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Miao J, Wei X, Cao C, Sun J, Xu Y, Zhang Z, Wang Q, Pan Y, Wang Z. Pig pangenome graph reveals functional features of non-reference sequences. J Anim Sci Biotechnol 2024; 15:32. [PMID: 38389084 PMCID: PMC10882747 DOI: 10.1186/s40104-023-00984-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied. RESULTS In this study, we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb. Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome. Furthermore, we observed that NRSs were rarely found within coding sequences, while NRS insertions were enriched in immune-related Gene Ontology terms. Notably, our investigation also unveiled a close association between novel genes and the immune capacity of pigs. We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs, and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X. Additionally, we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in Southern Chinese pigs. CONCLUSIONS Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.
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Affiliation(s)
- Jian Miao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xingyu Wei
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Caiyun Cao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jiabao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yuejin Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China.
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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2
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Woolley SA, Salavati M, Clark EL. Recent advances in the genomic resources for sheep. Mamm Genome 2023; 34:545-558. [PMID: 37752302 PMCID: PMC10627984 DOI: 10.1007/s00335-023-10018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.
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Affiliation(s)
- Shernae A Woolley
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Mazdak Salavati
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Scotland's Rural College, Parkgate, Barony Campus, Dumfries, DG1 3NE, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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3
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Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. Genomic insights into the conservation of wild and domestic animal diversity: A review. Gene 2023; 886:147719. [PMID: 37597708 DOI: 10.1016/j.gene.2023.147719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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4
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Gao G, Zhang H, Ni J, Zhao X, Zhang K, Wang J, Kong X, Wang Q. Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis. J Anim Sci Biotechnol 2023; 14:150. [PMID: 38001525 PMCID: PMC10675864 DOI: 10.1186/s40104-023-00944-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/06/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Domestic goose breeds are descended from either the Swan goose (Anser cygnoides) or the Greylag goose (Anser anser), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates a thorough identification of genetic variations, thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability. RESULTS To comprehensively facilitate population genomic and pan-genomic analyses in geese, we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples. By constructing the pan-genome for geese, we generated non-reference contigs totaling 612 Mb, unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes, 1,324 softcore genes, 2,734 shell genes, and 878 cloud genes in goose genomes. Furthermore, we detected an 81.97 Mb genomic region showing signs of genome selection, encompassing the TGFBR2 gene correlated with variations in body weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) and presence-absence variation revealed significant genomic associations with various goose meat quality, reproductive, and body composition traits. For instance, a gene encoding the SVEP1 protein was linked to carcass oblique length, and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length. Notably, the pan-genome analysis revealed enrichment of variable genes in the "hair follicle maturation" Gene Ontology term, potentially linked to the selection of feather-related traits in geese. A gene presence-absence variation analysis suggested a reduced frequency of genes associated with "regulation of heart contraction" in domesticated geese compared to their wild counterparts. Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation. CONCLUSION This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits, thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome, establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.
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Affiliation(s)
- Guangliang Gao
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Hongmei Zhang
- Department of Cardiovascular Ultrasound and Non-Invasive Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital,University of Electronic Science and Technology of China, Chengdu, 611731, China
- Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Jiangping Ni
- JiguangGene Biotechnology Co., Ltd., Nanjing, 210032, China
| | - Xianzhi Zhao
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Keshan Zhang
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Jian Wang
- Jiangsu Agri-Animal Vocational College, Taizhou, 225300, China
| | - Xiangdong Kong
- JiguangGene Biotechnology Co., Ltd., Nanjing, 210032, China.
| | - Qigui Wang
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China.
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China.
- Present Address: Poultry Science Institute, Chongqing Academy of Animal Science, No. 51 Changzhou Avenue, Rongchang District, Chongqing, 402460, P. R. China.
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5
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Bhati M, Mapel XM, Lloret-Villas A, Pausch H. Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue. Genetics 2023; 225:iyad161. [PMID: 37655920 PMCID: PMC10627265 DOI: 10.1093/genetics/iyad161] [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: 06/05/2023] [Revised: 06/05/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023] Open
Abstract
Structural variants (SVs) and short tandem repeats (STRs) are significant sources of genetic variation. However, the impacts of these variants on gene regulation have not been investigated in cattle. Here, we genotyped and characterized 19,408 SVs and 374,821 STRs in 183 bovine genomes and investigated their impact on molecular phenotypes derived from testis transcriptomes. We found that 71% STRs were multiallelic. The vast majority (95%) of STRs and SVs were in intergenic and intronic regions. Only 37% SVs and 40% STRs were in high linkage disequilibrium (LD) (R2 > 0.8) with surrounding SNPs/insertions and deletions (Indels), indicating that SNP-based association testing and genomic prediction are blind to a nonnegligible portion of genetic variation. We showed that both SVs and STRs were more than 2-fold enriched among expression and splicing QTL (e/sQTL) relative to SNPs/Indels and were often associated with differential expression and splicing of multiple genes. Deletions and duplications had larger impacts on splicing and expression than any other type of SV. Exonic duplications predominantly increased gene expression either through alternative splicing or other mechanisms, whereas expression- and splicing-associated STRs primarily resided in intronic regions and exhibited bimodal effects on the molecular phenotypes investigated. Most e/sQTL resided within 100 kb of the affected genes or splicing junctions. We pinpoint candidate causal STRs and SVs associated with the expression of SLC13A4 and TTC7B and alternative splicing of a lncRNA and CAPP1. We provide a catalog of STRs and SVs for taurine cattle and show that these variants contribute substantially to gene expression and splicing variation.
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Affiliation(s)
- Meenu Bhati
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Xena Marie Mapel
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | | | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
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6
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Neumann GB, Korkuć P, Reißmann M, Wolf MJ, May K, König S, Brockmann GA. Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle. Vet Res 2023; 54:95. [PMID: 37853447 PMCID: PMC10585868 DOI: 10.1186/s13567-023-01227-0] [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: 03/02/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.
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Affiliation(s)
- Guilherme B Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Monika Reißmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Manuel J Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
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7
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Xia X, Zhang F, Li S, Luo X, Peng L, Dong Z, Pausch H, Leonard AS, Crysnanto D, Wang S, Tong B, Lenstra JA, Han J, Li F, Xu T, Gu L, Jin L, Dang R, Huang Y, Lan X, Ren G, Wang Y, Gao Y, Ma Z, Cheng H, Ma Y, Chen H, Pang W, Lei C, Chen N. Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment. Genome Biol 2023; 24:211. [PMID: 37723525 PMCID: PMC10507960 DOI: 10.1186/s13059-023-03052-2] [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: 07/21/2022] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle. RESULTS In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a "north-south" gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle. CONCLUSIONS Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance.
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Affiliation(s)
- Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Shuang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Lixin Peng
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, China
| | - Zheng Dong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Bin Tong
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, China
| | - Fuyong Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Tieshan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Liangliang Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, 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, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Gang Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Yuanpeng Gao
- College of Veterinary Medicine, Northwest A&F University, Xianyang, Yangling, China
| | - Zhijie Ma
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China
| | - Weijun Pang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, 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, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, China.
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8
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Yang Z, Guarracino A, Biggs PJ, Black MA, Ismail N, Wold JR, Merriman TR, Prins P, Garrison E, de Ligt J. Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads. Front Genet 2023; 14:1225248. [PMID: 37636268 PMCID: PMC10448961 DOI: 10.3389/fgene.2023.1225248] [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: 05/19/2023] [Accepted: 08/01/2023] [Indexed: 08/29/2023] Open
Abstract
Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications.
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Affiliation(s)
- Zuyu Yang
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Patrick J. Biggs
- Molecular Biosciences Group, School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Public Health Laboratory, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Michael A. Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nuzla Ismail
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Jana Renee Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Tony R. Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Joep de Ligt
- Institute of Environmental Science and Research, Porirua, New Zealand
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9
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Salavati M, Clark R, Becker D, Kühn C, Plastow G, Dupont S, Moreira GCM, Charlier C, Clark EL. Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing. G3 (BETHESDA, MD.) 2023; 13:jkad108. [PMID: 37216666 PMCID: PMC10411599 DOI: 10.1093/g3journal/jkad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 02/27/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023]
Abstract
Understanding the genomic control of tissue-specific gene expression and regulation can help to inform the application of genomic technologies in farm animal breeding programs. The fine mapping of promoters [transcription start sites (TSS)] and enhancers (divergent amplifying segments of the genome local to TSS) in different populations of cattle across a wide diversity of tissues provides information to locate and understand the genomic drivers of breed- and tissue-specific characteristics. To this aim, we used Cap Analysis Gene Expression (CAGE) sequencing, of 24 different tissues from 3 populations of cattle, to define TSS and their coexpressed short-range enhancers (<1 kb) in the ARS-UCD1.2_Btau5.0.1Y reference genome (1000bulls run9) and analyzed tissue and population specificity of expressed promoters. We identified 51,295 TSS and 2,328 TSS-Enhancer regions shared across the 3 populations (dairy, beef-dairy cross, and Canadian Kinsella composite cattle from 2 individuals, 1 of each sex, per population). Cross-species comparative analysis of CAGE data from 7 other species, including sheep, revealed a set of TSS and TSS-Enhancers that were specific to cattle. The CAGE data set will be combined with other transcriptomic information for the same tissues to create a new high-resolution map of transcript diversity across tissues and populations in cattle for the BovReg project. Here we provide the CAGE data set and annotation tracks for TSS and TSS-Enhancers in the cattle genome. This new annotation information will improve our understanding of the drivers of gene expression and regulation in cattle and help to inform the application of genomic technologies in breeding programs.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Richard Clark
- Edinburgh Clinical Research Facility, Genetics Core, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Doreen Becker
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf 18196, Germany
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf 18196, Germany
- Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock 18059, Germany
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton T6G 2H1, Canada
| | - Sébastien Dupont
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège 4000, Belgium
| | | | - Carole Charlier
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège 4000, Belgium
- Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
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10
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Dai X, Bian P, Hu D, Luo F, Huang Y, Jiao S, Wang X, Gong M, Li R, Cai Y, Wen J, Yang Q, Deng W, Nanaei HA, Wang Y, Wang F, Zhang Z, Rosen BD, Heller R, Jiang Y. A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species. Genome Res 2023; 33:1284-1298. [PMID: 37714713 PMCID: PMC10547261 DOI: 10.1101/gr.277481.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/30/2023] [Indexed: 09/17/2023]
Abstract
Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.
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Affiliation(s)
- Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dexiang Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Funong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shaohua Jiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mian Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiayue Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qimeng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran 1983969412, Iran
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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11
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Smith TPL, Bickhart DM, Boichard D, Chamberlain AJ, Djikeng A, Jiang Y, Low WY, Pausch H, Demyda-Peyrás S, Prendergast J, Schnabel RD, Rosen BD. The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biol 2023; 24:139. [PMID: 37337218 DOI: 10.1186/s13059-023-02975-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/19/2023] [Indexed: 06/21/2023] Open
Abstract
The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-agreed pangenome representation to replace breed-specific reference assemblies for cattle genomics. The BPC invites partners sharing our vision to participate in the production of these assemblies and the development of a common, community-approved, pangenome reference as a public resource for the research community ( https://bovinepangenome.github.io/ ). This community-driven resource will provide the context for comparison between studies and the future foundation for cattle genomic selection.
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Affiliation(s)
- Timothy P L Smith
- US Meat Animal Research Center, USDA-ARS, Clay Center, NE, 68933, USA
| | | | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, ILRI Kenya, Nairobi, 30709-00100, Kenya
- Centre for Tropical Livestock Genetics and Health, Easter Bush, Midlothian, EH25 9RG, UK
| | - Yu Jiang
- Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling, 712100, China
| | - Wai Y Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Sebastian Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, 1900, La Plata, Argentina
- Consejo Superior de Investigaciones Científicas Y Tecnológicas (CONICET), CCT-La Plata, 1900, La Plata, Argentina
| | - James Prendergast
- Centre for Tropical Livestock Genetics and Health, Easter Bush, Midlothian, EH25 9RG, UK
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
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12
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Leonard AS, Crysnanto D, Mapel XM, Bhati M, Pausch H. Graph construction method impacts variation representation and analyses in a bovine super-pangenome. Genome Biol 2023; 24:124. [PMID: 37217946 PMCID: PMC10204317 DOI: 10.1186/s13059-023-02969-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown. RESULTS We create multi-species super-pangenomes using pggb, cactus, and minigraph with the Bos taurus taurus reference sequence and eleven haplotype-resolved assemblies from taurine and indicine cattle, bison, yak, and gaur. We recover 221 k nonredundant structural variations (SVs) from the pangenomes, of which 135 k (61%) are common to all three. SVs derived from assembly-based calling show high agreement with the consensus calls from the pangenomes (96%), but validate only a small proportion of variations private to each graph. Pggb and cactus, which also incorporate base-level variation, have approximately 95% exact matches with assembly-derived small variant calls, which significantly improves the edit rate when realigning assemblies compared to minigraph. We use the three pangenomes to investigate 9566 variable number tandem repeats (VNTRs), finding 63% have identical predicted repeat counts in the three graphs, while minigraph can over or underestimate the count given its approximate coordinate system. We examine a highly variable VNTR locus and show that repeat unit copy number impacts the expression of proximal genes and non-coding RNA. CONCLUSIONS Our findings indicate good consensus between the three pangenome methods but also show their individual strengths and weaknesses that need to be considered when analysing different types of variants from multiple input assemblies.
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Affiliation(s)
- Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Xena M Mapel
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Meenu Bhati
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.
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13
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Powell J, Talenti A, Fisch A, Hemmink JD, Paxton E, Toye P, Santos I, Ferreira BR, Connelley TK, Morrison LJ, Prendergast JGD. Profiling the immune epigenome across global cattle breeds. Genome Biol 2023; 24:127. [PMID: 37218021 DOI: 10.1186/s13059-023-02964-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Understanding the variation between well and poorly adapted cattle breeds to local environments and pathogens is essential for breeding cattle with improved climate and disease-resistant phenotypes. Although considerable progress has been made towards identifying genetic differences between breeds, variation at the epigenetic and chromatin levels remains poorly characterized. Here, we generate, sequence and analyse over 150 libraries at base-pair resolution to explore the dynamics of DNA methylation and chromatin accessibility of the bovine immune system across three distinct cattle lineages. RESULTS We find extensive epigenetic divergence between the taurine and indicine cattle breeds across immune cell types, which is linked to the levels of local DNA sequence divergence between the two cattle sub-species. The unique cell type profiles enable the deconvolution of complex cellular mixtures using digital cytometry approaches. Finally, we show distinct sub-categories of CpG islands based on their chromatin and methylation profiles that discriminate between classes of distal and gene proximal islands linked to discrete transcriptional states. CONCLUSIONS Our study provides a comprehensive resource of DNA methylation, chromatin accessibility and RNA expression profiles of three diverse cattle populations. The findings have important implications, from understanding how genetic editing across breeds, and consequently regulatory backgrounds, may have distinct impacts to designing effective cattle epigenome-wide association studies in non-European breeds.
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Affiliation(s)
- Jessica Powell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - Andrea Talenti
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Johanneke D Hemmink
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
| | - Edith Paxton
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Philip Toye
- The International Livestock Research Institute, PO Box 30709, Nairobi, 00100, Kenya
- Centre for Tropical Livestock Genetics and Health, ILRI Kenya, PO Box 30709, Nairobi, 00100, Kenya
| | - Isabel Santos
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Beatriz R Ferreira
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Tim K Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Liam J Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
- Centre for Tropical Livestock Genetics and Health, Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK.
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14
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Gong Y, Li Y, Liu X, Ma Y, Jiang L. A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? J Anim Sci Biotechnol 2023; 14:73. [PMID: 37143156 PMCID: PMC10161434 DOI: 10.1186/s40104-023-00860-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/01/2023] [Indexed: 05/06/2023] Open
Abstract
As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to have complex routes of origin and migration, suggesting a possible omission of some population-specific sequences in the current reference genome. Conversely, the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals (core genome) and is also able to display sequence information unique to each individual (variable genome). The progress of pangenome research in humans, plants and domestic animals has proved that the missing genetic components and the identification of large structural variants (SVs) can be explored through pangenomic studies. Many individual specific sequences have been shown to be related to biological adaptability, phenotype and important economic traits. The maturity of technologies and methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome. In the future, pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals, providing better insights into animal domestication, evolution and breeding. In this review, we mainly discuss how pangenome analysis reveals genetic variations in domestic animals (sheep, cattle, pigs, chickens) and their impacts on phenotypes and how this can contribute to the understanding of species diversity. Additionally, we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.
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Affiliation(s)
- Ying Gong
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yefang Li
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xuexue Liu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, 37 allées Jules Guesde, Toulouse, 31000, France
| | - Yuehui Ma
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Lin Jiang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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15
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Xia X, Qu K, Wang Y, Sinding MHS, Wang F, Hanif Q, Ahmed Z, Lenstra JA, Han J, Lei C, Chen N. Global dispersal and adaptive evolution of domestic cattle: a genomic perspective. STRESS BIOLOGY 2023; 3:8. [PMID: 37676580 PMCID: PMC10441868 DOI: 10.1007/s44154-023-00085-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/26/2023] [Indexed: 09/08/2023]
Abstract
Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.
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Affiliation(s)
- Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China
| | - Yan Wang
- Qingdao Municipal Bureau of Agriculture and Rural Affairs, Qingdao, 266000, China
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, 12350, Pakistan
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianlin Han
- Livestock Genetic Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, 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, 712100, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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16
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Parejo M, Talenti A, Richardson M, Vignal A, Barnett M, Wragg D. AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap. Sci Data 2023; 10:198. [PMID: 37037860 PMCID: PMC10086014 DOI: 10.1038/s41597-023-02097-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen's alleles and none from the many drones she mated with. Thus the ordered combination or 'phase' of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.
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Affiliation(s)
- M Parejo
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - A Talenti
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - M Richardson
- University of Edinburgh, King's Buildings Campus, Edinburgh, UK
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK
| | - A Vignal
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326, Castanet Tolosan, France
| | - M Barnett
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK
| | - D Wragg
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK.
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK.
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17
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Leeb T, Bannasch D, Schoenebeck JJ. Identification of Genetic Risk Factors for Monogenic and Complex Canine Diseases. Annu Rev Anim Biosci 2023; 11:183-205. [PMID: 36322969 DOI: 10.1146/annurev-animal-050622-055534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Advances in DNA sequencing and other technologies have greatly facilitated the identification of genetic risk factors for inherited diseases in dogs. We review recent technological developments based on selected examples from canine disease genetics. The identification of disease-causing variants in dogs with monogenic diseases may become a widely employed diagnostic approach in clinical veterinary medicine in the not-too-distant future. Diseases with complex modes of inheritance continue to pose challenges to researchers but have also become much more tangible than in the past. In addition to strategies for identifying genetic risk factors, we provide some thoughts on the interpretation of sequence variants that are largely inspired by developments in human clinical genetics.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland;
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California, Davis, California, USA;
| | - Jeffrey J Schoenebeck
- The Roslin Institute and Royal (Dick) School for Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom;
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18
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Pathak RK, Kim JM. Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science. Front Vet Sci 2022; 9:1008728. [PMID: 36439342 PMCID: PMC9691653 DOI: 10.3389/fvets.2022.1008728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/31/2022] [Indexed: 09/28/2023] Open
Abstract
Having played important roles in human growth and development, livestock animals are regarded as integral parts of society. However, industrialization has depleted natural resources and exacerbated climate change worldwide, spurring the emergence of various diseases that reduce livestock productivity. Meanwhile, a growing human population demands sufficient food to meet their needs, necessitating innovations in veterinary sciences that increase productivity both quantitatively and qualitatively. We have been able to address various challenges facing veterinary and farm systems with new scientific and technological advances, which might open new opportunities for research. Recent breakthroughs in multi-omics platforms have produced a wealth of genetic and genomic data for livestock that must be converted into knowledge for breeding, disease prevention and management, productivity, and sustainability. Vetinformatics is regarded as a new bioinformatics research concept or approach that is revolutionizing the field of veterinary science. It employs an interdisciplinary approach to understand the complex molecular mechanisms of animal systems in order to expedite veterinary research, ensuring food and nutritional security. This review article highlights the background, recent advances, challenges, opportunities, and application of vetinformatics for quality veterinary services.
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Affiliation(s)
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, South Korea
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19
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Talenti A, Powell J, Wragg D, Chepkwony M, Fisch A, Ferreira BR, Mercadante MEZ, Santos IM, Ezeasor CK, Obishakin ET, Muhanguzi D, Amanyire W, Silwamba I, Muma JB, Mainda G, Kelly RF, Toye P, Connelley T, Prendergast J. Optical mapping compendium of structural variants across global cattle breeds. Sci Data 2022; 9:618. [PMID: 36229544 PMCID: PMC9561109 DOI: 10.1038/s41597-022-01684-w] [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: 05/18/2022] [Accepted: 09/04/2022] [Indexed: 11/30/2022] Open
Abstract
Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution. Measurement(s) | Optical Mapping | Technology Type(s) | Optical Mapping | Factor Type(s) | Structural variants | Sample Characteristic - Organism | Bos taurus | Sample Characteristic - Location | United Kingdom • Kenya • Zambia • Uganda • Brazil • Nigeria |
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Affiliation(s)
- A Talenti
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom.
| | - J Powell
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - D Wragg
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom.,Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - M Chepkwony
- The International Livestock Research Institute, PO Box 30709, Nairobi, Kenya.,Centre for Tropical Livestock Genetics and Health, ILRI Kenya, Nairobi, 30709-00100, Kenya
| | - A Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - B R Ferreira
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - M E Z Mercadante
- Institute of Animal Science, Agriculture Department of São Paulo Government, Sertãozinho, SP, 14.174-000, Brazil
| | - I M Santos
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - C K Ezeasor
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - E T Obishakin
- Biotechnology Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria.,Biomedical Research Centre, Ghent University Global Campus, Songdo, Incheon, South Korea
| | - D Muhanguzi
- School of Biosecurity, Biotechnology and Laboratory Sciences (SBLS), College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O Box 7062, Kampala, Uganda
| | - W Amanyire
- School of Biosecurity, Biotechnology and Laboratory Sciences (SBLS), College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O Box 7062, Kampala, Uganda
| | - I Silwamba
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O BOX 32379, Lusaka, Zambia.,Department of Laboratory and Diagnostics, Livestock Services Cooperative Society, P.O. BOX 32025, Lusaka, Zambia
| | - J B Muma
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O BOX 32379, Lusaka, Zambia
| | - G Mainda
- Department of Veterinary Services, Ministry of Fisheries and Livestock, Central Veterinary Research Institute, P.O. Box 33980, Lusaka, Zambia
| | - R F Kelly
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom.,Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - P Toye
- The International Livestock Research Institute, PO Box 30709, Nairobi, Kenya
| | - T Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom. .,Centre for Tropical Livestock Genetics and Health, Easter Bush, Midlothian, EH25 9RG, UK.
| | - J Prendergast
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom. .,Centre for Tropical Livestock Genetics and Health, Easter Bush, Midlothian, EH25 9RG, UK.
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20
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Ros-Freixedes R, Johnsson M, Whalen A, Chen CY, Valente BD, Herring WO, Gorjanc G, Hickey JM. Genomic prediction with whole-genome sequence data in intensely selected pig lines. GENETICS SELECTION EVOLUTION 2022; 54:65. [PMID: 36153511 PMCID: PMC9509613 DOI: 10.1186/s12711-022-00756-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/05/2022] [Indexed: 12/03/2022]
Abstract
Background Early simulations indicated that whole-genome sequence data (WGS) could improve the accuracy of genomic predictions within and across breeds. However, empirical results have been ambiguous so far. Large datasets that capture most of the genomic diversity in a population must be assembled so that allele substitution effects are estimated with high accuracy. The objectives of this study were to use a large pig dataset from seven intensely selected lines to assess the benefits of using WGS for genomic prediction compared to using commercial marker arrays and to identify scenarios in which WGS provides the largest advantage. Methods We sequenced 6931 individuals from seven commercial pig lines with different numerical sizes. Genotypes of 32.8 million variants were imputed for 396,100 individuals (17,224 to 104,661 per line). We used BayesR to perform genomic prediction for eight complex traits. Genomic predictions were performed using either data from a standard marker array or variants preselected from WGS based on association tests. Results The accuracies of genomic predictions based on preselected WGS variants were not robust across traits and lines and the improvements in prediction accuracy that we achieved so far with WGS compared to standard marker arrays were generally small. The most favourable results for WGS were obtained when the largest training sets were available and standard marker arrays were augmented with preselected variants with statistically significant associations to the trait. With this method and training sets of around 80k individuals, the accuracy of within-line genomic predictions was on average improved by 0.025. With multi-line training sets, improvements of 0.04 compared to marker arrays could be expected. Conclusions Our results showed that WGS has limited potential to improve the accuracy of genomic predictions compared to marker arrays in intensely selected pig lines. Thus, although we expect that larger improvements in accuracy from the use of WGS are possible with a combination of larger training sets and optimised pipelines for generating and analysing such datasets, the use of WGS in the current implementations of genomic prediction should be carefully evaluated against the cost of large-scale WGS data on a case-by-case basis. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00756-0.
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21
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Riggio V, Tijjani A, Callaby R, Talenti A, Wragg D, Obishakin ET, Ezeasor C, Jongejan F, Ogo NI, Aboagye-Antwi F, Toure A, Nzalawahej J, Diallo B, Missohou A, Belem AMG, Djikeng A, Juleff N, Fourie J, Labuschagne M, Madder M, Marshall K, Prendergast JGD, Morrison LJ. Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle. Genet Sel Evol 2022; 54:58. [PMID: 36057548 PMCID: PMC9441065 DOI: 10.1186/s12711-022-00751-5] [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: 02/28/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. RESULTS We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS. CONCLUSIONS Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.
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Affiliation(s)
- Valentina Riggio
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK. .,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Abdulfatai Tijjani
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Ethiopia, P.O Box 5689, Addis Ababa, Ethiopia
| | - Rebecca Callaby
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Andrea Talenti
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Emmanuel T Obishakin
- Biotechnology Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria.,Biomedical Research Centre, Ghent University Global Campus, Songdo, Incheon, South Korea
| | - Chukwunonso Ezeasor
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Frans Jongejan
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Ndudim I Ogo
- National Veterinary Research Institute, Vom, Nigeria
| | - Fred Aboagye-Antwi
- Department of Animal Biology and Conservation Sciences, University of Ghana, Accra, Ghana
| | - Alassane Toure
- Laboratoire National d'Appui Au Dévéloppement Agricole(LANADA)/Laboratoire Central Vétérinaire de Bingerville, Bp: 206, Bingerville, Côte d'Ivoire
| | - Jahashi Nzalawahej
- Department of Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Ayao Missohou
- Ecole Inter-Etats des Sciences et Médecine Vétérinaires (EISMV) de Dakar, Dakar, Senegal
| | - Adrien M G Belem
- Université Polytechnique de Bobo-Dioulasso (UPB), Bobo -Dioulasso, Burkina Faso
| | - Appolinaire Djikeng
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Nick Juleff
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Michel Labuschagne
- Clinomics, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa.,Clinvet, Uitzich Road, Bainsvlei, Bloemfontein, 9338, South Africa
| | - Maxime Madder
- Clinglobal, B03/04, The Tamarin Commercial Hub, Jacaranda Avenue, Tamarin, 90903, Mauritius
| | - Karen Marshall
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, P.O. Box 30709, Nairobi, 00100, Kenya.,International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - James G D Prendergast
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Liam J Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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22
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Mo C, Wu Z, Shang X, Shi P, Wei M, Wang H, Xiao L, Cao S, Lu L, Zeng W, Yan H, Kong Q. Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana. DNA Res 2022; 29:6663990. [PMID: 35961033 PMCID: PMC9397507 DOI: 10.1093/dnares/dsac030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 12/03/2022] Open
Abstract
Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.
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Affiliation(s)
| | | | - Xiaohong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Pingli Shi
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Minghua Wei
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiyan Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Liuying Lu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Wendan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Huabing Yan
- To whom correspondence should be addressed. Tel. 86-13877165487. (H.Y.); Tel. 86-18942928088. (Q.K.)
| | - Qiusheng Kong
- To whom correspondence should be addressed. Tel. 86-13877165487. (H.Y.); Tel. 86-18942928088. (Q.K.)
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23
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Guarracino A, Heumos S, Nahnsen S, Prins P, Garrison E. ODGI: understanding pangenome graphs. BIOINFORMATICS (OXFORD, ENGLAND) 2022; 38:3319-3326. [PMID: 35552372 DOI: 10.1101/2021.11.10.467921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/18/2022] [Indexed: 05/24/2023]
Abstract
MOTIVATION Pangenome graphs provide a complete representation of the mutual alignment of collections of genomes. These models offer the opportunity to study the entire genomic diversity of a population, including structurally complex regions. Nevertheless, analyzing hundreds of gigabase-scale genomes using pangenome graphs is difficult as it is not well-supported by existing tools. Hence, fast and versatile software is required to ask advanced questions to such data in an efficient way. RESULTS We wrote Optimized Dynamic Genome/Graph Implementation (ODGI), a novel suite of tools that implements scalable algorithms and has an efficient in-memory representation of DNA pangenome graphs in the form of variation graphs. ODGI supports pre-built graphs in the Graphical Fragment Assembly format. ODGI includes tools for detecting complex regions, extracting pangenomic loci, removing artifacts, exploratory analysis, manipulation, validation and visualization. Its fast parallel execution facilitates routine pangenomic tasks, as well as pipelines that can quickly answer complex biological questions of gigabase-scale pangenome graphs. AVAILABILITY AND IMPLEMENTATION ODGI is published as free software under the MIT open source license. Source code can be downloaded from https://github.com/pangenome/odgi and documentation is available at https://odgi.readthedocs.io. ODGI can be installed via Bioconda https://bioconda.github.io/recipes/odgi/README.html or GNU Guix https://github.com/pangenome/odgi/blob/master/guix.scm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen 72076, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen 72076, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen 72076, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen 72076, Germany
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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24
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Leonard AS, Crysnanto D, Fang ZH, Heaton MP, Vander Ley BL, Herrera C, Bollwein H, Bickhart DM, Kuhn KL, Smith TPL, Rosen BD, Pausch H. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nat Commun 2022; 13:3012. [PMID: 35641504 PMCID: PMC9156671 DOI: 10.1038/s41467-022-30680-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.
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Affiliation(s)
- Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Michael P Heaton
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Carolina Herrera
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Kristen L Kuhn
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD, 20705, USA.
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
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25
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Guarracino A, Heumos S, Nahnsen S, Prins P, Garrison E. ODGI: understanding pangenome graphs. Bioinformatics 2022; 38:3319-3326. [PMID: 35552372 PMCID: PMC9237687 DOI: 10.1093/bioinformatics/btac308] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Motivation Pangenome graphs provide a complete representation of the mutual alignment of collections of genomes. These models offer the opportunity to study the entire genomic diversity of a population, including structurally complex regions. Nevertheless, analyzing hundreds of gigabase-scale genomes using pangenome graphs is difficult as it is not well-supported by existing tools. Hence, fast and versatile software is required to ask advanced questions to such data in an efficient way. Results We wrote Optimized Dynamic Genome/Graph Implementation (ODGI), a novel suite of tools that implements scalable algorithms and has an efficient in-memory representation of DNA pangenome graphs in the form of variation graphs. ODGI supports pre-built graphs in the Graphical Fragment Assembly format. ODGI includes tools for detecting complex regions, extracting pangenomic loci, removing artifacts, exploratory analysis, manipulation, validation and visualization. Its fast parallel execution facilitates routine pangenomic tasks, as well as pipelines that can quickly answer complex biological questions of gigabase-scale pangenome graphs. Availability and implementation ODGI is published as free software under the MIT open source license. Source code can be downloaded from https://github.com/pangenome/odgi and documentation is available at https://odgi.readthedocs.io. ODGI can be installed via Bioconda https://bioconda.github.io/recipes/odgi/README.html or GNU Guix https://github.com/pangenome/odgi/blob/master/guix.scm. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrea Guarracino
- Genomics Research Centre, Human Technopole, Viale Rita Levi-Montalcini 1, Milan, 20157, Italy
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, 72076, Germany.,Biomedical Data Science, Dept. of Computer Science, University of Tübingen, Tübingen, 72076, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, 72076, Germany.,Biomedical Data Science, Dept. of Computer Science, University of Tübingen, Tübingen, 72076, Germany
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, 38163, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, 38163, USA
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