The Experts below are selected from a list of 4779 Experts worldwide ranked by ideXlab platform
R B Onzima - One of the best experts on this subject based on the ideXlab platform.
-
genome wide characterization of selection signatures and runs of homozygosity in ugandan Goat Breeds
Frontiers in Genetics, 2018Co-Authors: R B Onzima, Maulik Upadhyay, Harmen P Doekes, Luiz F Brito, Mirte Bosse, E Kanis, M A M Groenen, R P M A CrooijmansAbstract:Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across Breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, F_ROH, based on runs of homozygosity (ROH), in six Ugandan Goat Breeds: Boer (n = 13), and the indigenous Breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29) and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all Breeds, based on marker-specific fixation index (F_ST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signalling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g. IL10RB and IL23A), growth and fatty acid composition (e.g. FGF9 and IGF1), and thermo-tolerance (e.g. MTOR and MAPK3). The study revealed little overlap between Breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g. GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous Goat Breeds showed very low levels of genomic inbreeding (with the mean F_ROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean F_ROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these Goat Breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan Goat Breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
-
genome wide population structure and admixture analysis reveals weak differentiation among ugandan Goat Breeds
Animal Genetics, 2018Co-Authors: R B Onzima, Maulik Upadhyay, E Kanis, M A M Groenen, R Mukiibi, R P M A CrooijmansAbstract:Uganda has a large population of Goats, predominantly from indigenous Breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer Goats. Knowledge about the genetic characteristics and relationships among these Ugandan Goat Breeds and the potential admixture with Boer Goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Goat Breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across Breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the Breeds. Principal components separated Kigezi and weakly Small East African from other indigenous Goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local Breeds. The Boer breed showed a unique cluster from the Ugandan indigenous Goat Breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the Breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes.
-
production system and participatory identification of breeding objective traits for indigenous Goat Breeds of uganda
Small Ruminant Research, 2017Co-Authors: R B Onzima, Solomon Gizaw, D R Kugonza, J A M Van Arendonk, E KanisAbstract:Abstract The success of breeding programs in improving indigenous livestock Breeds in Uganda has hitherto been limited due to lack of involvement of the key stakeholders. Thus, participatory approaches are being promoted for designing community based improvement programs. The aim of this study was to characterize the indigenous Goat production systems and assess in a participatory manner farmer preferred traits for establishing breeding objectives for indigenous Goat Breeds in Uganda. 217 farm households representing three Goat production systems (combinations of breed and region) were individually interviewed to assess the socio-economic characteristics of the regions and the preferences of the farmers for indigenous Goat Breeds. The three breed/region combinations were 78 households with the Small East African breed in Arua, 81 with the Mubende breed in Mubende and 58 with the Kigezi breed in Kabale. An index based approach was used to rank farmers’ choices of traits considered important for their production systems. Descriptive statistics show that overall the production systems were not significantly different in terms of the nature of the farms and the trait preferences of the farmers. The sale of live animals was considered a primary objective for keeping Goats by farmers across all the production systems studied. Adaptation traits (disease resistance, heat tolerance and survival) were considered critical in the farmers’ preferred breed. Production traits (better prolificacy and faster growth rate) and marketing ease were other characteristics considered by the farmers. The results from the study are useful for designing farmer-participatory breeding programs for Goats in the different production systems in Uganda.
R P M A Crooijmans - One of the best experts on this subject based on the ideXlab platform.
-
genome wide characterization of selection signatures and runs of homozygosity in ugandan Goat Breeds
Frontiers in Genetics, 2018Co-Authors: R B Onzima, Maulik Upadhyay, Harmen P Doekes, Luiz F Brito, Mirte Bosse, E Kanis, M A M Groenen, R P M A CrooijmansAbstract:Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across Breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, F_ROH, based on runs of homozygosity (ROH), in six Ugandan Goat Breeds: Boer (n = 13), and the indigenous Breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29) and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all Breeds, based on marker-specific fixation index (F_ST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signalling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g. IL10RB and IL23A), growth and fatty acid composition (e.g. FGF9 and IGF1), and thermo-tolerance (e.g. MTOR and MAPK3). The study revealed little overlap between Breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g. GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous Goat Breeds showed very low levels of genomic inbreeding (with the mean F_ROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean F_ROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these Goat Breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan Goat Breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
-
genome wide population structure and admixture analysis reveals weak differentiation among ugandan Goat Breeds
Animal Genetics, 2018Co-Authors: R B Onzima, Maulik Upadhyay, E Kanis, M A M Groenen, R Mukiibi, R P M A CrooijmansAbstract:Uganda has a large population of Goats, predominantly from indigenous Breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer Goats. Knowledge about the genetic characteristics and relationships among these Ugandan Goat Breeds and the potential admixture with Boer Goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Goat Breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across Breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the Breeds. Principal components separated Kigezi and weakly Small East African from other indigenous Goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local Breeds. The Boer breed showed a unique cluster from the Ugandan indigenous Goat Breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the Breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes.
Maulik Upadhyay - One of the best experts on this subject based on the ideXlab platform.
-
genome wide characterization of selection signatures and runs of homozygosity in ugandan Goat Breeds
Frontiers in Genetics, 2018Co-Authors: R B Onzima, Maulik Upadhyay, Harmen P Doekes, Luiz F Brito, Mirte Bosse, E Kanis, M A M Groenen, R P M A CrooijmansAbstract:Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across Breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, F_ROH, based on runs of homozygosity (ROH), in six Ugandan Goat Breeds: Boer (n = 13), and the indigenous Breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29) and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all Breeds, based on marker-specific fixation index (F_ST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signalling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g. IL10RB and IL23A), growth and fatty acid composition (e.g. FGF9 and IGF1), and thermo-tolerance (e.g. MTOR and MAPK3). The study revealed little overlap between Breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g. GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous Goat Breeds showed very low levels of genomic inbreeding (with the mean F_ROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean F_ROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these Goat Breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan Goat Breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.
-
genome wide population structure and admixture analysis reveals weak differentiation among ugandan Goat Breeds
Animal Genetics, 2018Co-Authors: R B Onzima, Maulik Upadhyay, E Kanis, M A M Groenen, R Mukiibi, R P M A CrooijmansAbstract:Uganda has a large population of Goats, predominantly from indigenous Breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer Goats. Knowledge about the genetic characteristics and relationships among these Ugandan Goat Breeds and the potential admixture with Boer Goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Goat Breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (HO) and expected (HE) heterozygosity across Breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the Breeds. Principal components separated Kigezi and weakly Small East African from other indigenous Goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local Breeds. The Boer breed showed a unique cluster from the Ugandan indigenous Goat Breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the Breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes.
Lorraine Pariset - One of the best experts on this subject based on the ideXlab platform.
-
landscape genomics and biased fst approaches reveal single nucleotide polymorphisms under selection in Goat Breeds of north east mediterranean
BMC Genetics, 2009Co-Authors: Lorraine Pariset, Stephane Joost, Paolo Ajmone Marsan, A ValentiniAbstract:Background In this study we compare outlier loci detected using a FST based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of Goat Breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring.
-
allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across Goat Breeds
Molecular Ecology Notes, 2006Co-Authors: I Cappuccio, Stephane Joost, Lorraine Pariset, S Dunner, Paolo Ajmonemarsan, O Cortes, Georg Erhardt, G Luhken, K Gutscher, S ZundelAbstract:Single-nucleotide polymorphisms (SNPs) are useful markers for biodiversity assessment, linkage analysis, traceability and paternity testing. To date, there are no available SNPs for Goat in the NCBI dbSNP database and only a few are reported in the literature. Within the European Union Econogene project, we characterized 27 SNPs in Goats using a targeted-gene approach. Polymorphisms were identified in a panel of 16 unrelated individuals belonging to eight different Goat Breeds selected throughout Europe. Genotypes of 30 Goats from each of the eight Breeds were determined for all the SNPs characterized and diversity measures were estimated. The caprine SNPs described will be a useful complement to the available genome markers.
-
assessment of population structure by single nucleotide polymorphisms snps in Goat Breeds
Journal of Chromatography B, 2006Co-Authors: Lorraine Pariset, I Cappuccio, Ajmone P Marsan, S Dunner, Gordon Luikart, P R England, Gaby Obexerruff, C Peter, Donata Marletta, Fabio PillaAbstract:Single nucleotide polymorphisms (SNPs) may be used in biodiversity studies and commercial tasks like traceability, paternity testing and selection for suitable genotypes. Twenty-seven SNPs were characterized and genotyped on 250 individuals belonging to eight Italian Goat Breeds. Multilocus genotype data were used to infer population structure and assign individuals to populations. To estimate the number of groups (K) to test in population structure analysis we used likelihood values and variance of the bootstrap samples, deriving optimal K from a drop in the likelihood and a rise in the variance plots against K.
Stephane Joost - One of the best experts on this subject based on the ideXlab platform.
-
landscape genomics and biased fst approaches reveal single nucleotide polymorphisms under selection in Goat Breeds of north east mediterranean
BMC Genetics, 2009Co-Authors: Lorraine Pariset, Stephane Joost, Paolo Ajmone Marsan, A ValentiniAbstract:Background In this study we compare outlier loci detected using a FST based method with those identified by a recently described method based on spatial analysis (SAM). We tested a panel of single nucleotide polymorphisms (SNPs) previously genotyped in individuals of Goat Breeds of southern areas of the Mediterranean basin (Italy, Greece and Albania). We evaluate how the SAM method performs with SNPs, which are increasingly employed due to their high number, low cost and easy of scoring.
-
identifying european marginal areas in the context of local sheep and Goat Breeds conservation a geographic information system approach
Agricultural Systems, 2007Co-Authors: Marco Bertaglia, Stephane Joost, Jutta RoosenAbstract:Abstract Local sheep and Goat Breeds are generally argued to be remarkably well adapted to marginal rural areas. The latter are often said to be particularly or solely suitable for extensive husbandry mostly based on small ruminants. However, many local sheep and Goat Breeds are presently endangered. Both conserving these Breeds and maintaining an active agricultural presence in marginal areas are presently two major priorities for agricultural and rural development policy in Europe. The objective of this paper is to analyse the spatial link between the geographic distribution of traditional, locally adapted sheep and Goat Breeds and the relative marginality of regions. The concept of marginal areas is discussed and defined and an index of relative marginality is computed in a Geographic Information System. The index combines land use, demographic and socio-economic data. The correlation between the marginality of a region measured by the index and the geographic distribution of sheep and Goat Breeds is analysed using a simple logit model. The broader interest of the index as a tool for agricultural and rural development policy applications is then discussed.
-
allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across Goat Breeds
Molecular Ecology Notes, 2006Co-Authors: I Cappuccio, Stephane Joost, Lorraine Pariset, S Dunner, Paolo Ajmonemarsan, O Cortes, Georg Erhardt, G Luhken, K Gutscher, S ZundelAbstract:Single-nucleotide polymorphisms (SNPs) are useful markers for biodiversity assessment, linkage analysis, traceability and paternity testing. To date, there are no available SNPs for Goat in the NCBI dbSNP database and only a few are reported in the literature. Within the European Union Econogene project, we characterized 27 SNPs in Goats using a targeted-gene approach. Polymorphisms were identified in a panel of 16 unrelated individuals belonging to eight different Goat Breeds selected throughout Europe. Genotypes of 30 Goats from each of the eight Breeds were determined for all the SNPs characterized and diversity measures were estimated. The caprine SNPs described will be a useful complement to the available genome markers.