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Olivier Hanotte - One of the best experts on this subject based on the ideXlab platform.
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The genome landscape of indigenous African cattle
Genome Biology, 2017Co-Authors: Jaemin Kim, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, Salim Bashir, Boubacar Diallo, Morris Agaba, Kwondo Kim, Woori Kwak, Samsun SungAbstract:Background The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems. Results We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine Breeds. We find the highest genetic diversity among African Zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in Zebu Breeds. Conclusions Our findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent.
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investigation of x and y specific single nucleotide polymorphisms in taurine bos taurus and indicine bos indicus cattle
Animal Genetics, 2007Co-Authors: Cecilia Anderung, Olivier Hanotte, Linda Hellborg, Jennifer M Seddon, Anders GotherstromAbstract:Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossBreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle Breeds (four Sanga Breeds, including Raya AZebu, Danakil, Caprivi, Nguni; and two Zebu Breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African Breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle Breeds.
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geographic distribution and frequency of a taurine bos taurus and an indicine bos indicus y specific allele amongst sub saharan african cattle Breeds
Molecular Ecology, 2000Co-Authors: Olivier Hanotte, C L Tawah, Daniel G Bradley, M A Okomo, Yasmi Verjee, Joel W Ochieng, J E O RegeAbstract:: We report for the first time, and for the whole of sub-Saharan Africa, the geographical distribution and the frequency of an indicine and a taurine Y specific allele amongst African cattle Breeds. A total of 984 males from 69 indigenous African populations from 22 countries were analysed at the microsatellite locus INRA 124. The taurine allele is probably the oldest one on the continent. However, the taurine and the indicine alleles were present in 291 males (30%), and 693 males (70%), respectively. More particularly, 96% of Zebu males (n = 470), 50% of taurine males (n = 263), 29% of sanga males (crossbreed Bos taurus x Bos indicus, n = 263) and 95% of Zebu x sanga crossbred males (n = 56) had the indicine allele. The Borgou, a breed classified as Zebu x taurine cross showed only the Zebu allele (n = 12). The indicine allele dominates today in the Abyssinian region, a large part of the Lake Victoria region and the sahelian belt of West Africa. All the sanga males (n = 64) but only one from the Abyssinian region had the indicine allele. The taurine allele is the commonest only among the sanga Breeds of the southern African region and the trypanotolerant taurine Breeds of West Africa. In West Africa and in the southern Africa regions, zones of introgression were detected with Breeds showing both Y chromosome alleles. Our data also reveal a pattern of male Zebu introgression in Mozambique and Zimbabwe, probably originating from the Mozambique coast. The sanga cattle from the Lake Victoria region and the Kuri cattle of Lake Chad, cattle populations surrounded by Zebu Breeds were, surprisingly, completely devoid of the indicine allele. Human migration, phenotypic preferences by the pastoralists, adaptation to specific habitats and to specific diseases are the main factors explaining the present-day distribution of the alleles in sub-Saharan Africa.
Anders Gotherstrom - One of the best experts on this subject based on the ideXlab platform.
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investigation of x and y specific single nucleotide polymorphisms in taurine bos taurus and indicine bos indicus cattle
Animal Genetics, 2007Co-Authors: Cecilia Anderung, Olivier Hanotte, Linda Hellborg, Jennifer M Seddon, Anders GotherstromAbstract:Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossBreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle Breeds (four Sanga Breeds, including Raya AZebu, Danakil, Caprivi, Nguni; and two Zebu Breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African Breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle Breeds.
Daniel G Bradley - One of the best experts on this subject based on the ideXlab platform.
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genetic and expression analysis of cattle identifies candidate genes in pathways responding to trypanosoma congolense infection
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Harry Noyes, Daniel G Bradley, Andy Brass, Isaiah Obara, Susan Anderson, Alan Archibald, Paul R Fisher, Abigail R Freeman, J P Gibson, Michael M GicheruAbstract:African bovine trypanosomiasis caused by Trypanosoma sp., is a major constraint on cattle productivity in sub-Saharan Africa. Some African Bos taurus Breeds are highly tolerant of infection, but the potentially more productive Bos indicus Zebu Breeds are much more susceptible. Zebu cattle are well adapted for plowing and haulage, and increasing their tolerance of trypanosomiasis could have a major impact on crop cultivation as well as dairy and beef production. We used three strategies to obtain short lists of candidate genes within QTL that were previously shown to regulate response to infection. We analyzed the transcriptomes of trypanotolerant N'Dama and susceptible Boran cattle after infection with Trypanosoma congolense. We sequenced EST libraries from these two Breeds to identify polymorphisms that might underlie previously identified quantitative trait loci (QTL), and we assessed QTL regions and candidate loci for evidence of selective sweeps. The scan of the EST sequences identified a previously undescribed polymorphism in ARHGAP15 in the Bta2 trypanotolerance QTL. The polymorphism affects gene function in vitro and could contribute to the observed differences in expression of the MAPK pathway in vivo. The expression data showed that TLR and MAPK pathways responded to infection, and the former contained TICAM1, which is within a QTL on Bta7. Genetic analyses showed that selective sweeps had occurred at TICAM1 and ARHGAP15 loci in African taurine cattle, making them strong candidates for the genes underlying the QTL. Candidate QTL genes were identified in other QTL by their expression profile and the pathways in which they participate.
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geographic distribution and frequency of a taurine bos taurus and an indicine bos indicus y specific allele amongst sub saharan african cattle Breeds
Molecular Ecology, 2000Co-Authors: Olivier Hanotte, C L Tawah, Daniel G Bradley, M A Okomo, Yasmi Verjee, Joel W Ochieng, J E O RegeAbstract:: We report for the first time, and for the whole of sub-Saharan Africa, the geographical distribution and the frequency of an indicine and a taurine Y specific allele amongst African cattle Breeds. A total of 984 males from 69 indigenous African populations from 22 countries were analysed at the microsatellite locus INRA 124. The taurine allele is probably the oldest one on the continent. However, the taurine and the indicine alleles were present in 291 males (30%), and 693 males (70%), respectively. More particularly, 96% of Zebu males (n = 470), 50% of taurine males (n = 263), 29% of sanga males (crossbreed Bos taurus x Bos indicus, n = 263) and 95% of Zebu x sanga crossbred males (n = 56) had the indicine allele. The Borgou, a breed classified as Zebu x taurine cross showed only the Zebu allele (n = 12). The indicine allele dominates today in the Abyssinian region, a large part of the Lake Victoria region and the sahelian belt of West Africa. All the sanga males (n = 64) but only one from the Abyssinian region had the indicine allele. The taurine allele is the commonest only among the sanga Breeds of the southern African region and the trypanotolerant taurine Breeds of West Africa. In West Africa and in the southern Africa regions, zones of introgression were detected with Breeds showing both Y chromosome alleles. Our data also reveal a pattern of male Zebu introgression in Mozambique and Zimbabwe, probably originating from the Mozambique coast. The sanga cattle from the Lake Victoria region and the Kuri cattle of Lake Chad, cattle populations surrounded by Zebu Breeds were, surprisingly, completely devoid of the indicine allele. Human migration, phenotypic preferences by the pastoralists, adaptation to specific habitats and to specific diseases are the main factors explaining the present-day distribution of the alleles in sub-Saharan Africa.
Jennifer M Seddon - One of the best experts on this subject based on the ideXlab platform.
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investigation of x and y specific single nucleotide polymorphisms in taurine bos taurus and indicine bos indicus cattle
Animal Genetics, 2007Co-Authors: Cecilia Anderung, Olivier Hanotte, Linda Hellborg, Jennifer M Seddon, Anders GotherstromAbstract:Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossBreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle Breeds (four Sanga Breeds, including Raya AZebu, Danakil, Caprivi, Nguni; and two Zebu Breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African Breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle Breeds.
Linda Hellborg - One of the best experts on this subject based on the ideXlab platform.
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investigation of x and y specific single nucleotide polymorphisms in taurine bos taurus and indicine bos indicus cattle
Animal Genetics, 2007Co-Authors: Cecilia Anderung, Olivier Hanotte, Linda Hellborg, Jennifer M Seddon, Anders GotherstromAbstract:Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossBreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle Breeds (four Sanga Breeds, including Raya AZebu, Danakil, Caprivi, Nguni; and two Zebu Breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African Breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle Breeds.
