1
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Belay S, Belay G, Nigussie H, Ahbara AM, Tijjani A, Dessie T, Tarekegn GM, Jian-Lin H, Mor S, Woldekiros HS, Dobney K, Lebrasseur O, Hanotte O, Mwacharo JM. Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats. Sci Rep 2024; 14:14908. [PMID: 38942813 PMCID: PMC11213886 DOI: 10.1038/s41598-024-65303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.
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Affiliation(s)
- Shumuye Belay
- Tigray Agricultural Research Institute, Mekelle, Ethiopia.
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia.
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia.
| | - Gurja Belay
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Helen Nigussie
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abulgasim M Ahbara
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Department of Zoology, Misurata University, Misurata, Libya
| | - Abdulfatai Tijjani
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Getinet M Tarekegn
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
- Institute of Biotechnology (IoB), Addis Ababa University, Addis Ababa, Ethiopia
| | - Han Jian-Lin
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Siobhan Mor
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Helina S Woldekiros
- Department of Anthropology, Washington University in St. Louis, St. Louis, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- University of Sydney, Sydney, Australia
| | - Ophelie Lebrasseur
- Palaeogenomics and Bioarchaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Joram M Mwacharo
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.
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2
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Nisa FU, Kaul H, Asif M, Amin I, Mrode R, Mansoor S, Mukhtar Z. Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale. Mamm Genome 2023; 34:602-614. [PMID: 37804434 DOI: 10.1007/s00335-023-10019-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/09/2023]
Abstract
Linkage disequilibrium (LD) affects genomic studies accuracy. High-density genotyping platforms identify SNPs across animal genomes, increasing LD evaluation resolution for accurate analysis. This study aimed to evaluate the decay and magnitude of LD in a cohort of 81 crossbred dairy cattle using the GGP_HDv3_C Bead Chip. After quality control, 116,710 Single Nucleotide Polymorphisms (SNPs) across 2520.241 Mb of autosomes were retained. LD extent was assessed between autosomal SNPs within a 10 Mb range using the r2 statistics. LD value declined as inter-marker distance increased. The average r2 value was 0.24 for SNP pairs < 10 kb apart, decreasing to 0.13 for 50-100 kb distances. Minor allele frequency (MAF) and sample size significantly impact LD. Lower MAF thresholds result in smaller r2 values, while higher thresholds show increased r2 values. Additionally, smaller sample sizes exhibit higher average r2 values, especially for larger physical distance intervals (> 50 kb) between SNP pairs. Effective population size and inbreeding coefficient were 150 and 0.028 for the present generation, indicating a decrease in genetic diversity over time. These findings imply that the utilization of high-density SNP panels and customized/breed-specific SNP panels represent a highly favorable approach for conducting genome-wide association studies (GWAS) and implementing genomic selection (GS) in the Bos indicus cattle breeds, whose genomes are still largely unexplored. Furthermore, it is imperative to devise a meticulous breeding strategy tailored to each herd, aiming to enhance desired traits while simultaneously preserving genetic diversity.
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Affiliation(s)
- Fakhar Un Nisa
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Haiba Kaul
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Raphael Mrode
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
- Animal and Veterinary Sciences, Scotland's Rural College, Edinburgh, UK
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan.
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3
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Jaafar MA, Heins BJ, Dechow C, Huson HJ. The impact of using different ancestral reference populations in assessing crossbred population admixture and influence on performance. Front Genet 2022; 13:910998. [PMID: 36226168 PMCID: PMC9549382 DOI: 10.3389/fgene.2022.910998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
Crossbreeding is a process in which animals from different breeds are mated together. The animals produced will exhibit a combination of both additive and non-additive genetic improvement from parental breeds that increase heterozygosity and negate inbreeding depression. However, crossbreeding may also break up the unique and often beneficial gene combinations in parental breeds, possibly reducing performance potential as the benefits of heterosis depends on the type of crossbreeding systems used and heritability of the traits. This effect of crossbreeding, especially on the genome architecture, is still poorly understood with respect to 3-breed crossbreeding systems. Thus, this study examined variation in genomic ancestry estimations relative to pedigree-based estimations and correlated breed composition to key production and health traits. Two rotational crossbred populations, referenced as ProCROSS and Grazecross were assessed and totaled 607 crossbred cattle. ProCROSS is a product of rotational crossbreeding of Viking Red (VKR), Holstein (HOL), and Montbeliarde (MON). In contrast, Grazecross consists of Viking Red (VKR), Normande (NOR), and Jersey (JER). Both breeding programs were aimed at capitalizing on the positive effect of heterosis. The VKR is a marketing term for Swedish Red, Danish Red, and Finnish Ayrshire breed which complicated breed determination. Therefore, genomic breed composition estimates were compared using two different representations of VKR, one of which was based on parents used in the crossing system and a second based on genotypes from the ancestral breeds that comprise VKR. Variation of breed composition estimates were assessed between pedigree and genome-based predictions. Lastly, Genomic estimations were correlated with production and health traits by comparing extreme performance groups to identify the relationship between breed ancestry and performance. With the exception of the JER breed composition in Grazecross, all other estimates of the purebred contribution to the ProCROSS and Grazecross showed a significant difference in their genomic breed estimation when using the VKR ancestral versus the VKR parental reference populations for admixture analysis. These observations were expected given the different relationship of each VKR representation to the crossbred cattle. Further analysis showed that regardless of which VKR reference population was used, the degree of MON and HOL breed composition plays a significant role in milk and fat production in ProCROSS, while the degree of VKR and NOR ancestry were related to improved health performance in Grazecross. In all, identifying the most appropriate and informative animals to use as reference animals in admixture analysis is an important factor when interpreting results of relationship and population structure, but some degree of uncertainty exists when assessing the relationship of breed composition to phenotypic performance.
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Affiliation(s)
- Mohd A. Jaafar
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Bradley J. Heins
- West Central Research and Outreach Centre, University of Minnesota, Morris, MN, United States
| | - Chad Dechow
- Department of Animal Science, Penn State University, State College, University Park, PA, United States
| | - Heather J. Huson
- Department of Animal Science, Cornell University, Ithaca, NY, United States
- *Correspondence: Heather J. Huson,
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4
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Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus). iScience 2022; 25:104672. [PMID: 35832892 PMCID: PMC9272374 DOI: 10.1016/j.isci.2022.104672] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/11/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.
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5
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Magnier J, Druet T, Naves M, Ouvrard M, Raoul S, Janelle J, Moazami-Goudarzi K, Lesnoff M, Tillard E, Gautier M, Flori L. The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean. G3 GENES|GENOMES|GENETICS 2022; 12:6523972. [PMID: 35137043 PMCID: PMC8982424 DOI: 10.1093/g3journal/jkac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.
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Affiliation(s)
- Jessica Magnier
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
| | | | | | | | - Jérôme Janelle
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | | | - Matthieu Lesnoff
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Emmanuel Tillard
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’Institut Agro, University of Montpellier, Montferrier sur Lez 34988, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’Institut Agro, University of Montpellier, Montpellier 34398, France
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6
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Cubric‐Curik V, Novosel D, Brajkovic V, Rota Stabelli O, Krebs S, Sölkner J, Šalamon D, Ristov S, Berger B, Trivizaki S, Bizelis I, Ferenčaković M, Rothammer S, Kunz E, Simčič M, Dovč P, Bunevski G, Bytyqi H, Marković B, Brka M, Kume K, Stojanović S, Nikolov V, Zinovieva N, Schönherz AA, Guldbrandtsen B, Čačić M, Radović S, Miracle P, Vernesi C, Curik I, Medugorac I. Large‐scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. Evol Appl 2021; 15:663-678. [PMID: 35505892 PMCID: PMC9046920 DOI: 10.1111/eva.13315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vlatka Cubric‐Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Dinko Novosel
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
- Department of Pathology Croatian Veterinary Institute Zagreb Croatia
| | - Vladimir Brajkovic
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Omar Rota Stabelli
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis Gene Center Ludwig Maximilians University Munich Munich Germany
| | - Johann Sölkner
- Division of Livestock Sciences Department of Sustainable Agricultural Systems BOKU‐University of Natural Resources and Life Sciences Vienna Vienna Austria
| | - Dragica Šalamon
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | | | - Beate Berger
- AREC Raumberg‐Gumpenstein Institute of Organic Farming and Biodiversity of Farm Animals Thalheim Austria
| | | | - Iosif Bizelis
- Faculty of Animal Science and Aquaculture Department of Animal Breeding & Husbandry Agricultural University of Athens Athens Greece
| | - Maja Ferenčaković
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Sophie Rothammer
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Elisabeth Kunz
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Mojca Simčič
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Peter Dovč
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Gojko Bunevski
- Faculty of Agricultural Sciences and Food University Ss. Cyril and Methodius Skopje Macedonia
| | - Hysen Bytyqi
- Faculty of Agriculture and Veterinary Department of Animal Science University of Prishtina Prishtina Kosovo
| | - Božidarka Marković
- Biotechnical Faculty Department of Livestock Science University of Montenegro Podgorica Montenegro
| | - Muhamed Brka
- Faculty of Agriculture and Food Science Institute of Animal Sciences University of Sarajevo Sarajevo Bosnia and Herzegovina
| | | | - Srđan Stojanović
- Ministry of Agriculture, Forestry and Water Management Beograd Serbia
| | - Vasil Nikolov
- Executive Agency for Selection and Reproduction in Animal Breeding Sofia Bulgaria
| | - Natalia Zinovieva
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry Moscow Region Russia
| | | | - Bernt Guldbrandtsen
- Department of Animal Sciences Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Mato Čačić
- Croatian Agricultural Agency Zagreb Croatia
| | - Siniša Radović
- Institute for Quaternary Palaeontology and Geology Croatian Academy of Sciences and Arts Zagreb Croatia
| | - Preston Miracle
- Department of Archaeology University of Cambridge Cambridge UK
| | - Cristiano Vernesi
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Ino Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Ivica Medugorac
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
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7
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Kambal S, Abdelrahim AE, Hanotte O, Nakao R, Alkhaibari AM, Salim B. Demographic expansion and high level of matrilineal diversity in two populations of East African Baggara cattle. J Anim Breed Genet 2021; 139:161-169. [PMID: 34520084 DOI: 10.1111/jbg.12648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022]
Abstract
Western Baggara cattle breed (WBCB) is an East African zebu inhabiting Sudan, well-known as beef-producing cattle. We investigated herein two phenotypically and geographically distinct populations of this breed, namely Nyalawi and Daeinawi, which are renowned for their unique meat production capabilities and adaptation attributes, with the aim to contribute to our understanding of their maternal genetic diversity and demography dynamics. Genetic polymorphism analysis of the full-length D-loop mtDNA region revealed 44 and 35 polymorphic sites defining 28 and 24 distinct haplotypes in the Nyalawi and the Daeinawi, respectively. Observed genetic diversity is high within the population with a low level of genetic differentiation between populations. Approximate Bayesian computation via the calculation of Bayesian skyline plots and neutrality tests support past expansion with a higher maternal effective population size (Ne ) in Nyalawi compared with the Daeinawi population and a population expansion beginning around 4,500 YBP and 3,500 YBP, respectively, before the arrival of zebu into the continent.
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Affiliation(s)
- Sumaya Kambal
- Department of Bioinformatics and Biostatistics, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan.,International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Amina E Abdelrahim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, Khartoum-North, Sudan
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK.,LiveGene - CTLGH, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ryo Nakao
- Department of Disease Control, Laboratory of Parasitology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Abeer M Alkhaibari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, Khartoum-North, Sudan
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8
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Abied A, Ahbara AM, Berihulay H, Xu L, Islam R, El-Hag FM, Rekik M, Haile A, Han JL, Ma Y, Zhao Q, Mwacharo JM. Genome Divergence and Dynamics in the Thin-Tailed Desert Sheep From Sudan. Front Genet 2021; 12:659507. [PMID: 34349777 PMCID: PMC8327097 DOI: 10.3389/fgene.2021.659507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
With climate change bound to affect food and feed production, emphasis will shift to resilient and adapted indigenous livestock to sustain animal production. However, indigenous livestock comprise several varieties, strains and ecotypes whose genomes are poorly characterized. Here, we investigated genomic variation in an African thin-tailed Desert Sheep sampled in Sudan, using 600K genotype data generated from 92 individuals representing five ecotypes. We included data from 18 fat-tailed and 45 thin-tailed sheep from China, to investigate shared ancestry and perform comparative genomic analysis. We observed a clear genomic differentiation between the African thin-tailed Desert Sheep and the Chinese thin-tailed and fat-tailed sheep, suggesting a broad genetic structure between the fat-tailed and thin-tailed sheep in general, and that at least two autosomal gene pools comprise the genome profile of the thin-tailed sheep. Further analysis detected two distinct genetic clusters in both the African thin-tailed Desert Sheep and the Chinese thin-tailed sheep, suggesting a fine-scale and complex genome architecture in thin-tailed sheep. Selection signature analysis suggested differences in adaptation, production, reproduction and morphology likely underly the fine-scale genetic structure in the African thin-tailed Desert Sheep. This may need to be considered in designing breeding programs and genome-wide association studies.
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Affiliation(s)
- Adam Abied
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Dry Land Research Centre and Animal Production, Agricultural Research Corporation, Khartoum, Sudan
| | - Abulgasim M Ahbara
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Haile Berihulay
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rabiul Islam
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Faisal M El-Hag
- Dry Land Research Centre and Animal Production, Agricultural Research Corporation, Khartoum, Sudan.,Arid Land Research Centre, Tottori University, Tottori, Japan
| | - Mourad Rekik
- International Center for Agricultural Research in the Dry Areas (ICARDA), Amman, Jordan
| | - Aynalem Haile
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia.,Animal and Veterinary Sciences, Scotland Rural College and Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, Midlothian, United Kingdom
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9
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Tarekegn GM, Khayatzadeh N, Liu B, Osama S, Haile A, Rischkowsky B, Zhang W, Tesfaye K, Dessie T, Mwai OA, Djikeng A, Mwacharo JM. Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats. Evol Appl 2021; 14:1716-1731. [PMID: 34295359 PMCID: PMC8287980 DOI: 10.1111/eva.13118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/15/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
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Affiliation(s)
- Getinet M. Tarekegn
- Department of Animal Production and TechnologySchool of Animal Sciences and Veterinary MedicineBahir Dar UniversityBahir DarEthiopia
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural SystemsDivision of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bin Liu
- Inner Mongolia Agricultural UniversityHohhotChina
| | - Sarah Osama
- The University of QueenslandSaint LuciaQLDAustralia
| | - Aynalem Haile
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | - Barbara Rischkowsky
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | | | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| | - Joram M. Mwacharo
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
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10
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Gebrehiwot NZ, Aliloo H, Strucken EM, Marshall K, Al Kalaldeh M, Missohou A, Gibson JP. Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations. Front Genet 2021; 12:584355. [PMID: 33841491 PMCID: PMC8025404 DOI: 10.3389/fgene.2021.584355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/22/2021] [Indexed: 11/24/2022] Open
Abstract
Several studies have evaluated computational methods that infer the haplotypes from population genotype data in European cattle populations. However, little is known about how well they perform in African indigenous and crossbred populations. This study investigates: (1) global and local ancestry inference; (2) heterozygosity proportion estimation; and (3) genotype imputation in West African indigenous and crossbred cattle populations. Principal component analysis (PCA), ADMIXTURE, and LAMP-LD were used to analyse a medium-density single nucleotide polymorphism (SNP) dataset from Senegalese crossbred cattle. Reference SNP data of East and West African indigenous and crossbred cattle populations were used to investigate the accuracy of imputation from low to medium-density and from medium to high-density SNP datasets using Minimac v3. The first two principal components differentiated Bos indicus from European Bos taurus and African Bos taurus from other breeds. Irrespective of assuming two or three ancestral breeds for the Senegalese crossbreds, breed proportion estimates from ADMIXTURE and LAMP-LD showed a high correlation (r ≥ 0.981). The observed ancestral origin heterozygosity proportion in putative F1 crosses was close to the expected value of 1.0, and clearly differentiated F1 from all other crosses. The imputation accuracies (estimated as correlation) between imputed and the real data in crossbred animals ranged from 0.142 to 0.717 when imputing from low to medium-density, and from 0.478 to 0.899 for imputation from medium to high-density. The imputation accuracy was generally higher when the reference data came from the same geographical region as the target population, and when crossbred reference data was used to impute crossbred genotypes. The lowest imputation accuracies were observed for indigenous breed genotypes. This study shows that ancestral origin heterozygosity can be estimated with high accuracy and will be far superior to the use of observed individual heterozygosity for estimating heterosis in African crossbred populations. It was not possible to achieve high imputation accuracy in West African crossbred or indigenous populations based on reference data sets from East Africa, and population-specific genotyping with high-density SNP assays is required to improve imputation.
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Affiliation(s)
- Netsanet Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Hassan Aliloo
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Eva M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Karen Marshall
- International Livestock Research Institute and Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya
| | - Mohammad Al Kalaldeh
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Ayao Missohou
- L'École Inter-États des Sciences et Médecine Vétérinaires de Dakar (EISMV), Dakar, Senegal
| | - John P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
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11
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Callaby R, Kelly R, Mazeri S, Egbe F, Benedictus L, Clark E, Doeschl-Wilson A, Bronsvoort B, Salavati M, Muwonge A. Genetic Diversity of Cameroon Cattle and a Putative Genomic Map for Resistance to Bovine Tuberculosis. Front Genet 2020; 11:550215. [PMID: 33281865 PMCID: PMC7705233 DOI: 10.3389/fgene.2020.550215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022] Open
Abstract
Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurization of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding European taurine cattle, such as Holsteins for increased resistance to bTB is feasible. The utility of such an approach is still unknown for African cattle populations. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture of cattle in Cameroon. We conducted a cross-sectional study of 2,346 slaughter cattle in Cameroon. Retropharyngeal lymph node samples were collected and cultured on Lowenstein Jensen media and the BACTEC MGIT 960 system, and M. bovis was identified using the Hain® Genotype kits. A total of 153 cattle were positive for M. bovis and were archived along with a random selection of negative samples. In this study, we genotyped archived samples from 212 cattle. Their genomic diversity was characterized using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous research on this study population have shown that Fulani cattle are more susceptible to bTB than mixed breeds. However, here we show that these apparent phenotypic differences in breeds are not reflected by clear genomic differences. At the genetic level, both the Fulani and mixed cattle show similar patterns of admixture with evidence of both taurine and indicine ancestry. There was little European taurine introgression within the studied population. Hierarchical clustering showed clusters of cattle that differed in their susceptibility to bTB. Our findings allude to bTB resistance being polygenic in nature. This study highlights the potential for genetic control of bTB in Africa and the need for further research into the genetics of bTB resistance within African cattle populations.
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Affiliation(s)
- Rebecca Callaby
- Centre for Tropical Livestock Genetics and Health, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert Kelly
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stella Mazeri
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Franklyn Egbe
- School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
| | - Lindert Benedictus
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Emily Clark
- Centre for Tropical Livestock Genetics and Health, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrea Doeschl-Wilson
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Barend Bronsvoort
- Centre for Tropical Livestock Genetics and Health, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Mazdak Salavati
- Centre for Tropical Livestock Genetics and Health, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom.,The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Muwonge
- The Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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12
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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13
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Peters SO, Hussain T, Adenaike AS, Hazzard J, Morenikeji OB, De Donato M, Paul S, Babar M, Yakubu A, Imumorin IG. Evolutionary Pattern of Interferon Alpha Genes in Bovidae and Genetic Diversity of IFNAA in the Bovine Genome. Front Immunol 2020; 11:580412. [PMID: 33117386 PMCID: PMC7561390 DOI: 10.3389/fimmu.2020.580412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
Interferons are secretory proteins induced in response to specific extracellular stimuli which stimulate intra- and intercellular networks for regulating innate and acquired immunity, resistance to viral infections, and normal and tumor cell survival and death. Type 1 interferons plays a major role in the CD8 T-cell response to viral infection. The genomic analysis carried out here for type I interferons within Bovidae family shows that cattle, bison, water buffalo, goat, and sheep (all Bovidae), have different number of genes of the different subtypes, with a large increase in the numbers, compared to human and mouse genomes. A phylogenetic analysis of the interferon alpha (IFNA) proteins in this group shows that the genes do not follow the evolutionary pattern of the species, but rather a cycle of duplications and deletions in the different species. In this study we also studied the genetic diversity of the bovine interferon alpha A (IFNAA), as an example of the IFNA genes in cattle, sequencing a fragment of the coding sequence in 18 breeds of cattle from Pakistan, Nigeria and USA. Similarity analysis allowed the allocation of sequences into 22 haplotypes. Bhagnari, Brangus, Sokoto Gudali, and White Fulani, had the highest number of haplotypes, while Angus, Hereford and Nari Master had the least. However, when analyzed by the average haplotype count, Angus, Bhagnari, Hereford, Holstein, Muturu showed the highest values, while Cholistani, Lohani, and Nari Master showed the lowest values. Haplotype 4 was found in the highest number of individuals (74), and in 15 breeds. Sequences for yak, bison, and water buffalo, were included within the bovine haplotypes. Medium Joining network showed that the sequences could be divided into 4 groups: one with highly similar haplotypes containing mostly Asian and African breeds, one with almost all of the Bos taurus American breeds, one mid-diverse group with mostly Asian and African sequences, and one group with highly divergent haplotypes with five N'Dama sequences and one from each of White Fulani, Dhanni, Tharparkar, and Bhagnari. The large genetic diversity found in IFNAA could be a very good indication of the genetic variation among the different genes of IFNA and could be an adaptation for these species in response to viral challenges they face.
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Affiliation(s)
- Sunday O. Peters
- Department of Animal Science, Berry College, Mount Berry, GA, United States
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Adeyemi S. Adenaike
- Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria
| | - Jordan Hazzard
- Department of Animal Science, Berry College, Mount Berry, GA, United States
| | - Olanrewaju B. Morenikeji
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
- Department of Biology, Hamilton College, Clinton, NY, United States
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Sujay Paul
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico
| | - Masroor Babar
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | | | - Ikhide G. Imumorin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
- Department of Biological Sciences, First Technical University, Ibadan, Nigeria
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14
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The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism. Nat Genet 2020; 52:1099-1110. [PMID: 32989325 DOI: 10.1038/s41588-020-0694-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 08/18/2020] [Indexed: 02/07/2023]
Abstract
Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750-1,050 yr ago, which has shaped the genome of today's cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism.
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15
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Reflections on IDEAL: What we have learnt from a unique calf cohort study. Prev Vet Med 2020; 181:105062. [PMID: 32615453 PMCID: PMC7456772 DOI: 10.1016/j.prevetmed.2020.105062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/07/2020] [Accepted: 06/10/2020] [Indexed: 11/20/2022]
Abstract
The year 2020 marks a decade since the final visit was made in the ‘Infectious Diseases of East African Livestock’ (IDEAL) project. However, data generation from samples obtained during this ambitious longitudinal study still continues. As the project launches its extensive open-access database and biobank to the scientific community, we reflect on the challenges overcome, the knowledge gained, and the advantages of such a project. We discuss the legacy of the IDEAL project and how it continues to generate evidence since being adopted by the Centre for Tropical Livestock Genetics and Health (CTLGH). We also examine the impact of the IDEAL project, from the authors perspective, for each of the stakeholders (the animal, the farmer, the consumer, the policy maker, the funding body, and the researcher and their institution) involved in the project and provide recommendations for future researchers who are interested in running longitudinal field studies.
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16
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Getachew T, Haile A, Mészáros G, Rischkowsky B, Huson H, Gizaw S, Wurzinger M, Mwai A, Sölkner J. Genetic diversity, population structure and runs of homozygosity in Ethiopian short fat-tailed and Awassi sheep breeds using genome-wide 50k SNP markers. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103899] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Mekonnen YA, Gültas M, Effa K, Hanotte O, Schmitt AO. Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed. Front Genet 2019; 10:1095. [PMID: 31803229 PMCID: PMC6872528 DOI: 10.3389/fgene.2019.01095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/11/2019] [Indexed: 12/23/2022] Open
Abstract
African animal trypanosomiasis (AAT) is caused by a protozoan parasite that affects the health of livestock. Livestock production in Ethiopia is severely hampered by AAT and various controlling measures were not successful to eradicate the disease. AAT affects the indigenous breeds in varying degrees. However, the Sheko breed shows better trypanotolerance than other breeds. The tolerance attributes of Sheko are believed to be associated with its taurine genetic background but the genetic controls of these tolerance attributes of Sheko are not well understood. In order to investigate the level of taurine background in the genome, we compare the genome of Sheko with that of 11 other African breeds. We find that Sheko has an admixed genome composed of taurine and indicine ancestries. We apply three methods: (i) The integrated haplotype score (iHS), (ii) the standardized log ratio of integrated site specific extended haplotype homozygosity between populations (Rsb), and (iii) the composite likelihood ratio (CLR) method to discover selective sweeps in the Sheko genome. We identify 99 genomic regions harboring 364 signature genes in Sheko. Out of the signature genes, 15 genes are selected based on their biological importance described in the literature. We also identify 13 overrepresented pathways and 10 master regulators in Sheko using the TRANSPATH database in the geneXplain platform. Most of the pathways are related with oxidative stress responses indicating a possible selection response against the induction of oxidative stress following trypanosomiasis infection in Sheko. Furthermore, we present for the first time the importance of master regulators involved in trypanotolerance not only for the Sheko breed but also in the context of cattle genomics. Our finding shows that the master regulator Caspase is a key protease which plays a major role for the emergence of adaptive immunity in harmony with the other master regulators. These results suggest that designing and implementing genetic intervention strategies is necessary to improve the performance of susceptible animals. Moreover, the master regulatory analysis suggests potential candidate therapeutic targets for the development of new drugs for trypanosomiasis treatment.
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Affiliation(s)
- Yonatan Ayalew Mekonnen
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
| | - Kefena Effa
- Animal Biosciences, National Program Coordinator for African Dairy Genetic Gain, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms amd Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Armin O Schmitt
- Breeding Informatics Group, Department of Animal Sciences, University of Göttingen, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), University of Göttingen, Göttingen, Germany
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18
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Utsunomiya YT, Milanesi M, Fortes MRS, Porto-Neto LR, Utsunomiya ATH, Silva MVGB, Garcia JF, Ajmone-Marsan P. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet 2019; 50:557-568. [PMID: 31475748 DOI: 10.1111/age.12836] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2019] [Indexed: 01/08/2023]
Abstract
Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Bld, 68 Cooper Rd, Brisbane, 4072, Qld, Australia
| | - L R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia QLD, Brisbane, 4067, Qld, Australia
| | - A T H Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M V G B Silva
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora, MG, 360381330, Brazil
| | - J F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
| | - P Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA and BioDNA, Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, Piacenza, 29122, Italy
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19
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Chhotaray S, Panigrahi M, Pal D, Ahmad SF, Bhanuprakash V, Kumar H, Parida S, Bhushan B, Gaur GK, Mishra BP, Singh RK. Genome-wide estimation of inbreeding coefficient, effective population size and haplotype blocks in Vrindavani crossbred cattle strain of India. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1600266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Supriya Chhotaray
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Dhan Pal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - V. Bhanuprakash
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - G. K. Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - B. P. Mishra
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - R. K. Singh
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Bareilly, India
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20
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Mrode R, Ojango JMK, Okeyo AM, Mwacharo JM. Genomic Selection and Use of Molecular Tools in Breeding Programs for Indigenous and Crossbred Cattle in Developing Countries: Current Status and Future Prospects. Front Genet 2019; 9:694. [PMID: 30687382 PMCID: PMC6334160 DOI: 10.3389/fgene.2018.00694] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 12/11/2018] [Indexed: 11/23/2022] Open
Abstract
Genomic selection (GS) has resulted in rapid rates of genetic gains especially in dairy cattle in developed countries resulting in a higher proportion of genomically proven young bulls being used in breeding. This success has been undergirded by well-established conventional genetic evaluation systems. Here, the status of GS in terms of the structure of the reference and validation populations, response variables, genomic prediction models, validation methods, and imputation efficiency in breeding programs of developing countries, where smallholder systems predominate and the basic components for conventional breeding are mostly lacking is examined. Also, the application of genomic tools and identification of genome-wide signatures of selection is reviewed. The studies on genomic prediction in developing countries are mostly in dairy and beef cattle usually with small reference populations (500-3,000 animals) and are mostly cows. The input variables tended to be pre-corrected phenotypic records and the small reference populations has made implementation of various Bayesian methods feasible in addition to GBLUP. Multi-trait single-step has been used to incorporate genomic information from foreign bulls, thus GS in developing countries would benefit from collaborations with developed countries, as many dairy sires used are from developed countries where they may have been genotyped and phenotyped. Cross validation approaches have been implemented in most studies resulting in accuracies of 0.20-0.60. Genotyping animals with a mixture of HD and LD chips, followed by imputation to the HD have been implemented with imputation accuracies of 0.74-0.99 reported. This increases the prospects of reducing genotyping costs and hence the cost-effectiveness of GS. Next-generation sequencing and associated technologies have allowed the determination of breed composition, parent verification, genome diversity, and genome-wide selection sweeps. This information can be incorporated into breeding programs aiming to utilize GS. Cost-effective GS in beef cattle in developing countries may involve usage of reproductive technologies (AI and in-vitro fertilization) to efficiently propagate superior genetics from the genomics pipeline. For dairy cattle, sexed semen of genomically proven young bulls could substantially improve profitability thus increase prospects of small holder farmers buying-in into genomic breeding programs.
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Affiliation(s)
- Raphael Mrode
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
- Animal and Veterinary Science, Scotland Rural College, Edinburgh, United Kingdom
| | - Julie M. K Ojango
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
| | - A. M. Okeyo
- Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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21
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Pitt D, Sevane N, Nicolazzi EL, MacHugh DE, Park SDE, Colli L, Martinez R, Bruford MW, Orozco‐terWengel P. Domestication of cattle: Two or three events? Evol Appl 2019; 12:123-136. [PMID: 30622640 PMCID: PMC6304694 DOI: 10.1111/eva.12674] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/19/2018] [Accepted: 06/10/2018] [Indexed: 02/06/2023] Open
Abstract
Cattle have been invaluable for the transition of human society from nomadic hunter-gatherers to sedentary farming communities throughout much of Europe, Asia and Africa since the earliest domestication of cattle more than 10,000 years ago. Although current understanding of relationships among ancestral populations remains limited, domestication of cattle is thought to have occurred on two or three occasions, giving rise to the taurine (Bos taurus) and indicine (Bos indicus) species that share the aurochs (Bos primigenius) as common ancestor ~250,000 years ago. Indicine and taurine cattle were domesticated in the Indus Valley and Fertile Crescent, respectively; however, an additional domestication event for taurine in the Western Desert of Egypt has also been proposed. We analysed medium density Illumina Bovine SNP array (~54,000 loci) data across 3,196 individuals, representing 180 taurine and indicine populations to investigate population structure within and between populations, and domestication and demographic dynamics using approximate Bayesian computation (ABC). Comparative analyses between scenarios modelling two and three domestication events consistently favour a model with only two episodes and suggest that the additional genetic variation component usually detected in African taurine cattle may be explained by hybridization with local aurochs in Africa after the domestication of taurine cattle in the Fertile Crescent. African indicine cattle exhibit high levels of shared genetic variation with Asian indicine cattle due to their recent divergence and with African taurine cattle through relatively recent gene flow. Scenarios with unidirectional or bidirectional migratory events between European taurine and Asian indicine cattle are also plausible, although further studies are needed to disentangle the complex human-mediated dispersion patterns of domestic cattle. This study therefore helps to clarify the effect of past demographic history on the genetic variation of modern cattle, providing a basis for further analyses exploring alternative migratory routes for early domestic populations.
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Affiliation(s)
- Daniel Pitt
- School of BiosciencesCardiff UniversityCardiffUK
| | | | | | - David E. MacHugh
- Animal Genomics LaboratoryUCD School of Agriculture and Food Science, UCD College of Health and Agricultural SciencesUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinDublinIreland
| | | | - Licia Colli
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e sul DNA AnticoUniversità Cattolica del S. Cuore di PiacenzaPiacenzaItaly
| | - Rodrigo Martinez
- Corporación Colombiana De Investigación Agropecuaria (Corpoica)Centro de investigaciones TibaitatáBogotáColombia
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22
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Cheruiyot EK, Bett RC, Amimo JO, Zhang Y, Mrode R, Mujibi FDN. Signatures of Selection in Admixed Dairy Cattle in Tanzania. Front Genet 2018; 9:607. [PMID: 30619449 PMCID: PMC6305962 DOI: 10.3389/fgene.2018.00607] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023] Open
Abstract
Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7 and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG, and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle.
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Affiliation(s)
- Evans Kiptoo Cheruiyot
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya.,USOMI Limited, Nairobi, Kenya
| | - Rawlynce Cheruiyot Bett
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya
| | - Joshua Oluoch Amimo
- Department of Animal Production, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya
| | - Yi Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Raphael Mrode
- International Livestock Research Institute, Nairobi, Kenya.,Scotland's Rural College, Edinburgh, United Kingdom
| | - Fidalis D N Mujibi
- USOMI Limited, Nairobi, Kenya.,Nelson Mandela African Institute of Science and Technology, Arusha, Tanzania
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23
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Bahbahani H, Afana A, Wragg D. Genomic signatures of adaptive introgression and environmental adaptation in the Sheko cattle of southwest Ethiopia. PLoS One 2018; 13:e0202479. [PMID: 30114214 PMCID: PMC6095569 DOI: 10.1371/journal.pone.0202479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/04/2018] [Indexed: 11/23/2022] Open
Abstract
Although classified as an African taurine breed, the genomes of Sheko cattle are an admixture of Asian zebu and African taurine ancestries. They populate the humid Bench Maji zone in Sheko and Bench districts in the south-western part of Ethiopia and are considered as a trypanotolerant breed with high potential for dairy production. Here, we investigate the genome of Sheko cattle for candidate signatures of adaptive introgression and positive selection using medium density genome-wide SNP data. Following locus-ancestry deviation analysis, 15 and 72 genome regions show substantial excess and deficiency in Asian zebu ancestry, respectively. Nine and 23 regions show candidate signatures of positive selection following extended haplotype homozygosity (EHH)-based analyses (iHS and Rsb), respectively. The results support natural selection before admixture for one iHS, one Rsb and three zebu ancestry-deficient regions. Genes and/or QTL associated with bovine immunity, fertility, heat tolerance, trypanotolerance and lactation are present within candidate selected regions. The identification of candidate regions under selection in Sheko cattle warrants further investigation of a larger sample size using full genome sequence data to better characterise the underlying haplotypes. The results can then support informative genomic breeding programmes to sustainably enhance livestock productivity in East African trypanosomosis infested areas.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
- * E-mail: ,
| | - Arwa Afana
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait City, Kuwait
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, United Kingdom
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24
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Tarekegn GM, Tesfaye K, Mwai OA, Djikeng A, Dessie T, Birungi J, Osama S, Zergaw N, Alemu A, Achieng G, Tutah J, Mutai C, Njuguna J, Mwacharo JM. Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats. Ecol Evol 2018; 8:1543-1553. [PMID: 29435231 PMCID: PMC5792515 DOI: 10.1002/ece3.3710] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 10/30/2017] [Accepted: 11/10/2017] [Indexed: 01/19/2023] Open
Abstract
The Horn of Africa forms one of the two main historical entry points of domestics into the continent and Ethiopia is particularly important in this regard. Through the analysis of mitochondrial DNA (mtDNA) d-loop region in 309 individuals from 13 populations, we reveal the maternal genetic variation and demographic dynamics of Ethiopian indigenous goats. A total of 174 variable sites that generated 231 haplotypes were observed. They defined two haplogroups that were present in all the 13 study populations. Reference haplotypes from the six globally defined goat mtDNA haplogroups show the two haplogroups present in Ethiopia to be A and G, the former being the most predominant. Although both haplogroups are characterized by an increase in effective population sizes (Ne) predating domestication, they also have experienced a decline in Ne at different time periods, suggesting different demographic histories. We observed seven haplotypes, six were directly linked to the central haplotypes of the two haplogroups and one was central to haplogroup G. The seven haplotypes were common between Ethiopia, Kenya, Egypt, and Saudi Arabia populations, suggesting common maternal history and the introduction of goats into East Africa via Egypt and the Arabian Peninsula, respectively. While providing new mtDNA data from a historically important region, our results suggest extensive intermixing of goats mediated by human socio-cultural and economic interactions. These have led to the coexistence of the two haplogroups in different geographic regions in Ethiopia resulting in a large caprine genetic diversity that can be exploited for genetic improvement.
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Affiliation(s)
- Getinet Mekuriaw Tarekegn
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
- Department of Animal Production and Technology, Biotechnology Research InstituteBahir Dar UniversityBahir DarEthiopia
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
- Swedish University of Agricultural SciencesUppsalaSweden
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and HealthThe University of EdinburghEdinburghUK
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Josephine Birungi
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Sarah Osama
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Netsanet Zergaw
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Alubel Alemu
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Gloria Achieng
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Jack Tutah
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Collins Mutai
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa‐International Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Joram M. Mwacharo
- Small Ruminant Genetics and Genomics GroupInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
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25
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Bahbahani H, Salim B, Almathen F, Al Enezi F, Mwacharo JM, Hanotte O. Signatures of positive selection in African Butana and Kenana dairy zebu cattle. PLoS One 2018; 13:e0190446. [PMID: 29300786 PMCID: PMC5754058 DOI: 10.1371/journal.pone.0190446] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/14/2017] [Indexed: 02/02/2023] Open
Abstract
Butana and Kenana are two types of zebu cattle found in Sudan. They are unique amongst African indigenous zebu cattle because of their high milk production. Aiming to understand their genome structure, we genotyped 25 individuals from each breed using the Illumina BovineHD Genotyping BeadChip. Genetic structure analysis shows that both breeds have an admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in Butana, 0.76 ± 0.006 in Kenana) and taurine (0.23 ± 0.009 in Butana, 0.24 ± 0.006 in Kenana) ancestries. We also observe a proportion of 0.02 to 0.12 of European taurine ancestry in ten individuals of Butana that were sampled from cattle herds in Tamboul area suggesting local crossbreeding with exotic breeds. Signatures of selection analyses (iHS and Rsb) reveal 87 and 61 candidate positive selection regions in Butana and Kenana, respectively. These regions span genes and quantitative trait loci (QTL) associated with biological pathways that are important for adaptation to marginal environments (e.g., immunity, reproduction and heat tolerance). Trypanotolerance QTL are intersecting candidate regions in Kenana cattle indicating selection pressure acting on them, which might be associated with an unexplored level of trypanotolerance in this cattle breed. Several dairy traits QTL are overlapping the identified candidate regions in these two zebu cattle breeds. Our findings underline the potential to improve dairy production in the semi-arid pastoral areas of Africa through breeding improvement strategy of indigenous local breeds.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait city, Kuwait
- * E-mail: ,
| | - Bashir Salim
- Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum Khartoum North, Sudan
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Hasa, Kingdom of Saudi Arabia
| | - Fahad Al Enezi
- Department of Biological Sciences, Faculty of Science, Kuwait University, Kuwait city, Kuwait
| | - Joram M. Mwacharo
- Small Ruminant Genomics Group, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
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26
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Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
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27
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Bahbahani H, Tijjani A, Mukasa C, Wragg D, Almathen F, Nash O, Akpa GN, Mbole-Kariuki M, Malla S, Woolhouse M, Sonstegard T, Van Tassell C, Blythe M, Huson H, Hanotte O. Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu. Front Genet 2017. [PMID: 28642786 PMCID: PMC5462927 DOI: 10.3389/fgene.2017.00068] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait UniversityKuwait, Kuwait
| | - Abdulfatai Tijjani
- School of Life Sciences, University of NottinghamNottingham, United Kingdom.,Centre for Genomics Research and Innovation, National Biotechnology Development AgencyAbuja, Nigeria
| | | | - David Wragg
- Centre for Tropical Livestock Genetics and Health, Roslin InstituteEdinburgh, United Kingdom
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal UniversityAl-Hasa, Saudi Arabia
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Development AgencyAbuja, Nigeria
| | - Gerald N Akpa
- Department of Animal Science, Ahmadu Bello UniversityZaria, Nigeria
| | - Mary Mbole-Kariuki
- School of Life Sciences, University of NottinghamNottingham, United Kingdom
| | - Sunir Malla
- Deep Seq Department, University of NottinghamNottingham, United Kingdom
| | - Mark Woolhouse
- Ashworth Laboratories, Centre for Immunity, Infection and Evolution, University of EdinburghEdinburgh, United Kingdom
| | | | - Curtis Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, United States
| | - Martin Blythe
- Deep Seq Department, University of NottinghamNottingham, United Kingdom
| | - Heather Huson
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, United States
| | - Olivier Hanotte
- School of Life Sciences, University of NottinghamNottingham, United Kingdom.,International Livestock Research Institute (ILRI)Addis Ababa, Ethiopia
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28
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Mdladla K, Dzomba EF, Muchadeyi FC. The potential of landscape genomics approach in the characterization of adaptive genetic diversity in indigenous goat genetic resources: A South African perspective. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0935-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Makina SO, Whitacre LK, Decker JE, Taylor JF, MacNeil MD, Scholtz MM, van Marle-Köster E, Muchadeyi FC, Makgahlela ML, Maiwashe A. Insight into the genetic composition of South African Sanga cattle using SNP data from cattle breeds worldwide. Genet Sel Evol 2016; 48:88. [PMID: 27846793 PMCID: PMC5111355 DOI: 10.1186/s12711-016-0266-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 11/04/2016] [Indexed: 01/05/2023] Open
Abstract
Background Understanding the history of cattle breeds is important because it provides the basis for developing appropriate selection and breed improvement programs. In this study, patterns of ancestry and admixture in Afrikaner, Nguni, Drakensberger and Bonsmara cattle of South Africa were investigated. We used 50 K single nucleotide polymorphism genotypes that were previously generated for the Afrikaner (n = 36), Nguni (n = 50), Drakensberger (n = 47) and Bonsmara (n = 44) breeds, and for 394 reference animals representing European taurine, African taurine, African zebu and Bos indicus. Results and discussion Our findings support previous conclusions that Sanga cattle breeds are composites between African taurine and Bos indicus. Among these breeds, the Afrikaner breed has significantly diverged from its ancestral forebears, probably due to genetic drift and selection to meet breeding objectives of the breed society that enable registration. The Nguni, Drakensberger and Bonsmara breeds are admixed, perhaps unintentionally in the case of Nguni and Drakensberger, but certainly by design in the case of Bonsmara, which was developed through crossbreeding between the Afrikaner, Hereford and Shorthorn breeds. Conclusions We established patterns of admixture and ancestry for South African Sanga cattle breeds, which provide a basis for developing appropriate strategies for their genetic improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0266-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sithembile O Makina
- Agricultural Research Council-Animal Production Institute, Private Bag X 2, Irene, 0062, South Africa.
| | - Lindsey K Whitacre
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael D MacNeil
- Agricultural Research Council-Animal Production Institute, Private Bag X 2, Irene, 0062, South Africa.,Department of Animal, Wildlife and Grassland Sciences, University of Free State, Bloemfontein, 9300, South Africa.,Delta G, Miles City, MT, 59301, USA
| | - Michiel M Scholtz
- Agricultural Research Council-Animal Production Institute, Private Bag X 2, Irene, 0062, South Africa.,Department of Animal, Wildlife and Grassland Sciences, University of Free State, Bloemfontein, 9300, South Africa
| | - Este van Marle-Köster
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X 20, Hatfield, 0028, South Africa
| | - Farai C Muchadeyi
- Agricultural Research Council-Biotechnology Platform, Private Bag X 5, Onderstepoort, 0110, South Africa
| | - Mahlako L Makgahlela
- Agricultural Research Council-Animal Production Institute, Private Bag X 2, Irene, 0062, South Africa
| | - Azwihangwisi Maiwashe
- Agricultural Research Council-Animal Production Institute, Private Bag X 2, Irene, 0062, South Africa.,Department of Animal, Wildlife and Grassland Sciences, University of Free State, Bloemfontein, 9300, South Africa
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31
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Mdladla K, Dzomba EF, Huson HJ, Muchadeyi FC. Population genomic structure and linkage disequilibrium analysis of South African goat breeds using genome-wide SNP data. Anim Genet 2016; 47:471-82. [PMID: 27306145 DOI: 10.1111/age.12442] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2016] [Indexed: 02/03/2023]
Abstract
The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies >0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2) = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of <150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances >100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in genetic studies of these populations.
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Affiliation(s)
- K Mdladla
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa.,Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - E F Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - H J Huson
- Department of Animal Science, Cornell University, 201 Morrison Hall, 507 Tower Road, Ithaca, NY, 14853, USA
| | - F C Muchadeyi
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa
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Review: Sustainability of crossbreeding in developing countries; definitely not like crossing a meadow…. Animal 2015; 10:262-73. [PMID: 26503101 DOI: 10.1017/s175173111500213x] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Crossbreeding, considering either terminal or rotational crossing, synthetic breed creation or breed replacement, is often promoted as an efficient strategy to increase farmers' income through the improvement of productivity of local livestock in developing countries. Sustainability of crossbreeding is however frequently challenged by constraints such as poor adaptation to the local environment or lack of logistic support. In this review, we investigate factors that may influence the long-term success or the failure of crossbreeding programs, based on the scientific literature and country reports submitted for The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture. Crossbreeding activities vary widely across species and countries. Its sustainability is dependent on different prerequisites such as continual access to adequate breeding stock (especially after the end of externally funded crossbreeding projects), the opportunity of improved livestock to express their genetic potential (e.g. through providing proper inputs) and integration within a reliable market chain. As formal crossbreeding programs are often associated with adoption of other technologies, they can be a catalyst for innovation and development for smallholders. Given the increasing global demand for animal products, as well as the potential environmental consequences of climate change, there is a need for practical research to improve the implementation of long-term crossbreeding programs in developing countries.
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Wambua L, Wambua PN, Ramogo AM, Mijele D, Otiende MY. Wildebeest-associated malignant catarrhal fever: perspectives for integrated control of a lymphoproliferative disease of cattle in sub-Saharan Africa. Arch Virol 2015; 161:1-10. [PMID: 26446889 PMCID: PMC4698299 DOI: 10.1007/s00705-015-2617-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/15/2015] [Indexed: 01/08/2023]
Abstract
Wildebeest-associated malignant catarrhal fever (WA-MCF), an acute lymphoproliferative disease of cattle caused by alcelaphine herpesvirus 1 (AlHV-1), remains a significant constraint to cattle production in nomadic pastoralist systems in eastern and southern Africa. The transmission of WA-MCF is dependent on the presence of the wildlife reservoir, i.e. wildebeest, belonging to the species Connochaetes taurinus and Connochaetes gnou; hence, the distribution of WA-MCF is largely restricted to Kenya, Tanzania and the Republic of South Africa, where wildebeest are present. WA-MCF is analogous to sheep-associated MCF (SA-MCF) in many aspects, with the latter having sheep as its reservoir host and a more global distribution, mainly in developed countries with intensive livestock production systems. However, unlike SA-MCF, the geographic seclusion of WA-MCF may have contributed to an apparent neglect in research efforts aimed at increased biological understanding and control of the disease. This review aims to highlight the importance of WA-MCF and the need for intensified research towards measures for its integrated control. We discuss current knowledge on transmission and geographical distribution in eastern and southern Africa and the burden of WA-MCF in affected vulnerable pastoral communities in Africa. Recent findings towards vaccine development and pertinent knowledge gaps for future research efforts on WA-MCF are also considered. Finally, integrated control of WA-MCF based on a logical three-pronged framework is proposed, contextualizing vaccine development, next-generation diagnostics, and diversity studies targeted to the viral pathogen and cattle hosts.
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Affiliation(s)
- Lillian Wambua
- School of Biological Sciences, University of Nairobi, P.O Box 30197, 00100, Nairobi, Kenya. .,International Center for Insect Physiology and Ecology, P.O Box 30772, 00100, Nairobi, Kenya.
| | - Peninah Nduku Wambua
- School of Biological Sciences, University of Nairobi, P.O Box 30197, 00100, Nairobi, Kenya.,International Center for Insect Physiology and Ecology, P.O Box 30772, 00100, Nairobi, Kenya
| | - Allan Maurice Ramogo
- International Center for Insect Physiology and Ecology, P.O Box 30772, 00100, Nairobi, Kenya
| | - Domnic Mijele
- Kenya Wildlife Service, P.O Box 40241, 00100, Nairobi, Kenya
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Bahbahani H, Clifford H, Wragg D, Mbole-Kariuki MN, Van Tassell C, Sonstegard T, Woolhouse M, Hanotte O. Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis. Sci Rep 2015; 5:11729. [PMID: 26130263 PMCID: PMC4486961 DOI: 10.1038/srep11729] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 06/03/2015] [Indexed: 12/02/2022] Open
Abstract
The small East African Shorthorn Zebu (EASZ) is the main indigenous cattle across East Africa. A recent genome wide SNP analysis revealed an ancient stable African taurine x Asian zebu admixture. Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. Four hundred and twenty-five EASZ and four reference populations (Holstein-Friesian, Jersey, N’Dama and Nellore) were analysed using 46,171 SNPs covering all autosomes and the X chromosome. Following FST and two extended haplotype homozygosity-based (iHS and Rsb) analyses 24 candidate genome regions within 14 autosomes and the X chromosome were revealed, in which 18 and 4 were previously identified in tropical-adapted and commercial breeds, respectively. These regions overlap with 340 bovine QTL. They include 409 annotated genes, in which 37 were considered as candidates. These genes are involved in various biological pathways (e.g. immunity, reproduction, development and heat tolerance). Our results support that different selection pressures (e.g. environmental constraints, human selection, genome admixture constrains) have shaped the genome of EASZ. We argue that these candidate regions represent genome landmarks to be maintained in breeding programs aiming to improve sustainable livestock productivity in the tropics.
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Affiliation(s)
- Hussain Bahbahani
- 1] School of Life Sciences, University of Nottingham, NG7 2RD, Nottingham, UK [2] Department of Biological Sciences, Faculty of Science, Kuwait University, Safat 13060, Kuwait
| | - Harry Clifford
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX, Oxford, UK
| | - David Wragg
- Institut National de la Recherche Agronomique (INRA), UMR 1338 Génétique, Physiologie et Systèmes d'Elevage (GenPhySE), 31326 Castanet Tolosan, France
| | - Mary N Mbole-Kariuki
- African Union - InterAfrican Bureau of Animal Resources (AU-IBAR), P. O. Box 30786, 00100 Nairobi, Kenya
| | - Curtis Van Tassell
- United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, USA
| | - Tad Sonstegard
- United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, USA
| | - Mark Woolhouse
- Centre for Immunity, Infection &Evolution, Ashworth Laboratories, Kings Buildings, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, NG7 2RD, Nottingham, UK
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Mwai O, Hanotte O, Kwon YJ, Cho S. African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:911-21. [PMID: 26104394 PMCID: PMC4478499 DOI: 10.5713/ajas.15.0002r] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers.
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Affiliation(s)
- Okeyo Mwai
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Young-Jun Kwon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea
| | - Seoae Cho
- CHO&KIM genomics, Seoul 151-919, Korea
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Njiiri NE, Bronsvoort BMD, Collins NE, Steyn HC, Troskie M, Vorster I, Thumbi SM, Sibeko KP, Jennings A, van Wyk IC, Mbole-Kariuki M, Kiara H, Poole EJ, Hanotte O, Coetzer K, Oosthuizen MC, Woolhouse M, Toye P. The epidemiology of tick-borne haemoparasites as determined by the reverse line blot hybridization assay in an intensively studied cohort of calves in western Kenya. Vet Parasitol 2015; 210:69-76. [PMID: 25858115 PMCID: PMC4427107 DOI: 10.1016/j.vetpar.2015.02.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 10/25/2022]
Abstract
The development of sensitive surveillance technologies using PCR-based detection of microbial DNA, such as the reverse line blot assay, can facilitate the gathering of epidemiological information on tick-borne diseases, which continue to hamper the productivity of livestock in many parts of Africa and elsewhere. We have employed a reverse line blot assay to detect the prevalence of tick-borne parasites in an intensively studied cohort of indigenous calves in western Kenya. The calves were recruited close to birth and monitored for the presence of infectious disease for up to 51 weeks. The final visit samples from 453 calves which survived for the study period were analyzed by RLB. The results indicated high prevalences of Theileria mutans (71.6%), T. velifera (62.8%), Anaplasma sp. Omatjenne (42.7%), A. bovis (39.9%), Theileria sp. (sable) (32.7%), T. parva (12.9%) and T. taurotragi (8.5%), with minor occurrences of eight other haemoparasites. The unexpectedly low prevalence of the pathogenic species Ehrlichia ruminantium was confirmed by a species-specific PCR targeting the pCS20 gene region. Coinfection analyses of the seven most prevalent haemoparasites indicated that they were present as coinfections in over 90% of the cases. The analyses revealed significant associations between several of the Theileria parasites, in particular T. velifera with Theileria sp. sable and T. mutans, and T. parva with T. taurotragi. There was very little coinfection of the two most common Anaplasma species, although they were commonly detected as coinfections with the Theileria parasites. The comparison of reverse line blot and serological results for four haemoparasites (T. parva, T. mutans, A. marginale and B. bigemina) indicated that, except for the mostly benign T. mutans, indigenous cattle seem capable of clearing infections of the three other, pathogenic parasites to below detectable levels. Although the study site was located across four agroecological zones, there was little restriction of the parasites to particular zones.
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Affiliation(s)
- Nyawira E Njiiri
- The International Livestock Research Institute, PO Box, 30709, 00100 Nairobi, Kenya; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | | | - Nicola E Collins
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Helena C Steyn
- Agricultural Research Council-Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort 0110, South Africa
| | - Milana Troskie
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Ilse Vorster
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - S M Thumbi
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK; Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164-7090, USA
| | - Kgomotso P Sibeko
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Amy Jennings
- The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK; The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Ilana Conradie van Wyk
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Mary Mbole-Kariuki
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK; African Union InterAfrican Bureau for Animal Resources (AU-IBAR), PO Box 30786, 00100 Nairobi, Kenya
| | - Henry Kiara
- The International Livestock Research Institute, PO Box, 30709, 00100 Nairobi, Kenya
| | - E Jane Poole
- The International Livestock Research Institute, PO Box, 30709, 00100 Nairobi, Kenya
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Koos Coetzer
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Marinda C Oosthuizen
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Mark Woolhouse
- Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Philip Toye
- The International Livestock Research Institute, PO Box, 30709, 00100 Nairobi, Kenya.
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Barbato M, Orozco-terWengel P, Tapio M, Bruford MW. SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front Genet 2015; 6:109. [PMID: 25852748 PMCID: PMC4367434 DOI: 10.3389/fgene.2015.00109] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/03/2015] [Indexed: 12/30/2022] Open
Abstract
Effective population size (Ne) is a key population genetic parameter that describes the amount of genetic drift in a population. Estimating Ne has been subject to much research over the last 80 years. Methods to estimate Ne from linkage disequilibrium (LD) were developed ~40 years ago but depend on the availability of large amounts of genetic marker data that only the most recent advances in DNA technology have made available. Here we introduce SNeP, a multithreaded tool to perform the estimate of Ne using LD using the standard PLINK input file format (.ped and.map files) or by using LD values calculated using other software. Through SNeP the user can apply several corrections to take account of sample size, mutation, phasing, and recombination rate. Each variable involved in the computation such as the binning parameters or the chromosomes to include in the analysis can be modified. When applied to published datasets, SNeP produced results closely comparable with those obtained in the original studies. The use of SNeP to estimate Ne trends can improve understanding of population demography in the recent past, provided a sufficient number of SNPs and their physical position in the genome are available. Binaries for the most common operating systems are available at https://sourceforge.net/projects/snepnetrends/.
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Affiliation(s)
- Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | - Miika Tapio
- MTT Agrifood Research Finland, Biotechnology and Food Research Jokioinen, Finland
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Woolhouse MEJ, Thumbi SM, Jennings A, Chase-Topping M, Callaby R, Kiara H, Oosthuizen MC, Mbole-Kariuki MN, Conradie I, Handel IG, Poole EJ, Njiiri E, Collins NE, Murray G, Tapio M, Auguet OT, Weir W, Morrison WI, Kruuk LEB, Bronsvoort BMDC, Hanotte O, Coetzer K, Toye PG. Co-infections determine patterns of mortality in a population exposed to parasite infection. SCIENCE ADVANCES 2015; 1:e1400026. [PMID: 26601143 PMCID: PMC4643819 DOI: 10.1126/sciadv.1400026] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/11/2015] [Indexed: 05/11/2023]
Abstract
Many individual hosts are infected with multiple parasite species, and this may increase or decrease the pathogenicity of the infections. This phenomenon is termed heterologous reactivity and is potentially an important determinant of both patterns of morbidity and mortality and of the impact of disease control measures at the population level. Using infections with Theileria parva (a tick-borne protozoan, related to Plasmodium) in indigenous African cattle [where it causes East Coast fever (ECF)] as a model system, we obtain the first quantitative estimate of the effects of heterologous reactivity for any parasitic disease. In individual calves, concurrent co-infection with less pathogenic species of Theileria resulted in an 89% reduction in mortality associated with T. parva infection. Across our study population, this corresponds to a net reduction in mortality due to ECF of greater than 40%. Using a mathematical model, we demonstrate that this degree of heterologous protection provides a unifying explanation for apparently disparate epidemiological patterns: variable disease-induced mortality rates, age-mortality profiles, weak correlations between the incidence of infection and disease (known as endemic stability), and poor efficacy of interventions that reduce exposure to multiple parasite species. These findings can be generalized to many other infectious diseases, including human malaria, and illustrate how co-infections can play a key role in determining population-level patterns of morbidity and mortality due to parasite infections.
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Affiliation(s)
- Mark E. J. Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
- Corresponding author. E-mail:
| | - Samuel M. Thumbi
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164–7090, USA
| | - Amy Jennings
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, The Roslin Building, Easter Bush, Midlothian EH25 9RG, UK
- The Roslin Institute, University of Edinburgh, The Roslin Building, Easter Bush, Midlothian EH25 9RG, UK
| | - Margo Chase-Topping
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Rebecca Callaby
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
- The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - Henry Kiara
- International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya
| | - Marinda C. Oosthuizen
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Mary N. Mbole-Kariuki
- International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Ilana Conradie
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Ian G. Handel
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, The Roslin Building, Easter Bush, Midlothian EH25 9RG, UK
- The Roslin Institute, University of Edinburgh, The Roslin Building, Easter Bush, Midlothian EH25 9RG, UK
| | - E. Jane Poole
- International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya
| | - Evalyne Njiiri
- International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya
| | - Nicola E. Collins
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Gemma Murray
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Miika Tapio
- Natural Resources Institute Finland (Luke), Green technology, FI-31600 Jokioinen, Finland
| | - Olga Tosas Auguet
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - Willie Weir
- Henry Wellcome Building, Institute of Biodiversity, Animal Health and Comparative Medicine, Garscube Campus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - W. Ivan Morrison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, The Roslin Building, Easter Bush, Midlothian EH25 9RG, UK
- The Roslin Institute, University of Edinburgh, The Roslin Building, Easter Bush, Midlothian EH25 9RG, UK
| | - Loeske E. B. Kruuk
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - B. Mark de C. Bronsvoort
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, The Roslin Building, Easter Bush, Midlothian EH25 9RG, UK
- The Roslin Institute, University of Edinburgh, The Roslin Building, Easter Bush, Midlothian EH25 9RG, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Koos Coetzer
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Philip G. Toye
- International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya
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Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds. Animal 2014; 9:218-26. [PMID: 25359181 DOI: 10.1017/s1751731114002560] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69,903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.
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40
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Abstract
Parasite burden varies widely between individuals within a population, and can covary with multiple aspects of individual phenotype. Here we investigate the sources of variation in faecal strongyle eggs counts, and its association with body weight and a suite of haematological measures, in a cohort of indigenous zebu calves in Western Kenya, using relatedness matrices reconstructed from single nucleotide polymorphism (SNP) genotypes. Strongyle egg count was heritable (h2 = 23·9%, s.e. = 11·8%) and we also found heritability of white blood cell counts (WBC) (h2 = 27·6%, s.e. = 10·6%). All the traits investigated showed negative phenotypic covariances with strongyle egg count throughout the first year: high worm counts were associated with low values of WBC, red blood cell count, total serum protein and absolute eosinophil count. Furthermore, calf body weight at 1 week old was a significant predictor of strongyle EPG at 16–51 weeks, with smaller calves having a higher strongyle egg count later in life. Our results indicate a genetic basis to strongyle EPG in this population, and also reveal consistently strong negative associations between strongyle infection and other important aspects of the multivariate phenotype.
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