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Leon-Apodaca AV, Kumar M, del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population. Genome Biol Evol 2024; 16:evae130. [PMID: 38913571 PMCID: PMC11221432 DOI: 10.1093/gbe/evae130] [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: 10/12/2023] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
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Affiliation(s)
- Ana V Leon-Apodaca
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Manoharan Kumar
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
| | - Andres del Castillo
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabriel C Conroy
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Robert W Lamont
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Kylie M Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Liz Borburgh
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Linda Behrendorff
- Queensland Parks and Wildlife Service, Department of Environment & Science, K’gari, Australia
| | - Sankar Subramanian
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA
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Leon-Apodaca AV, Kumar M, del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic consequences of isolation and inbreeding in an island dingo population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557950. [PMID: 37745583 PMCID: PMC10516007 DOI: 10.1101/2023.09.15.557950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.
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Affiliation(s)
| | - Manoharan Kumar
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
| | | | - Gabriel C. Conroy
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Robert W Lamont
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Steven Ogbourne
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Kylie M. Cairns
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney NSW 2052, Australia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Australia, Sydney NSW 2052, Australia
| | - Liz Borburgh
- School of Science, Technology & Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Linda Behrendorff
- Queensland Parks and Wildlife Service, Department of Environment & Science, K’gari, Australia
| | - Sankar Subramanian
- School of Science, Technology & Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland, Australia
| | - Zachary A. Szpiech
- Department of Biology, Pennsylvania State University, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, PA, USA
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Huang C, Zhao Q, Chen Q, Su Y, Ma Y, Ye S, Zhao Q. Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China. Genes (Basel) 2024; 15:313. [PMID: 38540373 PMCID: PMC10970279 DOI: 10.3390/genes15030313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/25/2024] [Accepted: 02/25/2024] [Indexed: 06/14/2024] Open
Abstract
Runs of Homozygosity (ROH) are continuous homozygous DNA segments in diploid genomes, which have been used to estimate the genetic diversity, inbreeding levels, and genes associated with specific traits in livestock. In this study, we analyzed the resequencing data from 10 local goat breeds in Yunnan province of China and five additional goat populations obtained from a public database. The ROH analysis revealed 21,029 ROH segments across the 15 populations, with an average length of 1.27 Mb, a pattern of ROH, and the assessment of the inbreeding coefficient indicating genetic diversity and varying levels of inbreeding. iHS (integrated haplotype score) was used to analyze high-frequency Single-Nucleotide Polymorphisms (SNPs) in ROH regions, specific genes related to economic traits such as coat color and weight variation. These candidate genes include OCA2 (OCA2 melanosomal transmembrane protein) and MLPH (melanophilin) associated with coat color, EPHA6 (EPH receptor A6) involved in litter size, CDKAL1 (CDK5 regulatory subunit associated protein 1 like 1) and POMC (proopiomelanocortin) linked to weight variation and some putative genes associated with high-altitude adaptability and immune. This study uncovers genetic diversity and inbreeding levels within local goat breeds in Yunnan province, China. The identification of specific genes associated with economic traits and adaptability provides actionable insights for utilization and conservation efforts.
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Affiliation(s)
- Chang Huang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yinxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
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Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [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] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
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Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
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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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Sharif MB, Fitak RR, Wallner B, Orozco-terWengel P, Frewin S, Fremaux M, Mohandesan E. Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses. Animals (Basel) 2022; 12:ani12243508. [PMID: 36552427 PMCID: PMC9774138 DOI: 10.3390/ani12243508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other domestic horses. We show that at least six maternal and six paternal lineages contributed unequally to the KH gene pool, and today's KH population possibly represents two sub-populations. Our results indicate that three horse breeds, namely Welsh ponies, Thoroughbreds and Arabian horses had a major influence in the genetic-makeup of the extant KH population. We show that mitochondrial genetic diversity in KHs (π = 0.00687 ± 0.00355) is closer to that of the Sable Island horses (π = 0.0034 ± 0.00301), and less than other feral horse populations around the world. Our current findings, combined with ongoing genomic research, will provide insight into the population-specific genetic variation and inbreeding among KHs. This will largely advance equine research and improve the management of future breeding programs of these treasured New Zealand horse.
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Affiliation(s)
- Muhammad Bilal Sharif
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Robert Rodgers Fitak
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, 4110 Libra Dr, Orlando, FL 32816, USA
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Veterinary University of Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - Simone Frewin
- Feed2U Ltd., 19 Wairere Valley Road, Paparoa 0571, New Zealand
| | - Michelle Fremaux
- InfogeneNZ (EPAGSC), School of Agriculture and Environment, Massey University, 1 Drysdale Drive, Palmerston North 4410, New Zealand
| | - Elmira Mohandesan
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Correspondence:
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Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022; 13:genes13122272. [PMID: 36553539 PMCID: PMC9777570 DOI: 10.3390/genes13122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Anna Tommasi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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