Population-genetic study of the polymorphism of structural genes and ISSR-PCR markers in some cattle breeds

The comparative analysis of genetic structures of five cattle breeds has been carried out using polymorphism of two different types of molecular-genetic markers--20 structural genes and 128 DNA loci (the DNA fragments flanked by inverted microsatellite loci repetitions--ISSR-PCR method). In spite of availability of breed-specific singularities of genotype distribution detected by the both methods the level of mean heterozygosity of structural genes was similar in all the investigated breeds. A part of polymorphic loci and the average value of the polymorphic information contents (PIC) of ISSR-PCR markers has appeared much higher in commercial breeds with high effective number in comparison with Ukrainian autochthonous breeds. The population-genetic processes detected by different methods are discussed.     

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.     

Serum proteins of the free-ranging European bison

The paper presents the values of total protein (TP) and protein fractions in the serum of 57 European bisons from the Bia?owieza Primeval Forest, 47 of these animals being free-ranging and 10 living in enclosures. It was found that the amount of TP and amount of alpha 1- and gamma-globulin fractions are significantly lower in adult females than males. The amount of TP and gamma-globulin fraction increase significantly with age in all examined Europeans bisons, whereas the amount of alpha 1- and alpha 2-globulin fractions increase only in free-ranging animals.     

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.     

Identification of bovine and novel interferon-tau alleles in the American plains bison (Bison bison) by analysis of hybrid cattle x bison blastocysts

The objective of this study was to generate bison x cattle hybrid embryos by in vitro fertilization, to assess their developmental potential, to determine the pattern of secretion of the embryonic signaling molecule interferon-tau (IFN-tau), and to identify novel IFN-tau mRNA polymorphism in the American plains bison. A total of 600 bovine oocytes were inseminated with frozen-thawed bison semen. Of these, 40.7% cleaved and 14.8% proceeded to the blastocyst stage. Individual blastocysts were cultured on a basement membrane (Matrigel) and their ability to attach and form outgrowths was monitored. A total of 36 blastocysts were cultured of which 22 formed outgrowths. During individual culture, medium samples were collected and their IFN-tau concentration was measured. On day 6 after onset of individual culture, attached outgrowths produced significantly more IFN-tau than unattached viable or degenerate blastocysts. At this time, female conceptuses also produced significantly more IFN-tau than their male cohorts. However, by day 12 this difference had disappeared. Total mRNA was extracted from three individual outgrowths and analyzed by RT-PCR. Subsequent sequencing of 28 clones showed several known bovine IFN-tau sequences as well as two novel sequences termed bisIFN-tau1 and 2. To determine the origin of these, DNA was extracted from bison semen and analyzed by PCR. One bovine IFN-tau sequence (bovIFN-tau1d) as well as bisIFN-tau2 and a third novel sequence bisIFN-tau3 were detected. This study demonstrates the feasibility of using hybrid embryos for the analysis of developmentally regulated gene expression in species where embryos may not be available.     

Phylogenetic relationships among the European and American bison and seven cattle breeds reconstructed using the BovineSNP50 Illumina Genotyping BeadChip

Here we present the first attempt to use the BovineSNP50 Illumina Genotyping BeadChip for genome-wide screening of European bison Bison bonasus bonasus (EB), two subspecies of American bison: the plains bison Bison bison bison (PB), the wood bison Bison bison athabascae (WB) and seven cattle Bos taurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the consequences of bottlenecks on the genetic distances amongst bison subspecies and cattle, and (3) detect loci under positive or stabilizing selection. A Bayesian clustering procedure (STRUCTURE) detected ten genetically distinct clusters, with separation among all seven cattle breeds and European and American bison, but no separation between plain and wood bison. A linkage disequilibrium based program (LDNE) was used to estimate the effective population size (N _e) for the cattle breeds; N _e was generally low, relative to the census size of the breeds (cattle breeds: mean N _e = 299.5, min N _e = 18.1, max N _e = 755.0). BOTTLENECK 1.2 detected signs of population bottlenecks in EB, PB and WB populations (sign test and standardized sign test: p = 0.0001). Evidence for loci under selection was found in cattle but not in bison. All extant wild populations of bison have shown to have survived severe bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups.     

Omasal ciliated protozoa in cattle, bison, and sheep

Omasal contents were collected from slaughtered cattle (n = 54), bison (n = 15), and sheep (n = 40) to determine numbers and generic distribution of ciliated protozoa. Total protozoan numbers were significantly lower in omasal contents than in ruminal contents of all three species, but the percent composition of all protozoan genera was similar between omasal and ruminal populations. The highest numbers of omasal protozoa found were 7.61 X 10(5)/g in cattle, 7.01 X 10(5)/g in bison, and 1.29 X 10(6)/g in sheep. Omasal dry matter was significantly higher than ruminal dry matter in all species and ranged up to 51.5% in cattle fed high-concentrate diets. The omasal pH was similar to the ruminal pH in all species. The number of omasal laminae averaged 149, 145, and 74 for cattle, bison, and sheep, respectively. Although protozoan concentrations in omasal contents were approximately 80% lower than those in ruminal contents, the omasum harbored relatively high numbers of ciliated protozoa. The resident omasal protozoa are extremely difficult to remove, particularly in cattle, and apparently are responsible for reinoculating transiently defaunated rumens.     

The buller syndrome in American bison bulls

Homosexual mounting (buller syndrome) was observed incidentally during approximately 3900 h of field observations of 2 populations of American bison (Bison bison) in the course of an 11-year study of social and reproductive behaviour. Buller behaviour was regularly observed in intact, free-ranging males up to the age of 4 years. This suggests that some level of this behaviour, which is an economically significant problem in cattle husbandry, may be a natural trait of feed-lot steers.     

Depauperate genetic variability detected in the American and European bison using genomic techniques

 

A total of 929 polymorphic SNPs in EB (out of 54, 000 SNPs screened using a BovineSNP50 Illumina Genotyping BeadChip), and 1, 524 and 1, 403 polymorphic SNPs in WB and PB, respectively, were analysed. EB, WB and PB have all undergone recent drastic reductions in population size. Accordingly, they exhibited extremely depauperate genomes, deviations from genetic equilibrium and a genome organization consisting of a mosaic of haplotype blocks: regions with low haplotype diversity and high levels of linkage disequilibrium. No evidence for positive or stabilizing selection was found in EB, WB and PB, likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow radical improvements of breeding practices in captive or managed populations, otherwise hampered by the limited availability of polymorphic markers. This result in improved possibilities for 1) estimating genetic relationships among individuals and 2) designing breeding strategies which attempt to preserve or reduce polymorphism in ecologically relevant genes and/or entire blocks.

Reviewers

This article was reviewed by: Fyodor Kondrashov and Shamil Sunyaev     

Omasal ciliated protozoa in cattle, bison, and sheep.

Omasal contents were collected from slaughtered cattle (n = 54), bison (n = 15), and sheep (n = 40) to determine numbers and generic distribution of ciliated protozoa. Total protozoan numbers were significantly lower in omasal contents than in ruminal contents of all three species, but the percent composition of all protozoan genera was similar between omasal and ruminal populations. The highest numbers of omasal protozoa found were 7.61 X 10(5)/g in cattle, 7.01 X 10(5)/g in bison, and 1.29 X 10(6)/g in sheep. Omasal dry matter was significantly higher than ruminal dry matter in all species and ranged up to 51.5% in cattle fed high-concentrate diets. The omasal pH was similar to the ruminal pH in all species. The number of omasal laminae averaged 149, 145, and 74 for cattle, bison, and sheep, respectively. Although protozoan concentrations in omasal contents were approximately 80% lower than those in ruminal contents, the omasum harbored relatively high numbers of ciliated protozoa. The resident omasal protozoa are extremely difficult to remove, particularly in cattle, and apparently are responsible for reinoculating transiently defaunated rumens.     

The seasonal fertility of North American bison (Bison bison) bulls

The objective of this study was to determine the presence and magnitude of seasonal fluctuations in semen quality and other reproductive indices in bison bulls. Testicles from 288 commercially slaughtered bison bulls were collected monthly over a 1-year period. Carcass and testicle weight were determined and measurements of seminiferous tubule lumen, diameter, and epithelial thickness were made. Sperm cell morphology and defects were described and quantified using epididymal semen from each testicle. Twenty-one Plains (Bison bison bison) and Wood bison (Bison bison athabascae) breeding bulls, averaging 6.0 years of age (range 2.5-8.0), from three farms were selected for semen collection and evaluation on the basis of producer co-operation. Semen was collected by electro-ejaculation on four seasonal occasions during a 12-month period. Ejaculate quality was judged on the basis of volume, density, gross and individual motility, morphology, live/dead ratio, and concentration. Sperm cell morphologies were evaluated microscopically and classified according to criteria used for bovine semen. Fecal testosterone was measured at each semen collection using a commercial competitive binding radioimmunoassay. There was an increase in carcass weights over the study period and testis weights were moderately correlated (r=0.44) with carcass weights. However, mean testes weights were heavier (P<0.05) in the summer than in winter, spring, or fall periods. There were no differences in the proportion of normal and abnormal epididymal sperm between seasons but there were seasonal changes in the testicular parenchyma. Seminiferous tubule and lumen diameter, and epithelial thickness were greatest (P<0.05) in summer. Live bulls gained weight between April and November, but lost weight over the winter. Normal sperm cell percentages as well as individual sperm cell motility in electro-ejaculated sperm samples were higher (P<0.05) at the pre-breeding collection relative to other collections, but no change in sperm cell concentrations occurred over the study period. Fecal testosterone concentrations were highest at the pre-breeding period (June) but decreased (P<0.05) in each subsequent collection to reach their lowest levels in the April. While many changes in seen characteristics were not significant, overall results indicate the presence of some reproductive seasonality and increased testicular capacity in the summer breeding season. Bulls showing marginal semen quality in the winter but otherwise carrying desirable genetic traits may warrant another evaluation in late spring prior to being culled from a breeding program.     

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.     

Defecation rate in captive European bison, Bison bonasus

Data on the digestive characteristics of European bison, Bison bonasus (L.), are needed for studies of their role as the largest extant herbivore in Europe and a potential keystone species of the temperate forest ecosystem. Very little published data are available, particularly on the defecation rate which affects population estimates from dropping counts and also the individual seed deposition rate. We gathered data from a captive bison group kept at the Show Reserve of the Bia?owie?a National Park. Droppings accumulated in the enclosure over a 72-h period were counted in winter 2010. In addition, the group was observed over approximately 6-h periods three times in winter and 16 times in summer. The count of accumulated droppings over a 72-h period gave eight defecations per day. The summer direct observations recorded 7.5 defecations per day and winter observation 5.4 defecations per day. These estimates are within the range for other bovids of similar size. The difference between summer and winter observation-based estimates may be accounted for by a higher frequency of defecation in early morning and late afternoon, periods not covered in winter observations. Given the published density of seedlings emerging from droppings of the ～470 free-living bison in the nearby forest, eight defecations a day mean that seed deposition by European bison may contribute significantly to realize seed dispersal and plant establishment.     

Restriction fragment length polymorphism (RFLP) of exon 2 of the MhcBibi-DRB3 gene in American bison (Bison bison)

Polymerase chain reaction (PCR) primers specific to exon 2 of the bovine lymphocyte antigen (BoLA)-DRB3 gene were successfully used to amplify the equivalent region in 469 American bison (Bison bison). In domestic cattle, alleles of DRB3 are assigned through a restriction fragment length polymorphism (RFLP) analysis of the patterns of fragment lengths observed after digestion with the restriction enzymes RsaI, BstYI and HaeIII. In bison, using the same procedure, the observed RFLP patterns provided evidence for the strong conservation of restriction sites previously reported in cattle.     

African and European mitochondrial haplotypes in South American Creole cattle

South American Creole cattle are direct descendants of the animals brought to the New World by the Spanish and Portuguese during the 16th century. A portion of the mitochondrial D-loop was sequenced in 36 animals from five Creole cattle populations in Argentina and four in Bolivia. Individuals belonging to the potentially ancestral Spanish breed Retinta were also analysed. Sequence comparisons revealed three main groups: two with the characteristics of European breeds and a third showing the transitions representative of the African taurine breeds. The African sequences were found in two populations from Argentina and three populations from Bolivia, whose only connections go back to colonial times. The most probable explanation for the finding is that animals could have been moved from Africa to Spain during the long-lasting Arabian occupation that started in the seventh century, and from the Iberian Peninsula to America eight centuries later. However, since African haplotypes were not found in the Spanish sample, the possibility of cattle transported directly from Africa cannot be disregarded.     

Cases of spermiogenesis in young European bison

Development of spermiogenesis and sizes of seminiferous tubules of the testes and epididymal duct were studied in 45 young European bisonBison bonasus (Linnaeus, 1758) males from an enclosed breeding centre and a free-ranging population in the Białowieża Forest. Of 13 males in age class II (up to two years), four showed the presence of elongated late spermatids: one male aged 15 months from the enclosed breeding centre and three from the free-ranging population (2 males aged 18 months and one about 24 months old). Of 7 males from age class III (up to 3 years), four showed spermiogenesis, of which the youngest, 26 and 32 months old, were from enclosed breeding. Spermiogenesis was observed in males with high body weight in a given age class. In males of age class I (up to one year old), the mean diameter of the seminiferous tubules was 49.8 μm, in class II — 110.7 μm, and in class III — 162 μm, the mean diameter of the epididymal duct being 110.8 μm, 187.2 μm and 273.4 μm, respectively. Measurements of seminiferous tubules and epididymal duct were significantly correlated with age and body weight of males and differed significantly between the three age classes.