Search

Methods: Up to 237 individuals belonging to 10 different taurine (Bos taurus), zebu (B. indicus), and taurine × zebu sanga cattle populations sampled in Benin, Burkina Faso, and Niger were typed using the BovineHD BeadChip of Illumina to ascertain the patterns and importance of heterozygosity-rich regions (HRRs) in West African cattle. To account for among-population gene flow, individuals were further classified into three groups (Qtaurine, Qzebu, and admixed) according to maximum likelihood estimates of individual ancestries ( q ^ ) obtained using the program Admixture v1.23. Results and discussion: The 967 HRRs identified on 27 out of 29 bovine chromosomes in 231 cattle individuals were further summarized into 103 HRR islands, covering 40.7 Mb of the bovine genome. Only HRR islands identified in at least 10% of the animals typed or 10% of the individuals classified according to cattle type or admixture class were considered relevant to characterize the West African cattle genomic background. Only one and three HRR islands were considered taurine- and zebu-specific, respectively. Most (14) relevant HRR islands identified were present in cattle individuals despite the cattle type or admixture class into which they were classified (waHRR), suggesting that HRR can give advantages for adaptation to harsh environments. A total of 202 potential candidate genes were identified on the 14 waHRR islands. Most of them belonged to gene families coding zinc finger, protocadherin, adhesion G protein-coupled receptors, solute carrier, and arachidonate lipoxygenase proteins, involved in immune response, with a putative role in adaptation. Furthermore, waHRRs were also enriched on 18 and 11 different genes coding olfactory receptors and pregnancy-associated glycoproteins, respectively, giving additional support to the suggested importance of the HRR islands identified for the adaptive ability of West African cattle. Our research identified new genomic areas that can be targeted for further research in cattle adaptive ability. [ABSTRACT FROM AUTHOR]

Background: Goats were domesticated in the Fertile Crescent about 10,000 years before present (YBP) and subsequently spread across Eurasia and Africa. This dispersal is expected to generate a gradient of declining genetic diversity with increasing distance from the areas of early livestock management. Previous studies have reported the existence of such genetic cline in European goat populations, but they were based on a limited number of microsatellite markers. Here, we have analyzed data generated by the AdaptMap project and other studies. More specifically, we have used the geographic coordinates and estimates of the observed (Ho) and expected (He) heterozygosities of 1077 European, 1187 African and 617 Asian goats belonging to 38, 43 and 22 different breeds, respectively, to find out whether genetic diversity and distance to Ganj Dareh, a Neolithic settlement in western Iran for which evidence of an early management of domestic goats has been obtained, are significantly correlated. Results: Principal component and ADMIXTURE analyses revealed an incomplete regional differentiation of European breeds, but two genetic clusters representing Northern Europe and the British-Irish Isles were remarkably differentiated from the remaining European populations. In African breeds, we observed five main clusters: (1) North Africa, (2) West Africa, (3) East Africa, (4) South Africa, and (5) Madagascar. Regarding Asian breeds, three well differentiated West Asian, South Asian and East Asian groups were observed. For European and Asian goats, no strong evidence of significant correlations between Ho and He and distance to Ganj Dareh was found. In contrast, in African breeds we detected a significant gradient of diversity, which decreased with distance to Ganj Dareh. Conclusions: The detection of a genetic cline associated with distance to the Ganj Dareh in African but not in European or Asian goat breeds might reflect differences in the post-domestication dispersal process and subsequent migratory movements associated with the management of caprine populations from these three continents. [ABSTRACT FROM AUTHOR]

Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH‐based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H‐Line), 766 individuals for the low variability line (L‐Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (FPED) information, on ROH identified using the SW method (FROHSW) and on ROH identified using the CR method (FROHCR). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between FPED and FROH were high, particularly for FROHSW. Moreover, correlations between FROHSW and FPED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of FROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH‐based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with FPED. Differences in robustness between lines were not attributable to a higher homozygosis in the L‐Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness. [ABSTRACT FROM AUTHOR]

Contributions to gene diversity and allelic richness were computed in a total of 2,260 domestic pig genotypes, sharing 53,626 autosomal SNPs, belonging to 98 pig subpopulations worldwide (41 Asian, 696 genotypes; 20 American, 262 genotypes; and 37 European, 686 genotypes), using 616 pig samples belonging to 5 different Cosmopolitan pig breeds as an outgroup, to ascertain if local pig subpopulation can be considered reservoirs of genetic diversity for the whole domestic pig species worldwide. Assessments were carried out for the whole dataset and separately for the American-European and Asian subsets. Effective population size was computed at the subpopulation level using molecular coancestry and linkage disequilibrium information to ensure that estimates of contributions to diversity were not affected by demographic issues. Most American and European pig subpopulations tended to have favorable contributions to both gene diversity and allelic richness. However, contributions to allelic richness were more consistent than those obtained for gene diversity, whether the computations are performed using either the whole dataset or the American–Asian subset, suggesting that allelic richness can be a key parameter to identify putative reservoirs for the species. The Asian pig subpopulations never contributed favorably to the allelic richness of the domestic pig metapopulation. Although these results can partially be explained by the highly divergent origins of the American-European and the Asian pig subpopulations, it cannot be discarded that the results obtained for the Asian subpopulations are biased due to a worse calling performance of the pig SNP arrays used for genotyping. The use of other potentially less biased sources of genotypic information is advisable to compare the Asian and American-European pig subpopulations genetic diversity. [ABSTRACT FROM AUTHOR]

Celtic‐Iberian pig breeds were majority in Spain and Portugal until the first half of the 20th century. In the 1990s, they were nearly extinct as a result of the introduction of foreign improved pig breeds. Despite its historical importance, the genetic background of the Celtic‐Iberian pig strain is poorly documented. In this study, we have identified genomic regions that might contain signatures of selection peculiar of the Celtic‐Iberian genetic lineage. A total of 153 DNA samples of Celtic‐Iberian pigs (Spanish Gochu Asturcelta and Portuguese Bísara breeds), Iberian pigs (Spanish Iberian and Portuguese Alentejano breeds), Cinta Senese pig, Korean local pig and Cosmopolitan pig (Hampshire, Landrace and Large White individuals) were analysed. A pairwise‐comparison approach was applied: the Gochu Asturcelta and the Bísara samples as test populations and the five other pig populations as reference populations. Three different statistics (XP‐EHH, FST and ΔDAF) were computed on each comparison. Strict criteria were used to identify selection sweeps in order to reduce the noise brought on by the Gochu Asturcelta and Bísara breeds' severe population bottlenecks. Within test population, SNPs used to construct potential candidate genomic areas under selection were only considered if they were identified in four of ten two‐by‐two pairwise comparisons and in at least two of three statistics. Genomic regions under selection constructed within test population were subsequently overlapped to construct candidate regions under selection putatively unique to the Celtic‐Iberian pig strain. These genomic regions were finally used for enrichment analyses. A total of 39 candidate regions, mainly located on SSC5 and SSC9 and covering 3130.5 kb, were identified and could be considered representative of the ancient genomic background of the Celtic‐Iberian strain. Enrichment analysis allowed to identify a total of seven candidate genes (NOL12, LGALS1, PDXP, SH3BP1, GGA1, WIF1, and LYPD6). Other studies reported that the WIF1 gene is associated with ear size, one of the characteristic traits of the Celtic‐Iberian pig strain. The function of the other candidate genes could be related to reproduction, adaptation and immunity traits, indirectly fitting with the rusticity of a non‐improved pig strain traditionally exploited under semi‐extensive conditions. [ABSTRACT FROM AUTHOR]

Abstract We present here a simple approach to obtain reliable estimates of the effective population size in real world populations via the computation of the increase in inbreeding for each individual (delta Fi) in a given population. The values of delta Fi are computed as t-root of 1 - (1 - Fi) where Fi is the inbreeding coefficient and t is the equivalent complete generations for each individual. The values of delta F computed for a pre-defined reference subset can be averaged and used to estimate effective size. A standard error of this estimate of Ne can be further computed from the standard deviation of the individual increase in inbreeding. The methodology is demonstrated by applying it to several simulated examples and to a real pedigree in which other methodologies fail when considering reference subpopulations. The main characteristics of the approach and its possible use are discussed both for predictive purposes and for analyzing genealogies.

Abstract Background Introgression of Sahel livestock genes southwards in West Africa may be favoured by human activity and the increase of the duration of the dry seasons since the 1970’s. The aim of this study is to assess the gene flow patterns in Burkina Faso goat and to ascertain the most likely factors influencing geographic patterns of genetic variation in the Burkina Faso goat population. Results A total of 520 goat were sampled in 23 different locations of Burkina Faso and genotyped for a set of 19 microsatellites. Data deposited in the Dryad repository: http://dx.doi.org/10.5061/dryad.41h46j37. Although overall differentiation is poor (FST = 0.067 ± 0.003), the goat population of Burkina Faso is far from being homogeneous. Barrier analysis pointed out the existence of: a) genetic discontinuities in the Central and Southeast Burkina Faso; and b) genetic differences within the goat sampled in the Sahel or the Sudan areas of Burkina Faso. Principal component analysis and admixture proportion scores were computed for each population sampled and used to construct interpolation maps. Furthermore, Population Graph analysis revealed that the Sahel and the Sudan environmental areas of Burkina Faso were connected through a significant number of extended edges, which would be consistent with the hypothesis of long-distance dispersal. Genetic variation of Burkina Faso goat followed a geographic-related pattern. This pattern of variation is likely to be related to the presence of vectors of African animal trypanosomosis. Partial Mantel test identified the present Northern limit of trypanosome vectors as the most significant landscape boundary influencing the genetic variability of Burkina Faso goat (p = 0.008). The contribution of Sahel goat genes to the goat populations in the Northern and Eastern parts of the Sudan-Sahel area of Burkina Faso was substantial. The presence of perennial streams explains the existence of trypanosome vectors. The South half of the Nakambé river (Southern Ouagadougou) and the Mouhoun river loop determined, respectively, the Eastern and Northern limits for the expansion of Sahelian goat genes. Furthermore, results from partial Mantel test suggest that the introgression of Sahelian goat genes into Djallonké goat using human-influenced genetic corridors has a limited influence when compared to the biological boundary defined by the northern limits for the distribution of the tsetse fly. However, the genetic differences found between the goat sampled in Bobo Dioulasso and the other populations located in the Sudan area of Burkina Faso may be explained by the broad goat trade favoured by the main road of the country. Conclusions The current analysis clearly suggests that genetic variation in Burkina Faso goat: a) follows a North to South clinal; and b) is affected by the distribution of the tsetse fly that imposes a limit to the Sahelian goat expansion due to their trypanosusceptibility. Here we show how extensive surveys on livestock populations can be useful to indirectly assess the consequences of climate change and human action in developing countries.