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Gudra D, Valdovska A, Jonkus D, Kairisa D, Galina D, Ustinova M, Viksne K, Fridmanis D, Kalnina I. Genetic characterization of the Latvian local goat breed and genetic traits associated with somatic cell count. Animal 2024; 18:101154. [PMID: 38703755 DOI: 10.1016/j.animal.2024.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 05/06/2024] Open
Abstract
The Latvian local goat (LVK) breed represents the only native domestic goat breed in Latvia, but its limited population places it within the endangered category. However, the LVK breed has not yet undergone a comprehensive genetic characterization. Therefore, we completed whole genome sequencing to reveal the genetic foundation of the LVK breed while identifying genetic traits linked to the somatic cell count (SCC) levels. The study included 40 genomes of LVK goats sequenced to acquire at least 35x or 10x coverage. A Principal component analysis, a genetic distance tree, and an admixture analysis showed LVK's similarity to some European breeds, such as Finnish Landrace, Alpine, and Saanen, which aligns with the breed's history. An analysis of genome-wide heterozygosity, nucleotide diversity, and LD analysis indicated that the LVK population exhibits substantial levels of genetic diversity. LVK genome was dominated by short runs of homozygosity (ROHs, ≤ 500 kb) with a median length of 25 kb. With FROH 2.49%, average inbreeding levels were low; however, FROH ranged broadly from 0.13 to 12.2%. With the exception of one pure-blood breeding buck exhibiting FROH of 9.3% and FSNP of 8.5%, animals with at least 66% LVK ancestry showed moderate or no inbreeding. Overall, this study demonstrated that the LVK goats can be differentiated from imported breeds, although the population has a complex genetic structure. We were able to identify potential genetic traits associated with SCC levels, although the kinship of the animals and the heterogenic substructure of the population might have largely influenced the association analysis. We identified 26 genetic variants associated with SCC levels, which included the potentially relevant SNP rs662053371 in the OSBPL8 gene, indicating a potential signal linked to lipid metabolism in goats. To conclude, these findings present valuable insight into the genetic structure of the LVK breed for the conservation of local genetic resources.
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Affiliation(s)
- D Gudra
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - A Valdovska
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia.
| | - D Jonkus
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Kairisa
- Faculty of Agriculture, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - D Galina
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, Helmana iela 8 K, LV-3004 Jelgava, Latvia; Scientific Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, Lielā iela 2, LV-3001 Jelgava, Latvia
| | - M Ustinova
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - K Viksne
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - D Fridmanis
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
| | - I Kalnina
- Human Genetics and Disease Mechanisms Department, Latvian Biomedical Research and Study Centre, Rātsupītes iela 1 K-1, LV-1067 Riga, Latvia
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Manunza A, Ramirez-Diaz J, Cozzi P, Lazzari B, Tosser-Klopp G, Servin B, Johansson AM, Grøva L, Berg P, Våge DI, Stella A. Genetic diversity and historical demography of underutilised goat breeds in North-Western Europe. Sci Rep 2023; 13:20728. [PMID: 38007600 PMCID: PMC10676416 DOI: 10.1038/s41598-023-48005-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023] Open
Abstract
In the last decade, several studies aimed at dissecting the genetic architecture of local small ruminant breeds to discover which variations are involved in the process of adaptation to environmental conditions, a topic that has acquired priority due to climate change. Considering that traditional breeds are a reservoir of such important genetic variation, improving the current knowledge about their genetic diversity and origin is the first step forward in designing sound conservation guidelines. The genetic composition of North-Western European archetypical goat breeds is still poorly exploited. In this study we aimed to fill this gap investigating goat breeds across Ireland and Scandinavia, including also some other potential continental sources of introgression. The PCA and Admixture analyses suggest a well-defined cluster that includes Norwegian and Swedish breeds, while the crossbred Danish landrace is far apart, and there appears to be a close relationship between the Irish and Saanen goats. In addition, both graph representation of historical relationships among populations and f4-ratio statistics suggest a certain degree of gene flow between the Norse and Atlantic landraces. Furthermore, we identify signs of ancient admixture events of Scandinavian origin in the Irish and in the Icelandic goats. The time when these migrations, and consequently the introgression, of Scandinavian-like alleles occurred, can be traced back to the Viking colonisation of these two isles during the Viking Age (793-1066 CE). The demographic analysis indicates a complicated history of these traditional breeds with signatures of bottleneck, inbreeding and crossbreeding with the improved breeds. Despite these recent demographic changes and the historical genetic background shaped by centuries of human-mediated gene flow, most of them maintained their genetic identity, becoming an irreplaceable genetic resource as well as a cultural heritage.
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Affiliation(s)
- Arianna Manunza
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy.
| | - Johanna Ramirez-Diaz
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | - Paolo Cozzi
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | - Barbara Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
| | | | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 75007, Uppsala, Sweden
| | - Lise Grøva
- Norwegian Institute of Bioeconomy Research, Gunnars vei 6, NO-6630, Tingvoll, Norway
| | - Peer Berg
- Faculty of Biosciences, NMBU, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, ÅS, Norway
| | - Dag Inge Våge
- Faculty of Biosciences, NMBU, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, ÅS, Norway
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council, via Edoardo Bassini, 15, 20133, Milan, Italy
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Sallam AM, Reyer H, Wimmers K, Bertolini F, Aboul-Naga A, Braz CU, Rabee AE. Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds. BMC Genomics 2023; 24:573. [PMID: 37752425 PMCID: PMC10521497 DOI: 10.1186/s12864-023-09679-6] [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: 02/28/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
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Affiliation(s)
- Ahmed M Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt.
| | - Henry Reyer
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6b, 18059, Rostock, Germany
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Adel Aboul-Naga
- Animal Production Research Institute, Agricultural Research Center, Dokki, Cairo, Egypt
| | - Camila U Braz
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Alaa Emara Rabee
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 Gregory Dr, Urbana, 61801, USA
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Hewett AM, Stoffel MA, Peters L, Johnston SE, Pemberton JM. Selection, recombination and population history effects on runs of homozygosity (ROH) in wild red deer (Cervus elaphus). Heredity (Edinb) 2023; 130:242-250. [PMID: 36801920 PMCID: PMC10076382 DOI: 10.1038/s41437-023-00602-z] [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: 05/11/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
The distribution of runs of homozygosity (ROH) may be shaped by a number of interacting processes such as selection, recombination and population history, but little is known about the importance of these mechanisms in shaping ROH in wild populations. We combined an empirical dataset of >3000 red deer genotyped at >35,000 genome-wide autosomal SNPs and evolutionary simulations to investigate the influence of each of these factors on ROH. We assessed ROH in a focal and comparison population to investigate the effect of population history. We investigated the role of recombination using both a physical map and a genetic linkage map to search for ROH. We found differences in ROH distribution between both populations and map types indicating that population history and local recombination rate have an effect on ROH. Finally, we ran forward genetic simulations with varying population histories, recombination rates and levels of selection, allowing us to further interpret our empirical data. These simulations showed that population history has a greater effect on ROH distribution than either recombination or selection. We further show that selection can cause genomic regions where ROH is common, only when the effective population size (Ne) is large or selection is particularly strong. In populations having undergone a population bottleneck, genetic drift can outweigh the effect of selection. Overall, we conclude that in this population, genetic drift resulting from a historical population bottleneck is most likely to have resulted in the observed ROH distribution, with selection possibly playing a minor role.
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Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Martin A Stoffel
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Lucy Peters
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
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Zhong T, Wang X, Huang C, Yang L, Zhao Q, Chen X, Freitas-de-Melo A, Zhan S, Wang L, Dai D, Cao J, Guo J, Li L, Zhang H, Niu L. A genome-wide perspective on the diversity and selection signatures in indigenous goats using 53 K single nucleotide polymorphism array. Animal 2023; 17:100706. [PMID: 36758301 DOI: 10.1016/j.animal.2023.100706] [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: 08/27/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Tibetan goats, Taihang goats, Jining grey goats, and Meigu goats are the representative indigenous goats in China, found in Qinghai-Tibet Plateau, Western pastoral area, Northern and Southern agricultural regions. Very few studies have conducted a comprehensive analysis of the genomic diversity and selection of these breeds. We genotyped 96 unrelated individuals, using goat 53 K Illumina BeadChip array, of the following goat breeds: Tibetan (TG), Taihang (THG), Jining grey (JGG), and Meigu (MGG). A total of 45 951 single nucleotide polymorphisms were filtered to estimate the genetic diversity and selection signatures. All breeds had a high proportion (over 95%) of polymorphic loci. The observed and excepted heterozygosity ranged from 0.338 (MGG) to 0.402 (JGG) and 0.339 (MGG) to 0.395 (JGG), respectively. Clustering analysis displayed a genetically distinct lineage for each breed, and their Fst were greater than 0.25, indicating that they had a higher genetic differentiation between groups. Furthermore, effective population size reduced in all four populations, indicating a loss of genetic diversity. In addition, runs of homozygosity were mainly distributed in 5-10 Mb. Lastly, we identified signature genes, which were closely related to high-altitude adaptation (ADIRF) and prolificity (CNTROB, SMC3, and PTEN). This study provides a valuable resource for future studies on genome-wide perspectives on the diversity and selection signatures of Chinese indigenous goats.
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Affiliation(s)
- Tao Zhong
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinlu Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunhua Huang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Liu Yang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianjun Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xiaoyong Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Aline Freitas-de-Melo
- Departamento de Biociencias Veterinarias, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Siyuan Zhan
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linjie Wang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dinghui Dai
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxue Cao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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SHARMA REKHA, SEHRAWAT RENUKA, AHLAWAT SONIKA, GURJAR ML, TANTIA MS. Genetic diversity evaluation of Sojat goat population of India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2022. [DOI: 10.56093/ijans.v92i12.117981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sojat goat forms the part and parcel of the lives of the farmers in the Barmer region of Rajasthan. These are large-sized goats, white in colour, and have dual utility. These goats fetch premium price during the Eid festival. Assessment of diversity is essential for germplasm characterization and management. Genomic microsatellite markers being a valuable tool for estimating genetic diversity were selected for exploring existing genetic variability in the Sojat goat population. The standard metrics of genomic diversity detected moderate variability with a total of 162 alleles across 22 loci in this lesser-known population. The expected number of alleles had a mean value of 3.40±0.39. Similarly, a moderate magnitude of diversity was recorded in the Sojat population as the mean observed heterozygosity was 0.54±0.05. Expected heterozygosity was higher than the observed (0.60±0.06), indicating a deviation from Hardy-Weinberg Equilibrium (HWE) and the possibility of inbreeding due to the non-random mating in the population. Accordingly, significant heterozygote deficiency was noticed (F=0.08±0.03). The population did not suffer a reduction in effective population size in the last few generations. Mutation drift equilibrium did not reveal significant heterozygosity excess under different models of microsatellite evolution and no shift was recorded in the frequency distribution of alleles. To conclude, the results provided the first insights into the genetic diversity of Sojat goats. A moderate genetic variability with heterozygote deficiency within the population warrants immediate attention for scientific management of this unique goat population to conserve the existing genetic variation and to avoid any escalation of inbreeding.
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Li G, Tang J, Huang J, Jiang Y, Fan Y, Wang X, Ren J. Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds. Front Genet 2022; 13:774196. [PMID: 35559012 PMCID: PMC9086400 DOI: 10.3389/fgene.2022.774196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.
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Affiliation(s)
- Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.,Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Jinyan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang, China
| | - Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
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Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats. J Anim Sci Biotechnol 2022; 13:35. [PMID: 35264251 PMCID: PMC8908635 DOI: 10.1186/s40104-022-00684-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/19/2022] [Indexed: 12/30/2022] Open
Abstract
Background Inbreeding depression can adversely affect traits related to fitness, reproduction and productive performance. Although current research suggests that inbreeding levels are generally low in most goat breeds, the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data. Results We genotyped 1040 goats with the Goat SNP50 BeadChip. This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns. We detected 38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1, 2, 4, 6, 14, 16 and 17. Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes. Four regions on chromosomes 8 and 25 were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count. Notably, these regions contain several genes related with immunity, such as SYK, IL27, CCL19 and CCL21. Moreover, one region on chromosome 2 was significantly associated with inbreeding depression for milk yield. Conclusions Although genomic inbreeding levels are low in Murciano-Granadina goats, significant evidence of inbreeding depression for the logarithm of the somatic cell count, a phenotype closely associated with udder health and milk yield, have been detected in this population. Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis, which is one of the main causes of dairy goat culling. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00684-5.
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The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management. Genes (Basel) 2022; 13:genes13020213. [PMID: 35205258 PMCID: PMC8872249 DOI: 10.3390/genes13020213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
The Montecristo wild goat is an endangered feral population that has been on the homonymous island in the Tuscan Archipelago since ancient times. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neolithic times or between the 6th and 13th century of the Common Era. To investigate the evolutionary history and relationships of this population we assembled a 50K SNP dataset including 55 Mediterranean breeds and two nuclei of Montecristo goats sampled on the island and from an ex situ conservation project. Diversity levels, gene flow, population structure, and genetic relationships were assessed through multiple approaches. The insular population scored the lowest values of both observed and expected heterozygosity, highlighting reduced genetic variation, while the ex situ nucleus highlighted a less severe reduction. Multivariate statistics, network, and population structure analyses clearly separated the insular nucleus from all other breeds, including the population of Montecristo goats from the mainland. Moreover, admixture and gene flow analyses pinpointed possible genetic inputs received by the two Montecristo goat nuclei from different sources, while Runs of Homozygosity (ROHs) indicated an ancient bottleneck/founder effect in the insular population and recent extensive inbreeding in the ex situ one. Overall, our results suggest that Montecristo goats experienced several demographic fluctuations combined with admixture events over time and highlighted a noticeable differentiation between the two nuclei.
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Denoyelle L, Talouarn E, Bardou P, Colli L, Alberti A, Danchin C, Del Corvo M, Engelen S, Orvain C, Palhière I, Rupp R, Sarry J, Salavati M, Amills M, Clark E, Crepaldi P, Faraut T, Masiga CW, Pompanon F, Rosen BD, Stella A, Van Tassell CP, Tosser-Klopp G. VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity. Genet Sel Evol 2021; 53:86. [PMID: 34749642 PMCID: PMC8573910 DOI: 10.1186/s12711-021-00659-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00659-6.
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Affiliation(s)
- Laure Denoyelle
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.,Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Estelle Talouarn
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.,Sigenae, INRAE, 31326, Castanet-Tolosan, France
| | - Licia Colli
- Dipartimento Di Scienze Animali, Della Nutrizione E Degli Alimenti, BioDNA Centro Di Ricerca Sulla Biodiversità E Sul DNA Antico, Facoltà Di Scienze Agrarie, Alimentari E Ambientali, Università Cattolica del Sacro Cuore, Milan, Italy
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Coralie Danchin
- Institut de L'Elevage, Maison Nationale Des Eleveurs, 149 Rue de Bercy, 75595, Paris cedex 12, France
| | - Marcello Del Corvo
- Dipartimento Di Scienze Animali, Della Nutrizione E Degli Alimenti, BioDNA Centro Di Ricerca Sulla Biodiversità E Sul DNA Antico, Facoltà Di Scienze Agrarie, Alimentari E Ambientali, Università Cattolica del Sacro Cuore, Milan, Italy
| | - Stéfan Engelen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Céline Orvain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Isabelle Palhière
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Mazdak Salavati
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Emily Clark
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Paola Crepaldi
- Depth. Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Clet Wandui Masiga
- Tropical Institute of Development Innovations (TRIDI), P O Box 23158, Kampala, Uganda
| | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Alessandra Stella
- Istituto Di Biologia E Biotecnologia Agraria, Consiglio Nazionale Delle Ricerche, Milan, Italy
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
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11
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Cardoso TF, Luigi‐Sierra MG, Castelló A, Cabrera B, Noce A, Mármol‐Sánchez E, García‐González R, Fernández‐Arias A, Alabart JL, López‐Olvera JR, Mentaberre G, Granados‐Torres JE, Cardells‐Peris J, Molina A, Sànchez A, Clop A, Amills M. Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats ( Capra pyrenaica). Evol Appl 2021; 14:2618-2634. [PMID: 34815743 PMCID: PMC8591326 DOI: 10.1111/eva.13299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/07/2021] [Accepted: 08/02/2021] [Indexed: 01/11/2023] Open
Abstract
Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very often with hunting purposes), but they were not systematically planned or recorded. On the other hand, recent data suggest the occurrence of hybridization events between Iberian wild goats and domestic goats (Capra hircus). Augmentation translocations and interspecific hybridization might have contributed to increase the diversity of Iberian wild goats. With the aim of investigating this issue, we have genotyped 118 Iberian wild goats from Tortosa-Beceite, Sierra Nevada, Muela de Cortes, Gredos, Batuecas, and Ordesa and Monte Perdido by using the Goat SNP50 BeadChip (Illumina). The analysis of genotypic data indicated that Iberian wild goat populations are strongly differentiated and display low diversity. Only three Iberian wild goats out from 118 show genomic signatures of mixed ancestry, a result consistent with a scenario in which past augmentation translocations have had a limited impact on the diversity of Iberian wild goats. Besides, we have detected eight Iberian wild goats from Tortosa-Beceite with signs of domestic goat introgression. Although rare, hybridization with domestic goats could become a potential threat to the genetic integrity of Iberian wild goats; hence, measures should be taken to avoid the presence of uncontrolled herds of domestic or feral goats in mountainous areas inhabited by this iconic wild ungulate.
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Affiliation(s)
- Tainã Figueiredo Cardoso
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
| | - María Gracia Luigi‐Sierra
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
| | - Anna Castelló
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Betlem Cabrera
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Antonia Noce
- Leibniz‐Institute for Farm Animal Biology (FBN)DummerstorfGermany
| | - Emilio Mármol‐Sánchez
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
| | | | - Alberto Fernández‐Arias
- Servicio de Caza y PescaDepartamento de Agricultura, Ganadería y Medio AmbienteGobierno de AragónZaragozaSpain
| | - José Luis Alabart
- Unidad de Producción y Sanidad AnimalCentro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)Instituto Agroalimentario de Aragón ‐ IA2 (CITA‐Universidad de Zaragoza)Gobierno de AragónZaragozaSpain
| | - Jorge Ramón López‐Olvera
- Wildlife Ecology & Health Group and Servei d’Ecopatologia de Fauna Salvatge (SEFaS)Departament de Medicina i Cirurgia AnimalsUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Gregorio Mentaberre
- Wildlife Ecology & Health Group and Departament de Ciència AnimalEscola Tècnica Superior d’Enginyeria Agraria (ETSEA)Universitat de Lleida (UdL)LleidaSpain
| | | | - Jesús Cardells‐Peris
- SAIGAS (Servicio de Análisis, Investigación y Gestión de Animales Silvestres) and Wildlife Ecology & Health Group, Faculty of VeterinaryUniversidad Cardenal Herrera‐CEU, CEU UniversitiesValenciaSpain
| | - Antonio Molina
- Departamento de GenéticaUniversidad de CórdobaCórdobaSpain
| | - Armand Sànchez
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Alex Clop
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
| | - Marcel Amills
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterraSpain
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12
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Pogorevc N, Simčič M, Khayatzadeh N, Sölkner J, Berger B, Bojkovski D, Zorc M, Dovč P, Medugorac I, Horvat S. Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds. BMC Genomics 2021; 22:546. [PMID: 34273960 PMCID: PMC8285797 DOI: 10.1186/s12864-021-07802-z] [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: 11/16/2020] [Accepted: 06/13/2021] [Indexed: 12/05/2022] Open
Abstract
Background Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Results Distinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Conclusions Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07802-z.
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Affiliation(s)
- Neža Pogorevc
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Mojca Simčič
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Negar Khayatzadeh
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor Mendel Str. 33, A-1180, Vienna, Austria
| | - Johann Sölkner
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor Mendel Str. 33, A-1180, Vienna, Austria
| | - Beate Berger
- Department Animal Genetic Resources, AREC Raumberg-Gumpenstein, Institute of Organic Farming and Biodiversity of Farm Animals, 4601 Thalheim b., Wels, Austria
| | - Danijela Bojkovski
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Minja Zorc
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Peter Dovč
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Lena-Christ-Straβe 48, 8215, Martinsried/Planegg, Germany
| | - Simon Horvat
- Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia.
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13
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Nandolo W, Mészáros G, Wurzinger M, Banda LJ, Gondwe TN, Mulindwa HA, Nakimbugwe HN, Clark EL, Woodward-Greene MJ, Liu M, Liu GE, Van Tassell CP, Rosen BD, Sölkner J. Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics 2021; 22:398. [PMID: 34051743 PMCID: PMC8164248 DOI: 10.1186/s12864-021-07703-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. Results A total of 253,553 CNV (244,876 deletions and 8677 duplications) were identified, corresponding to an overall average of 1393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. Conclusions This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07703-1.
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Affiliation(s)
- Wilson Nandolo
- University of Natural Resources and Life Sciences, Vienna, Austria.,Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria Wurzinger
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Liveness J Banda
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Timothy N Gondwe
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | | | | | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland, UK
| | - M Jennifer Woodward-Greene
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.,National Agricultural Library, USDA-ARS, Beltsville, MD, USA
| | - Mei Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
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14
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Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations. Animals (Basel) 2021; 11:ani11061510. [PMID: 34071004 PMCID: PMC8224610 DOI: 10.3390/ani11061510] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary In the local populations, the increase in inbreeding is a relevant problem for the reduction in production, reproduction, and adaptive traits. The application of genomic technologies has facilitated the assessment of inbreeding in these populations. The current study aims to investigate the patterns of homozygosity in five Italian local goat populations. The results showed the different selection histories and breeding schemes of these goat populations. The analysis also indicated the importance of this information to avoid future loss of diversity and to produce information for designing optimal breeding and conservation programs. Abstract The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.
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15
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Microsatellite-Based Genetic Characterization of the Indigenous Katjang Goat in Peninsular Malaysia. Animals (Basel) 2021; 11:ani11051328. [PMID: 34066910 PMCID: PMC8148601 DOI: 10.3390/ani11051328] [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: 02/28/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Genetic characterization is one of the tools to assess the genetic diversity of livestock breeds towards the goals of conservation and sustainable use. This research aimed to assess the genetic diversity, population, genetic relationship, and structure of the Malaysian indigenous Katjang goat breed, which has been reported to be at risk of extinction by the Food and Agriculture Organization of the United Nations (FAO). Through assessment from microsatellite DNA markers, this breed was found to have low genetic diversity and showed evidence of high inbreeding. This breed might also have undergone population bottlenecks in the past. Through combined data analysis with other breeds and populations, available through data from published research, the Katjang goat population was found to have interconnection and form the centre of the network; it was also found to be the centroid of the multidimensional scaling plot. The findings of this research help in the understanding of the current genetic diversity of this breed and the need for its conservation. Abstract The Katjang goat is the only indigenous domestic goat breed in Malaysia. Following a national baseline survey from 2001 to 2002, this breed was reported to the FAO as being at risk of extinction. In this study, 36 microsatellite markers were screened, and 25 polymorphic markers were used to analyze the genetic structure of the Katjang goat breed in Peninsular Malaysia. A sample set of data derived from another 10 populations from three published research studies was used as an outgroup for an inter-population genetic study. The analysis showed that the mean value of the observed heterozygosity was 0.29 ± 0.14, and the expected heterozygosity was 0.72 ± 0.14, which indicated low genetic diversity. The inbreeding coefficient, FIS, was high, at 0.46. Significant (p < 0.01) deviations from the Hardy Weinberg equilibrium were noted for all loci. The bottleneck analysis using the Wilcoxon Rank test under the two-phase model of mutation was significant (p < 0.01) for heterozygosity excess, which suggested that the Katjang breed had undergone significant population reduction in the past. Through combined analysis of data from publicly available research, almost the entire population of Katjang goats represent the centroid and are grouped together on a multidimensional scaling plot, except for the Terengganu population. Network analysis revealed that the goat population from Pahang formed the centrality of the network.
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16
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Dettori ML, Petretto E, Pazzola M, Vidal O, Amills M, Vacca GM. Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers. Animals (Basel) 2020; 10:E2194. [PMID: 33255190 PMCID: PMC7761473 DOI: 10.3390/ani10122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022] Open
Abstract
A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The FST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations.
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Affiliation(s)
- Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Elena Petretto
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Oriol Vidal
- Departament de Biologia, Universitat de Girona, 17003 Girona, Spain;
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Department of Animal Genetics, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
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17
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Dementieva NV, Kudinov AA, Larkina TA, Mitrofanova OV, Dysin AP, Terletsky VP, Tyshchenko VI, Griffin DK, Romanov MN. Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity. Animals (Basel) 2020; 10:ani10101887. [PMID: 33076516 PMCID: PMC7602725 DOI: 10.3390/ani10101887] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary To maintain the uniqueness of conserved chicken populations of local and imported breeds is of great importance. In this study, we genotyped small populations belonging to 14 breeds and 7 crossbreds using an Illumina Chicken 60K SNP (Single Nucleotide Polymorphisms) BeadChip and looked for appropriate methods to characterize their purity/variability. It was not straightforward to identify crossbred individuals, and the best approach was based on calculating the length and number of homozygous regions, or runs of homozygosity (ROH), in the populations studied. The latter enabled most accurate identification of crossbreds and can be served as an effective tool in testing genome-wide purity of chicken breeds. Abstract Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Andrei A. Kudinov
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Tatiana A. Larkina
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Artyom P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Valeriy P. Terletsky
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia; (N.V.D.); (A.A.K.); (T.A.L.); (O.V.M.); (A.P.D.); (V.P.T.); (V.I.T.)
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
- Correspondence:
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Estimates of Autozygosity Through Runs of Homozygosity in Farmed Coho Salmon. Genes (Basel) 2020; 11:genes11050490. [PMID: 32365758 PMCID: PMC7290985 DOI: 10.3390/genes11050490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 11/17/2022] Open
Abstract
The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon (Oncorhynchus kisutch) breeding nuclei, genotyped using a 200 K Affymetrix Axiom® myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two “pure” lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available.
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19
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Berg P, Groeneveld L, Brekke C, Våge D, Sørheim K, Grøva L. Genetic characterization of a small closed island population of Norwegian coastal goat. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1729852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- P. Berg
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - C. Brekke
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - D.I. Våge
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - K.M. Sørheim
- Norwegian Centre for Organic Agriculture, Tingvoll, Norway
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20
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Kierkegaard LS, Groeneveld LF, Kettunen A, Berg P. The status and need for characterization of Nordic animal genetic resources. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1722216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | | | - Anne Kettunen
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Nofima AS, Ås, Norway
| | - Peer Berg
- Farm Animal Section, NordGen – The Nordic Genetic Resource Center, Ås, Norway
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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21
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Michailidou S, Tsangaris GT, Tzora A, Skoufos I, Banos G, Argiriou A, Arsenos G. Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds. PLoS One 2019; 14:e0226179. [PMID: 31830089 PMCID: PMC6907847 DOI: 10.1371/journal.pone.0226179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/21/2019] [Indexed: 12/02/2022] Open
Abstract
Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina’s Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright’s fixation index FST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.
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Affiliation(s)
- S. Michailidou
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thermi, Greece
- * E-mail:
| | - G. Th. Tsangaris
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - A. Tzora
- School of Agriculture, Department of Agriculture, Division of Animal Production, University of Ioannina, Kostakioi Artas, Greece
| | - I. Skoufos
- School of Agriculture, Department of Agriculture, Division of Animal Production, University of Ioannina, Kostakioi Artas, Greece
| | - G. Banos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Scotland's Rural College and The Roslin Institute University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - A. Argiriou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thermi, Greece
| | - G. Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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22
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Nandolo W, Mészáros G, Banda LJ, Gondwe TN, Lamuno D, Mulindwa HA, Nakimbugwe HN, Wurzinger M, Utsunomiya YT, Woodward-Greene MJ, Liu M, Liu G, Van Tassell CP, Curik I, Rosen BD, Sölkner J. Timing and Extent of Inbreeding in African Goats. Front Genet 2019; 10:537. [PMID: 31214253 PMCID: PMC6558083 DOI: 10.3389/fgene.2019.00537] [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: 10/31/2018] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
Genetic characterization of African goats is one of the current priorities in the improvement of goats in the continent. This study contributes to the characterization effort by determining the levels and number of generations to common ancestors ("age") associated with inbreeding in African goat breeds and identifies regions that contain copy number variation mistyped as being homozygous. Illumina 50k single nucleotide polymorphism genotype data for 608 goats from 31 breeds were used to compute the level and age of inbreeding at both local (marker) and global levels (FG) using a model-based approach based on a hidden Markov model. Runs of homozygosity (ROH) segments detected using the Viterbi algorithm led to ROH-based inbreeding coefficients for all ROH (FROH) and for ROH longer than 2 Mb (FROH > 2Mb). Some of the genomic regions identified as having ROH are likely to be hemizygous regions (copy number deletions) mistyped as homozygous regions. Although the proportion of these miscalled ROH is small and does not substantially affect estimates of levels of inbreeding for individual animals, the inbreeding metrics were adjusted by removing these regions from the ROH. All the inbreeding metrics varied widely across breeds, with overall means of 0.0408, 0.0370, and 0.0691 and medians of 0.0125, 0.0098, and 0.0366 for FROH, FROH > 2Mb, and FG, respectively. Several breeds (including Menabe and Sofia from Madagascar) had high proportions of recent inbreeding, while Small East African, Ethiopian, and most of the West African breeds (including West African Dwarf) had more ancient inbreeding.
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Affiliation(s)
- Wilson Nandolo
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria.,Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi.,Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Gábor Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Liveness Jessica Banda
- Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Timothy N Gondwe
- Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Doreen Lamuno
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | | | | | - Maria Wurzinger
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Yuri T Utsunomiya
- School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo State University (UNESP), São Paulo, Brazil
| | - M Jennifer Woodward-Greene
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Mei Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - George Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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23
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Bertolini F, Cardoso TF, Marras G, Nicolazzi EL, Rothschild MF, Amills M. Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats. Genet Sel Evol 2018; 50:59. [PMID: 30449279 PMCID: PMC6241033 DOI: 10.1186/s12711-018-0424-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 10/15/2018] [Indexed: 01/15/2023] Open
Abstract
Background Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were to characterize the number and length of runs of homozygosity (ROH) and to detect ROH hotspots in order to gain new insights into the consequences of neutral and selection processes on the genome-wide homozygosity patterns of goats. Results The proportion of the goat genome covered by ROH is, in general, less than 15% with an inverse relationship between ROH length and frequency i.e. short ROH (< 3 Mb) are the most frequent ones. Our data also indicate that ~ 60% of the breeds display low FROH coefficients (< 0.10), while ~ 30 and ~ 10% of the goat populations show moderate (0.10 < FROH < 0.20) or high (> 0.20) FROH values. For populations from Asia, the average number of ROH is smaller and their coverage is lower in goats from the Near East than in goats from Central Asia, which is consistent with the role of the Fertile Crescent as the primary centre of goat domestication. We also observed that local breeds with small population sizes tend to have a larger fraction of the genome covered by ROH compared to breeds with tens or hundreds of thousands of individuals. Five regions on three goat chromosomes i.e. 11, 12 and 18, contain ROH hotspots that overlap with signatures of selection. Conclusions Patterns of homozygosity (average number of ROH of 77 and genome coverage of 248 Mb; FROH < 0.15) are similar in goats from different geographic areas. The increased homozygosity in local breeds is the consequence of their small population size and geographic isolation as well as of founder effects and recent inbreeding. The existence of three ROH hotspots that co-localize with signatures of selection demonstrates that selection has also played an important role in increasing the homozygosity of specific regions in the goat genome. Finally, most of the goat breeds analysed in this work display low levels of homozygosity, which is favourable for their genetic management and viability. Electronic supplementary material The online version of this article (10.1186/s12711-018-0424-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. .,National Institute of Aquatic Resources, Technical University of Denmark (DTU), Lyngby, 2800, Denmark.
| | - Tainã Figueiredo Cardoso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Gabriele Marras
- Fondazione Parco Tecnologico Padano (PTP), 26900, Lodi, Italy
| | | | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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24
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Colli L, Milanesi M, Talenti A, Bertolini F, Chen M, Crisà A, Daly KG, Del Corvo M, Guldbrandtsen B, Lenstra JA, Rosen BD, Vajana E, Catillo G, Joost S, Nicolazzi EL, Rochat E, Rothschild MF, Servin B, Sonstegard TS, Steri R, Van Tassell CP, Ajmone-Marsan P, Crepaldi P, Stella A. Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes. Genet Sel Evol 2018; 50:58. [PMID: 30449284 PMCID: PMC6240949 DOI: 10.1186/s12711-018-0422-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/15/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. RESULTS A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. CONCLUSIONS After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.
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Affiliation(s)
- Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy. .,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy.
| | - Marco Milanesi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,School of Veterinary Medicine, Department of Support, Production and Animal Health, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Andrea Talenti
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, USA.,National Institute of Aquatic Resources, Technical University of Denmark, DTU, Lyngby, Denmark
| | - Minhui Chen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark.,Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alessandra Crisà
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Kevin Gerard Daly
- Population Genetics Lab, Smurfit Institute of Genetics, Trinity College of Dublin, Dublin, Ireland
| | - Marcello Del Corvo
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Århus, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Elia Vajana
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Bertrand Servin
- GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France
| | | | - Roberto Steri
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA) - Research Centre for Animal Production and Aquaculture, Monterotondo, Rome, Italy
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA
| | - Paolo Ajmone-Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del S. Cuore, Piacenza, Italy.,BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, University of Milan, Milan, Italy
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano, Lodi, Italy.,Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy
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