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Mahar K, Gurao A, Kumar A, Pratap Singh L, Chitkara M, Gowane GR, Ahlawat S, Niranjan SK, Pundir RK, Kataria RS, Dige MS. Genomic inbreeding analysis reveals resilience and genetic diversity in Indian yak populations. Gene 2024; 928:148787. [PMID: 39053660 DOI: 10.1016/j.gene.2024.148787] [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: 01/15/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The yak (Bos grunniens), renowned for its adaptability to extreme cold and hypoxic conditions, stands as a remarkable domestic animal crucial for sustaining livelihoods in harsh climates. We conducted a comprehensive analysis of the whole genome sequence data from three distinct Indian yak populations: Arunachali yak (n = 10), Himachali yak (n = 10), and Ladakhi yak (n = 10). The genomic data for Indian yaks were meticulously generated by our laboratory and compared with their Chinese counterpart, the Jinchuan yak (n = 8), for a more nuanced understanding. Our investigation revealed a total of 37,437 runs of homozygosity (ROH) segments in 34 animals representing four distinct yak populations. The Jinchuan yak population exhibited the highest proportion, constituting 80.8 % of total ROHs, predominantly as small segments (<0.1 Mb), accounting for 63 % of the overall ROHs. Further analysis uncovered a significantly higher degree of inbreeding in Chinese yaks compared to their Indian counterparts. The Indian yak populations, in contrast, demonstrated relatively lower and consistent levels of inbreeding. Moreover, we identified ROH hotspots that covered at least 60 % of individuals in our study, indicating their pivotal role in environmental adaptation. A total of five hotspot regions were detected, housing genes such as ENSBGRG00000015023 (WNT2), YIPF4, SPAST, TLN2, and DSG4. These genes are associated with traits including hair follicle initiation, nutrient stress response, microtubule assembly, development of cardiac muscle, hair follicle, and coat color. This observation strongly suggests that there is substantial selection acting on these genes, emphasizing their important role in environmental adaptation among yak populations.
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Affiliation(s)
- Karan Mahar
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Ankita Gurao
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Amod Kumar
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Lalit Pratap Singh
- Division of Animal Biotechnology, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Meenakshi Chitkara
- Division of Animal Biotechnology, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Gopal R Gowane
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Sonika Ahlawat
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - S K Niranjan
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R K Pundir
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R S Kataria
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - M S Dige
- Division of Animal Genetic Resources, ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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Wang P, Ou G, Li G, Li H, Zhao T. Analysis of genetic diversity and structure of endangered Dengchuan cattle population using a single-nucleotide polymorphism chip. Anim Biotechnol 2024; 35:2349625. [PMID: 38733367 DOI: 10.1080/10495398.2024.2349625] [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: 05/13/2024]
Abstract
This study aimed to evaluate the genetic diversity and structure within the Dengchuan cattle population and effectively protect and utilize their germplasm resources. Herein, the single-nucleotide polymorphisms (SNPs) of 100 Dengchuan cattle (46 bulls and 54 cows) were determined using the GGP Bovine 100K SNP Beadchip. The results showed that among the Dengchuan cattle, a total of 101,220 SNPs were detected, and there were 83,534 SNPs that passed quality control, of which 85.7% were polymorphic. The average genetic distance based on identity-by-state (IBS) within the conservation population of Dengchuan cattle was 0.26 ± 0.02. A total of 3,999 genome-length runs of homozygosity (ROHs) were detected in the Dengchuan cattle, with ROH lengths primarily concentrated in the range of 1-5 Mb, accounting for 87.02% of the total. The average inbreeding coefficient based on ROHs was 4.6%, within the conservation population of Dengchuan cattle, whereas it was 4.9% for bulls, and the Wright inbreeding coefficient (FIS) value was 2.4%, demonstrating a low level of inbreeding within the Dengchuan cattle population. Based on neighbor-joining tree analysis, the Dengchuan cattle could be divided into 16 families. In summary, the conservation population of Dengchuan cattle displays relatively abundant diversity and a moderate genetic relationship. Inbreeding was observed among a few individuals, but the overall inbreeding level of the population remained low. It is important to maintain this low level of inbreeding when introducing purebred bloodlines to expand the core group. This approach will ensure the long-term conservation of Dengchuan cattle germplasm resources and prevent loss of genetic diversity.
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Affiliation(s)
- Pingping Wang
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Guoyu Ou
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Genchang Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Huiying Li
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
| | - Tianzhang Zhao
- College of Agriculture and Biological Science, Dali University, Dali, Yunnan, China
- Co-Innovation Center for Cangshan Mountain and Erhai Lake Integrated Protection and Green Development of Yunnan Province, Dali University, Dali, Yuannan, China
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Goli RC, Mahar K, Manohar PS, Chishi KG, Prabhu IG, Choudhary S, Rathi P, Chinnareddyvari CS, Haritha P, Metta M, Shetkar M, Kumar A, N D CP, Vidyasagar, Sukhija N, Kanaka KK. Insights from homozygous signatures of cervus nippon revealed genetic architecture for components of fitness. Mamm Genome 2024:10.1007/s00335-024-10064-1. [PMID: 39191871 DOI: 10.1007/s00335-024-10064-1] [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: 05/07/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024]
Abstract
This study investigates the genomic landscape of Sika deer populations, emphasizing the detection and characterization of runs of homozygosity (ROH) and their contribution towards components of fitness. Using 85,001 high-confidence SNPs, the investigation into ROH distribution unveiled nuanced patterns of autozygosity across individuals especially in 2 out of the 8 farms, exhibiting elevated ROH levels and mean genome coverage under ROH segments. The prevalence of shorter ROH segments (0.5-4 Mb) suggests historical relatedness and potential selective pressures within these populations. Intriguingly, despite observed variations in ROH profiles, the overall genomic inbreeding coefficient (FROH) remained relatively low across all farms, indicating a discernible degree of genetic exchange and effective mitigation of inbreeding within the studied Sika deer populations. Consensus ROH (cROH) were found to harbor genes for important functions viz., EGFLAM gene which is involved in the vision function of the eye, SKP2 gene which regulates cell cycle, CAPSL involved in adipogenesis, SPEF2 which is essential for sperm flagellar assembly, DCLK3 involved in the heat stress. This first ever study on ROH in Sika deer, to shed light on the adaptive role of genes in these homozygous regions. The insights garnered from this study have broader implications in the management of genetic diversity in this vulnerable species.
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Affiliation(s)
- Rangasai Chandra Goli
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Karan Mahar
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Peela Sai Manohar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Kiyevi G Chishi
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | | | - Sonu Choudhary
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Pallavi Rathi
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Chandana Sree Chinnareddyvari
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Pala Haritha
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Muralidhar Metta
- College of Veterinary Science, SVVU, Garividi, Andhra Pradesh, India
| | - Mahantesh Shetkar
- College of Veterinary Sciences and Animal Husbandry, DUVASU, Mathura, Uttar Pradesh, India
| | - Amit Kumar
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Chethan Patil N D
- Department of Agricultural Economics & Extension, Lovely Professional University, Punjab, India
| | - Vidyasagar
- Veterinary College, KVAFSU, Bidar, Karnataka, India
| | - Nidhi Sukhija
- CSB-Central Tasar Research and Training Institute, Ranchi, Jharkhand, India.
| | - K K Kanaka
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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Liu Y, Kuang W, Yue B, Zhou C. Genomic diversity and demographic history of the endangered Sichuan hill-partridge (Arborophila rufipectus). J Hered 2024; 115:532-540. [PMID: 38635970 DOI: 10.1093/jhered/esae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/17/2024] [Indexed: 04/20/2024] Open
Abstract
Species conservation can be improved by knowledge of genetic diversity and demographic history. The Sichuan hill-partridge (Arborophila rufipectus, SP) is an endangered species endemic to the mountains in southwestern China. However, little is known about this species' genomic variation and demographic history. Here, we present a comprehensive whole-genome analysis of six SP individuals from the Laojunshan National Nature Reserve in Sichuan Province, China. We observe a relatively high genetic diversity and low level of recent inbreeding in the studied SP individuals. This suggests that the current population carries genetic variability that may benefit the long-term survival of this species, and that the present population may be larger than currently recognized. Analyses of demographic history showed that fluctuations in the effective population size of SP are inconsistent with changes of the historical climate. Strikingly, evidence from demographic modeling suggests SPs population decreased dramatically 15,100 years ago after the Last Glacial Maximum, possibly due to refugial isolation and later human interference. These results provide the first detailed and comprehensive genomic insights into genetic diversity, genomic inbreeding levels, and demographic history of the Sichuan hill-partridge, which are crucial for the conservation and management of this endangered species.
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Affiliation(s)
- Yi Liu
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Neijiang Normal University, Neijiang, China
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Weimin Kuang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Bisong Yue
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuang Zhou
- Key Laboratory of Bioresources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
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Brejon Lamartinière E, Tremble K, Dentinger BTM, Dasmahapatra KK, Hoffman JI. Runs of homozygosity reveal contrasting histories of inbreeding across global lineages of the edible porcini mushroom, Boletus edulis. Mol Ecol 2024; 33:e17470. [PMID: 39034770 DOI: 10.1111/mec.17470] [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: 02/07/2024] [Revised: 06/26/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024]
Abstract
Inbreeding, the mating of individuals that are related through common ancestry, is of central importance in evolutionary and conservation biology due to its impacts on individual fitness and population dynamics. However, while advanced genomic approaches have revolutionised the study of inbreeding in animals, genomic studies of inbreeding are rare in plants and lacking in fungi. We investigated global patterns of inbreeding in the prized edible porcini mushroom Boletus edulis using 225 whole genomes from seven lineages distributed across the northern hemisphere. Genomic inbreeding was quantified using runs of homozygosity (ROHs). We found appreciable variation both among and within lineages, with some individuals having over 20% of their genomes in ROHs. Much of this variation could be explained by a combination of elevation and latitude, and to a lesser extent by predicted habitat suitability during the last glacial maximum. In line with this, the majority of ROHs were short, reflecting ancient common ancestry dating back approximately 200-1700 generations ago, while longer ROHs indicative of recent common ancestry (less than approximately 50 generations ago) were infrequent. Our study reveals the inbreeding legacy of major climatic events in a widely distributed forest mutualist, aligning with prevailing theories and empirical studies of the impacts of historical glaciation events on the dominant forest tree species of the northern hemisphere.
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Affiliation(s)
- Etienne Brejon Lamartinière
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Keaton Tremble
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Bryn T M Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Natural History Museum of Utah, Salt Lake City, Utah, USA
| | | | - Joseph I Hoffman
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Münster, Germany
- British Antarctic Survey, Cambridge, UK
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Liu SQ, Xu YJ, Chen ZT, Li H, Zhang Z, Wang QS, Pan YC. Genome-wide detection of runs of homozygosity and heterozygosity in Tunchang pigs. Animal 2024; 18:101236. [PMID: 39096602 DOI: 10.1016/j.animal.2024.101236] [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: 08/28/2023] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 08/05/2024] Open
Abstract
Tunchang pigs, mainly distributed throughout Hainan Province of China, are well-known for their superior meat quality, crude feed tolerance, and adaptability to high temperatures and humidity. Runs of homozygosity (ROH) can provide valuable information about the inbreeding coefficient in individuals and selection signals that may reveal candidate genes associated with key functional traits. Runs of heterozygosity (ROHet) are commonly associated with balance selection, which can help us understand the adaptive evolutionary history of domestic animals. In this study, we investigated ROHs and ROHets in 88 Tunchang pigs. We also compared the estimates of inbreeding coefficients in individuals calculated based on four methods. In summary, we detected a total of 16 ROH islands in our study, and 100 genes were found within ROH regions. These genes were correlated with economically important traits such as reproduction (e.g., SERPIND1, HIRA), meat quality (e.g., PI4KA, TBX1), immunity (e.g., ESS2, RANBP1), adaption to heat stress (TXNRD2 and DGCR8), and crude food tolerance (TRPM6). Moreover, we discovered 18 ROHet islands harbouring genes associated with reproduction (e.g., ARHGEF12, BMPR2), immune system (e.g., BRD4, DNMT3B). These findings may help us design effective breeding and conservation strategies for this unique breed.
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Affiliation(s)
- S Q Liu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
| | - Y J Xu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
| | - Z T Chen
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China
| | - H Li
- Hainan Longjian Animal Husbandry Development Co. Ltd, Lantian Road, Haikou 570203, China
| | - Z Zhang
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China
| | - Q S Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
| | - Y C Pan
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China; Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East 310058, China; Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China.
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7
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Zeitler L, Gilbert KJ. Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates. Genome Biol Evol 2024; 16:evae139. [PMID: 38935434 PMCID: PMC11245710 DOI: 10.1093/gbe/evae139] [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: 02/27/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024] Open
Abstract
Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also create long ROHs. While ROHs are frequently used to understand inbreeding in the context of conservation and selective breeding, as well as for consanguinity of populations and their demographic history, it remains unclear how ROH characteristics are altered by selfing and if this confounds expected signatures of inbreeding due to demographic change. Using simulations, we study the impact of the mode of reproduction and demographic history on ROHs. We apply random forests to identify unique characteristics of ROHs, indicative of different sources of inbreeding. We pinpoint distinct features of ROHs that can be used to better characterize the type of inbreeding the population was subjected to and to predict outcrossing rates and complex demographic histories. Using additional simulations and four empirical datasets, two from highly selfing species and two from mixed-maters, we predict the selfing rate and validate our estimations. We find that self-fertilization rates are successfully identified even with complex demography. Population genetic summary statistics improve algorithm accuracy particularly in the presence of additional inbreeding, e.g. from population bottlenecks. Our findings highlight the importance of ROHs in disentangling confounding factors related to various sources of inbreeding and demonstrate situations where such sources cannot be differentiated. Additionally, our random forest models provide a novel tool to the community for inferring selfing rates using genomic data.
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Affiliation(s)
- Leo Zeitler
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland
| | - Kimberly J Gilbert
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg 1700, Switzerland
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Li X, Lan F, Chen X, Yan Y, Li G, Wu G, Sun C, Yang N. Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding. BMC Genomics 2024; 25:638. [PMID: 38926812 PMCID: PMC11210043 DOI: 10.1186/s12864-024-10551-4] [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: 08/12/2023] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding. RESULTS In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight. CONCLUSIONS In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.
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Affiliation(s)
- Xiaochang Li
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Fangren Lan
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoman Chen
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Yiyuan Yan
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Guangqi Li
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Guiqin Wu
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
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Zhang X, Yang L, Xie Z, Gan J, Zhu P, Song J, Kang H, Zhang Z, Liu L, Xiang H, Li H. Genetic assessment and candidate genes identification for breed-specific characteristics of Qingyuan partridge chicken based on runs of homozygosity. BMC Genomics 2024; 25:577. [PMID: 38858651 PMCID: PMC11163754 DOI: 10.1186/s12864-024-10492-y] [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: 10/17/2023] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH. RESULTS The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands. CONCLUSIONS These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.
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Affiliation(s)
- Xing Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Liu Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Key Laboratory of National Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant, China Conservation and Research Centre for the Giant Panda, Panda National Park, Chengdu, 611830, China
| | - Zhuojun Xie
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Jiankang Gan
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China
| | - Piao Zhu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Jiani Song
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Huimin Kang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Zhengfen Zhang
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China.
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10
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Sheriff O, Ahbara AM, Haile A, Alemayehu K, Han JL, Mwacharo JM. Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats. Front Genet 2024; 15:1353026. [PMID: 38854428 PMCID: PMC11156998 DOI: 10.3389/fgene.2024.1353026] [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: 12/09/2023] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.
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Affiliation(s)
- Oumer Sheriff
- Department of Animal Science, Assosa University, Assosa, Ethiopia
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abulgasim M. Ahbara
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
| | - Aynalem Haile
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Kefyalew Alemayehu
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
- Ethiopian Agricultural Transformation Institute, Amhara Agricultural Transformation Center, Bahir Dar, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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11
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Kar D, Ganguly I, Singh S, Bhatia AK, Dixit SP. Genome-wide runs of homozygosity signatures in diverse Indian goat breeds. 3 Biotech 2024; 14:81. [PMID: 38375512 PMCID: PMC10874352 DOI: 10.1007/s13205-024-03921-y] [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: 08/22/2023] [Accepted: 01/05/2024] [Indexed: 02/21/2024] Open
Abstract
The present study analyzed ROH and consensus ROH regions in 102 animals of eleven diverse Indian goat (Capra hircus) breeds using whole genome sequencing. A total of 51,705 ROH and 21,271 consensus regions were identified. The mean number of ROH per animal was highest in the meat breed, Jharkhand Black (2693) and lowest in the pashmina breed, Changthangi (60). The average length of ROH (ALROH) was maximum in Kanniadu (974.11 Kb) and minimum in Tellicherry (146.98 Kb). Long ROH is typically associated with more recent inbreeding, whereas short ROH is connected to more ancient inbreeding. The overall ROH-based genomic inbreeding (FROH) was highest for Jharkhand Black (0.602) followed by Kanniadu (0.120) and Sangamneri (0.108) among all breeds. FROH of Jharkhand Black was higher than Kanniadu up to 5 Mb ROH length category. However, in > 20 Mb ROH length category, Kanniadu (0.98) exhibited significantly higher FROH than Jharkhand Black (0.46). This implies that Kanniadu had higher levels of recent inbreeding than Jharkhand Black. Despite this, due to the presence of both recent and ancient inbreeding, Jharkhand Black demonstrated higher overall FROH compared to Kanniadu. ROH patterns revealed dual purpose (meat and dairy) and pashmina breeds as less consanguineous while recent inbreeding was apparent in meat breeds. Analysis of ROH consensus regions identified selection sweeps in key genes governing intramuscular fat deposition, meat tenderisation, lean meat production and carcass weight (CDK4, ALOX15, CASP9, PRDM16, DVL1) in meat breeds; milk fat percentage and mammary gland development (POLD1, NOTCH2, ARHGAP35) in dual purpose (meat and dairy) breeds; while cold adaptation and hair follicle development (APOBEC1, DNAJC3, F2RL1, FGF9) in pashmina breed. MAPK, RAS, BMP and Wnt signaling pathways associated with hair follicle morphogenesis in Changthangi were also identified. PCA analysis based on ROH consensus regions revealed that meat breeds are more diverse than other goat breeds/populations. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03921-y.
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Affiliation(s)
- Dibyasha Kar
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Indrajit Ganguly
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Sanjeev Singh
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Avnish Kumar Bhatia
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - S. P. Dixit
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
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12
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Cole JB. Perspective: Can we actually do anything about inbreeding? J Dairy Sci 2024; 107:643-648. [PMID: 37777000 DOI: 10.3168/jds.2023-23958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023]
Affiliation(s)
- John B Cole
- URUS Group LP, Madison, WI 53718; Department of Animal Sciences, University of Florida, Gainesville, FL 32611; Department of Animal Science, North Carolina State University, Raleigh, NC 27695.
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13
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Illa SK, Mumtaz S, Nath S, Mukherjee S, Mukherjee A. Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle. J Appl Genet 2024; 65:167-180. [PMID: 38110827 DOI: 10.1007/s13353-023-00816-1] [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: 02/10/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023]
Abstract
Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average FPED (Pedigree based inbreeding coefficient), FROH (Genomic inbreeding coefficient), FHOM (Inbreeding estimated as the ratio of observed and expected homozygous genotypes), FGRM (Inbreeding estimated on genomic relationship method) and FGRM0.5 (Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.
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Affiliation(s)
- Satish Kumar Illa
- Livestock Research Station, Garividi, Sri Venkateswara Veterinary University, Tirupati, Andhra Pradesh State, India
| | - Shabahat Mumtaz
- Animal Husbandry Department, Kolkata, West Bengal State, India
| | - Sapna Nath
- College of Veterinary Science, Garividi, Sri Venkateswara Veterinary University, Tirupati, Andhra Pradesh State, India
| | - Sabyasachi Mukherjee
- Animal Genetics & Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana State, India.
| | - Anupama Mukherjee
- Animal Genetics & Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana State, India.
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14
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Santos WB, Pereira CB, Maiorano AM, Arce CDS, Baldassini WA, Pereira GL, Chardulo LAL, Neto ORM, Oliveira HN, Curi RA. Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line. J Anim Breed Genet 2023; 140:583-595. [PMID: 37282810 DOI: 10.1111/jbg.12812] [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: 10/03/2022] [Revised: 03/30/2023] [Accepted: 05/28/2023] [Indexed: 06/08/2023]
Abstract
With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.
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Affiliation(s)
- Wellington B Santos
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Camila B Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Amanda M Maiorano
- Department of Animal Science, Federal University of Uberlândia, Uberlândia, Brazil
| | | | - Welder A Baldassini
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Guilherme L Pereira
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Luis Artur L Chardulo
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Otávio R M Neto
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
| | - Henrique N Oliveira
- Department of Animal Science, São Paulo State University, Jaboticabal, Brazil
| | - Rogério A Curi
- Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil
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15
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Saif-Ur-Rehman M, Hassan FU, Reecy J, Deng T. Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan. Anim Biotechnol 2023; 34:1384-1396. [PMID: 35044288 DOI: 10.1080/10495398.2022.2026369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.
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Affiliation(s)
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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16
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Arias KD, Gutiérrez JP, Fernández I, Álvarez I, Goyache F. Approaching autozygosity in a small pedigree of Gochu Asturcelta pigs. Genet Sel Evol 2023; 55:74. [PMID: 37880572 PMCID: PMC10601182 DOI: 10.1186/s12711-023-00846-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 10/03/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major difficulties. Homozygosity estimators show large variation due to different causes, namely, Mendelian sampling, population structure, and differences among chromosomes. Therefore, the ascertainment of how inbreeding is reflected in the genome is still an issue. The aim of this research was to study the usefulness of genomic information for the assessment of genetic diversity in the highly endangered Gochu Asturcelta pig breed. Pedigree depth varied from 0 (founders) to 4 equivalent discrete generations (t). Four homozygosity parameters (runs of homozygosity, FROH; heterozygosity-rich regions, FHRR; Li and Horvitz's, FLH; and Yang and colleague's FYAN) were computed for each individual, adjusted for the variability in the base population (BP; six individuals) and further jackknifed over autosomes. Individual increases in homozygosity (depending on t) and increases in pairwise homozygosity (i.e., increase in the parents' mean) were computed for each individual in the pedigree, and effective population size (Ne) was computed for five subpopulations (cohorts). Genealogical parameters (individual inbreeding, individual increase in inbreeding, and Ne) were used for comparisons. RESULTS The mean F was 0.120 ± 0.074 and the mean BP-adjusted homozygosity ranged from 0.099 ± 0.081 (FLH) to 0.152 ± 0.075 (FYAN). After jackknifing, the mean values were slightly lower. The increase in pairwise homozygosity tended to be twofold higher than the corresponding individual increase in homozygosity values. When compared with genealogical estimates, estimates of Ne obtained using FYAN tended to have low root-mean-squared errors. However, Ne estimates based on increases in pairwise homozygosity using both FROH and FHRR estimates of genomic inbreeding had lower root-mean-squared errors. CONCLUSIONS Parameters characterizing homozygosity may not accurately depict losses of variability in small populations in which breeding policy prohibits matings between close relatives. After BP adjustment, the performance of FROH and FHRR was highly consistent. Assuming that an increase in homozygosity depends only on pedigree depth can lead to underestimating it in populations with shallow pedigrees. An increase in pairwise homozygosity computed from either FROH or FHRR is a promising approach for characterizing autozygosity.
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Affiliation(s)
- Katherine D Arias
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394, Gijón, Spain.
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Ayalew W, Wu X, Tarekegn GM, Sisay Tessema T, Naboulsi R, Van Damme R, Bongcam-Rudloff E, Edea Z, Enquahone S, Yan P. Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation. Animals (Basel) 2023; 13:3269. [PMID: 37893993 PMCID: PMC10603685 DOI: 10.3390/ani13203269] [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: 09/01/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.
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Affiliation(s)
- Wondossen Ayalew
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Getinet Mekuriaw Tarekegn
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
- Scotland’s Rural College (SRUC), Roslin Institute Building, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tesfaye Sisay Tessema
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Rakan Naboulsi
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Tomtebodavägen 18A, 17177 Stockholm, Sweden
| | - Renaud Van Damme
- Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden; (R.V.D.); (E.B.-R.)
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Bioinformatics Section, Swedish University of Agricultural Sciences, P.O. Box 7023, S-750 07 Uppsala, Sweden; (R.V.D.); (E.B.-R.)
| | - Zewdu Edea
- Ethiopian Bio and Emerging Technology Institute, Addis Ababa P.O. Box 5954, Ethiopia;
| | - Solomon Enquahone
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (G.M.T.); (T.S.T.)
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
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18
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Yin S, Li Z, Yang F, Guo H, Zhao Q, Zhang Y, Yin Y, Wu X, He J. A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond. Int J Mol Sci 2023; 24:14550. [PMID: 37833998 PMCID: PMC10572203 DOI: 10.3390/ijms241914550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1-5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.
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Affiliation(s)
- Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Haimin Guo
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Qinghua Zhao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
| | - Yulong Yin
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
- Animal Nutrition Genome and Germplasm Innovation Research Center, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China
| | - Xiaolin Wu
- Council on Dairy Cattle Breeding, Bowie, MD 20716, USA
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
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Yin C, Wang Y, Zhou P, Shi H, Ma X, Yin Z, Liu Y. Genomic Scan for Runs of Homozygosity and Selective Signature Analysis to Identify Candidate Genes in Large White Pigs. Int J Mol Sci 2023; 24:12914. [PMID: 37629094 PMCID: PMC10454931 DOI: 10.3390/ijms241612914] [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: 06/28/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Large White pigs are extensively utilized in China for their remarkable characteristics of rapid growth and the high proportion of lean meat. The economic traits of pigs, comprising reproductive and meat quality traits, play a vital role in swine production. In this study, 2295 individuals, representing three different genetic backgrounds Large White pig populations were used: 500 from the Canadian line, 295 from the Danish line, and 1500 from the American line. The GeneSeek 50K GGP porcine HD array was employed to genotype the three pig populations. Firstly, genomic selective signature regions were identified using the pairwise fixation index (FST) and locus-specific branch length (LSBL). By applying a top 1% threshold for both parameters, a total of 888 candidate selective windows were identified, harbouring 1571 genes. Secondly, the investigation of regions of homozygosity (ROH) was performed utilizing the PLINK software. In total, 25 genomic regions exhibiting a high frequency of ROHs were detected, leading to the identification of 1216 genes. Finally, the identified potential functional genes from candidate genomic regions were annotated, and several important candidate genes associated with reproductive traits (ADCYAP1, U2, U6, CETN1, Thoc1, Usp14, GREB1L, FGF12) and meat quality traits (MiR-133, PLEKHO1, LPIN2, SHANK2, FLVCR1, MYL4, SFRP1, miR-486, MYH3, STYX) were identified. The findings of this study provide valuable insights into the genetic basis of economic traits in Large White pigs and may have potential use in future pig breeding programs.
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Affiliation(s)
- Chang Yin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Yuwei Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Peng Zhou
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Haoran Shi
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Xinyu Ma
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Yang Liu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (C.Y.); (Y.W.); (P.Z.); (H.S.); (X.M.)
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20
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Marchesini A, Silverj A, Torre S, Rota-Stabelli O, Girardi M, Passeri I, Fracasso I, Sebastiani F, Vernesi C. First genome-wide data from Italian European beech (Fagus sylvatica L.): Strong and ancient differentiation between Alps and Apennines. PLoS One 2023; 18:e0288986. [PMID: 37471380 PMCID: PMC10358878 DOI: 10.1371/journal.pone.0288986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 07/10/2023] [Indexed: 07/22/2023] Open
Abstract
The European beech (Fagus sylvatica L.) is one of the most widespread forest trees in Europe whose distribution and intraspecific diversity has been largely shaped by repeated glacial cycles. Previous studies, mainly based on palaeobotanical evidence and a limited set of chloroplast and nuclear genetic markers, highlighted a complex phylogeographic scenario, with southern and western Europe characterized by a rather heterogeneous genetic structure, as a result of recolonization from different glacial refugia. Despite its ecological and economic importance, the genome of this broad-leaved tree has only recently been assembled, and its intra-species genomic diversity is still largely unexplored. Here, we performed whole-genome resequencing of nine Italian beech individuals sampled from two stands located in the Alpine and Apennine mountain ranges. We investigated patterns of genetic diversity at chloroplast, mitochondrial and nuclear genomes and we used chloroplast genomes to reconstruct a temporally-resolved phylogeny. Results allowed us to test European beech differentiation on a whole-genome level and to accurately date their divergence time. Our results showed comparable, relatively high levels of genomic diversity in the two populations and highlighted a clear differentiation at chloroplast, mitochondrial and nuclear genomes. The molecular clock analysis indicated an ancient split between the Alpine and Apennine populations, occurred between the Günz and the Riss glaciations (approximately 660 kyrs ago), suggesting a long history of separation for the two gene pools. This information has important conservation implications in the context of adaptation to ongoing climate changes.
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Affiliation(s)
- Alexis Marchesini
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
- Research Institute on Terrestrial Ecosystems (IRET), The National Research Council of Italy (CNR), Porano (Terni), Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Andrea Silverj
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | - Sara Torre
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Omar Rota-Stabelli
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige, Italy
- Department CIBIO, University of Trento, Trento, Italy
- Plant Protection Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
| | - Matteo Girardi
- Conservation Genomics Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
| | - Iacopo Passeri
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
- Faculty of Science and Technology, Free University of Bolzano-Bozen, Bolzano, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection (IPSP), The National Research Council of Italy (CNR), Sesto Fiorentino (Florence), Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, S. Michele all’Adige (Trento), Italy
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Perfilyeva A, Bespalova K, Bespalov S, Begmanova M, Kuzovleva Y, Vishnyakova O, Nazarenko I, Abylkassymova G, Perfilyeva Y, Plakhov K, Djansugurova L, Bekmanov B. Homozygosity mapping in the Kazakh national dog breed Tazy. Sci Rep 2023; 13:10735. [PMID: 37400480 DOI: 10.1038/s41598-023-37990-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023] Open
Abstract
The Tazy is a breed of sighthound common in Kazakhstan. The identification of runs of homozygosity (ROH) is an informative approach to assessing the history and possible patterns of directional selection pressure. To our knowledge, the present study is the first to provide an overview of the ROH pattern in the Tazy dogs from a genome-wide perspective. The ROH of the Tazy was found to be mainly composed of shorter segments (1-2 Mb), accounting for approximately 67% of the total ROH. The estimated ROH-based inbreeding coefficients (FROH) ranged from 0.028 to 0.058 with a mean of 0.057. Five genomic regions under positive selection were identified on chromosomes 18, 22, and 25. The regions on chromosomes 18 and 22 may be breed specific, while the region on chromosome 22 overlaps with regions of hunting traits in other hunting dog breeds. Among the 12 candidate genes located in these regions, the gene CAB39L may be a candidate that affects running speed and endurance of the Tazy dog. Eight genes could belong to an evolutionarily conserved complex as they were clustered in a large protein network with strong linkages. The results may enable effective interventions when incorporated into conservation planning and selection of the Tazy breed.
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Affiliation(s)
- Anastassiya Perfilyeva
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Kira Bespalova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan.
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, 050040, Almaty, Kazakhstan.
| | - Sergey Bespalov
- Department of Theriology, Institute of Zoology, 050060, Almaty, Kazakhstan
| | - Mamura Begmanova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Yelena Kuzovleva
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Olga Vishnyakova
- Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", 050008, Almaty, Kazakhstan
| | - Inna Nazarenko
- Republican Federation of Public Associations of Hunters and Hunting Societies "Kansonar", 020000, Astana, Kazakhstan
| | - Gulnar Abylkassymova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Yuliya Perfilyeva
- Laboratory of Molecular Immunology and Immunobiotechnology, M.A. Aitkhozhin's Institute of Molecular Biology and Biochemistry, 050012, Almaty, Kazakhstan
| | - Konstantin Plakhov
- Laboratory of Biocenology and Hunting Management, Institute of Zoology, 050060, Almaty, Kazakhstan
| | - Leyla Djansugurova
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
| | - Bakhytzhan Bekmanov
- Department of Molecular Genetics, Institute of Genetics and Physiology, 050060, Almaty, Kazakhstan
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, 050040, Almaty, Kazakhstan
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22
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Chen C, Zhu B, Tang X, Chen B, Liu M, Gao N, Li S, Gu J. Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide. Genes (Basel) 2023; 14:1211. [PMID: 37372391 DOI: 10.3390/genes14061211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had varying degrees of impact on various horse breeds. However, recent inbreeding events were uncommon, particularly among indigenous horse breeds. Consequently, the ROH-based genomic inbreeding coefficient could aid in monitoring the level of inbreeding. Using the Thoroughbred population as a case study, we discovered 24 ROH islands containing 72 candidate genes associated with artificial selection traits. We found that the candidate genes in Thoroughbreds were involved in neurotransmission (CHRNA6, PRKN, and GRM1), muscle development (ADAMTS15 and QKI), positive regulation of heart rate and heart contraction (HEY2 and TRDN), regulation of insulin secretion (CACNA1S, KCNMB2, and KCNMB3), and spermatogenesis (JAM3, PACRG, and SPATA6L). Our findings provide insight into horse breed characteristics and future breeding strategies.
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Affiliation(s)
- Chujie Chen
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bo Zhu
- Novogene Bioinformatics Institute, Beijing 100015, China
| | - Xiangwei Tang
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bin Chen
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Mei Liu
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Ning Gao
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Sheng Li
- Maxun Biotechnology Institute, Changsha 410024, China
| | - Jingjing Gu
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
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23
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Abdoli R, Mirhoseini SZ, Ghavi Hossein-Zadeh N, Zamani P, Moradi MH, Ferdosi MH, Sargolzaei M, Gondro C. Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep. Heredity (Edinb) 2023; 130:358-367. [PMID: 37016136 PMCID: PMC10238534 DOI: 10.1038/s41437-023-00611-y] [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: 12/03/2021] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.
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Affiliation(s)
- Ramin Abdoli
- Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Gilan, Iran.
| | - Seyed Ziaeddin Mirhoseini
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran.
| | - Navid Ghavi Hossein-Zadeh
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran
| | - Pouya Zamani
- Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, 65178-33131, Iran
| | - Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arāk, 38156-8-8349, Iran
| | - Mohammad Hossein Ferdosi
- AGBU, a joint venture of NSW Department of Primary Industries and University of New England, University of New England, Armidale, NSW, 2351, Australia
| | - Mehdi Sargolzaei
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada
| | - Cedric Gondro
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, 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: 6] [Impact Index Per Article: 6.0] [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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25
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Rocha RDFB, Garcia AO, Otto PI, da Silva MVB, Martins MF, Machado MA, Panetto JCDC, Guimarães SEF. Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle. Mamm Genome 2023:10.1007/s00335-023-09989-w. [PMID: 37000236 DOI: 10.1007/s00335-023-09989-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/11/2023] [Indexed: 04/01/2023]
Abstract
Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (FROH) and pedigree-based inbreeding (Fped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH1-2Mb: 58.17%), representing ancient inbreeding, ROH2-4Mb (22.74%), ROH4-8Mb (11.34%), ROH8-16Mb (5.51%), and ROH>16Mb (2.24%). Combining our results, we conclude that the increase in general FROH and Fped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with FROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.
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Affiliation(s)
| | | | - Pamela Itajara Otto
- Department of Animal Science, Universidade Federal de Santa Maria, Santa Maria, Rio Grande Do Sul, Brazil
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26
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Dash S, Singh A, Dixit SP, Kumar A, Behera R. Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India. Trop Anim Health Prod 2023; 55:129. [PMID: 36952060 DOI: 10.1007/s11250-023-03534-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Abstract
The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (n = 19), Tharparkar (n = 17), and Gir (n = 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (FROH) revealed that Gir had the highest FROH (0.099) proposing more inbreeding rate in this population. Effective population size (Ne) decreased slowly over the last 60 generations and at 13 generations ago; Ne was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (r = 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.
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Affiliation(s)
- Soumya Dash
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India.
- School of Crop Health Policy Support Research, ICAR-National Institute of Biotic Stress Management, Raipur, 493225, Chhattisgarh, India.
| | - Avtar Singh
- Animal Genetics and Breeding Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S P Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Avnish Kumar
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Rajalaxmi Behera
- Regional Centre, ICAR-Directorate of Poultry Research, Bhubaneswar, 751003, Odisha, India
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The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India. Genes Genomics 2023; 45:813-825. [PMID: 36807878 DOI: 10.1007/s13258-023-01367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. OBJECTIVE The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. METHODS For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). RESULTS A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. CONCLUSIONS This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.
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Abumadini MS, Al Ghamdi KS, Alqahtani AH, Almedallah DK, Callans L, Jarad JA, Cyrus C, Koeleman BPC, Keating BJ, Pankratz N, Al-Ali AK. Genome-wide copy number variant screening of Saudi schizophrenia patients reveals larger deletions in cases versus controls. Front Mol Neurosci 2023; 16:1069375. [PMID: 36846569 PMCID: PMC9950097 DOI: 10.3389/fnmol.2023.1069375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
Introduction Genome-wide association studies have discovered common polymorphisms in regions associated with schizophrenia. No genome-wide analyses have been performed in Saudi schizophrenia subjects. Methods Genome-wide genotyping data from 136 Saudi schizophrenia cases and 97 Saudi controls in addition to 4,625 American were examined for copy number variants (CNVs). A hidden Markov model approach was used to call CNVs. Results CNVs in schizophrenia cases were twice as large on average than CNVs in controls (p = 0.04). The analyses focused on extremely large >250 kilobases CNVs or homozygous deletions of any size. One extremely large deletion was noted in a single case (16.5 megabases on chromosome 10). Two cases had an 814 kb duplication of chromosome 7 spanning a cluster of genes, including circadian-related loci, and two other cases had 277 kb deletions of chromosome 9 encompassing an olfactory receptors gene family. CNVs were also seen in loci previously associated with schizophrenia, namely a 16p11 proximal duplication and two 22q11.2 deletions. Discussion Runs of homozygosity (ROHs) were analyzed across the genome to investigate correlation with schizophrenia risk. While rates and sizes of these ROHs were similar in cases and controls, we identified 10 regions where multiple cases had ROHs and controls did not.
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Affiliation(s)
- Mahdi S. Abumadini
- Department of Psychiatry, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Kholoud S. Al Ghamdi
- Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdullah H. Alqahtani
- Department of Psychiatry, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Dana K. Almedallah
- Department of Psychiatry, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Lauren Callans
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, United States
| | - Jumanah A. Jarad
- Department of Psychiatry, King Fahd Hospital of the University, Al-Khobar and College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Cyril Cyrus
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Bobby P. C. Koeleman
- Department of Genetics, Division Lab, University Medical Center Utrecht, Utrecht, Netherlands
| | - Brendan J. Keating
- Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA, United States
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States
| | - Amein K. Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia,*Correspondence: Amein K. Al-Ali, ✉
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Yasmin T, Andres EM, Ashraf K, Basra MAR, Raza MH. Genome-wide analysis of runs of homozygosity in Pakistani controls with no history of speech or language-related developmental phenotypes. Ann Hum Biol 2023; 50:100-107. [PMID: 36786444 PMCID: PMC10284496 DOI: 10.1080/03014460.2023.2180087] [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: 08/03/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Runs of homozygosity (ROHs) analysis of controls provide a convenient resource to minimize the association of false positive results of disease-associated ROHs and genetic variants for simple and complex disorders in individuals from the same population. Evidence for the value of ROHs to speech or language-related traits is restricted due to the absence of population-matched behaviourally defined controls and limited family-based studies. AIM This study aims to identify common ROHs in the Pakistani population, focussing on the total length and frequency of ROHs of variable sizes, shared ROHs, and their genomic distribution. SUBJECTS AND METHODS We performed homozygosity analysis (in PLINK) of 86 individuals (39 males, 47 females) with no history of speech or language-related phenotypes (controls) who had been genotyped with the Illumina Infinium QC Array-24. RESULTS ROHs of 1-<4 megabases (Mb) were frequent in unrelated individuals. We observed ROHs over 20 Mb among six individuals. Over 30 percent of the identified ROHs were shared among several individuals, indicating consanguinity's effect on the Pakistani population. CONCLUSION Our findings serve as a foundation for family-based genetic studies of consanguineous families with speech or language-related disorders to ultimately narrow the homozygosity regions of interest to identify pathogenic variants.
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Affiliation(s)
- Tahira Yasmin
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Erin M. Andres
- Thompson Center for Autism & Neurodevelopment, University of Missouri, Columbia, MO, USA
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, 66045, USA
| | - Komal Ashraf
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Muhammad Asim Raza Basra
- Centre for Clinical and Nutritional Chemistry, School of Chemistry, University of The Punjab, Lahore, Pakistan
| | - Muhammad Hashim Raza
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, 66045, USA
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30
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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Martin CA, Sheppard EC, Illera JC, Suh A, Nadachowska-Brzyska K, Spurgin LG, Richardson DS. Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird. Mol Ecol 2023; 32:1972-1989. [PMID: 36704917 DOI: 10.1111/mec.16865] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations and drive speciation. Across island systems, contemporary patterns of genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow and genetic drift. Here, we investigate genome-wide diversity and the distribution of runs of homozygosity (ROH) using whole-genome resequencing of individuals (>22× coverage) from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii)-a passerine that has recently undergone island speciation. We show the most dramatic reduction in diversity occurs between the mainland sister species (the tawny pipit) and Berthelot's pipit and is lowest in the populations that have experienced sequential bottlenecks (i.e., the Madeiran and Selvagens populations). Pairwise sequential Markovian coalescent (PSMC) analyses estimated that Berthelot's pipit diverged from its sister species ~2 million years ago, with the Madeiran archipelago founded 50,000 years ago, and the Selvagens colonized 8000 years ago. We identify many long ROH (>1 Mb) in these most recently colonized populations. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). However, the extensive long and short ROH detected in the Selvagens suggest strong recent inbreeding and bottleneck effects, with as much as 38% of the autosomes consisting of ROH >250 kb. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | | | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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Lavanchy E, Goudet J. Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization. Mol Ecol Resour 2023; 23:787-802. [PMID: 36626297 DOI: 10.1111/1755-0998.13755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/22/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Genomic measures of inbreeding based on identical-by-descent (IBD) segments are increasingly used to measure inbreeding and mostly estimated on SNP arrays and whole-genome sequencing (WGS) data. However, some softwares recurrently used for their estimation assume that genomic positions which have not been genotyped are nonvariant. This might be true for WGS data, but not for reduced genomic representations and can lead to spurious IBD segments estimation. In this project, we simulated the outputs of WGS, two SNP arrays of different sizes and RAD-sequencing for three populations with different sizes and histories. We compare the results of IBD segments estimation with two softwares: runs of homozygosity (ROHs) estimated with PLINK and homozygous-by-descent (HBD) segments estimated with RZooRoH. We demonstrate that to obtain meaningful estimates of inbreeding, RZooRoH requires a SNPs density 11 times smaller compared to PLINK: ranks of inbreeding coefficients were conserved among individuals above 22 SNPs/Mb for PLINK and 2 SNPs/Mb for RZooRoH. We also show that in populations with simple demographic histories, distribution of ROHs and HBD segments are correctly estimated with both SNP arrays and WGS. PLINK correctly estimated distribution of ROHs with SNP densities above 22 SNPs/Mb, while RZooRoH correctly estimated distribution of HBD segments with SNPs densities above 11 SNPs/Mb. However, in a population with a more complex demographic history, RZooRoH resulted in better distribution of IBD segments estimation compared to PLINK even with WGS data. Consequently, we advise researchers to use either methods relying on excess homozygosity averaged across SNPs or model-based HBD segments calling methods for inbreeding estimations.
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Affiliation(s)
- Eléonore Lavanchy
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
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Falchi L, Cesarani A, Mastrangelo S, Senczuk G, Portolano B, Pilla F, Macciotta NPP. Analysis of runs of homozygosity of cattle living in different climate zones. J Anim Sci 2023; 101:skad061. [PMID: 36802370 PMCID: PMC10066727 DOI: 10.1093/jas/skad061] [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: 09/27/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.
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Affiliation(s)
- Laura Falchi
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, 07100 Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, 30602 Athens, USA
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy
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Cesarani A, Mastrangelo S, Congiu M, Portolano B, Gaspa G, Tolone M, Macciotta NPP. Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds. J Anim Breed Genet 2023; 140:28-38. [PMID: 36239218 PMCID: PMC10092622 DOI: 10.1111/jbg.12741] [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: 04/22/2022] [Accepted: 09/22/2022] [Indexed: 12/13/2022]
Abstract
The effects of inbreeding in livestock species breeds have been well documented and they have a negative impact on profitability. The objective of this study was to evaluate the levels of inbreeding in Sarda (SAR, n = 785) and Valle del Belice (VdB, n = 473) dairy sheep breeds and their impact on milk production traits. Two inbreeding coefficients (F) were estimated: using pedigree (FPED ), or runs of homozygosity (ROH; FROH ) at different minimum ROH lengths and different ROH classes. After the quality control, 38,779 single nucleotide polymorphisms remained for further analyses. A mixed-linear model was used to evaluate the impact of inbreeding coefficients on production traits within each breed. VdB showed higher inbreeding coefficients compared to SAR, with both breeds showing lower estimates as the minimum ROH length increased. Significant inbreeding depression was found only for milk yield, with a loss of around 7 g/day (for SAR) and 9 g/day (VdB) for a 1% increase of FROH . The present study confirms how the use of genomic information can be used to manage intra-breed diversity and to calculate the effects of inbreeding on phenotypic traits.
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Affiliation(s)
- Alberto Cesarani
- Dipartimento di Agraria, Università di Sassari, Sassari, Italy.,Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, USA
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Michele Congiu
- Dipartimento di Agraria, Università di Sassari, Sassari, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Giustino Gaspa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Grugliasco, Italy
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
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Ballan M, Schiavo G, Bovo S, Schiavitto M, Negrini R, Frabetti A, Fornasini D, Fontanesi L. Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds. Anim Genet 2022; 53:849-862. [PMID: 36073189 PMCID: PMC9826494 DOI: 10.1111/age.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/01/2022] [Accepted: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome.
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Affiliation(s)
- Mohamad Ballan
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Giuseppina Schiavo
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Samuele Bovo
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | - Michele Schiavitto
- Associazione Nazionale Coniglicoltori Italiani (ANCI), Contrada Giancola SncVolturara AppulaItaly
| | | | | | | | - Luca Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
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Rodriguez OL, Silver CA, Shields K, Smith ML, Watson CT. Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta, and beta loci. CELL GENOMICS 2022; 2:100228. [PMID: 36778049 PMCID: PMC9903726 DOI: 10.1016/j.xgen.2022.100228] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/25/2022] [Accepted: 11/05/2022] [Indexed: 12/02/2022]
Abstract
T cell receptors (TCRs) recognize peptide fragments presented by the major histocompatibility complex (MHC) and are critical to T cell-mediated immunity. Recent data have indicated that genetic diversity within TCR-encoding gene regions is underexplored, limiting understanding of the impact of TCR loci polymorphisms on TCR function in disease, even though TCR repertoire signatures (1) are heritable and (2) associate with disease phenotypes. To address this, we developed a targeted long-read sequencing approach to generate highly accurate haplotype resolved assemblies of the TCR beta (TRB) and alpha/delta (TRA/D) loci, facilitating the genotyping of all variant types, including structural variants. We validate our approach using two mother-father-child trios and 5 unrelated donors representing multiple populations. This resulted in improved genotyping accuracy and the discovery of 84 undocumented V, D, J, and C alleles, demonstrating the utility of this framework for improving our understanding of TCR diversity and function in disease.
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Affiliation(s)
- Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Catherine A. Silver
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa L. Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA,Corresponding author
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Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types. Animals (Basel) 2022; 12:ani12233293. [PMID: 36496815 PMCID: PMC9736150 DOI: 10.3390/ani12233293] [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: 09/28/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ROH islands, which may be signals of recent selection events. Eight to fourteen ROH islands were identified per breed, which spanned multiple genes. Many were involved in important horse breed characteristics, including WFIKNN2, CACNA1G, STXBP4, NOG, FAM184B, QDPR, LCORL, and the zinc finger protein family. Regions of the genome with zero ROH occurrences were also of major interest in specific populations. Depending on the breed, we detected between 2 to 57 no-ROH regions and identified 27 genes in these regions that were common for five breeds. These genes were involved in, e.g., muscle contractility (CACNA1A) and muscle development (miR-23, miR-24, miR-27). To sum up, the obtained results can be furthered analyzed in the topic of identification of markers unique for specific horse breed characteristics.
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Wang G, Wang F, Pei H, Li M, Bai F, Lei C, Dang R. Genome-wide analysis reveals selection signatures for body size and drought adaptation in Liangzhou donkey. Genomics 2022; 114:110476. [PMID: 36057425 DOI: 10.1016/j.ygeno.2022.110476] [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: 12/28/2021] [Revised: 07/21/2022] [Accepted: 08/12/2022] [Indexed: 01/14/2023]
Abstract
Liangzhou donkey is a domestic animal breed distributed on the edge of the Tengger Desert in Gansu Province of China. It has small body size and strong adaptability to dry environments. Here, we sequenced 10 Liangzhou donkey genomes and compared them to the 55 genomes of 8 representative donkey breeds worldwide. The population structure analysis revealed that Liangzhou donkey harboured the ancestry with the Asian domestic donkeys (0.863) and European domestic donkeys (0.137). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the genetic diversity in Liangzhou donkey. In addition, we analyzed the genetic basis of the small body size and drought adaptation of Liangzhou donkey by using Fst, θπ-ratio, XP-EHH, CLR and θπ methods. We found that the NCAPG-LCORL on chromosome 3 may be a candidate region for small body size trait of Liangzhou donkey. The CYP4A11 gene located on chromosome 5 showed strong sign of selection sweep. CYP4A11 can convert arachidonic acid into 19(S)-HETE, which can promote water reabsorption in renal tubule and enhance the ability of Liangzhou donkey to adapt to dry environment. These results contribute to a better understanding of the underlying population structure of Liangzhou donkeys and provides a valuable resource for future research on donkey breeding in response to climate change.
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Affiliation(s)
- Gang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Haoyu Pei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Mei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China
| | - Fuxia Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang 712100, Shaanxi Province, China.
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Bosse M, van Loon S. Challenges in quantifying genome erosion for conservation. Front Genet 2022; 13:960958. [PMID: 36226192 PMCID: PMC9549127 DOI: 10.3389/fgene.2022.960958] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.
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Affiliation(s)
- Mirte Bosse
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mirte Bosse,
| | - Sam van Loon
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Lozada-Soto EA, Tiezzi F, Jiang J, Cole JB, VanRaden PM, Maltecca C. Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle. J Dairy Sci 2022; 105:8956-8971. [PMID: 36153159 DOI: 10.3168/jds.2022-22116] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022]
Abstract
Maintaining a genetically diverse dairy cattle population is critical to preserving adaptability to future breeding goals and avoiding declines in fitness. This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle. We analyzed a sizable genomic data set containing 4,173,679 pedigreed and genotyped animals of the Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey breeds. Runs of homozygosity (ROH) of 2 Mb or longer in length were identified in each animal. The within-breed means for number and the combined length of ROH were highest in Jerseys (62.66 ± 8.29 ROH and 426.24 ± 83.40 Mb, respectively; mean ± SD) and lowest in Ayrshires (37.24 ± 8.27 ROH and 265.05 ± 85.00 Mb, respectively). Short ROH were the most abundant, but moderate to large ROH made up the largest proportion of genome autozygosity in all breeds. In addition, we identified ROH islands in each breed. This revealed selection patterns for milk production, productive life, health, and reproduction in most breeds and evidence for parallel selective pressure for loci on chromosome 6 between Ayrshire and Brown Swiss and for loci on chromosome 20 between Holstein and Jersey. We calculated inbreeding coefficients using 3 different approaches, pedigree-based (FPED), marker-based using a genomic relationship matrix (FGRM), and segment-based using ROH (FROH). The average inbreeding coefficient ranged from 0.06 in Ayrshires and Brown Swiss to 0.08 in Jerseys and Holsteins using FPED, from 0.22 in Holsteins to 0.29 in Guernsey and Jerseys using FGRM, and from 0.11 in Ayrshires to 0.17 in Jerseys using FROH. In addition, the effective population size at past generations (5-100 generations ago), the yearly rate of inbreeding, and the effective population size in 3 recent periods (2000-2009, 2010-2014, and 2015-2018) were determined in each breed to ascertain current and historical trends of genetic diversity. We found a historical trend of decreasing effective population size in the last 100 generations in all breeds and breed differences in the effect of the recent implementation of genomic selection on inbreeding accumulation.
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Affiliation(s)
| | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, 50144 Florence, Italy
| | - Jicai Jiang
- Department of Animal Science, North Carolina State University, Raleigh 27607
| | | | - Paul M VanRaden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh 27607
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Wu X, Zhou R, Wang Y, Zhang W, Zheng X, Zhao G, Zhang X, Yin Z, Ding Y. Genome‐wide scan for runs of homozygosity in Asian wild boars and Anqing six‐end‐white pigs. Anim Genet 2022; 53:867-871. [DOI: 10.1111/age.13250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/26/2022] [Accepted: 08/02/2022] [Indexed: 01/28/2023]
Affiliation(s)
- Xudong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Ren Zhou
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Yuanlang Wang
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Wei Zhang
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Xianrui Zheng
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Guiying Zhao
- College of Animal Science and Technology Yunnan Agricultural University Kunming China
| | - Xiaodong Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Zongjun Yin
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Yueyun Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
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Krepischi ACV, Villela D, da Costa SS, Mazzonetto PC, Schauren J, Migliavacca MP, Milanezi F, Santos JG, Guida G, Guarischi-Sousa R, Campana G, Kok F, Schlesinger D, Kitajima JP, Campagnari F, Bertola DR, Vianna-Morgante AM, Pearson PL, Rosenberg C. Chromosomal microarray analyses from 5778 patients with neurodevelopmental disorders and congenital anomalies in Brazil. Sci Rep 2022; 12:15184. [PMID: 36071085 PMCID: PMC9452501 DOI: 10.1038/s41598-022-19274-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
Chromosomal microarray analysis (CMA) has been recommended and practiced routinely since 2010 both in the USA and Europe as the first-tier cytogenetic test for patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies. However, in Brazil, the use of CMA is still limited, due to its high cost and complexity in integrating the results from both the private and public health systems. Although Brazil has one of the world’s largest single-payer public healthcare systems, nearly all patients referred for CMA come from the private sector, resulting in only a small number of CMA studies in Brazilian cohorts. To date, this study is by far the largest Brazilian cohort (n = 5788) studied by CMA and is derived from a joint collaboration formed by the University of São Paulo and three private genetic diagnostic centers to investigate the genetic bases of neurodevelopmental disorders and congenital abnormalities. We identified 2,279 clinically relevant CNVs in 1886 patients, not including the 26 cases of UPD found. Among detected CNVs, the corresponding frequency of each category was 55.6% Pathogenic, 4.4% Likely Pathogenic and 40% VUS. The diagnostic yield, by taking into account Pathogenic, Likely Pathogenic and UPDs, was 19.7%. Since the rational for the classification is mostly based on Mendelian or highly penetrant variants, it was not surprising that a second event was detected in 26% of those cases of predisposition syndromes. Although it is common practice to investigate the inheritance of VUS in most laboratories around the world to determine the inheritance of the variant, our results indicate an extremely low cost–benefit of this approach, and strongly suggest that in cases of a limited budget, investigation of the parents of VUS carriers using CMA should not be prioritized.
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Affiliation(s)
- Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Rua do Matão 277, São Paulo, ZIP Code 05508-090, Brazil.,Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Silvia Souza da Costa
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Rua do Matão 277, São Paulo, ZIP Code 05508-090, Brazil
| | | | | | | | | | | | - Gustavo Guida
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | | | | | | | | | | | - Debora R Bertola
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Rua do Matão 277, São Paulo, ZIP Code 05508-090, Brazil.,Instituto da Criança Do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Angela M Vianna-Morgante
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Rua do Matão 277, São Paulo, ZIP Code 05508-090, Brazil
| | - Peter L Pearson
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Rua do Matão 277, São Paulo, ZIP Code 05508-090, Brazil
| | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, Rua do Matão 277, São Paulo, ZIP Code 05508-090, Brazil. .,Diagnósticos da América S.A., DASA, São Paulo, Brazil.
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Genomic inbreeding and runs of homozygosity analysis of indigenous cattle populations in southern China. PLoS One 2022; 17:e0271718. [PMID: 36006904 PMCID: PMC9409551 DOI: 10.1371/journal.pone.0271718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous segments from the common ancestor of parents. Evaluating ROH pattern can help to understand inbreeding level and genetic basis of important traits. In this study, three representative cattle populations including Leiqiong cattle (LQC), Lufeng cattle (LFC) and Hainan cattle (HNC) were genotyped using the Illumina BovineHD SNPs array (770K) to assess ROH pattern at genome wide level. Totally, we identified 26,537 ROH with an average of 153 ROH per individual. The sizes of ROH ranged from 0.5 to 53.26Mb, and the average length was 1.03Mb. The average of FROH ranged from 0.10 (LQC) to 0.15 (HNC). Moreover, we identified 34 ROH islands (with frequency > 0.5) across genome. Based on these regions, we observed several breed-specific candidate genes related to adaptive traits. Several common genes related to immunity (TMEM173, MZB1 and SIL1), and heat stress (DNAJC18) were identified in all three populations. Three genes related to immunity (UGP2), development (PURA) and reproduction (VPS54) were detected in both HNC and LQC. Notably, we identified several breed-specific genes related to sperm development (BRDT and SPAG6) and heat stress (TAF7) in HNC, and immunity (CDC23 and NME5) and development (WNT87) in LFC. Our findings provided valuable insights into understanding the genomic homozygosity pattern and promoting the conservation of genetic resources of Chinese indigenous cattle.
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Chokoe TC, Hadebe K, Muchadeyi FC, Nephawe KA, Dzomba EF, Mphahlele TD, Matelele TC, Mtileni BJ. Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker. Front Genet 2022; 13:909472. [PMID: 36017496 PMCID: PMC9395594 DOI: 10.3389/fgene.2022.909472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.
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Affiliation(s)
- T. C. Chokoe
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
- School of Agriculture & Environmental Sciences, University of Limpopo, Polokwane, South Africa
- *Correspondence: T. C. Chokoe,
| | - K. Hadebe
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - F. C. Muchadeyi
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - K. A. Nephawe
- Department of Animal Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - E. F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of Kwazulu-Natal, Scottsville, South African
| | - T. D. Mphahlele
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - T. C. Matelele
- Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - B. J. Mtileni
- Department of Animal Sciences, Tshwane University of Technology, Pretoria, South Africa
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Berghöfer J, Khaveh N, Mundlos S, Metzger J. Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs. BMC Genomics 2022; 23:564. [PMID: 35933356 PMCID: PMC9357325 DOI: 10.1186/s12864-022-08801-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Past selection events left footprints in the genome of domestic animals, which can be traced back by stretches of homozygous genotypes, designated as runs of homozygosity (ROHs). The analysis of common ROH regions within groups or populations displaying potential signatures of selection requires high-quality SNP data as well as carefully adjusted ROH-defining parameters. In this study, we used a simultaneous testing of rule- and model-based approaches to perform strategic ROH calling in genomic data from different pig populations to detect genomic regions under selection for specific phenotypes. RESULTS Our ROH analysis using a rule-based approach offered by PLINK, as well as a model-based approach run by RZooRoH demonstrated a high efficiency of both methods. It underlined the importance of providing a high-quality SNP set as input as well as adjusting parameters based on dataset and population for ROH calling. Particularly, ROHs ≤ 20 kb were called in a high frequency by both tools, but to some extent covered different gene sets in subsequent analysis of ROH regions common for investigated pig groups. Phenotype associated ROH analysis resulted in regions under potential selection characterizing heritage pig breeds, known to harbour a long-established breeding history. In particular, the selection focus on fitness-related traits was underlined by various ROHs harbouring disease resistance or tolerance-associated genes. Moreover, we identified potential selection signatures associated with ear morphology, which confirmed known candidate genes as well as uncovered a missense mutation in the ABCA6 gene potentially supporting ear cartilage formation. CONCLUSIONS The results of this study highlight the strengths and unique features of rule- and model-based approaches as well as demonstrate their potential for ROH analysis in animal populations. We provide a workflow for ROH detection, evaluating the major steps from filtering for high-quality SNP sets to intersecting ROH regions. Formula-based estimations defining ROHs for rule-based method show its limits, particularly for efficient detection of smaller ROHs. Moreover, we emphasize the role of ROH detection for the identification of potential footprints of selection in pigs, displaying their breed-specific characteristics or favourable phenotypes.
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Affiliation(s)
- Jan Berghöfer
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Nadia Khaveh
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Stefan Mundlos
- Research Group Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Charité-Universitätsmedizin Berlin, BCRT, Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Julia Metzger
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany.
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Toro-Ospina AM, Herrera Rios AC, Pimenta Schettini G, Vallejo Aristizabal VH, Bizarria dos Santos W, Zapata CA, Ortiz Morea EG. Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia). Genes (Basel) 2022; 13:genes13071232. [PMID: 35886015 PMCID: PMC9318017 DOI: 10.3390/genes13071232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.
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Affiliation(s)
- Alejandra M. Toro-Ospina
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Correspondence:
| | - Ana C. Herrera Rios
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Science and Humanities Faculty, Digital University Institute of Antioquia, IUDigital, Medellin, Antioquia 50010, Colombia
| | - Gustavo Pimenta Schettini
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA;
| | - Viviana H. Vallejo Aristizabal
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Wellington Bizarria dos Santos
- School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, Sao Paulo 14884-900, Brazil;
| | - Cesar A. Zapata
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Edna Gicela Ortiz Morea
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
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Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle. Animals (Basel) 2022; 12:ani12121546. [PMID: 35739882 PMCID: PMC9219517 DOI: 10.3390/ani12121546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 12/01/2022] Open
Abstract
In this study, runs of homozygosity (ROH) and quantitative trait locus/association (QTL) for semen parameters in selected Chinese and South African beef cattle breed were estimated. The computed results showed 7516 ROH were observed between classes 0−5 Mb with no ROH observed in classes >40 Mb. Distribution of ROH showed high level of genomic coverage for ANG, NGU, CSI, and BEL breeds. Approximately 13 genomic regions with QTL were controlling sperm motility, sperm concentration, semen volume, sperm count, sperm head abnormalities, sperm tail abnormalities, sperm integrity, and percentage of abnormal sperm traits. Nine candidate genes, CDF9, MARCH1, WDR19, SLOICI, ST7, DOP1B, CFAF9, INHBA, and ADAMTS1, were suggested to be associated with above mentioned QTL traits. The results for inbreeding coefficient showed moderate correlation between FROH vs FHOM at 0.603 and high correlation between FROH 0−5 Mb 0.929, and lowest correlation for 0−>40 Mb 0.400. This study suggested recent inbreeding in CSI, BEL, ANG, BON, SIM, and NGU breeds. Furthermore, it highlighted varied inbreeding levels and identified QTL for semen traits and genes of association. These results can assist in implementation of genetic improvement strategies for bulls and provide awareness and proper guidelines in developing breeding programs.
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Kumar H, Panigrahi M, Panwar A, Rajawat D, Nayak SS, Saravanan KA, Kaisa K, Parida S, Bhushan B, Dutt T. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. J Comput Biol 2022; 29:943-960. [PMID: 35639362 DOI: 10.1089/cmb.2021.0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.
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Affiliation(s)
- Harshit Kumar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Anuradha Panwar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Divya Rajawat
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Sonali Sonejita Nayak
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - K A Saravanan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Kaiho Kaisa
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Subhashree Parida
- Divisions of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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Jiang Y, Li X, Liu J, Zhang W, Zhou M, Wang J, Liu L, Su S, Zhao F, Chen H, Wang C. Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data. BMC Genomics 2022; 23:373. [PMID: 35581549 PMCID: PMC9115978 DOI: 10.1186/s12864-022-08583-9] [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: 11/18/2021] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Background Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (FROH) and homozygosity (FHOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein. Results The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10–20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. FROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, FROH and FHOM values were highly correlated (0.952–0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits. Conclusion Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08583-9.
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Affiliation(s)
- Yao Jiang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaojin Li
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jiali Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Zhang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Mei Zhou
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jieru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Linqing Liu
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Shiguang Su
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongquan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Chonglong Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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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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