Validation of 15 microsatellites for parentage testing in North American bison, Bison bison and domestic cattle

Fifteen bovine microsatellites were evaluated for use in parentage testing in 725 bison from 14 public populations, 178 bison from two private ranches and 107 domestic cattle from five different breeds. The number of alleles per locus ranged from five to 16 in bison and from five to 13 in cattle. On average, expected heterozygosity, polymorphism information content (PIC) and probability of exclusion values were slightly lower in bison than in cattle. A core set of 12 loci was further refined to produce a set of multiplexed markers suitable for routine parentage testing. Assuming one known parent, the core set of markers provides exclusion probabilities in bison of 0.9955 and in cattle of 0.9995 averaged across all populations or breeds tested. Tests of Hardy-Weinberg and linkage equilibrium showed only minor deviations. This core set of 12 loci represent a powerful and efficient method for determining parentage in North American bison and domestic cattle.     

Effects of bison and cattle on growth, reproduction, and abundances of five tallgrass prairie forbs

Forb populations were sampled on Kansas tallgrass prairie to examine the effects of native (bison) and domestic (cattle) ungulates on plant growth, reproduction, and species abundances. Five locally and regionally abundant native tallgrass prairie perennials, Baptisia bracteata, Oenothera speciosa, Vernonia baldwinii, Solidago missouriensis, and Salvia azurea, were selected for study. Replicate watershed-level treatments included three grazing regimes (ungrazed, grazed by cattle, and grazed by bison), and two spring fire frequencies (annually burned and burned at 4-yr intervals). The results show that forb responses to ungulates in tallgrass prairie are complex and vary significantly among plant species, ungulate species, fire regimes, and plant life history stages. Some forbs (e.g., B. bracteata, O. speciosa, and V. baldwinii) increased in growth and reproduction in grazed sites, indicating competitive release in response to selective grazing of the dominant warm-season matrix grasses. Forbs that reduced performance in grazed sites are likely negatively affected by disturbances generated by ungulate nongrazing activities, because none of the forbs studied were directly consumed by bison or cattle. Large grazers had no detectable effect on the frequency of plant damage by other herbivores or pathogens. Significant effects of grazers on patterns of flowering and seed production were not congruent with their effects on population densities, indicating that variation in sexual reproduction plays a minor role in regulating local population abundances. Furthermore, the native and domestic ungulates differ significantly in their effects on forb growth and reproduction.     

Conservation genomics: disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations

Introgressive hybridization is one of the major threats to species conservation, and is often induced by human influence on the natural habitat of wildlife species. The ability to accurately identify introgression is critical to understanding its importance in evolution and effective conservation management of species. Hybridization between North American bison (Bison bison) and domestic cattle (Bos taurus) as a result of human activities has been recorded for over 100 years, and domestic cattle mitochondrial DNA was previously detected in bison populations. In this study, linked microsatellite markers were used to identify domestic cattle chromosomal segments in 14 genomic regions from 14 bison populations. Cattle nuclear introgression was identified in five populations, with an average frequency per population ranging from 0.56% to 1.80%. This study represents the first use of linked molecular markers to examine introgression between mammalian species and the first demonstration of domestic cattle nuclear introgression in bison. To date, six public bison populations have been identified with no evidence of mitochondrial or nuclear domestic cattle introgression, providing information critical to the future management of bison genetic resources. The ability to identify even low levels of introgression resulting from historic hybridization events suggests that the use of linked molecular markers to identify introgression is a significant development in the study of introgressive hybridization across a broad range of taxa.     

Genetic relationships among European cattle breeds

Genetic relationships among 37 European cattle breeds were investigated using blood group and serum protein polymorphisms. The 18 859 animals included in the study represented a random sample from pedigree populations in the UK. Within-breed variation was estimated by average heterozygosity and number of alleles observed, and breed relationships were evaluated by genetic distance. Standard errors of the heterozygosity, number of alleles and genetic distance were obtained by bootstrapping. The significance of breed differences was tested using an exact test of differentiation. French, Italian and Channel Island breeds were found to have generally higher heterozygosities and a greater number of alleles than breeds from mainland Britain and North Europe. Genetic distances ranged between 0·011 (±0·005) and 0·309 (±0·071). Two major breed groups were identified; a group of French, Italian and Channel Island breeds together with the Simmental and Gelbvieh, and a second group consisting of the mainland British and North European breeds. The exact test of breed differentiation showed all breeds to be significantly different from one another ( P < 0·0001). Overall relationships among breeds reflected their geographical origin and common ancestry rather than the agricultural use for which the breeds have been selected.     

Cattle ancestry in bison: explanations for higher mtDNA than autosomal ancestry

Understanding and documenting the process of hybridization and introgression between related species is a major focus of recent evolutionary research using molecular techniques. Many North American bison herds have cattle ancestry introduced by crossbreeding over a century ago. Molecular estimates of this ancestry have shown much higher levels for cattle mtDNA than for autosomal cattle genes. A large part of this difference appears to be the result of partial reproductive isolation between the two species where only bison bull × domestic cow crosses are successful, and all the surviving progeny are females. In addition, selection against autosomal cattle genes in bison may have contributed to differential levels of cattle ancestry. The impact of selection against cattle mtDNA and gene flow of bison mtDNA are examined to explain particular combinations of mtDNA and autosomal cattle ancestry. A bottleneck, after the level of cattle ancestry in bison was reduced to a low level, is consistent with the high variance over autosomal loci observed for cattle ancestry, and differential selection among cattle loci in bison does not need to be invoked. Further examination of the cattle genome in bison may shed light on whether these markers, or their associated regions, are indeed neutral.     

Assessing priorities for conservation in Tuscan cattle breeds using microsatellites

Preservation of rare genetic stocks requires assessment of within-population genetic diversity and between-population differentiation to make inferences on their degree of uniqueness. A total of 194 Tuscan cattle (44 Calvana, 35 Chianina, 25 Garfagnina, 31 Maremmana, 31 Mucca Pisana and 28 Pontremolese) individuals were genotyped for 34 microsatellite markers. Moreover, 56 samples belonging to Argentinean Creole and Asturiana de la Montaña cattle breeds were used as an outgroup. Genetic diversity was quantified in terms of molecular coancestry and allelic richness. STRUCTURE analyses showed that the Tuscan breeds have well-differentiated genetic backgrounds, except for the Calvana and Chianina breeds, which share the same genetic ancestry. The between-breed Nei's minimum distance (D_m) matrices showed that the pair Calvana–Chianina was less differentiated (0.049 ± 0.006). The endangered Tuscan breeds (Calvana, Garfagnina, Mucca Pisana and Pontremolese) made null or negative contributions to diversity, except for the Mucca Pisana contribution to allelic richness (C_T = 1.8%). The Calvana breed made null or negative within-breed contributions (f¯_W = 0.0%; C_W = −0.4%). The Garfagnina and Pontremolese breeds made positive contributions to between-breed diversity but negative and high within-breed contributions, thus suggesting population bottleneck with allelic losses and increase of homozygosity in the population. Exclusion of the four endangered Tuscan cattle breeds did not result in losses in genetic diversity (f¯_T = −0.7%; C_T = −1.2%), whereas exclusion of the non-endangered breeds (Chianina and Maremmana) did (f¯_T = 2.1%; C_T = 3.9%); the simple exclusion of the Calvana breed from the former group led to losses in genetic diversity (f¯_T = 0.47%; C_T = 2.34%), indicating a diverse significance for this breed. We showed how quantifying both within-population diversity and between-population differentiation in terms of allelic frequencies and allelic richness provides different and complementary information on the genetic backgrounds assessed and may help to implement priorities and strategies for conservation in livestock.     

采用微卫星标记分析13个中外牛品种的遗传变异和品种间的遗传关系

本研究应用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)推荐的10对微卫星引物,结合荧光–多重PCR技术,检测了10个中国地方黄牛品种和3个外来牛品种的基因型。通过计算基因频率、多态信息含量和遗传杂合度,以Nei’s遗传距离和Nei’s标准遗传距离为基础,采用非加权组对算术平均聚类法构建了聚类图,分析了13个牛品种的群体内遗传变异和群体间遗传关系。并以聚类分析和群体结构分析为基础,将13个中外黄牛品种分为三类:Ⅰ类属于普通黄牛品种,包括延边牛、沿江牛、长白地方牛、蒙古牛、阿勒泰白头牛、哈萨克牛、复州牛和西藏牛;Ⅱ类属于含有瘤牛血统的黄牛品种,包括日喀则驼峰牛和阿沛甲咂牛;Ⅲ类属于外来牛品种,包括德国黄牛、西门塔尔牛和夏洛来牛。研究结果为加强我国地方黄牛品种种质特性研究以及地方牛品种资源的保护与利用提供了科学的依据。     

Effectiveness of bovine microsatellites in resolving paternity cases in American bison, Bison bison L.

A set of 33 cattle microsatellite primer pairs was tested with the DNA of American bison from a captive population in Belgium and evaluated for usefulness in parentage testing. Two primer sets did not amplify and three were monomorphic. Among the polymorphic markers, the number of alleles ranged from two to nine. Heterozygosity, polymorphism information content (PIC) and probability of exclusion (PE) values were low by comparison with those obtained with the same markers in cattle. Two methods of estimating PE were used, one which assumed equal allele frequencies between parental sexes and another which took into account differences in allele frequencies between parental sexes. An internationally accepted set of nine microsatellites gives cumulative PE values of 0·98 and 0·97, respectively, for the two methods. The potential of this marker set to identify bison × cattle hybrids is discussed. Because bison and cattle have a common ancestor, these microsatellites are a useful way to establish genetic distances and can lead to the construction of phylogenetic trees.     

Genetic relationships between feral cattle from Chirikof Island, Alaska and other breeds

The origin of cattle on Chirikof Island, off the coast of Alaska, is not well documented. We assessed genetic differentiation of cattle isolated on Chirikof Island from several breeds commonly used for commercial production in North America including breeds popularly believed to have contributed to the Chirikof Island population. A set of 34 microsatellite loci was used to genotype Angus, Charolais, Hereford, Highland, Limousin, Red Angus, Salers, Shorthorn, Simmental, Tarentaise and Texas Longhorn cattle sampled from North America and the Chirikof Island population. Resulting F(ST) statistics for these loci ranged from 0.06 to 0.22 and on average, 14% of total genetic variation was between breeds. Whether population structure was modelled as a bifurcating tree or genetic network, Chirikof Island cattle appeared to be unique and strongly differentiated relative to the other breeds that were sampled. Bayesian clustering for multiple-locus assignment to genetic groups indicated low levels of admixture in the Chirikof Island population. Thus, the Chirikof Island population may be a novel genetic resource of some importance for conservation and industry.     

Differential introgression of uniparentally inherited markers in bison populations with hybrid ancestries

Historical hybridization between Bison bison (bison) and Bos taurus (cattle) has been well documented and resulted in cattle mitochondrial DNA (mtDNA) introgression, previously identified in six different bison populations. In order to examine Y chromosome introgression, a microsatellite marker (BYM-1) with non-overlapping allele size distributions in bison and cattle was isolated from a bacterial artificial chromosome (BAC) clone, and was physically assigned to the Y chromosome by fluorescence in situ hybridization. BYM-1 genotypes for a sample of 143 male bison from 10 populations, including all six populations where cattle mtDNA haplotypes were previously identified, indicated that cattle Y chromosome introgression had not occurred in these bison populations. The differential permeability of uniparentally inherited markers to introgression is consistent with observations of sterility among first generation hybrid males and a sexual asymmetry in the direction of hybridization favouring matings between male bison and female cattle.     

Temporal changes in genetic variation of north European cattle breeds

Temporal changes in genetic variation within and between 13 North European cattle breeds were evaluated using erythrocyte antigen systems and transferrin protein as genetic markers. Current data on allele frequency distributions of markers in large commercial and smaller endangered native cattle breeds were compared to data published during 1956 to 1975. Intrabreed genetic variation was quantified by conventional parameters (e.g. heterozygosity, average number of alleles per locus) and migration by the effective migration rate. The neighbour-joining dendrogram of relationships between old and present cattle populations was constructed using Nei's standard genetic distance. Variance effective population size was estimated from changes in allele frequencies over time. Comparison of old and new data indicated some significant changes in allele frequencies. In six of the breeds, a few low-frequency alleles in the old data were absent in the present samples. Heterozygosity remained stable in most breeds. The harmonic means for variance effective population size ranged between 30 and 257. Current results indicate that despite marked declines in total population sizes, North European native cattle breeds have retained a reasonably high genetic diversity. However, their genes contribute less than previously to genetic variation of Nordic production breeds. Commercial breeds do not appear to have a larger effective population size than native breeds. The present effective population sizes imply that Nordic breeds could have lost from 1 to 11% of their heterozygosity over a 20-40-year period.     

Genetic diversity,introgression and relationships among West/Central African cattle breeds

Genetic diversity, introgression and relationships were studied in 521 individuals from 9 African Bos indicus and 3 Bos taurus cattle breeds in Cameroon and Nigeria using genotype information on 28 markers (16 microsatellite, 7 milk protein and 5 blood protein markers). The genotypes of 13 of the 16 microsatellite markers studied on three European (German Angus, German Simmental and German Yellow) and two Indian (Nelore and Ongole) breeds were used to assess the relationships between them and the African breeds. Diversity levels at microsatellite loci were higher in the zebu than in the taurine breeds and were generally similar for protein loci in the breeds in each group. Microsatellite allelic distribution displayed groups of alleles specific to the Indian zebu, African taurine and European taurine. The level of the Indian zebu genetic admixture proportions in the African zebus was higher than the African taurine and European taurine admixture proportions, and ranged from 58.1% to 74.0%. The African taurine breed, Muturu was free of Indian zebu genes while its counter Namchi was highly introgressed (30.2%). Phylogenic reconstruction and principal component analysis indicate close relationships among the zebu breeds in Cameroon and Nigeria and a large genetic divergence between the main cattle groups – African taurine, European taurine and Indian zebu, and a central position for the African zebus. The study presents the first comprehensive information on the hybrid composition of the individual cattle breeds of Cameroon and Nigeria and the genetic relationships existing among them and other breeds outside of Africa. Strong evidence supporting separate domestication events for the Bos species is also provided.     

Detection of mitochondrial DNA from domestic cattle in bison on Santa Catalina Island

In 1924, 14 American bison (Bison bison) were introduced to Santa Catalina Island, California and sporadically supplemented thereafter with additional animals. To reduce the herd and its impact on native vegetation, over 2000 animals have been exported during the past four decades. Today, the herd is estimated to contain around 250 individuals. Genetic analysis was performed on 98 animals removed from the island in 2004. Forty-four samples (45%) had domestic cattle mitochondrial DNA (mtDNA), 12 (12%) had previously reported bison haplotypes and 42 (43%) had a new haplotype differing by one base pair from a previously reported bison haplotype. A complement of five restriction enzymes was found to be useful in identifying bison with domestic cattle mtDNA.     

Resistance to malignant catarrhal fever in American bison (Bison bison) is associated with MHC class IIa polymorphisms

The Rhadinovirus ovine herpesvirus-2 (OvHV-2) is the most common causative agent of malignant catarrhal fever (MCF) in clinically susceptible ruminants including cattle and bison. American bison (Bison bison) are highly susceptible to clinical MCF. Nevertheless, approximately 20% of bison on ranches or in feedlots become infected with the virus without developing clinical disease. Defining the genetic basis for differences in susceptibility between bison could facilitate development of improved control strategies for MCF. One genetic region that influences susceptibility to infectious diseases is the major histocompatibility complex (MHC). In this study, a Bison bison (Bibi) DRB3 oligonucleotide microarray was used to type 189 bison from 10 herds where MCF outbreaks had occurred. Binary logistic regression was used to classify DRB3 alleles as resistant (R), susceptible (S) or neutral (N). Animals were reclassified using six DRB3 genotype categories: N/N, N/R, N/S, R/S, R/R and S/S. Analysis of homogeneity across herds showed that there was a herd effect. Consequently, a penalized logistic regression model was run with herd and genotype categories as the explanatory variables. The R/R genotype was associated with resistance to MCF (P = 0.0327), while the S/S genotype was associated with clinical MCF (P = 0.0069). This is the first evidence that MHC class IIa polymorphism is associated with resistance or susceptibility to OvHV-2-induced MCF.     

中国黄牛品种多样性及其保护

总结关于中国黄牛起源和品种多样的文献,依据头颅骨分类,毛色,血液蛋白多态性,体型体态,梁色体组型,线粒体DNA和考古论证的资料可知,在各地的牛种中,中国的无峰牛来自于两种原牛,在长城以北有长角型的普通牛的分支土雷诺蒙古利亚（truano-mognolia)和青藏高原有矮型的短角型普通牛（draft pimigenius),有峰牛来自于三种原牛,来自北非,西亚的瘤牛,印度瘤牛和东南亚瘤牛,这些牛的后裔大多以混血种形态存在,关中和中原地区牛受西亚瘤牛的影响,胸垂较发达,多皱折,体格圈套 ,云南部分高峰牛受印度瘤牛影响,东南地区高峰牛为古代准牛属爪哇牛被东南亚瘤牛吸收杂交的后裔,属矮小型,体躯体而皱折贫乏,肩峰属头位,耳端较尖而不下垂,在起源上,藏牛为原始种,海南高峰牛（zebu sinsis)为一个瘤牛的发源地,云南高峰牛是一个特殊种,击阳牛是含有非洲瘤牛血淮的特殊种,全国的黄牛在总体上可分为两大系统三大类型,根据体态特征分为无峰,低身和有峰三种,按地理分布为蒙古,黄淮和长珠三组,现代国民经济发展引进30个外国品种,加速了地方品种的灭绝,本文还提出了农牛保种应以特殊品种和边缘地区以及特有生态区牛种为主要的主张。     

Superovulation and embryo transfer in wood bison (Bison bison athabascae)

Two experiments were done to develop an effective superovulatory treatment protocol in wood bison for the purpose of embryo collection and transfer. In experiment 1, donor bison were assigned randomly to four treatment groups (N = 5 per group) to examine the effects of method of synchronization (follicular ablation vs. estradiol-progesterone treatment) and ovarian follicular superstimulation (single slow-release vs. split dose of FSH). Recipient bison were synchronized with donor bison by either follicular ablation (N = 8) or estradiol-progesterone treatment (N = 9). In experiment 2, bison were assigned randomly to four treatment groups (N = 5 per group) to examine the ovarian response to two versus four doses of FSH, and the effect of progesterone (ovarian superstimulation with or without an intravaginal progesterone-releasing device). Donor bison were inseminated with fresh chilled wood bison semen 12 and 24 hours after treatment with GnRH (experiment 1) or LH (experiment 2). The ovarian response was assessed using ultrasonography. In experiment 1, the number of large follicles (≥7 mm) increased in response to both FSH treatments, but the diameter of the largest follicle detected 4 and 5 days after the start of ovarian superstimulation was greater in bison treated with a single dose of FSH than in those treated with two doses (P < 0.05). A total of 10 ova and/or embryos were collected. One blastocyst was transferred to each of five recipient bison resulting in the birth of two live wood bison calves. In experiment 2, two doses of FSH resulted in a greater number of large follicles (≥9 mm) on Days 4, 5, and 6 (P < 0.05) after beginning of superstimulation (Day 0), and more ovulations than four doses of FSH (11.2 ± 2.4 vs. 6.4 ± 0.8; P < 0.05). Embryo collection was performed on only five donors, and a total of 19 ova and/or embryos were recovered. In summary, fewer FSH treatments were as good or better than multiple treatments, consistent with the notion that minimizing handling stress improves the superovulatory response in bison. Follicular ablation and estradiol plus progesterone treatment were effective for inducing ovarian synchronization in embryo donor and recipient bison, and an intravaginal progesterone-releasing device during superstimulatory treatment did not influence the superovulatory response or embryo collection. Delaying ovulation-inducing treatment (GnRH or LH) to 5 days after superstimulatory treatment resulted in a greater number of ovulations and improved embryo collection efficiency (experiment 2). Embryo collection and transfer resulted in live offspring from wild wood bison.     

A microsatellite within the bovine K-casein gene reveals a polymorphism correlating strongly with polymorphisms previously described at the protein as well as the DNA level

The polymorphism of a (TA)n(CA)n repeat microsatellite present in the third intaron of the bovine K-casein gene (CASK) has been investigated. The existence of six alleles differing only in the number of dinucleotide repeats has been established. A total of 330 animals belonging to nine different pure bred Bos Taurus French breeds or to a cross-bred Bos taurus*Bos indicus population (Créole) were genotyped. The distribution of the microsatellite alleles was examined and clear breed differences were noted. Genotyping of animals by isoelectric focusing (IEF) or restriction fragment length polymorphism (RFLP) (TaqI) was performed, in order to examine the relationship of the microsatellite polymorphism to other previously described CASK polymorphisms, at the protein and DNA levels. Strong correlation was seen, indicating that evolution of the various polymorphisms was not independent, and nine CASK haplotypes were observed.     

Genetic variation in BoLA microsatellite loci in Portuguese cattle breeds

Major histocompatibility complex (MHC) typing based on microsatellites can be a valuable approach to understanding the selective processes occurring at linked or physically close MHC genes and can provide important information on variability and relationships of populations. Using microsatellites within or in close proximity with bovine lymphocyte antigen (BoLA) genes, we investigated the polymorphisms in the bovine MHC, known as the BoLA, in eight Portuguese cattle breeds. Additional data from non-BoLA microsatellite loci were also used to compare the variability between these regions. Diversity was higher in BoLA than in non-BoLA microsatellites, as could be observed by the number of alleles, allelic richness and observed heterozygosity. Brava de Lide, a breed selected for aggressiveness and nobility, presented the lowest values of observed heterozygosity and allelic richness in both markers. Results from neutrality tests showed few statistically significant differences between the observed Hardy–Weinberg homozygosity ( F ) and the expected homozygosity ( F _E), indicating the apparent neutrality of the BoLA microsatellites within the analysed breeds. Nevertheless, we detected a trend of lower values of observed homozygosity compared with the expected one. We also detected some differences in the levels of allelic variability among the four BoLA microsatellites. Our data showed a higher number of alleles at the BoLA-DRB3 locus than at the BoLA-DRBP1 locus. These differences could be related to their physical position in the chromosome and may reflect functional requirements for diversity.