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.     

Brucella abortus in captive bison. I. Serology, bacteriology, pathogenesis, and transmission to cattle

Two groups of six, non-brucellosis vaccinated, brucellosis seronegative pregnant American bison (Bison bison) were individually challenged with 1 x 10(7) colony forming units (CFU) of Brucella abortus strain 2308. Three days after challenge, each bison group was placed in a common paddock with six non-vaccinated, brucellosis susceptible, pregnant domestic heifers. In a parallel study, two groups of six susceptible, pregnant cattle were simultaneously challenged with the identical dose as the bison and each group was placed with six susceptible cattle in order to compare bison to cattle transmission to that observed in cattle to cattle transmission. Blood samples were collected from bison and cattle weekly for at least 1 mo prior to exposure to B. abortus and for 180 days post-exposure (PE). Sera from the bison and cattle were evaluated by the Card, rivanol precipitation, standard plate agglutination, standard tube agglutination, cold complement fixation tube, warm complement fixation tube, buffered acidified plate antigen, rapid screening, bovine conjugated enzyme linked immunosorbent assay, bison or bovine conjugated enzyme linked immunosorbent assay, and the hemolysis-in-gel techniques for the presence of antibodies to Brucella spp. At the termination of pregnancy by abortion or birth of a live-calf, quarter milk samples, vaginal swabs, and placenta were collected from the dam. Rectal swabs were collected from live calves, and mediastinal lymph nodes, abomasal contents and lung were taken at necropsy from aborted fetuses for culture of Brucella spp. These tissues and swabs were cultured on restrictive media for the isolation and identification of Brucella spp. Pathogenesis of brucellosis in bison was studied in an additional group of six pregnant bison which were challenged with 1 x 10(7) CFU of B. abortus strain 2308. One animal was euthanatized each week PE. Tissues were collected at necropsy and later examined bacteriologically and histologically. Lesions of brucellosis in bison did not significantly differ grossly or histologically from those in cattle. There were six abortions and two nonviable calves in the bison group, as compared to nine abortions in the 12 similarly inoculated cattle. As determined by bacterial isolations, transmission of B. abortus from bison to cattle (five of 12 susceptible cattle became infected) did not differ statistically from cattle to cattle transmission (six of 12 susceptible cattle became infected) under identical conditions. No single serologic test was constantly reliable to diagnosing B. abortus infected bison for 8 wk PE.(ABSTRACT TRUNCATED AT 400 WORDS)     

Polymorphism of bovine microsatellite DNA sequences in the lowland European bison

Investigations of genetic polymorphism of microsatellite DNA sequences were conducted in 22 individuals of the European bisonBison bonasus (Linneaus, 1758) from Bia?owie?a Primeval Forest. For this purpose 27 cattle microsatellite primer pairs were used. Among the 27 microsatellite markers examined, an amplification product was obtained for 21 loci. This rendered it possible to identify total of 40 alleles in the bison population tested. In addition, eight loci were proved to be monomorphic. A majority of the 40 alleles identified was identical with the alleles identified at the corresponding loci in cattle. Only two alleles seem to be specific for the European bison. The value of heterozygosity for the examined loci in bison population from Bia?owie?a was low and ranged from 0.13 to 0.53. Hence, the polymorphism information content was low as well. Based on our results the microsatellite DNA markers identified in cattle may be used to analyse the genetic structure of the population of European bison.     

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.     

Development of a linkage map and QTL scan for growth traits in North American bison

PCR protocols incorporating fluorescently labeled multiplexed primer combinations were developed to produce a linkage map for bison. Three hundred fifty eight microsatellite loci spanning all 29 autosomes were genotyped via 83 PCR multiplexes and nine individual amplifications. A total of 292 markers were integrated into an autosomal linkage map for bison. The sex averaged bison map (2,647 cM) was approximately 9% longer than the corresponding USDA MARC map, which covered 2,415 cM. Utilizing weaning, yearling and 17-month weights from two private bison herds, a QTL scan was conducted using the developed linkage map. LOD peaks suggestive of QTL were identified on chromosomes 2, 7, 15, and 24 for weaning weight, chromosomes 4, 14, and 15 for yearling weight and chromosomes 8, 14, and 25 for 17-month weight. Four of the identified chromosomes have conserved synteny with regions harboring growth QTL in cattle.     

Kappa-casein polymorphisms among cattle breeds and bison herds

Summary
We identified the Hind III restriction site polymorphism of K-casein in cattle reported by Pinder et al. ( Animal Genetics 22, 11, 1991) and found an additonal polymorphism ( Rsa I) in cattle and bison. The Hin dIII and Rsa I restriction sites were mapped and three haplotypes (alleles) were identified. Preliminary screening of 39 cattle and 71 bison revealed one allele restricted to cattle, one restricted to bison, and one shared by the species. No fixed allelic differences were observed among cattle breeds or among bison herds or subspecies.     

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.     

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.     

DNA fingerprinting and genetic diversity of the European bison (Bison bonasus), American bison (Bison bison), and gray Ukrainian cattle (Bos taurus)

To describe genetic variability and population diversity in domesticated populations of American bison (Bison bison), aurochs (Bison bonasus), and gray Ukrainian cattle (Bos taurus) different variants of DNA fingerprinting technique (utilizing the M13 phage DNA, (TTAGGG)4 synthetic oligonucleotide, and three arbitrary primers as hybridization probes) were used. Several parameters characterizing polymorphism and genetic diversity levels in each population (species) were evaluated on the basis of the profiles obtained. Dendrograms reflecting similarities between individual animals were constructed. Genetic variability of minisatellite and telomeric markers observed in the gray Ukrainian cattle flock was higher than that in aurochs and bisons. Comparison of the intrapopulation similarity (S) and gene diversity (H) indices along with the analysis of clusters in the dendrograms showed that the relatedness between the aurochs individuals was much higher than between the individual animals in the bison and gray Ukrainian cattle flocks. Furthermore, the gray Ukrainian cattle flock was represented by more distant relatives than the bison flock. It is suggested that reduced genetic variability and the appearance of deviant genotype observed in the two bison lines under selection, resulted from close inbreeding and the founder effect. The diagnostic value and efficacy of utilization of different molecular markers for estimation of genetic diversity and relatedness in domesticated animal populations is discussed.     

Microsatellite characterization of Cimarron Uruguayo dogs

Various genetic markers, including microsatellites, have been used to analyze the genetic polymorphism and heterozygosity in canine breeds. In this work, we used nine microsatellite markers to investigate the genetic variability in Cimarron Uruguayo dogs, the only officially recognized native canine breed in Uruguay. DNA from 30 Cimarron Uruguayo dogs from northeastern and southern Uruguay was analyzed. The allelic frequencies for each microsatellite, the genetic variability and the consanguinity were calculated, as were the polymorphic information content (PIC) and the probability of exclusion (PE). All of the microsatellites studied were polymorphic. FH 2361, FH 2305 and PEZ 03 were the most informative, with PIC values > 0.7, in agreement with results for other canine breeds. The PE values for the markers were within the ranges previously described and were generally greater for microsatellites with higher PIC values. The heterozygosity value (0.649) was considered high since only nine microsatellites were analyzed. Compared with data for other breeds, the results obtained here indicate that Cimarron Uruguayo dogs have high genetic diversity.     

Ruminal ciliated protozoa in bison

Ruminal contents from 79 slaughtered bison and 2 ruminally cannulated bison were collected to obtain information on total numbers and species distribution of ciliated protozoa. The bison originated from numerous herds throughout the Great Plains and were grouped into three dietary categories: (i) only forage; (ii) forage with moderate levels of supplementation; and (iii) feedlot concentrate-silage diet. Total ciliate counts were highest in bison receiving grain supplementation (210.1 x 10(4)/g) and lowest in bison consuming only forage (27.1 x 10(4)/g). All protozoan species found in bison have been reported in domestic livestock, although Ophryoscolex sp., a relatively common protozoan in cattle, was detected at low concentrations in only eight bison. The uncommon holotrich Microcetus lappus was present in five bison in concentrations reaching 8.4% of the total ciliate population. Charonina ventriculi, another infrequently observed species, was present in 18 bison, with the highest concentrations in forage-fed animals. Thirty bison possessed a type B protozoan population, characterized by Epidinium sp., Eudiplodinium maggii, and Eudiplodinium bovis. Thirty-eight bison possessed a mixed A-B population, characterized by Polyplastron sp. coexisting with low numbers of Eudiplodinium maggii or Epidinium sp. or both. Thirteen bison possessed populations lacking any remnant type B ciliate species. At least 29 of the bison possessing Polyplastron sp. were known to have been in contact with cattle, whereas all bison isolated from cattle had type B populations. The reduction of type B populations in bison becomes increasingly likely as bison production expands into areas inhabited by domestic livestock.     

Ruminal ciliated protozoa in bison.

Ruminal contents from 79 slaughtered bison and 2 ruminally cannulated bison were collected to obtain information on total numbers and species distribution of ciliated protozoa. The bison originated from numerous herds throughout the Great Plains and were grouped into three dietary categories: (i) only forage; (ii) forage with moderate levels of supplementation; and (iii) feedlot concentrate-silage diet. Total ciliate counts were highest in bison receiving grain supplementation (210.1 x 10(4)/g) and lowest in bison consuming only forage (27.1 x 10(4)/g). All protozoan species found in bison have been reported in domestic livestock, although Ophryoscolex sp., a relatively common protozoan in cattle, was detected at low concentrations in only eight bison. The uncommon holotrich Microcetus lappus was present in five bison in concentrations reaching 8.4% of the total ciliate population. Charonina ventriculi, another infrequently observed species, was present in 18 bison, with the highest concentrations in forage-fed animals. Thirty bison possessed a type B protozoan population, characterized by Epidinium sp., Eudiplodinium maggii, and Eudiplodinium bovis. Thirty-eight bison possessed a mixed A-B population, characterized by Polyplastron sp. coexisting with low numbers of Eudiplodinium maggii or Epidinium sp. or both. Thirteen bison possessed populations lacking any remnant type B ciliate species. At least 29 of the bison possessing Polyplastron sp. were known to have been in contact with cattle, whereas all bison isolated from cattle had type B populations. The reduction of type B populations in bison becomes increasingly likely as bison production expands into areas inhabited by domestic livestock.     

Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites

To guide genetic conservation programmes with objective criteria, general genetic variability has to be taken into account. This study was conducted to determine the genetic variation between 10 cattle breeds by using 17 microsatellite loci and 13 biochemical markers (11 blood groups, the transferrin and β-casein loci). Microsatellite loci were amplified in 31–50 unrelated individuals from 10 cattle breeds: Charolais, Limousin, Breton Black Pied, Parthenais, Montbéliard, Vosgien, Maine-Anjou, Normande, Jersey and Holstein. Neighbor-joining trees were calculated from genetic distance estimates. The robustness of tree topology was obtained by bootstrap resampling of loci. A total of 210 alleles of the 17 microsatellites were detected in this study and average heterozygosities ranged from 0·53 in the Jersey breed to 0·66 in the Parthenais breed. In general, low bootstrap values were obtained: with the 17 microsatellites, the highest bootstrap values concerned the Holstein/Maine-Anjou grouping with an occurrence of 74%; with the biochemical markers, this node had an occurrence of 79% and the Charolais/Limousin grouping appeared with an occurrence of 74%; when microsatellites and biochemical polymorphism were analysed together, the occurrence of the Holstein/Maine-Anjou grouping was 90% and that of the Charolais/Limousin grouping was 42%. These results suggest that 30 microsatellites, a number currently considered as sufficient to distinguish closely related breeds is, in fact, probably insufficient.     

Experimental infections of Babesia bigemina in American bison

Babesia bigemina was experimentally transmitted from cattle to bison and back to cattle. One spleen-intact and two splenectomized American bison (Bison bison) inoculated with a B. bigemina stabilate exhibited clinical and hematological signs of babesiosis within 10 days of exposure. Blood from the infected bison produced disease in a splenectomized bovine steer.     

Female segregation patterns of the putative Y-chromosome-specific microsatellite markers INRA124 and INRA126 do not support their use for cattle population studies

Here we tested the segregation and paternal compatibility of markers INRA124 and INRA126 on female DNA in 10 different cattle families, in order to clarify the usefulness of these microsatellites for the study of male-mediated population processes in cattle. Their performance was compared with that of four microsatellites located in the PAR-BTAY ( UMN0108 , UMN0803 , UMN0929 and UMN0905 ) and another one male-specific microsatellite ( INRA189 ). INRA124 and INRA126 amplified the same sized fragment in both sexes. Same size alleles were sequenced and the high homology found allowed us to rule out non-specific female amplification. INRA124 showed full parental compatibility, whilst the locus INRA126 showed 55% parental incompatibility. Based on these observations, it is recommended that markers INRA124 and INRA126 should not be used in studies to characterize male-mediated genetic events in cattle.     

Characterization of Bison bison major histocompatibility complex class IIa haplotypes

American bison (Bison bison) and domestic cattle (Bos taurus and Bos indicus) evolved from a common ancestor 1–1.4 million years ago. Nevertheless, they show dramatic differences in their susceptibility to infectious diseases, including malignant catarrhal fever (MCF). Although bison are highly susceptible to ovine herpesvirus-2 (OvHV-2) associated MCF, about 20% of healthy domesticated and wild bison are positive for OvHV-2 antibody. We are interested in testing the hypothesis that, within the bison population, the polymorphism of major histocompatibility complex (MHC) class II genes influences resistance to MCF. However, since little was known about the MHC class II genes of bison, it was necessary to first characterize class II haplotypes present in Bi. bison (Bibi). Thus, the MHC class II haplotypes carried by 14 bison were characterized by the PCR-based cloning and sequencing of their DRB3, DQA, and DQB alleles. Twelve MHC class II haplotypes were identified in the 14 bison. These haplotypes comprised six previously reported and six new Bibi-DRB3 alleles, along with 11 Bibi-DQA and 10 Bibi-DQB alleles. For each bison class II allele, it was possible to identify closely related cattle sequences. The closest bison and bovine DQA, DQB, and DRB3 alleles, on average, differed by only 1.3, 3.5, and 5.8 amino acids, respectively. Furthermore, bison MHC haplotypes with both nonduplicated and duplicated DQ genes were identified; these haplotypes appear to have originated from the same ancestral haplotypes as orthologous cattle haplotypes. This study was supported by USDA-Agricultural Research Service grant CWU-5348-32000-018-00D. While working on this project, Dr. Bharat Bhushan was supported by a fellowship from the World-Bank-sponsored National Agricultural Technology Project of the Indian Council of Agricultural Research, Indian Ministry of Agriculture, New Delhi, India     

Genetic characterization in four sciaenid species from the Arabian Sea

Four sciaenid species Johnieops dussumieri, Kathala axillaris, Pennahia macropthalmus and Otolithes ruber were analysed electrophoretically for genetic variation at 18 loci (16 in P. macropthalmus and O. ruber ). Twelve loci were polymorphic in J. dussumieri , 10 in K. axillaris , three in P. macropthalmus and 12 in O. ruber ( P <0·99). Average heterozygosity ranged from 0·033 ± 0·100 to 0·070 ± 0·122. The allele frequencies of 14 loci were used to estimate Nei's genetic distance (). The values ranged from 0·334 to 0·612. Three isozyme loci ( LDH-B*, MDH-2* and G3PDH-1* ) were found to be the most reliable species-specific markers.     

Bovine coccidia in American bison.

Three species of coccidia, found in American bison sampled in Wyoming, are identified. The described coccidial species, common to cattle, have not been reported previosuly from American bison, (Bison bison). Identification of the parasites was determined by oocyst structural measurements and by oocyst sporulation times.     

Inheritance of amplified fragment length polymorphism markers and their utility in population genetic analysis of Plecoglossus altivelis

The reproducibility, mode of inheritance and polymorphism of amplified fragment length polymorphism (AFLP) markers were examined in ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae). The AFLP markers were highly reproducible, their inheritance following Mendelian expectations. The number of fragments amplified (34–134), polymorphic ratio (0·15–0·78) and average heterozygosity (0·02–0·25) of the AFLP markers showed significant variation among six primer pairs and among ayu populations, including a landlocked Lake‐Biwa population, two amphidromous populations ( P. a. altivelis ) and two Ryukyu‐ayu populations ( P. a. ryukyuensis ). Although AFLP analysis provided similar results in intra‐population diversity and relationships among populations to those found by analyses of allozymes, microsatellites and mitochondrial DNA sequences, AFLPs showed higher polymorphisms and hence greater distinction between genetically close populations.     

Characterization of Anaplasma marginale isolated from North American bison

Anaplasma marginale (Rickettsiales: Anaplasmataceae), a tick-borne pathogen of cattle, is endemic in tropical and subtropical regions of the world. Although serologic tests have identified American bison, Bison bison, as being infected with A. marginale, the present study was undertaken to confirm A. marginale infection and to characterize isolates obtained from naturally infected bison in the United States and Canada. Major surface protein (MSP1a and MSP4) sequences of bison isolates were characterized in comparison with New World cattle isolates. Blood from one U.S. bison was inoculated into a susceptible, splenectomized calf, which developed acute anaplasmosis, demonstrating infectivity of this A. marginale bison isolate for cattle. The results of this study showed that these A. marginale isolates obtained from bison were similar to ones from naturally infected cattle.