An autosomal genetic linkage map of the sheep genome

Verification of pedigree information with paternity testing in Karacabey Merino sheep

Complex tests of DNA sequences, genetic research, and the use of specific DNA polymorphisms as genetic markers have all advanced rapidly in recent years. It is widely used in DNA-based parental testing. Therefore, it has replaced the blood types routinely used in pedigree tests. The study aimed to evaluate the 14 microsatellite loci in the study in terms of paternity test parameters and to investigate the usability of the relevant loci in determining the parentage of the Karacabey Merino breed. In this study, paternity testing was performed on 5 rams of the Karacabey Merino breed and their probable 98 offspring using 14 microsatellite loci. A total of 290 alleles were observed in the study. The observed heterozygosity ratio (Ho) based on loci was between 0.82 and 0.98, and the expected heterozygosity ratio (He) was between 0.87 and 0.93. Individual exclusion probability (PE) values for the loci were calculated to be between 0.596 and 0.761, with combined exclusion probability (CPE) values of 0.99999995. According to the results of the study, paternity tests using 14 microsatellite markers in Karacabey Merino sheep can be used with high accuracy.

Spatial genetic structure and Ovis haplogroup as a tool for an adaptive conservation management of the endangered Cyprus mouflon

The mouflon (Ovis gmelini ophion) is the largest wild terrestrial mammal of Cyprus. Regarded as the local flagship species, its population range is limited to the mountainous Paphos Forest and adjacent areas including part of Troodos National Forest Park (> 700 Km²). This species, protected by both national and international legislation, is classified as Endangered by the IUCN, with livestock intrusion, poaching and habitat loss as the main threatening factors. We determined the spatial genetic structure by investigating sexes separately and shed further light on the Cyprus mouflon placement among Ovis haplogroups (HGs) to enforce its protection within an adaptive conservation framework. We genotyped 108 samples collected across the entire species' range at both14 loci of the microsatellite DNA and the mitochondrial DNA Control Region (CR). Microsatellite genotyping indicated that the wild population retained low genetic variability, which, however, was not associated with a level of inbreeding raising particular concern (F_IS = 0.12). An overall weak spatial genetic structure was disclosed, consistently with the limited extension of the mouflon range, the lack of significant physical barriers to dispersal and the intense gene flow mostly occurring along a northeast-southwest axis across the forest. Nevertheless, evidences of structure were found for females in compliance with their philopatric behaviour. The disclosure of unique features compared to Mediterranean and Near East conspecifics, such as the occurrence of a six-fold 76 bp-long repeated motif in the Cyprus mouflon CR, along with the outcome of a phylogenetic reconstruction (based on a far higher number of Ovis GenBank records and Cyprus haplotypes than in previous studies) inspired the proposal of a new haplogroup (HGC2) which included the Anatolian mouflon (O. g. anatolica, former HGX) as sister taxon. While both high habitat heterogeneity and low human disturbance were the main drivers in determining the overall spatial structure, future conservation efforts to preserve this valuable genetic resource should focus on avoiding possible introgressive hybridisation with co-grazing livestock to the edge of its range.

Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty-first century

The continuous development and application of technology for genetic improvement is a key element for advancing sheep production in the United States. The US sheep industry has contracted over time but appears to be at a juncture where a greater utilization of technology can facilitate industry expansion to new markets and address inefficiencies in traditional production practices. Significant transformations include the increased value of lamb in relation to wool, and a downtrend in large-scale operations but a simultaneous rise in small flocks. Additionally, popularity of hair breeds not requiring shearing has surged, particularly in semi-arid and subtropical US environments. A variety of domestically developed composite breeds and newly established technological approaches are now widely available for the sheep industry to use as it navigates these ongoing transformations. These genetic resources can also address long-targeted areas of improvement such as growth, reproduction and parasite resistance. Moderate progress in production efficiency has been achieved by producers who have employed estimated breeding values, but widespread adoption of this technology has been limited. Genomic marker panels have recently shown promise for reducing disease susceptibility, identifying parentage and providing a foundation for marker-assisted selection. As the ovine genome is further explored and genomic assemblies are improved, the sheep research community in the USA can capitalize on new-found information to develop and apply genetic technologies to improve the production efficiency and profitability of the sheep industry.

Assessing possible hybridization among managed Nubian ibex in North America

Hybridization among closely related species is a concern in zoo and aquarium populations where unpedigreed animals are frequently exchanged with the private sector. In this study, we examine possible hybridization in a group of Nubian ibex (Capra nubiana) imported into the Association of Zoos and Aquariums' (AZA) Species Survival Program (SSP) from a private institution. These individuals appeared smaller in stature than adult SSP Nubian ibex and were excluded from breeding recommendations over the concern that they were hybrids. Twenty-six microsatellites were used to rule out recent hybridization with domestic goats, Siberian ibex (Capra sibirica), and Alpine ibex (Capra ibex). We argue that natural phenotypic variation across the large geographic range of Nubian ibex may account for the small stature of the imported ibex, as private institutions may have historically acquired individuals from locations that differed from the SSP founders. However, the imported Nubian ibex appeared genetically differentiated from the SSP Nubian ibex and may represent a source of genetic variation for the managed population.

A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora)

A high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24 cM and covered nearly the whole genome (99.4%) with a resolution of 0.47 cM. 1,457 scaffolds spanning 435.15 Mb were anchored onto 24 linkage groups, accounting for 80.7% of the draft genome assembly of the yellow drum. Comparative genomic analyses with medaka and zebrafish genomes showed superb chromosome-scale synteny between yellow drum and medaka. QTL mapping and association analysis congruously revealed 22 QTLs for growth-related traits and 13 QTLs for sex dimorphism. Some important candidate genes such as PLA2G4A, BRINP3 and P2RY1 were identified from these growth-related QTL regions. A gene family including DMRT1, DMRT2 and DMRT3 was identified from these sex-related QTL regions on the linkage group LG9. We demonstrate that this linkage map can facilitate the ongoing marker-assisted selection and genomic and genetic studies for yellow drum.

Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

BACKGROUND

Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding programs. Better understanding of linkage disequilibrium (LD) and ancestral effective population size (Ne) through quantifying this diversity and comparison between populations allows for more informed decisions with regards to selective breeding taking population genetic diversity into account. The estimation of N e can be determined via genetic markers and requires knowledge of genetic distances between these markers. Single nucleotide polymorphisms (SNP) data from a sample of 12,597 New Zealand crossbred and purebred sheep genotyped with the Illumina Ovine SNP50 BeadChip was used to perform a genome-wide scan of LD and N e . Three methods to estimate genetic distances were investigated: 1) M1: a ratio fixed across the whole genome of one Megabase per centiMorgan; 2) M2: the ratios of genetic distance (using M3, below) over physical distance fixed for each chromosome; and, 3) M3: a genetic map of inter-SNP distances estimated using CRIMAP software (v2.503).

RESULTS

The estimates obtained with M2 and M3 showed much less variability between autosomes than those with M1, which tended to give lower N e results and higher LD decay. The results suggest that N e has decreased since the development of sheep breeds in Europe and this reduction in Ne has been accelerated in the last three decades. The N e estimated for five generations in the past ranged from 71 to 237 for Texel and Romney breeds, respectively. A low level of genetic kinship and inbreeding was estimated in those breeds suggesting avoidance of mating close relatives.

CONCLUSIONS

M3 was considered the most accurate method to create genetic maps for the estimation of LD and Ne. The findings of this study highlight the history of genetic selection in New Zealand crossbred and purebred sheep and these results will be very useful to understand genetic diversity of the population with respect to genetic selection. In addition, it will help geneticists to identify genomic regions which have been preferentially selected within a variety of breeds and populations.

Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle

We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). The heritability of global recombination rate (GRR) was estimated at 0.13 in males and 0.08 in females, with a genetic correlation of 0.66 indicating that shared variants are influencing GRR in both sexes. A genome-wide association study identified seven quantitative trait loci (QTL) for GRR. Fine-mapping following sequence-based imputation in 14,401 animals pinpointed likely causative coding (5) and noncoding (1) variants in genes known to be involved in meiotic recombination (HFM1, MSH4, RNF212, MLH3, MSH5) for 5/7 QTL, and noncoding variants (3) in RNF212B for 1/7 QTL. This suggests that this RNF212 paralog might also be involved in recombination. Most of the identified mutations had significant effects in both sexes, with three of them each accounting for ∼10% of the genetic variance in males.

Copy number variants in the sheep genome detected using multiple approaches

Background

Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Most surveys of CNV in livestock have been conducted in the cattle genome, and often utilise only a single approach for the detection of copy number differences. Here we performed a study of CNV in sheep, using multiple methods to identify and characterise copy number changes. Comprehensive information from small pedigrees (trios) was collected using multiple platforms (array CGH, SNP chip and whole genome sequence data), with these data then analysed via multiple approaches to identify and verify CNVs.

Results

In total, 3,488 autosomal CNV regions (CNVRs) were identified in this study, which substantially builds on an initial survey of the sheep genome that identified 135 CNVRs. The average length of the identified CNVRs was 19 kb (range of 1 kb to 3.6 Mb), with shorter CNVRs being more frequent than longer CNVRs. The total length of all CNVRs was 67.6Mbps, which equates to 2.7 % of the sheep autosomes. For individuals this value ranged from 0.24 to 0.55 %, and the majority of CNVRs were identified in single animals. Rather than being uniformly distributed throughout the genome, CNVRs tended to be clustered. Application of three independent approaches for CNVR detection facilitated a comparison of validation rates. CNVs identified on the Roche-NimbleGen 2.1M CGH array generally had low validation rates with lower density arrays, while whole genome sequence data had the highest validation rate (>60 %).

Conclusions

This study represents the first comprehensive survey of the distribution, prevalence and characteristics of CNVR in sheep. Multiple approaches were used to detect CNV regions and it appears that the best method for verifying CNVR on a large scale involves using a combination of detection methodologies. The characteristics of the 3,488 autosomal CNV regions identified in this study are comparable to other CNV regions reported in the literature and provide a valuable and sizeable addition to the small subset of published sheep CNVs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2754-7) contains supplementary material, which is available to authorized users.

Utility of several microsatellite markers for the genetic characterisation of three ex situ populations of threatened caprine taxa (<i>Capra aegagrus</i>, <i>C. cylindricornis</i> and <i>C. falconeri</i>)

Abstract. Caprines belong to the most endangered group of mammals and artiodactyls suffering from many negative human impacts. Fortunately, many of them are protected and managed by national and international legislation and in situ and ex situ conservation actions. Although many microsatellite markers have been developed for wild and domestic caprines, they remain uninvestigated in respect of their utility for some taxa. We examined the utility of the International Society for Animal Genetics microsatellite set for genetic characterisations of three wild and one domestic Capra species from captive or semi-captive ex situ populations in Europe. Our data suggest the utility of this microsatellite set for detecting shared and species-specific alleles, characterising the genetic variability, and determining phylogenetic relationships and intraspecific structures in investigated taxa. We detected a depleted genetic variability in Capra falconeri and Capra cylindricornis in European ex situ populations; unrelated individuals are therefore needed for improving genetic variability parameters, as they are for the extralimital population of Capra aegagrus in the Vřísek game reserve (Czech Republic), for which we identified no genetic introgression from the domestic goat and great dissimilarity with some analysed individuals from European zoos. Current results here indicate some difficulties with the historical evidence, for example with respect to the origin and purity of particular individuals under breeding programmes.

The sheep genome illuminates biology of the rumen and lipid metabolism

Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.

Mutation discovery for Mendelian traits in non-laboratory animals: a review of achievements up to 2012

Within two years of the re-discovery of Mendelism, Bateson and Saunders had described six traits in non-laboratory animals (five in chickens and one in cattle) that show single-locus (Mendelian) inheritance. In the ensuing decades, much progress was made in documenting an ever-increasing number of such traits. In 1987 came the first discovery of a causal mutation for a Mendelian trait in non-laboratory animals: a non-sense mutation in the thyroglobulin gene (TG), causing familial goitre in cattle. In the years that followed, the rate of discovery of causal mutations increased, aided mightily by the creation of genome-wide microsatellite maps in the 1990s and even more mightily by genome assemblies and single-nucleotide polymorphism (SNP) chips in the 2000s. With sequencing costs decreasing rapidly, by 2012 causal mutations were being discovered in non-laboratory animals at a rate of more than one per week. By the end of 2012, the total number of Mendelian traits in non-laboratory animals with known causal mutations had reached 499, which was half the number of published single-locus (Mendelian) traits in those species. The distribution of types of mutations documented in non-laboratory animals is fairly similar to that in humans, with almost half being missense or non-sense mutations. The ratio of missense to non-sense mutations in non-laboratory animals to the end of 2012 was 193:78. The fraction of non-sense mutations (78/271 = 0.29) was not very different from the fraction of non-stop codons that are just one base substitution away from a stop codon (21/61 = 0.34).

Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome

Homologous recombination affects myriad aspects of genome evolution, from standing levels of nucleotide diversity to the efficacy of natural selection. Rates of crossing over show marked variability at all scales surveyed, including species-, population-, and individual-level differences. Even within genomes, crossovers are nonrandomly distributed in a wide diversity of taxa. Although intra- and intergenomic heterogeneities in crossover distribution have been documented in Drosophila, the scale and degree of crossover rate heterogeneity remain unclear. In addition, the genetic features mediating this heterogeneity are unknown. Here we quantify fine-scale heterogeneity in crossover distribution in a 2.1-Mb region of the Drosophila melanogaster X chromosome by localizing crossover breakpoints in 2500 individuals, each containing a single crossover in this specific X chromosome region. We show 90-fold variation in rates of crossing over at a 5-kb scale, place this variation in the context of several aspects of genome evolution, and identify several genetic features associated with crossover rates. Our results shed new light on the scale and magnitude of crossover rate heterogeneity in D. melanogaster and highlight potential features mediating this heterogeneity.

No mutations of FecB and FecG(H) in Iranian Lory sheep

The Booroola fecundity gene (FecB) and growth differentiation factor 9 (GDF9) gene belong to the transforming growth factor β (TGF-β) superfamily. The mutations of these genes have additive effects on the prolificacy in sheep. The aim of the present study was to determine the possible mutations of FecB and FecG(H) genes in Lory sheep breed of the Lorestan province, Iran. Sixty blood samples were collected and DNA was extracted from whole fresh blood. For detection of FecB and FecG(H) mutations, the PCR products were incubated with AvaII and DdeI restricted enzymes. Based on the results we did not find the FecB and FecG(H) mutations in this sheep breed population, so these mutations cannot the cause of the high prolificacy of Lory sheep breed and more study are needed to determine the genetic or environmental causes of high prolificacy of this sheep breed.

Evolution of population genetic structure of the British roe deer by natural and anthropogenic processes (Capreolus capreolus)

Human influence typically impacts on natural populations of conservation interest. These interactions are varied and sometimes complex, and may be negative and unintended or associated with conservation and management strategy. Understanding the details of how these interactions influence and are influenced by natural evolutionary processes is essential to the development of effective conservation strategies. In this study, we investigate a species in Britain that has experienced both negative impact through overhunting in historical times and management efforts through culls and translocations. At the same time, there are regional populations that have been less affected by human influence. We use mtDNA and nuclear microsatellite DNA markers to investigate patterns of connectivity and diversity and find multiple insular populations in Britain that probably evolved within the Holocene (when the habitat was free of ice). We identify three concurrent processes. First, surviving indigenous populations show highly provincial patterns of philopatry, maintaining and generating population structure on a small geographic scale. Second, founder populations into habitat extirpated of native populations have expanded, but remained largely insular. Third, introductions into established populations generate some admixture. We discuss the implications for the evolution of diversity of the integration of natural processes with anthropogenic influences on population size and distribution.

Use of entropy in the analysis of nominal traits in sheep

In the analysis of dependencies between nominal traits entropy and its function, mutual information seems to be a proper descriptive statistic. This is shown by characterizing the relationships between the prolificacy of dams and selected genetic attributes: the genotype of transferrin, the genotype of hemoglobin, and the type of birth, as well as the environmental attribute, i.e., year of birth. The entropy method may improve the exactitude of investigations concerning the influence of different factors on production trait. The index of relative uniformity, introduced in this study, proved to be an adequate tool for the determination of similarity in the examined flocks. The application of mutual information in the determination of values of the dependence measures in the analyzed experiment was justified.

Isolation and Characterization of Cross-Amplification Microsatellite Panels for Species of Procapra (Bovidae; Antilopinae)

The three Procapra species, Tibetan gazelle (P. picticaudata), Mongolian gazelle (P. gutturosa) and Przewalski’s gazelle (P. przewalskii) are endemic to Asia. Several intraspecific genetic issues have been studied with species-specific microsatellite loci in these Asian gazelles. However, cross-species microsatellite panels are absent, which inhibits comparative conservation and evolutionary studies of the Procapra. In this study, we isolated 20 cross-species microsatellite loci for Procapra from both related species and the genomic library of P. przewalskii. Fifty-three samples of the three gazelles were used to characterize the markers. Allele numbers ranged from three to 20, with a mean of 7.93 per locus. Observed heterozygosity (H_O) averaged 0.680 and expected heterozygosity (H_E) 0.767. The mean polymorphic information content (PIC) was 0.757 for P. picticaudata, 0.803 for P. gutturosa and 0.590 for P. przewalskii. Nine loci were significantly deviated from Hardy-Weinberg (H-W) equilibrium in the three species. Significant linkage disequilibrium was detected in four pairs of loci in P. przewalskii, five pairs in P. gutturosa and 51 pairs in P. picticaudata. Considering the abundance of published loci and their high success rates of cross-amplification, testing and utilization of loci from related species is efficient for wild species of Bovidae. The cross-species microsatellite loci we developed will facilitate further interspecies genetic studies in Procapra.

Loss of MHC and neutral variation in Peary caribou: genetic drift is not mitigated by balancing selection or exacerbated by MHC allele distributions

Theory and empirical results suggest that the rate of loss of variation at Mhc and neutral microsatellite loci may differ because selection influences Mhc genes, and because a high proportion of rare alleles at Mhc loci may result in high rates of loss via drift. Most published studies compare Mhc and microsatellite variation in various contemporary populations to infer the effects of population size on genetic variation, even though different populations are likely to have different demographic histories that may also affect contemporary genetic variation. We directly compared loss of variation at Mhc and microsatellite loci in Peary caribou by comparing historical and contemporary samples. We observed that similar proportions of genetic variation were lost over time at each type of marker despite strong evidence for selection at Mhc genes. These results suggest that microsatellites can be used to estimate genome-wide levels of variation, but also that adaptive potential is likely to be lost following population bottlenecks. However, gene conversion and recombination at Mhc loci may act to increase variation following bottlenecks.

A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome

The pregnant sheep has provided seminal insights into reproduction related to animal and human development (ovarian function, fertility, implantation, fetal growth, parturition and lactation). Fetal sheep physiology has been extensively studied since 1950, contributing significantly to the basis for our understanding of many aspects of fetal development and behaviour that remain in use in clinical practice today. Understanding mechanisms requires the combination of systems approaches uniquely available in fetal sheep with the power of genomic studies. Absence of the full range of sheep genomic resources has limited the full realization of the power of this model, impeding progress in emerging areas of pregnancy biology such as developmental programming. We have examined the expressed fetal sheep heart transcriptome using high-throughput sequencing technologies. In so doing we identified 36,737 novel transcripts and describe genes, gene variants and pathways relevant to fundamental developmental mechanisms. Genes with the highest expression levels and with novel exons in the fetal heart transcriptome are known to play central roles in muscle development. We show that high-throughput sequencing methods can generate extensive transcriptome information in the absence of an assembled and annotated genome for that species. The gene sequence data obtained provide a unique genomic resource for sheep specific genetic technology development and, combined with the polymorphism data, augment annotation and assembly of the sheep genome. In addition, identification and pathway analysis of novel fetal sheep heart transcriptome splice variants is a first step towards revealing mechanisms of genetic variation and gene environment interactions during fetal heart development.

A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus)

The striped bass (Morone saxatilis) and its relatives (genus Morone) are of great importance to fisheries and aquaculture in North America. As part of a collaborative effort to employ molecular genetics technologies in striped bass breeding programs, we previously developed nearly 500 microsatellite markers. The objectives of this study were to construct a microsatellite linkage map of striped bass and to examine conserved synteny between striped bass and three-spined stickleback (Gasterosteus aculeatus). Of 480 microsatellite markers screened for polymorphism, 289 informative markers were identified and used to genotype two half-sib mapping families. Twenty-six linkage groups were assembled, and only two markers remain unlinked. The sex-averaged map spans 1,623.8 cM with an average marker density of 5.78 cM per marker. Among 287 striped bass microsatellite markers assigned to linkage groups, 169 (58.9%) showed homology to sequences on stickleback chromosomes or scaffolds. Comparison between the stickleback genome and the striped bass linkage map revealed conserved synteny between these two species. This is the first linkage map for any of the Morone species. This map will be useful for molecular mapping and marker-assisted selection of genes of interest in striped bass breeding programs. The conserved synteny between striped bass and stickleback will facilitate fine mapping of genome regions of interest and will serve as a new resource for comparative mapping with other Perciform fishes such as European sea bass (Dicentrarchus labrax), gilthead sea bream (Sparus aurata), and tilapia (Oreochromis ssp.).

Deficiency in DNA methylation increases meiotic crossover rates in euchromatic but not in heterochromatic regions in Arabidopsis

Meiotic recombination is tightly regulated by cis- and trans-acting factors. Although DNA methylation and chromatin remodeling affect chromosome structure, their impact on meiotic recombination is not well understood. To study the effect of DNA methylation on the landscape of chromosomal recombination, we analyzed meiotic recombination in the decreased DNA methylation 1 (ddm1) mutant. DDM1 is a SWI2/SNF2-like chromatin-remodeling protein necessary for DNA methylation and heterochromatin maintenance in Arabidopsis thaliana. The rate of meiotic recombination between markers located in euchromatic regions was significantly higher in both heterozygous (DDM1/ddm1) and homozygous (ddm1/ddm1) backgrounds than in WT plants. The effect on recombination was similar for both male and female meiocytes. Contrary to expectations, ddm1 had no effect on the number of crossovers between markers in heterochromatic pericentric regions that underwent demethylation. These results are surprising, because the pericentromeric regions are hypermethylated and were expected to be the regions most affected by demethylation. Thus, DDM1 loss of function may trigger changes that enhance meiotic recombination in euchromatin regions but are not sufficient to induce the same events in heterochromatic segments. This work uncovers the repressive role of methylation on meiotic recombination in euchromatic regions and suggests that additional factors may have a role in controlling the suppression of recombination in heterochromatin.

The use of DNA markers in deciding conservation priorities in sheep and other livestock

The genetic diversity of most livestock species is reducing and it is not possible to preserve all livestock breeds. In order to preserve as much of the genetic diversity as possible we must first have a robust method of measuring the genetic differences between breeds. The analysis of microsatellite allele frequency is now the method of choice. Using sheep as an example, this paper describes the methods used for both microsatellite amplification and the analysis of the data once it has been collected.

Cross-species amplification of bovid microsatellites in central African duikers (genus Cephalophus) and other sympatric artiodactyls

The present study set out to evaluate cross-species amplification of 34 bovid microsatellites in six central African duikers: Cephalophus callipygus, C. monticola, C. silvicultor, C. nigrifrons, C. dorsalis and C. leucogaster. Of these loci, 16 amplified across all species and appeared polymorphic when initially tested in polyacrylamide gel electrophoresis. Twelve of these loci were subsequently assembled into three multiplex panels of four loci each. These multiplexes successfully amplified across all six duiker species in the present study and the sympatric artiodactyls Tragelaphus spekei and Hyemoschus aquaticus. The only exception was the locus BM848 that did not amplify from C. leucogaster. For species with sufficient sample sizes (C. callipygus and C. monticola), the number of alleles ranged from three to ten and four to fifteen, respectively. Three loci deviated from Hardy-Weinberg equilibrium in C. callipygus and five in C. monticola. We attribute the latter result to possibilities of local population substructuring or to an excess of homozygotes because of null alleles. These multiplex assemblies will greatly facilitate studies of individual identification, parentage analysis, population size estimation and fine-scale analyses of population genetic structure in central African artiodactyls.

A linkage map of sheep chromosome X (OARX) aligned to human chromosome X (HSAX)

We have constructed a genetic linkage map of the sheep X chromosome (OARX) containing 22 new gene loci from across the human X chromosome (HSAX). The female OARX linkage map has a total length of 152.6 cM with average gene spacing of 5.5 cM. Comparison with HSAX confirms one previously reported major breakpoint and inversion, and other minor rearrangements between OARX and HSAX. Comparison of the linkage map with sheep sequence data OAR 1.0 reveals a different arrangement of markers on the q arm, which may more accurately reflect the genuine arrangement of this region.

Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population

The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms.

Association between major histocompatibility complex microsatellites, fecal egg count, blood packed cell volume and blood eosinophilia in Pelibuey sheep infected with Haemonchus contortus

The objective of this study was to assess the correlation among traits associated with resistance or susceptibility to Haemonchus contortus infestation and to evaluate the participation of the ovine major histocompatibility complex (MHC) in Pelibuey sheep, a prevalent breed in tropical and sub-tropical regions in Mexico and elsewhere. Association among the fecal egg count (FEC), blood packed cell volume (PCV), antibody (AB) levels, serum proteins (SP) and blood eosinophil count (EOS) was assessed in 52 lambs experimentally infected with H. contortus, and the participation of the MHC was evaluated using polymorphisms in three microsatellites, located at the class I (OMHC1) and class II (OLADRB1, OLADRB2) regions of the MHC. Spearman correlation analysis among the traits showed a negative association (P<0.01) between FEC and PCV (-0.35), EOS (-0.50), SP (-0.30) and AB (-0.57), and a positive correlation of antibodies with EOS (0.50). The homozygotes for the OMHC1-188 and OLADRB2-282 alleles were associated with a reduction in FEC (-813 and -551, respectively). Conversely, the OMHC1-200 and OMHC1-206 alleles were associated with an increase in FEC (1704 and 1008, respectively). Furthermore, the OLADRB1-482 allele was associated with an increase of 163 EOS by allele copy, while the OMHC1-200 allele showed a reduction of 95 EOS in homozygotes. The associations among microsatellite MHC loci and the remaining variables were not significant. These results reinforce the evidence that MHC polymorphisms have an important role in parasite resistance or susceptibility in Pelibuey sheep and could be used as genetic markers to assist selection and improve parasite resistance to H. contortus.

A first comparative map of copy number variations in the sheep genome

We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle and goat genomes indicated that overlaps between sheep and both other species CNVRs are highly significant (P<0.0001), suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVRs include genes with important biological functions. Further studies are needed to evaluate their functional relevance.

Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene

Microphthalmia in sheep is an autosomal recessive inherited congenital anomaly found within the Texel breed. It is characterized by extremely small or absent eyes and affected lambs are absolutely blind. For the first time, we use a genome-wide ovine SNP array for positional cloning of a Mendelian trait in sheep. Genotyping 23 cases and 23 controls using Illumina's OvineSNP50 BeadChip allowed us to localize the causative mutation for microphthalmia to a 2.4 Mb interval on sheep chromosome 22 by association and homozygosity mapping. The PITX3 gene is located within this interval and encodes a homeodomain-containing transcription factor involved in vertebrate lens formation. An abnormal development of the lens vesicle was shown to be the primary event in ovine microphthalmia. Therefore, we considered PITX3 a positional and functional candidate gene. An ovine BAC clone was sequenced, and after full-length cDNA cloning the PITX3 gene was annotated. Here we show that the ovine microphthalmia phenotype is perfectly associated with a missense mutation (c.338G>C, p.R113P) in the evolutionary conserved homeodomain of PITX3. Selection against this candidate causative mutation can now be used to eliminate microphthalmia from Texel sheep in production systems. Furthermore, the identification of a naturally occurring PITX3 mutation offers the opportunity to use the Texel as a genetically characterized large animal model for human microphthalmia.