized bull), she was bred by AI at 12 and 24 hr after the onset of estrus. The four females not observed in estrus, including the one marked during the first 48 hr, were bred by AI at 80 and 92 hr after the second PG injection. Of the two gaur females observed in estrus, one female was first mated by the vasectomized bull at 77 hr and the second female was mated at 98 hr after PG. Both females exhibited very short durations of receptivity (less than 4 hr). The second female observed in estrus became pregnant after AI and gave birth to a healthy gaur calf after a 299-day gestation. It appears that female gaur can be synchronized with PG techniques developed for domestic cattle. These data should provide useful information for programs studying and maintaining this endangered species and may have relevance for the cattle industry, since the gaur could provide a source of diverse ancestral genetic material.     

Refinement of bovine chromosome 2 linkage map near the mh locus reveals rearrangements between the bovine and human genomes

The locus responsible for the appearance of muscular hypertrophy (mh) in double muscled cattle breeds has recently been shown to encode a secreted growth factor designated myostatin (MSTN). This conclusion was based in part on the placement of MSTN in the interval to which mh had been mapped on bovine chromosome 2 (BTA2). During the mapping phase of the study, numerous yeast artificial chromosome (YAC) clones were isolated that contained genetic markers closely linked to mh. Other YACs and cosmids were identified that contained genes selected from human chromosome 2q (HSA2q), with the goal of defining the position of breakpoints in conserved synteny between the bovine and human comparative maps, thereby permitting accurate selection of positional candidate genes. An efficient subcloning procedure was developed to obtain microsatellites (ms) from YAC clones, to increase the number of informative meioses in herds segregating for mh. The same procedure was used to place the human orthologues of engrailed-1 (EN1), interleukin 1 beta (IL1B), and paired-box-containing 8 (PAX8) genes on the cattle map to further define the positions of breakpoints in conserved synteny and gene order. Twenty-three of 28 ms identified from YAC subclone libraries were informative in the mapping families. Seven mapped to the centromeric end of BTA2, which contains the mh locus, improving marker density and informativeness. The two MSTN and four EN1 gene-associated ms markers developed from YACs, map to positions 1·5 and 61·6 cm in the BTA2 linkage group, respectively. In addition, ms markers developed from cosmids containing either IL1B or PAX8, map to positions 56·6 and 56·9 cm in the BTA11 linkage group, respectively. These linkage data confirm the location and orientation of orthologous segments of HSA2q that were previously indistinguishable on the bovine map, and demonstrates the presence of microrearrangements of gene order (segments <10 cm ) and conserved synteny between the human and bovine genomes.     

Genome‐wide association study identifies loci linked to serum electrolyte traits in Chinese Holstein cattle

We aimed to identify QTL for serum electrolyte traits by performing a GWAS of calcium, chloride, sodium, potassium and magnesium ion concentrations in Chinese Holstein cattle. We detected five SNPs that had significant associations with calcium ion concentrations and identified GATA2 from Bos taurus chromosome (BTA)22 as having the highest significance. Among the genes with significant results, we speculate that TMEM123 might be related to calcium channel proteins according to the functions of the TMEM family.     

The bovine 5′ AMPK gene family: mapping and single nucleotide polymorphism detection

The 5-AMP-activated protein kinase (AMPK) family is an ancient stress response system whose primary function is regulation of cellular ATP. Activation of AMPK, which is instigated by environmental and nutritional stresses, initiates energy-conserving measures that protect the cell by inhibition and phosphorylation of key enzymes in energy-consuming biochemical pathways. The seven genes that comprise the bovine AMPK family were mapped in cattle by using a radiation hybrid panel. The seven genes mapped to six different cattle chromosomes, each with a LOD score greater than 10.0. PRKAA1 mapped to BTA 20, PRKAA2 and PRKAB2 to BTA 3, PRKAB1 to BTA 17, PRKAG1 to BTA 5, PRKAG2 to BTA 4, and PRKAG3 to BTA 2. Five of the seven genes mapped to regions expected from human/cattle comparative maps. PRKAB2 and PRKAG3, however, have not been mapped in humans. We predict these genes to be located on HSA 1 and 2, respectively. Additionally, one synonymous and one non-synonymous single nucleotide polymorphism (SNP) were detected in PRKAG3 in Bos taurus cattle. In an effort to determine ancestral origins, various herds of mixed breed cattle as well as other ruminant species were characterized for sequence variation in this region of PRKAG3. Owing to the physiological importance of this gene family, we believe that its individual genes are candidate genes for conferring resistance to diseases in cattle.     

Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences

The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.     

Syntenic Assignment of Human Chromosome 1 Homologous Loci in the Bovine

Three mouse chromosomes (MMU 1, 3, and 4) carry homologs of human chromosome 1 (HSA 1) genes. A similar situation is found in the bovine, where five bovine chromosomes (BTA 2, 3, 5, 16, and unassigued syntenic group U25) contain homologs of HSA 1 loci. To evaluate further the syntenic relationship of HSA 1 homologs in cattle, 10 loci have been physically mapped through segregation analysis in bovine-rodent hybrid somatic cells. These loci, chosen for their location on HSA 1, are antithrombin 3 (AT3), renin (REN), complement component receptor 2 (CR2), phosphofructokinase muscle type (PFKM), Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog (FGR), α fucosidase (FUCA1), G-protein β1 subunit (GNB1), α 1A amylase, (AMY1), the neuroblastoma RAS viral (v-ras) oncogene homolog (NRAS), and α skeletal actin (ACTA1). AT3, REN, CR2, and GNB1 mapped to BTA 16, PFKM to BTA 5, AMY1A and NRAS to BTA 3, FGR and FUCA1 to BTA 2, and ACTA1 to BTA 28.     

Myostatin maps to the interval containing the bovine mh locus

Myostatin (GDF-8) is a member of the transforming growth factor-β superfamily and plays a role in muscle growth and development. Mice having targeted disruption of this gene display marked increases in muscle mass, a phenotype similar to the muscular hypertrophy (mh) in several cattle breeds. Physical mapping data developed from YAC clones indicate the bovine myostatin gene lies close to the centromere of bovine Chromosome (Chr) 2 (BTA2) at 2q11, indistinguishable from the cytogenetic location of the mh locus. In addition, a polymorphism in the second intron of the gene was used to show that myostatin maps within the interval previously shown to contain mh. These data suggest myostatin may be the gene causing muscular hypertrophy in cattle. Received: 19 June 1997 / Accepted: 2 July 1997     

Synteny mapping in river buffalo

The cosegregation of ten coding loci has been investigated, in a panel of 37 somatic cell hybrids resulting from the fusion of a hamster cell line and river buffalo lymphocytes, by use of Southern hybridization technique. Five syntenic groups, TCRB-PGY3, ASS-ABL, FUCA1P-CRYG, MBP-YES1, and CGN1-ACTA1, previously assigned to cattle as U13, U16, U17, U28, and U29 respectively, were also found to be syntenic in buffalo. Based on the extensive syntenic conservation and banding homology between cattle and river buffalo, comparative mapping predicts the localization of these syntenic groups on river buffalo Chromosomes (Chrs) :BBU7, BBU12, BBU2q, BBU22, and BBU4q respectively as they have been previously localized on cattle Chrs BTA4, BTA11, BTA2, BTA24 & BTA28. Received: 2 April 1996 / Accepted: 4 July 1996     

A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 7 and comparative mapping to the cattle and human genomes

A preliminary radiation hybrid (RH) map containing 50 loci on chromosome 7 of the domestic river buffalo Bubalus bubalis (BBU; 2n = 50) was constructed based on a comparative mapping approach. The RH map of BBU7 includes thirty-seven gene markers and thirteen microsatellites. All loci have been previously assigned to Bos taurus (BTA) chromosome BTA6, which is known for its association with several economically important milk production traits in cattle. The map consists of two linkage groups spanning a total length of 627.9 cR(5,000). Comparative analysis of the BBU7 RH(5,000) map with BTA6 in cattle gave new evidence for strong similarity between the two chromosomes over their entire length and exposed minor differences in locus order. Comparison of the BBU7 RH(5,000) map with the Homo sapiens (HSA) genome revealed similarity with a large chromosome segment of HSA4. Comparative analysis of loci in both species revealed more variability than previously known in gene order and several chromosome rearrangements including centromere relocation. The data obtained in our study define the evolutionarily conserved segment on BBU7 and HSA4 to be between 3.5 megabases (Mb) and 115.8 Mb in the HSA4 (genome build 36) DNA sequence.     

Studying Large Mammals With Imperfect Detection: Status and Habitat Preferences of Wild Cattle and Large Carnivores in Eastern Cambodia

Studying large mammal species in tropical forests is a conservation challenge with species’ behavior and ecology often increasing the probability of non‐detection during surveys. Consequently, knowledge of the distribution, status, and natural history of many large mammal species in Southeast Asia is limited. I developed occupancy models from camera‐trapping data, thereby accounting for imperfect detection at sampling sites, to clarify the status and habitat requirements of four globally threatened or near threatened large mammals (banteng Bos javanicus, gaur Bos gaurus, dhole Cuon alpinus, and leopard Panthera pardus) in Mondulkiri Protected Forest, eastern Cambodia. Camera traps were operational for >3500 trap nights with 202 photographic encounters of the four study species. Model averaged occupancy estimates were between 5 percent (leopard) and 140 percent (gaur) higher than naive estimates (i.e., proportion of camera‐trap sites species recorded from) thus highlighting the importance of accounting for detectability during conservation surveys. I recommend the use of an occupancy framework when using camera‐trap data to study the status, ecology, and habitat preferences of poorly known and elusive species. The results highlight the importance of mixed deciduous and semi‐evergreen forest for wild cattle in eastern Cambodia and I emphasize that these habitats must be considered in conservation planning across the Lower Mekong Dry Forest Ecoregion.     

Karyotype analysis of mithun (Bos frontalis) and mithun bull x Brahman cow hybrids

We examined the cytogenetics of mithun (Bos frontalis), a domesticated version of the Asian gaur, and hybrids (F(1) generation) produced by artificial insemination of Brahman cows (Bos indicus) with mithun semen. Reproductive potential was also examined in the F(1) generation and a backcrossed heifer for utilization of heterosis. Metaphase chromosome spreads were examined by conventional staining and fluorescence in situ hybridization hybridized with the entire chromosome 1 of mithun as a specific probe. Chromosome 1 of mithun was found to be equivalent to Bos taurus chromosomes 2 and 28. The karyotype of the female mithun (N = 4) comprised 58 chromosomes, including 54 acrocentric and four large submetacentric chromosomes, without the four acrocentric chromosomes found in the domesticated species B. indicus. However, one of the four female mithuns with a normal mithun phenotype had an abnormal karyotype (2n = 59), indicating introgression from B. taurus or B. indicus. The F(1) karyotypes (N = 6, 3♂3♀) of the mithun bull × Brahman cow cross had 2n = 59, intermediate between their parents; they were consistent heterozygous carriers with a centric fusion involving rob(2;28), as expected. Two pronounced red signals were seen in the mithun karyotypes, three red signals in the mithun × Brahman hybrids, and four red signals in the Brahman cattle, in good agreement with centric fusion of bovine rob(2;28). The female backcross hybrid (N = 1) with 2n = 59 had a similar chromosome configuration to the F(1) karyotypes and had rob(2;28). Such female backcross hybrids normally reproduce; however, the F(1) bulls (N = 3) had not yet generated normal sperm at 24 months.     

Comparative FISH-mapping of the survival of motor neuron gene (SMN) in domestic bovids

A comparative fluorescence in situ mapping of the SMN gene was performed on R-banded chromosome preparations of cattle (Bos taurus, BTA, 2n = 60), river buffalo (Bubalus bubalis, BBU, 2n = 50), sheep (Ovis aries, OAR, 2n = 54) and goat (Capra hircus, CHI, 2n = 60), as well as on those of a calf from Piedmont breed affected by arthrogryposis. SMN was located on BTA20q13.1, OAR16q13.1, CHI20q13.1 and BBU19q13. These chromosomes and chromosome bands are believed to be homeologous, confirming the high degree of chromosome homeologies among bovids. The position of SMN was refined in cattle, compared to the two previous localizations, while it is a new gene assignment in the other three bovids. A comparative fiber-FISH performed on extended chromatin of both normal cattle and calf affected by arthrogryposis revealed more extended FITC signals in the calf, compared to the normal cattle (control), suggesting a possible duplication of the SMN gene in the calf affected by arthrogryposis. .     

Diversity and phylogeny of mitochondrial DNA isolated from mithun Bos frontalis located in Bhutan

We sequenced the 16S rRNA gene in mitochondrial DNA to characterize mithun located in Bhutan and to increase our understanding of its origin. We compared mithun with yak, European cattle, Bhutanese zebu and Indian zebu. Sequencing revealed low nucleotide diversity within the mithun population and their phylogenetic proximity to gaur. A close relationship between Bhutanese mithun and gaur was confirmed by an additional comparison with wild gaur specimens from three locations in Bhutan. Direct domestication of mithun from gaur was supported, while maternal contribution from the cattle lineage during domestication was not supported.     

Myostatin rapid sequence evolution in ruminants predates domestication

Myostatin (GDF-8) is a negative regulator of skeletal muscle development. This gene has previously been implicated in the double muscling phenotype in mice and cattle. A systematic analysis of myostatin sequence evolution in ruminants was performed in a phylogenetic context. The myostatin coding sequence was determined from duiker (Sylvicapra grimmia caffra), eland (Taurotragus derbianus), gaur (Bos gaurus), ibex (Capra ibex), impala (Aepyceros melampus rednilis), pronghorn (Antilocapra americana), and tahr (Hemitragus jemlahicus). Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (K_a/K_s) indicates that positive selection may have been operating on this gene during the time of divergence of Bovinae and Antilopinae, starting from approximately 23 million years ago, a period that appears to account for most of the sequence difference between myostatin in these groups. These periods of positive selective pressure on myostatin may correlate with changes in skeletal muscle mass during the same period.     

Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle

A putative functional mutation (rs109231213) near PLAG1 (BTA14) associated with stature was studied in beef cattle. Data from 8199 Bos taurus, Bos indicus and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF‐I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P < 10^?4). Frequency of the mutant C allele of rs109231213 differed among B. indicus (0.52), B. taurus (0.96) and Tropical Composite (0.68). Most chromosomes carrying the C allele had the same surrounding 10 SNP haplotype, probably because the C allele was introgressed into Brahman from B. taurus cattle. A region of reduced heterozygosity surrounds the C allele; this is small in B. taurus but 20 Mb long in Brahmans, indicating recent and strong selection for the mutant allele. Thus, the C allele appears to mark a mutation that has been selected almost to fixation in the B. taurus breeds studied here and introduced into Brahman cattle during grading up and selected to a frequency of 0.52 despite its negative effects on fertility.     

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

Background

Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattle are widely studied, whereas our knowledge of the genetic mechanisms of adaptation to local environments is still scarce. To address this issue for cold climates we used an integrated approach for detecting genomic intervals related to body temperature maintenance under acute cold stress. Our approach combined genome-wide association studies (GWAS) and scans for signatures of selection applied to a cattle population (Hereford and Kazakh Whiteheaded beef breeds) bred in Siberia. We utilized the GGP HD150K DNA chip containing 139,376 single nucleotide polymorphism markers.

Results

We detected a single candidate region on cattle chromosome (BTA)15 overlapping between the GWAS results and the results of scans for selective sweeps. This region contains two genes, MSANTD4 and GRIA4. Both genes are functional candidates to contribute to the cold-stress resistance phenotype, due to their indirect involvement in the cold shock response (MSANTD4) and body thermoregulation (GRIA4).

Conclusions

Our results point to a novel region on BTA15 which is a candidate region associated with the body temperature maintenance phenotype in Siberian cattle. The results of our research and the follow up studies might be used for the development of cattle breeds better adapted to cold climates of the Russian Federation and other Northern countries with similar climates.