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Nandanpawar P, Sahoo B, Sahoo L, Murmu K, Reang D, Kumar AP, Chaudhari A, Das P. Unveiling population structure and selection signatures of riverine and genetically improved rohu, Labeo rohita using genome wide SNPs. Mol Biol Rep 2024; 51:926. [PMID: 39167228 DOI: 10.1007/s11033-024-09866-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024]
Abstract
BACKGROUND Captive breeding, along with artificial selection can significantly impact population structure by influencing allele frequencies and driving populations towards specific adaptation. Selective sweeps are powerful forces in shaping genetic variation within populations and can drive rapid spread of beneficial alleles while simultaneously reducing genetic diversity in localized regions of the genome. The present work was undertaken to assess the genetic structure and consequences of artificial selection in 10th generation of genetically improved rohu by comparing with wild populations. METHODS AND RESULTS The present study used 11,022 high-quality genome wide SNPs to compare the population genetic structure and signatures of selection between Jayanti rohu population and its wild counterpart. Outlier analysis revealed presence of 14 adaptive SNPs, out of which 5 were classified to be under decisive selection pressure. Notably, Jayanti rohu (JR) displayed 297 private alleles exclusive to its population. Chromosomes 7 and 16 emerged as potential hotspots containing a majority of the identified SNPs. Structure and principal component analysis revealed two distinct clusters, effectively distinguishing the JR and wild rohu populations. Phylogenetic analysis indicated a separate cluster of JR population distant from wild groups. CONCLUSION The results of present study shall help in elucidating patterns of genetic variation and characterizing selection signatures associated with captive bred and natural populations of rohu. The genomic resources generated through this work shall be helpful in improving the traceability of selectively bred germplasm for developing future strategies of genetic management.
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Affiliation(s)
- Priyanka Nandanpawar
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India.
| | - Bismay Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Lakshman Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Khuntia Murmu
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
| | - Dhalongsaih Reang
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Annam Pavan Kumar
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Aparna Chaudhari
- ICAR-Central Institute of Fisheries Education, Panch Marg, Versova, Mumbai, Maharashtra, 400 061, India
| | - Paramananda Das
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751002, India
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2
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Nawaz MY, Savegnago RP, Lim D, Lee SH, Gondro C. Signatures of selection in Angus and Hanwoo beef cattle using imputed whole genome sequence data. Front Genet 2024; 15:1368710. [PMID: 39161420 PMCID: PMC11331311 DOI: 10.3389/fgene.2024.1368710] [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: 01/11/2024] [Accepted: 07/09/2024] [Indexed: 08/21/2024] Open
Abstract
In this study, we detected signatures of selection in Hanwoo and Angus beef cattle using allele frequency and haplotype-based methods based on imputed whole genome sequence variants. Our dataset included 13,202 Angus animals with 10,057,633 imputed SNPs and 10,437 Hanwoo animals with 13,241,550 imputed SNPs. The dataset was subset down to 6,873,624 SNPs in common between the two populations to identify within population (runs of homozygosity, extended haplotype homozygosity) and between population signals of selection (allele fixation index, extended haplotype homozygosity). Assuming these selection signals were complementary to each other, they were combined into a decorrelated composite of multiple signals to identify regions under selection for each of the breeds. 27 genomic regions spanning 25.15 Mb and harboring 360 genes were identified in Angus on chromosomes 1,3, 4, 5, 6, 7, 8, 12, 13, 14, 16, 20, 21 and 28. Similarly, in Hanwoo, 59 genes and 17 genomic regions spanning 5.21 Mb on chromosomes 2, 4, 5, 6, 7, 8, 9, 10, 13, 17, 20 and 24 were identified. Apart from a small region on chromosome 13, there was no major overlap of selection signals between the two breeds reflecting their largely different selection histories, environmental challenges, breeding objectives and breed characteristics. Positional candidate genes identified in selected genomic regions in Angus have been previously associated with growth, immunity, reproductive development, feed efficiency and adaptation to environment while the candidate genes identified in Hanwoo included important genes regulating meat quality, fat deposition, cholesterol metabolism, lipid synthesis, neuronal development, and olfactory reception.
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Affiliation(s)
- Muhammad Yasir Nawaz
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | | | - Dajeong Lim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Republic of Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Republic of Korea
| | - Cedric Gondro
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
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3
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Gao Z, Lu Y, Chong Y, Li M, Hong J, Wu J, Wu D, Xi D, Deng W. Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery. Int J Mol Sci 2024; 25:7147. [PMID: 39000250 PMCID: PMC11240973 DOI: 10.3390/ijms25137147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/23/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Beef is a major global source of protein, playing an essential role in the human diet. The worldwide production and consumption of beef continue to rise, reflecting a significant trend. However, despite the critical importance of beef cattle resources in agriculture, the diversity of cattle breeds faces severe challenges, with many breeds at risk of extinction. The initiation of the Beef Cattle Genome Project is crucial. By constructing a high-precision functional annotation map of their genome, it becomes possible to analyze the genetic mechanisms underlying important traits in beef cattle, laying a solid foundation for breeding more efficient and productive cattle breeds. This review details advances in genome sequencing and assembly technologies, iterative upgrades of the beef cattle reference genome, and its application in pan-genome research. Additionally, it summarizes relevant studies on the discovery of functional genes associated with key traits in beef cattle, such as growth, meat quality, reproduction, polled traits, disease resistance, and environmental adaptability. Finally, the review explores the potential of telomere-to-telomere (T2T) genome assembly, structural variations (SVs), and multi-omics techniques in future beef cattle genetic breeding. These advancements collectively offer promising avenues for enhancing beef cattle breeding and improving genetic traits.
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Affiliation(s)
- Zhendong Gao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ying Lu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yuqing Chong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengfei Li
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jieyun Hong
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiao Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dongwang Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dongmei Xi
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Weidong Deng
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Kunming 650201, China
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4
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Rowan TN, Schnabel RD, Decker JE. Uncovering the architecture of selection in two Bos taurus cattle breeds. Evol Appl 2024; 17:e13666. [PMID: 38405336 PMCID: PMC10883790 DOI: 10.1111/eva.13666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/18/2023] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
Directional selection alters the genome via hard sweeps, soft sweeps, and polygenic selection. However, mapping polygenic selection is difficult because it does not leave clear signatures on the genome like a selective sweep. In populations with temporally stratified genotypes, the Generation Proxy Selection Mapping (GPSM) method identifies variants associated with generation number (or appropriate proxy) and thus variants undergoing directional allele frequency changes. Here, we use GPSM on two large datasets of beef cattle to detect associations between an animal's generation and 11 million imputed SNPs. Using these datasets with high power and dense mapping resolution, GPSM detected a total of 294 unique loci actively under selection in two cattle breeds. We observed that GPSM has a high power to detect selection in the very recent past (<10 years), even when allele frequency changes are small. Variants identified by GPSM reside in genomic regions associated with known breed-specific selection objectives, such as fertility and maternal ability in Red Angus, and carcass merit and coat color in Simmental. Over 60% of the selected loci reside in or near (<50 kb) annotated genes. Using haplotype-based and composite selective sweep statistics, we identify hundreds of putative selective sweeps that likely occurred earlier in the evolution of these breeds; however, these sweeps have little overlap with recent polygenic selection. This makes GPSM a complementary approach to sweep detection methods when temporal genotype data are available. The selected loci that we identify across methods demonstrate the complex architecture of selection in domesticated cattle.
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Affiliation(s)
- Troy N. Rowan
- Division of Animal SciencesUniversity of MissouriColumbiaMissouriUSA
- Genetics Area ProgramUniversity of MissouriColumbiaMissouriUSA
- Department of Animal ScienceUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
- Department of Large Animal Clinical Sciences, College of Veterinary MedicineUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Robert D. Schnabel
- Division of Animal SciencesUniversity of MissouriColumbiaMissouriUSA
- Genetics Area ProgramUniversity of MissouriColumbiaMissouriUSA
- Institute for Data Science and InformaticsUniversity of MissouriColumbiaMissouriUSA
| | - Jared E. Decker
- Division of Animal SciencesUniversity of MissouriColumbiaMissouriUSA
- Genetics Area ProgramUniversity of MissouriColumbiaMissouriUSA
- Institute for Data Science and InformaticsUniversity of MissouriColumbiaMissouriUSA
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5
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Harish A, Lopes Pinto FA, Eriksson S, Johansson AM. Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds. BMC Genomics 2024; 25:89. [PMID: 38254050 PMCID: PMC10802049 DOI: 10.1186/s12864-024-09959-9] [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: 07/11/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Several indigenous cattle breeds in Sweden are endangered. Conservation of their genetic diversity and genomic characterization is a priority.Whole-genome sequences (WGS) with a mean coverage of 25X, ranging from 14 to 41X were obtained for 30 individuals of the breeds Fjällko, Fjällnära, Bohuskulla, Rödkulla, Ringamåla, and Väneko. WGS-based genotyping revealed 22,548,028 variants in total, comprising 18,876,115 single nucleotide polymorphisms (SNPs) and 3,671,913 indels. Out of these, 1,154,779 SNPs and 304,467 indels were novel. Population stratification based on roughly 19 million SNPs showed two major groups of the breeds that correspond to northern and southern breeds. Overall, a higher genetic diversity was observed in the southern breeds compared to the northern breeds. While the population stratification was consistent with previous genome-wide SNP array-based analyses, the genealogy of the individuals inferred from WGS based estimates turned out to be more complex than expected from previous SNP-array based estimates. Polymorphisms and their predicted phenotypic consequences were associated with differences in the coat color phenotypes between the northern and southern breeds. Notably, these high-consequence polymorphisms were not represented in SNP arrays, which are used routinely for genotyping of cattle breeds.This study is the first WGS-based population genetic analysis of Swedish native cattle breeds. The genetic diversity of native breeds was found to be high. High-consequence polymorphisms were linked with desirable phenotypes using whole-genome genotyping, which highlights the pressing need for intensifying WGS-based characterization of the native breeds.
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Affiliation(s)
- Ajith Harish
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden.
| | - Fernando A Lopes Pinto
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden.
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6
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Barría A, Peñaloza C, Papadopoulou A, Mahmuddin M, Doeschl‐Wilson A, Benzie JAH, Houston RD, Wiener P. Genetic differentiation following recent domestication events: A study of farmed Nile tilapia ( Oreochromis niloticus) populations. Evol Appl 2023; 16:1220-1235. [PMID: 37360025 PMCID: PMC10286235 DOI: 10.1111/eva.13560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Nile tilapia (Oreochromis niloticus) is among the most farmed finfish worldwide, distributed across different environmental conditions. Its wide distribution has mainly been facilitated by several breeding programs and widespread dissemination of genetically improved strains. In the first Nile tilapia study exploiting a whole-genome pooled sequencing (Poolseq) approach, we identified the genetic structure and signatures of selection in diverse, farmed Nile tilapia populations, with a particular focus on the GIFT strain, developed in the 1980s, and currently managed by WorldFish (GIFTw). We also investigated important farmed strains from The Philippines and Africa. Using both SNP array data and Poolseq SNPs, we characterized the population structure of these samples. We observed the greatest separation between the Asian and African populations and greater admixture in the Asian populations than in the African ones. We also established that the SNP array data were able to successfully resolve relationships between these diverse Nile tilapia populations. The Poolseq data identified genomic regions with high levels of differentiation (F ST) between GIFTw and the other populations. Gene ontology terms associated with mesoderm development were significantly enriched in the genes located in these regions. A region on chromosome Oni06 was genetically differentiated in pairwise comparisons between GIFTw and all other populations. This region contains genes associated with muscle-related traits and overlaps with a previously published QTL for fillet yield, suggesting that these traits may have been direct targets for selection on GIFT. A nearby region was also identified using XP-EHH to detect genomic differentiation using the SNP array data. Genomic regions with high or extended homozygosity within each population were also identified. This study provides putative genomic landmarks associated with the recent domestication process in several Nile tilapia populations, which could help to inform their genetic management and improvement.
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Affiliation(s)
- Agustin Barría
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark Genetics Norway ASBergenNorway
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Present address:
Benchmark GeneticsMidlothianUK
| | - Athina Papadopoulou
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Center of Environment Fisheries and Aquaculture ScienceWeymouthUK
| | | | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
| | - John A. H. Benzie
- WorldFishBayan LepasPenangMalaysia
- School of Biological Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
- Benchmark GeneticsMidlothianUK
| | - Pamela Wiener
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh Easter BushMidlothianUK
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7
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Ghildiyal K, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Lei C, Bhushan B, Dutt T. Selection signatures for fiber production in commercial species: A review. Anim Genet 2023; 54:3-23. [PMID: 36352515 DOI: 10.1111/age.13272] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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8
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Abbasi-Moshaii B, Moradi MH, Yin T, Rahimi-Mianji G, Nejati-Javaremi A, König S. Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle. J Anim Breed Genet 2023; 140:92-105. [PMID: 35988016 DOI: 10.1111/jbg.12737] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/02/2022] [Indexed: 12/13/2022]
Abstract
Domestication and selection significantly changed phenotypic and behavioural traits in modern domestic animals. In this study, to identify the genomic regions associated with mastitis, genomic data of German Holstein dairy cattle were analysed. The samples were genotyped using the Bovine 50 K SNP chip. For each defined healthy and sick group, 133 samples from 13,276 genotyped dairy cows were selected based on mastitis random residual effects. Grouping was done to infer selection signatures based on XP-EHH statistic. The results revealed that for the top 0.01 percentile of the obtained XP-EHH values, five genomic regions on chromosomes 8, 11, 12, 14 and 26 of the control group, and four regions on chromosomes 3, 4 (two regions) and 22 of the case group, have been under selection. Also, consideration of the top 0.1 percentile of the XP-EHH values, clarified 21 and 15 selective sweeps in the control and case group, respectively. This study identified some genomic regions containing potential candidate genes associated with resistance and susceptibility to mastitis, immune system and inflammation, milk traits, udder morphology and different types of cancers. In addition, these regions overlap with some quantitative trait loci linked to clinical mastitis, immunoglobulin levels, somatic cell score, udder traits, milk fat and protein, milk yield, milking speed and veterinary treatments. It is noteworthy that we found two regions in the healthy group (on chromosomes 12 and 14) with strong signals, which were not described previously. It is likely that future research could link these identified genomic regions to mastitis. The results of the current study contribute to the identification of causal mutations, genomic regions and genes affecting mastitis incidence in dairy cows.
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Affiliation(s)
- Bita Abbasi-Moshaii
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany.,Department of Animal Science and Fisheries, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | | | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Ghodratollah Rahimi-Mianji
- Department of Animal Science and Fisheries, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | - Ardeshir Nejati-Javaremi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany
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9
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Han H, McGivney BA, Allen L, Bai D, Corduff LR, Davaakhuu G, Davaasambuu J, Dorjgotov D, Hall TJ, Hemmings AJ, Holtby AR, Jambal T, Jargalsaikhan B, Jargalsaikhan U, Kadri NK, MacHugh DE, Pausch H, Readhead C, Warburton D, Dugarjaviin M, Hill EW. Common protein-coding variants influence the racing phenotype in galloping racehorse breeds. Commun Biol 2022; 5:1320. [PMID: 36513809 PMCID: PMC9748125 DOI: 10.1038/s42003-022-04206-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/01/2022] [Indexed: 12/14/2022] Open
Abstract
Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.
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Affiliation(s)
- Haige Han
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Beatrice A. McGivney
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Lucy Allen
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Dongyi Bai
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Leanne R. Corduff
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Gantulga Davaakhuu
- grid.425564.40000 0004 0587 3863Institute of Biology, Mongolian Academy of Sciences, Peace Avenue 54B, Ulaanbaatar, 13330 Mongolia
| | - Jargalsaikhan Davaasambuu
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Dulguun Dorjgotov
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Thomas J. Hall
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Andrew J. Hemmings
- grid.417905.e0000 0001 2186 5933Royal Agricultural University, Cirencester, Gloucestershire GL7 6JS UK
| | - Amy R. Holtby
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland
| | - Tuyatsetseg Jambal
- grid.440461.30000 0001 2191 7895School of Industrial Technology, Mongolian University of Science and Technology, Ulaanbaatar, 661 Mongolia
| | - Badarch Jargalsaikhan
- grid.444534.60000 0000 8485 883XDepartment of Obstetrics and Gynecology, Mongolian National University of Medical Sciences, Ulaanbaatar, 14210 Mongolia
| | - Uyasakh Jargalsaikhan
- Ajnai Sharga Horse Racing Team, Encanto Town 210-11, Ikh Mongol State Street, 26th Khoroo, Bayanzurkh district Ulaanbaatar, 13312 Mongolia
| | - Naveen K. Kadri
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - David E. MacHugh
- grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland ,grid.7886.10000 0001 0768 2743UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
| | - Hubert Pausch
- grid.5801.c0000 0001 2156 2780Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Carol Readhead
- grid.20861.3d0000000107068890Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125 USA
| | - David Warburton
- grid.42505.360000 0001 2156 6853The Saban Research Institute, Children’s Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027 USA
| | - Manglai Dugarjaviin
- grid.411638.90000 0004 1756 9607Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018 China
| | - Emmeline W. Hill
- grid.496984.ePlusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, A96 W5T3 Ireland ,grid.7886.10000 0001 0768 2743UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8 Ireland
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10
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Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences. PLoS One 2022; 17:e0276309. [PMID: 36288367 PMCID: PMC9605288 DOI: 10.1371/journal.pone.0276309] [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: 08/04/2021] [Accepted: 10/04/2022] [Indexed: 11/04/2022] Open
Abstract
Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2-71.3 Mb), BTA5 (10.0-19.7 Mb), BTA20 (10.0-19.9 and 20.0-22.7 Mb), and BTA25 (0.5-9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.
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Álvarez Cecco P, Rogberg Muñoz A, Balbi M, Bonamy M, Munilla S, Forneris NS, Peral García P, Cantet RJC, Giovambattista G, Fernández ME. Genome-wide scan for signatures of selection in the Brangus cattle genome. J Anim Breed Genet 2022; 139:679-694. [PMID: 35866697 DOI: 10.1111/jbg.12733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/01/2022] [Indexed: 11/28/2022]
Abstract
Brangus is a composite cattle breed developed with the objective of combining the advantages of Angus and Zebuine breeds (Brahman, mainly) in tropical climates. The aim of this work was to estimate breed composition both genome-wide and locally, at the chromosome level, and to uncover genomic regions evidencing positive selection in the Argentinean Brangus population/nucleus. To do so, we analysed marker data from 478 animals, including Brangus, Angus and Brahman. Average breed composition was 35.0% ± 9.6% of Brahman, lower than expected according to the theoretical fractions deduced by the usual cross-breeding practice in this breed. Local ancestry analysis evidenced that breed composition varies between chromosomes, ranging from 19.6% for BTA26 to 56.1% for BTA5. Using approaches based on allelic frequencies and linkage disequilibrium, genomic regions with putative selection signatures were identified in several chromosomes (BTA1, BTA5, BTA6 and BTA14). These regions harbour genes involved in horn development, growth, lipid metabolism, reproduction and immune response. We argue that the overlapping of a chromosome segment originated in one of the parental breeds and over-represented in the sample with the location of a signature of selection constitutes evidence of a selection process that has occurred in the breed since its take off in the 1950s. In this regard, our results could contribute to the understanding of the genetic mechanisms involved in cross-bred cattle adaptation and productivity in tropical environments.
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Affiliation(s)
- Paulo Álvarez Cecco
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Andrés Rogberg Muñoz
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INPA - Instituto de Investigaciones en Producción Animal (UBA - CONICET), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marianela Balbi
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Martín Bonamy
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Sebastián Munilla
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INPA - Instituto de Investigaciones en Producción Animal (UBA - CONICET), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Natalia Soledad Forneris
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INPA - Instituto de Investigaciones en Producción Animal (UBA - CONICET), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pilar Peral García
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Rodolfo Juan Carlos Cantet
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,INPA - Instituto de Investigaciones en Producción Animal (UBA - CONICET), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guillermo Giovambattista
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Elena Fernández
- IGEVET - Instituto de Genética Veterinaria (UNLP - CONICET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
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12
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Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert. Sci Rep 2022; 12:12264. [PMID: 35851076 PMCID: PMC9293982 DOI: 10.1038/s41598-022-15986-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
The southern margin of the Taklimakan Desert is characterized by low rainfall, heavy sandstorms, sparse vegetation and harsh ecological environment. The indigenous sheep in this area are rich in resources, with the advantages of perennial estrus and good resistance to stress in most sheep. Exploring the molecular markers of livestock adaptability in this environment will provide the molecular basis for breeding research to cope with extreme future changes in the desert environment. In this study, we analyzed the population genetic structure and linkage imbalance of five sheep breeds with three different agricultural geographic characteristics using four complementary genomic selection signals: fixation index (FST), cross-population extended haplotype homozygosity (xp-EHH), Rsb (extended haplotype homozygosity between-populations) and iHS (integrated haplotype homozygosity score). We used Illumina Ovine SNP 50K Genotyping BeadChip Array, and gene annotation and enrichment analysis were performed on selected regions of the obtained genome. The ovary of Qira Black sheep (Follicular phase, Luteal phase, 30th day of pregnancy, 45th day of pregnancy) was collected, and the differentially expressed genes were screened by transcriptomic sequencing. Genome-wide selective sweep results and transcriptome data were combined for association analysis to obtain candidate genes associated with perennial estrus and stable reproduction. In order to verify the significance of the results, 15 resulting genes were randomly selected for fluorescence quantitative analysis. The results showed that Dolang sheep and Qira Black sheep evolved from Kazak sheep. Linkage disequilibrium analysis showed that the decay rate of sheep breeds in the Taklimakan Desert was higher than that in Yili grassland. The signals of FST, xp-EHH, Rsb and iHS detected 526, 332, 308 and 408 genes, respectively, under the threshold of 1% and 17 overlapping genes under the threshold of 5%. A total of 29 genes were detected in association analysis of whole-genome and transcriptome data. This study reveals the genetic mechanism of perennial estrus and environmental adaptability of indigenous sheep breeds in the Taklimakan Desert. It provides a theoretical basis for the conservation and exploitation of genetic resources of indigenous sheep breeds in extreme desert environment. This provides a new perspective for the quick adaptation of sheep and other mammals to extreme environments and future climate changes.
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13
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Wyss P, Song C, Bina M. Along the Bos taurus genome, uncover candidate imprinting control regions. BMC Genomics 2022; 23:478. [PMID: 35764919 PMCID: PMC9241299 DOI: 10.1186/s12864-022-08694-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background In mammals, Imprinting Control Regions (ICRs) regulate a subset of genes in a parent-of-origin-specific manner. In both human and mouse, previous studies identified a set of CpG-rich motifs occurring as clusters in ICRs and germline Differentially Methylated Regions (gDMRs). These motifs consist of the ZFP57 binding site (ZFBS) overlapping a subset of MLL binding units known as MLL morphemes. MLL or MLL1 (Mixed Lineage Leukemia 1) is a relatively large multidomain protein that plays a central role in the regulation of transcription. The structures of both MLL1 and MLL2 include a domain (MT) that binds CpG-rich DNA and a conserved domain (SET) that methylates lysine 4 in histone H3 producing H3K4me3 marks in chromatin. Results Since genomic imprinting impacts many developmental and key physiological processes, we followed a previous bioinformatics strategy to pinpoint ICR positions in the Bos taurus genome. Initial genome-wide analyses involved finding the positions of ZFP57 binding sites, and the CpG-rich motifs (ZFBS-morph overlaps) along cattle chromosomal DNA. By creating plots displaying the density of ZFBS-morph overlaps, we removed background noise and thus improved signal detection. With the density-plots, we could view the positions of peaks locating known and candidate ICRs in cattle DNA. Our evaluations revealed the correspondence of peaks in plots to reported known and inferred ICRs/DMRs in cattle. Beside peaks pinpointing such ICRs, the density-plots also revealed additional peaks. Since evaluations validated the robustness of our approach, we inferred that the additional peaks may correspond to candidate ICRs for imprinted gene expression. Conclusion Our bioinformatics strategy offers the first genome-wide approach for systematically localizing candidate ICRs. Furthermore, we have tailored our datasets for upload onto the UCSC genome browser so that researchers could find known and candidate ICRs with respect to a wide variety of annotations at all scales: from the positions of Single Nucleotide Polymorphisms (SNPs), to positions of genes, transcripts, and repeated DNA elements. Furthermore, the UCSC genome browser offers tools to produce enlarged views: to uncover the genes in the vicinity of candidate ICRs and thus discover potential imprinted genes for experimental validations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08694-3.
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Affiliation(s)
- Phillip Wyss
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Carol Song
- Information Technology, Purdue University, West Lafayette, IN, 47907, USA
| | - Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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Zhang S, Yao Z, Li X, Zhang Z, Liu X, Yang P, Chen N, Xia X, Lyu S, Shi Q, Wang E, Ru B, Jiang Y, Lei C, Chen H, Huang Y. Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data. BMC Genomics 2022; 23:460. [PMID: 35729510 PMCID: PMC9215082 DOI: 10.1186/s12864-022-08645-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, including fast growth, early onset of puberty, and good meat quality. In this study, we analyzed the genetic diversity, population structure, and genomic region under the selection of Pinan cattle based on whole-genome sequencing data of 30 Pinan cattle and 169 published cattle genomic data worldwide. RESULTS: Estimating ancestry composition analysis showed that the composition proportions for our Pinan cattle were mainly Piedmontese and a small amount of Nanyang cattle. The analyses of nucleotide diversity and linkage disequilibrium decay indicated that the genomic diversity of Pinan cattle was higher than that of European cattle and lower than that of Chinese indigenous cattle. De-correlated composite of multiple selection signals, which combines four different statistics including θπ, CLR, FST, and XP-EHH, was computed to detect the signatures of selection in the Pinan cattle genome. A total of 83 genes were identified, affecting many economically important traits. Functional annotation revealed that these selected genes were related to immune (BOLA-DQA2, BOLA-DQB, LSM14A, SEC13, and NAALADL2), growth traits (CYP4A11, RPL26, and MYH10), embryo development (REV3L, NT5E, CDX2, KDM6B, and ADAMTS9), hornless traits (C1H21orf62), and climate adaptation (ANTXR2). CONCLUSION In this paper, we elucidated the genomic characteristics, ancestry composition, and selective signals related to important economic traits in Pinan cattle. These results will provide the basis for further genetic improvement of Pinan cattle and reference for other hybrid cattle related studies.
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Affiliation(s)
- Shunjin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Zhi Yao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Xinmiao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou Henan, 450002, China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou Henan, 450008, China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 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, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou Henan, 450002, China
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou Henan, 450002, China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou Henan, 450002, China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou Henan, 450008, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling Shaanxi, 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, 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, No. 22 Xinong Road, Yangling Shaanxi, 712100, China.
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15
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Duarte INH, Bessa AFDO, Rola LD, Genuíno MVH, Rocha IM, Marcondes CR, Regitano LCDA, Munari DP, Berry DP, Buzanskas ME. Cross-population selection signatures in Canchim composite beef cattle. PLoS One 2022; 17:e0264279. [PMID: 35363779 PMCID: PMC8975110 DOI: 10.1371/journal.pone.0264279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait.
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Affiliation(s)
| | | | - Luciana Diniz Rola
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | - Iasmin Marques Rocha
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | | | - Danísio Prado Munari
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Donagh Pearse Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy Co. Cork., Ireland
| | - Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
- * E-mail:
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Kour A, Niranjan SK, Malayaperumal M, Surati U, Pukhrambam M, Sivalingam J, Kumar A, Sarkar M. Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak. Genes (Basel) 2022; 13:254. [PMID: 35205299 PMCID: PMC8872319 DOI: 10.3390/genes13020254] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima's D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.
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Affiliation(s)
- Aneet Kour
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; (S.K.N.); (A.K.)
| | - Mohan Malayaperumal
- ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India; (M.M.); (U.S.)
| | - Utsav Surati
- ICAR-National Dairy Research Institute, Karnal 132001, Haryana, India; (M.M.); (U.S.)
| | - Martina Pukhrambam
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
| | | | - Amod Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; (S.K.N.); (A.K.)
| | - Mihir Sarkar
- ICAR-National Research Centre on Yak, Dirang 790101, Arunachal Pradesh, India; (M.P.); (M.S.)
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17
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Johnsson M, Jungnickel MK. Evidence for and localization of proposed causative variants in cattle and pig genomes. Genet Sel Evol 2021; 53:67. [PMID: 34461824 PMCID: PMC8404348 DOI: 10.1186/s12711-021-00662-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. RESULTS For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome. CONCLUSIONS Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.
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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - Melissa K. Jungnickel
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland, UK
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18
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Rowan TN, Durbin HJ, Seabury CM, Schnabel RD, Decker JE. Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle. PLoS Genet 2021; 17:e1009652. [PMID: 34292938 PMCID: PMC8297814 DOI: 10.1371/journal.pgen.1009652] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 06/09/2021] [Indexed: 12/19/2022] Open
Abstract
Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional selection and local adaptation are changing populations; but, identifying loci underlying polygenic or environmental selection has been difficult. We use genomic data on tens of thousands of cattle from three populations, distributed over time and landscapes, in linear mixed models with novel dependent variables to map signatures of selection on complex traits and local adaptation. We identify 207 genomic loci associated with an animal's birth date, representing ongoing selection for monogenic and polygenic traits. Additionally, hundreds of additional loci are associated with continuous and discrete environments, providing evidence for historical local adaptation. These candidate loci highlight the nervous system's possible role in local adaptation. While advanced technologies have increased the rate of directional selection in cattle, it has likely been at the expense of historically generated local adaptation, which is especially problematic in changing climates. When applied to large, diverse cattle datasets, these selection mapping methods provide an insight into how selection on complex traits continually shapes the genome. Further, understanding the genomic loci implicated in adaptation may help us breed more adapted and efficient cattle, and begin to understand the basis for mammalian adaptation, especially in changing climates. These selection mapping approaches help clarify selective forces and loci in evolutionary, model, and agricultural contexts.
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Affiliation(s)
- Troy N. Rowan
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genetics Area Program, University of Missouri, Columbia, Missouri, United States of America
- Department of Animal Science, University of Tennessee, Knoxville, Tennessee, United States of America
- College of Veterinary Medicine, Large Animal Clinical Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Harly J. Durbin
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genetics Area Program, University of Missouri, Columbia, Missouri, United States of America
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genetics Area Program, University of Missouri, Columbia, Missouri, United States of America
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, United States of America
| | - Jared E. Decker
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
- Genetics Area Program, University of Missouri, Columbia, Missouri, United States of America
- Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, United States of America
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Martinez-Castillero M, Then C, Altarriba J, Srihi H, López-Carbonell D, Díaz C, Martinez P, Hermida M, Varona L. Detection of Genomic Regions with Pleiotropic Effects for Growth and Carcass Quality Traits in the Rubia Gallega Cattle Breed. Animals (Basel) 2021; 11:ani11061682. [PMID: 34200089 PMCID: PMC8227173 DOI: 10.3390/ani11061682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. We have developed a ssGWAS by backsolving the SNP effects after implementing a ssGBLUP. The results showed an apparent heterogeneity of the additive genetic variance across the genome. Some of the genomic regions explaining the most of this additive variance were shared across traits, indicating the presence of pleiotropic effects, which were reflected in their genetic correlations. Abstract The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) by backsolving the SNP (single nucleotide polymorphisms) effects. Therefore, the objective of this study was to identify genomic regions associated with the genetic variability in growth and carcass quality traits. We implemented a ssGBLUP by using a database that included records for Birth Weight (BW-327,350 records-), Weaning Weight (WW-83,818-), Cold Carcass Weight (CCW-91,621-), Fatness (FAT-91,475-) and Conformation (CON-91,609-). The pedigree included 464,373 individuals, 2449 of which were genotyped. After a process of filtering, we ended up using 43,211 SNP markers. We used the GBLUP and SNPBLUP model equivalences to obtain the effects of the SNPs and then calculated the percentage of variance explained by the regions of the genome between 1 Mb. We identified 7 regions of the genome for CCW; 8 regions for BW, WW, FAT and 9 regions for CON, which explained the percentage of variance above 0.5%. Furthermore, a number of the genome regions had pleiotropic effects, located at: BTA1 (131–132 Mb), BTA2 (1–11 Mb), BTA3 (32–33 Mb), BTA6 (36–38 Mb), BTA16 (24–26 Mb), and BTA 21 (56–57 Mb). These regions contain, amongst others, the following candidate genes: NCK1, MSTN, KCNA3, LCORL, NCAPG, and RIN3.
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Affiliation(s)
- Maria Martinez-Castillero
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
- Correspondence:
| | - Carlos Then
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Juan Altarriba
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Houssemeddine Srihi
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - David López-Carbonell
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Clara Díaz
- Instituto Nacional de Investigación y Tecnología Agraria (INIA), 28040 Madrid, Spain;
| | - Paulino Martinez
- Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002 Lugo, Spain; (P.M.); (M.H.)
| | - Miguel Hermida
- Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002 Lugo, Spain; (P.M.); (M.H.)
| | - Luis Varona
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
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Wiener P, Robert C, Ahbara A, Salavati M, Abebe A, Kebede A, Wragg D, Friedrich J, Vasoya D, Hume DA, Djikeng A, Watson M, Prendergast JGD, Hanotte O, Mwacharo JM, Clark EL. Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations. Genome Biol Evol 2021; 13:evab014. [PMID: 33501931 PMCID: PMC7955157 DOI: 10.1093/gbe/evab014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.
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Affiliation(s)
- Pamela Wiener
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Christelle Robert
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, United Kingdom
- Department of Zoology, Misurata University, Misurata, Libya
| | - Mazdak Salavati
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Ayele Abebe
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - David Wragg
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Juliane Friedrich
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Deepali Vasoya
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Appolinaire Djikeng
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - James G D Prendergast
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Olivier Hanotte
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- School of Life Sciences, University of Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- Animal and Veterinary Sciences Group, Scotland’s Rural College (SRUC), Midlothian, United Kingdom
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Emily L Clark
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
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21
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Mei C, Gui L, Hong J, Raza SHA, Aorigele C, Tian W, Garcia M, Xin Y, Yang W, Zhang S, Zan L. Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:959-967. [PMID: 33614243 PMCID: PMC7868925 DOI: 10.1016/j.omtn.2020.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
Abstract
Mongolian cattle (MG, Bos taurus) and Minnan cattle (MN, Bos indicus) are two different breeds of Chinese indigenous cattle, representing North type and South type, respectively. However, their value and potential have not yet been discovered at the genomic level. In this study, 26 individuals of MN and MG were sequenced for the first time at an average of 13.9- and 12.8-fold, respectively. Large numbers of different variations were identified. In addition, the analyses of phylogenetic and population structure showed that these two cattle breeds are distinct from each other, and results of linkage disequilibrium analysis revealed that these two cattle breeds have undergone various degrees of intense natural or artificial selection. Subsequently, 496 and 306 potential selected genes (PSRs) were obtained in MN and MG, containing 1,096 and 529 potential selected genes (PSGs), respectively. These PSGs, together with the analyzed copy number variation (CNV)-related genes, showed potential relations with their phenotypic characteristics, including environmental adaptability (e.g., DVL2, HSPA4, CDHR4), feed efficiency (e.g., R3HDM1, PLAG1, XKR4), and meat/milk production (e.g., PDHB, LEMD3, APOF). The results of this study help to gain new insights into the genetic characteristics of two distinct cattle breeds and will contribute to future cattle breeding.
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Affiliation(s)
- Chugang Mei
- Northwest A&F University, Yangling 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling 712100, China
| | - Linsheng Gui
- Northwest A&F University, Yangling 712100, Shaanxi, China.,Qinghai University, Xining 810008, China
| | - Jieyun Hong
- Northwest A&F University, Yangling 712100, Shaanxi, China.,Yunnan Agricultural University, Kunming 650031, China
| | | | - Chen Aorigele
- Inner Mongolia Agricultural University, Hohhot 010000, China
| | - Wanqiang Tian
- Yangling Vocational & Technical College, Yangling 712100, China
| | | | - Yaping Xin
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wucai Yang
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Song Zhang
- Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Linsen Zan
- Northwest A&F University, Yangling 712100, Shaanxi, China.,National Beef Cattle Improvement Center, Yangling 712100, China
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Strillacci MG, Vevey M, Blanchet V, Mantovani R, Sartori C, Bagnato A. The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System. Animals (Basel) 2020; 10:ani10122385. [PMID: 33322839 PMCID: PMC7764440 DOI: 10.3390/ani10122385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022] Open
Abstract
The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were -0.003, -0.01 and -0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.
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Affiliation(s)
- Maria Giuseppina Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 20133 Milano, Italy;
| | - Mario Vevey
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy; (M.V.); (V.B.)
| | - Veruska Blanchet
- Associazione Nazionale Bovini di Razza Valdostana, Fraz. Favret, 5, 11020 Gressan, Italy; (M.V.); (V.B.)
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (R.M.); (C.S.)
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università degli Studi di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (R.M.); (C.S.)
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 20133 Milano, Italy;
- Correspondence: ; Tel.: +39-02-5033-4583
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23
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Zinovieva NA, Dotsev AV, Sermyagin AA, Deniskova TE, Abdelmanova AS, Kharzinova VR, Sölkner J, Reyer H, Wimmers K, Brem G. Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis. PLoS One 2020; 15:e0242200. [PMID: 33196682 PMCID: PMC7668599 DOI: 10.1371/journal.pone.0242200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.
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Affiliation(s)
- Natalia Anatolievna Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
- * E-mail:
| | - Arsen Vladimirovich Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Alexander Alexandrovich Sermyagin
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Tatiana Evgenievna Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Alexandra Sergeevna Abdelmanova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Veronika Ruslanovna Kharzinova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology [FBN], Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology [FBN], Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine [VMU], Vienna, Austria
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Peripolli E, Reimer C, Ha NT, Geibel J, Machado MA, Panetto JCDC, do Egito AA, Baldi F, Simianer H, da Silva MVGB. Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data. BMC Genomics 2020; 21:624. [PMID: 32917133 PMCID: PMC7488563 DOI: 10.1186/s12864-020-07035-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. RESULTS A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. CONCLUSION The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
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Affiliation(s)
- Elisa Peripolli
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, 14884-900, Brazil
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Ngoc-Thuy Ha
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Johannes Geibel
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Marco Antonio Machado
- National Council for Scientific and Technological Development (CNPq), Lago Sul, 71605-001, Brazil
- Embrapa Dairy Cattle, Juiz de Fora, 36038-330, Brazil
| | | | | | - Fernando Baldi
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, 14884-900, Brazil
| | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
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25
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Ghoreishifar SM, Eriksson S, Johansson AM, Khansefid M, Moghaddaszadeh-Ahrabi S, Parna N, Davoudi P, Javanmard A. Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genet Sel Evol 2020; 52:52. [PMID: 32887549 PMCID: PMC7487911 DOI: 10.1186/s12711-020-00571-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023] Open
Abstract
Background Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). Conclusions We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden.
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | - Nahid Parna
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | - Arash Javanmard
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
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Edea Z, Jung KS, Shin SS, Yoo SW, Choi JW, Kim KS. Signatures of positive selection underlying beef production traits in Korean cattle breeds. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:293-305. [PMID: 32568261 PMCID: PMC7288235 DOI: 10.5187/jast.2020.62.3.293] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/15/2020] [Indexed: 01/01/2023]
Abstract
The difference in the breeding programs and population history may have diversely
shaped the genomes of Korean native cattle breeds. In the absence of phenotypic
data, comparisons of breeds that have been subjected to different selective
pressures can aid to identify genomic regions and genes controlling qualitative
and complex traits. In this study to decipher genetic variation and identify
evidence of divergent selection, 3 Korean cattle breeds were genotyped using the
recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array.
The three Korean cattle breeds clustered according to their coat color
phenotypes and breeding programs. The Heugu breed reliably showed smaller
effective population size at all generations considered. Across the autosomal
chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and
Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the
two pairwise comparisons. The most important signals of selection were detected
on bovine chromosomes 14 (24.39–25.13 Mb) and 18 (13.34–15.07 Mb),
containing genes related to body size, and coat color (XKR4,
LYN, PLAG1, SDR16C5,
TMEM68, CDH15, MC1R, and
GALNS). Some of the candidate genes are also associated
with meat quality traits (ACSF3, EIF2B1,
BANP, APCDD1, and GALM)
and harbor quantitative trait locus (QTL) for beef production traits. Further
functional analysis revealed that the candidate genes (DBI,
ACSF3, HINT2, GBA2,
AGPAT5, SCAP, ELP6,
APOB, and RBL1) were involved in gene
ontology (GO) terms relevant to meat quality including fatty acid oxidation,
biosynthesis, and lipid storage. Candidate genes previously known to affect beef
production and quality traits could be used in the beef cattle selection
strategies.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kyoung Sub Jung
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Sung-Sub Shin
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Song-Won Yoo
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Jae Won Choi
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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27
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Butty AM, Chud TCS, Miglior F, Schenkel FS, Kommadath A, Krivushin K, Grant JR, Häfliger IM, Drögemüller C, Cánovas A, Stothard P, Baes CF. High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data. Sci Rep 2020; 10:8044. [PMID: 32415111 PMCID: PMC7229195 DOI: 10.1038/s41598-020-64680-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/15/2020] [Indexed: 12/15/2022] Open
Abstract
Multiple methods to detect copy number variants (CNV) relying on different types of data have been developed and CNV have been shown to have an impact on phenotypes of numerous traits of economic importance in cattle, such as reproduction and immunity. Further improvements in CNV detection are still needed in regard to the trade-off between high-true and low-false positive variant identification rates. Instead of improving single CNV detection methods, variants can be identified in silico with high confidence when multiple methods and datasets are combined. Here, CNV were identified from whole-genome sequences (WGS) and genotype array (GEN) data on 96 Holstein animals. After CNV detection, two sets of high confidence CNV regions (CNVR) were created that contained variants found in both WGS and GEN data following an animal-based (n = 52) and a population-based (n = 36) pipeline. Furthermore, the change in false positive CNV identification rates using different GEN marker densities was evaluated. The population-based approach characterized CNVR, which were more often shared among animals (average 40% more samples per CNVR) and were more often linked to putative functions (48 vs 56% of CNVR) than CNV identified with the animal-based approach. Moreover, false positive identification rates up to 22% were estimated on GEN information. Further research using larger datasets should use a population-wide approach to identify high confidence CNVR.
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Affiliation(s)
- Adrien M Butty
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Tatiane C S Chud
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Arun Kommadath
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Kirill Krivushin
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jason R Grant
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, BE, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, BE, Switzerland
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada. .,Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, BE, Switzerland.
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28
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Aramburu O, Ceballos F, Casanova A, Le Moan A, Hemmer-Hansen J, Bekkevold D, Bouza C, Martínez P. Genomic Signatures After Five Generations of Intensive Selective Breeding: Runs of Homozygosity and Genetic Diversity in Representative Domestic and Wild Populations of Turbot ( Scophthalmus maximus). Front Genet 2020; 11:296. [PMID: 32346384 PMCID: PMC7169425 DOI: 10.3389/fgene.2020.00296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
Massive genotyping of single nucleotide polymorphisms (SNP) has opened opportunities for analyzing the way in which selection shapes genomes. Artificial or natural selection usually leaves genomic signatures associated with selective sweeps around the responsible locus. Strong selective sweeps are most often identified either by lower genetic diversity than the genomic average and/or islands of runs of homozygosity (ROHi). Here, we conducted an analysis of selective sweeps in turbot (Scophthalmus maximus) using two SNP datasets from a Northeastern Atlantic population (36 individuals) and a domestic broodstock (46 individuals). Twenty-six families (∼ 40 offspring per family) from this broodstock and three SNP datasets applying differing filtering criteria were used to adjust ROH calling parameters. The best-fitted genomic inbreeding estimate (FROH) was obtained by the sum of ROH longer than 1 Mb, called using a 21,615 SNP panel, a sliding window of 37 SNPs and one heterozygous SNP per window allowed. These parameters were used to obtain the ROHi distribution in the domestic and wild populations (49 and 0 ROHi, respectively). Regions with higher and lower genetic diversity within each population were obtained using sliding windows of 37 SNPs. Furthermore, those regions were mapped in the turbot genome against previously reported genetic markers associated with QTL (Quantitative Trait Loci) and outlier loci for domestic or natural selection to identify putative selective sweeps. Out of the 319 and 278 windows surpassing the suggestive pooled heterozygosity thresholds (ZHp) in the wild and domestic population, respectively, 78 and 54 were retained under more restrictive ZHp criteria. A total of 116 suggestive windows (representing 19 genomic regions) were linked to either QTL for production traits, or outliers for divergent or balancing selection. Twenty-four of them (representing 3 genomic regions) were retained under stricter ZHp thresholds. Eleven QTL/outlier markers were exclusively found in suggestive regions of the domestic broodstock, 7 in the wild population and one in both populations; one (broodstock) and two (wild) of those were found in significant regions retained under more restrictive ZHp criteria in the broodstock and the wild population, respectively. Genome mining and functional enrichment within regions associated with selective sweeps disclosed relevant genes and pathways related to aquaculture target traits, including growth and immune-related pathways, metabolism and response to hypoxia, which showcases how this genome atlas of genetic diversity can be a valuable resource to look for candidate genes related to natural or artificial selection in turbot populations.
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Affiliation(s)
- Oscar Aramburu
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Johannesburg, South Africa
| | - Adrián Casanova
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alan Le Moan
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Jakob Hemmer-Hansen
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Lugo, Spain.,Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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29
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Karimi K, Farid AH, Sargolzaei M, Myles S, Miar Y. Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data. Front Genet 2020; 11:223. [PMID: 32231688 PMCID: PMC7083153 DOI: 10.3389/fgene.2020.00223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
Knowledge of linkage disequilibrium (LD) patterns is necessary to determine the minimum density of markers required for genomic studies and to infer historical changes as well as inbreeding events in the populations. In this study, we used genotyping-by-sequencing (GBS) approach to detect single nucleotide polymorphisms (SNPs) across American mink genome and further to estimate LD, effective population size (Ne), and inbreeding rates based on excess of homozygosity (FHOM) and runs of homozygosity (ROH). A GBS assay was constructed based on the sequencing of ApeKI-digested libraries from 285 American mink using Illumina HiSeq Sequencer. Data of 13,321 SNPs located on 46 scaffolds was used to perform LD analysis. The average LD (r2 ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r2 < 0.2 was observed at inter-marker distances of >40 kb, suggesting that at least 60,000 informative SNPs would be required for genomic selection in American mink. The Ne was estimated to be 116 at five generations ago. In addition, the most rapid decline of population size was observed between 100 and 200 generations ago. Our results showed that short extensions of homozygous genotypes (500 kb to 1 Mb) were abundant across the genome and accounted for 33% of all ROH identified. The average inbreeding coefficient based on ROH longer than 1 Mb was 0.132 ± 0.042. The estimations of FHOM ranged from −0.44 to 0.34 among different samples with an average of 0.15 over all individuals. This study provided useful insights to determine the density of SNP panel providing enough statistical power and accuracy in genomic studies of American mink. Moreover, these results confirmed that GBS approach can be considered as a useful tool for genomic studies in American mink.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - A Hossain Farid
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,Select Sires Inc., Plain City, OH, United States
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
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30
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Bhati M, Kadri NK, Crysnanto D, Pausch H. Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data. BMC Genomics 2020; 21:27. [PMID: 31914939 PMCID: PMC6950892 DOI: 10.1186/s12864-020-6446-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/31/2019] [Indexed: 02/07/2023] Open
Abstract
Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10− 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.
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Affiliation(s)
- Meenu Bhati
- Animal Genomics, ETH Zürich, Zürich, Switzerland.
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31
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Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed. Genes Genomics 2019; 42:203-215. [DOI: 10.1007/s13258-019-00888-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
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32
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Banos G, Clark EL, Bush SJ, Dutta P, Bramis G, Arsenos G, Hume DA, Psifidi A. Genetic and genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep. PLoS One 2019; 14:e0214346. [PMID: 31765378 PMCID: PMC6876840 DOI: 10.1371/journal.pone.0214346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/31/2019] [Indexed: 11/19/2022] Open
Abstract
Milk yield is the most important dairy sheep trait and constitutes the key genetic improvement goal via selective breeding. Mastitis is one of the most prevalent diseases, significantly impacting on animal welfare, milk yield and quality, while incurring substantial costs. Our objectives were to determine the feasibility of a concomitant genetic improvement programme for enhanced milk production and resistance to mastitis. Individual records for milk yield, and four mastitis-related traits (milk somatic cell count, California Mastitis Test score, total viable bacterial count in milk and clinical mastitis presence) were collected monthly throughout lactation for 609 ewes of the Chios breed. All ewes were genotyped with a mastitis specific custom-made 960 single nucleotide polymorphism (SNP) array. We performed targeted genomic association studies, (co)variance component estimation and pathway enrichment analysis, and characterised gene expression levels and the extent of allelic expression imbalance. Presence of heritable variation for milk yield was confirmed. There was no significant genetic correlation between milk yield and mastitis traits. Environmental factors appeared to favour both milk production and udder health. There were no overlapping of SNPs associated with mastitis resistance and milk yield in Chios sheep. Furthermore, four distinct Quantitative Trait Loci (QTLs) affecting milk yield were detected on chromosomes 2, 12, 16 and 19, in locations other than those previously identified to affect mastitis resistance. Five genes (DNAJA1, GHR, LYPLA1, NUP35 and OXCT1) located within the QTL regions were highly expressed in both the mammary gland and milk transcriptome, suggesting involvement in milk synthesis and production. Furthermore, the expression of two of these genes (NUP35 and OXCT1) was enriched in immune tissues implying a potentially pleiotropic effect or likely role in milk production during udder infection, which needs to be further elucidated in future studies. In conclusion, the absence of genetic antagonism between milk yield and mastitis resistance suggests that simultaneous genetic improvement of both traits be achievable.
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Affiliation(s)
- Georgios Banos
- Scotland’s Rural College, Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Emily L. Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Stephen J. Bush
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, England, United Kingdom
| | - Prasun Dutta
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
| | - Georgios Bramis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Arsenos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - David A. Hume
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - Androniki Psifidi
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom
- Royal Veterinary College, University of London, Hatfield, England, United Kingdom
- * E-mail: ,
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33
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Zhou J, Liu L, Chen CJ, Zhang M, Lu X, Zhang Z, Huang X, Shi Y. Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle. BMC Genomics 2019; 20:827. [PMID: 31703627 PMCID: PMC6842163 DOI: 10.1186/s12864-019-6224-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/24/2019] [Indexed: 01/01/2023] Open
Abstract
Background Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore more critical for dual-purpose cattle to increase net income and maintain well-being. With dual-purpose Xinjiang Brown cattle adapted to the Xinjiang Region in northwestern China, we conducted genome-wide association studies (GWAS) to dissect the genetic architecture related to milk, reproductive, and mastitis resistance traits. Phenotypic data were collected for 2410 individuals measured during 1995–2017. By adding another 445 ancestors, a total of 2855 related individuals were used to derive estimated breeding values for all individuals, including the 2410 individuals with phenotypes. Among phenotyped individuals, we genotyped 403 cows with the Illumina 150 K Bovine BeadChip. Results GWAS were conducted with the FarmCPU (Fixed and random model circulating probability unification) method. We identified 12 markers significantly associated with six of the 10 traits under the threshold of 5% after a Bonferroni multiple test correction. Seven of these SNPs were in QTL regions previously identified to be associated with related traits. One identified SNP, BovineHD1600006691, was significantly associated with both age at first service and age at first calving. This SNP directly overlapped a QTL previously reported to be associated with calving ease. Within 160 Kb upstream and downstream of each significant SNP identified, we speculated candidate genes based on functionality. Four of the SNPs were located within four candidate genes, including CDH2, which is linked to milk fat percentage, and GABRG2, which is associated with milk protein yield. Conclusions These findings are beneficial not only for breeding through marker-assisted selection, but also for genome editing underlying the related traits to enhance the overall performance of dual-purpose cattle.
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Affiliation(s)
- Jinghang Zhou
- School of Agriculture, Ningxia University, Yinchuan, China.,Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Liyuan Liu
- School of Agriculture, Ningxia University, Yinchuan, China.,Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Chunpeng James Chen
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Menghua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Xin Lu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA.
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China.
| | - Yuangang Shi
- School of Agriculture, Ningxia University, Yinchuan, China.
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34
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Yin T, Jaeger M, Scheper C, Grodkowski G, Sakowski T, Klopčič M, Bapst B, König S. Multi-breed genome-wide association studies across countries for electronically recorded behavior traits in local dual-purpose cows. PLoS One 2019; 14:e0221973. [PMID: 31665138 PMCID: PMC6821105 DOI: 10.1371/journal.pone.0221973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/16/2019] [Indexed: 12/20/2022] Open
Abstract
Basic bovine behavior is a crucial parameter influencing cattle domestication. In addition, behavior has an impact on cattle productivity, welfare and adaptation. The aim of the present study was to infer quantitative genetic and genomic mechanisms contributing to natural dual-purpose cow behavior in grazing systems. In this regard, we genotyped five dual-purpose breeds for a dense SNP marker panel from four different European countries. All cows from the across-country study were equipped with the same electronic recording devices. In this regard, we analyzed 97,049 longitudinal sensor behavior observations from 319 local dual-purpose cows for rumination, feeding, basic activity, high active, not active and ear temperature. According to the specific sensor behaviors and following a welfare protocol, we computed two different welfare indices. For genomic breed characterizations and multi-breed genome-wide association studies, sensor traits and test-day production records were merged with 35,826 SNP markers per cow. For the estimation of variance components, we used the pedigree relationship matrix and a combined similarity matrix that simultaneously included both pedigree and genotypes. Heritabilities for feeding, high active and not active were in a moderate range from 0.16 to 0.20. Estimates were very similar from both relationship matrix-modeling approaches and had quite small standard errors. Heritabilities for the remaining sensor traits (feeding, basic activity, ear temperature) and welfare indices were lower than 0.09. Five significant SNPs on chromosomes 11, 17, 27 and 29 were associated with rumination, and two different SNPs significantly influenced the sensor traits “not active” (chromosome 13) and “feeding” (chromosome 23). Gene annotation analyses inferred 22 potential candidate genes with a false discovery rate lower than 20%, mostly associated with rumination (13 genes) and feeding (8 genes). Mendelian randomization based on genomic variants (i.e., the instrumental variables) was used to infer causal inference between an exposure and an outcome. Significant regression coefficients among behavior traits indicate that all specific behavioral mechanisms contribute to similar physiological processes. The regression coefficients of rumination and feeding on milk yield were 0.10 kg/% and 0.12 kg/%, respectively, indicating their positive influence on dual-purpose cow productivity. Genomically, an improved welfare behavior of grazing cattle, i.e., a higher score for welfare indices, was significantly associated with increased fat and protein percentages.
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Affiliation(s)
- Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Maria Jaeger
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
| | - Gregorz Grodkowski
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Tomasz Sakowski
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Marija Klopčič
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Domzale, Slovenia
| | - Beat Bapst
- Genetic evaluation center, Qualitas AG, Switzerland
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, Gießen, Germany
- * E-mail:
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35
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McHugo GP, Browett S, Randhawa IAS, Howard DJ, Mullen MP, Richardson IW, Park SDE, Magee DA, Scraggs E, Dover MJ, Correia CN, Hanrahan JP, MacHugh DE. A Population Genomics Analysis of the Native Irish Galway Sheep Breed. Front Genet 2019; 10:927. [PMID: 31649720 PMCID: PMC6792165 DOI: 10.3389/fgene.2019.00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022] Open
Abstract
The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as 'at-risk'. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recent genetic history of the breed. These analyses support the hypothesis that British Leicester sheep were used in the formation of the Galway. When compared to conventional and endangered breeds, the Galway breed was intermediate in effective population size, genomic inbreeding and runs of homozygosity. This indicates that, although the Galway breed is declining, it is still relatively genetically diverse and that conservation and management plans informed by genomic information may aid its recovery. The Galway breed also exhibited distinct genomic signatures of artificial or natural selection when compared to other breeds, which highlighted candidate genes that may be involved in production and health traits.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sam Browett
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Imtiaz A S Randhawa
- Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Dawn J Howard
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | - Michael P Mullen
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | | | | | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Erik Scraggs
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - James P Hanrahan
- Animal and Grassland Research and Innovation Centre, Athenry, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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36
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Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle. BMC Genomics 2019; 20:494. [PMID: 31200634 PMCID: PMC6570941 DOI: 10.1186/s12864-019-5822-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 05/21/2019] [Indexed: 01/18/2023] Open
Abstract
Background Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs. Results We performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China. Population genetic analyses revealed the genetic structures of these populations were mostly related to the geographic locations. Notably, we detected 294 and 1263 candidate regions under selection using the di and iHS approaches, respectively. A series of group-specific and breed-specific candidate genes were identified, which are involved in immune response, sexual maturation, stature related, birth and bone weight, embryonic development, coat colors and adaptation. Furthermore, haplotype diversity and network pattern for candidate genes, including LPGAT1, LCORL, PPP1R8, RXFP2 and FANCA, suggest that these genes have been under differential selection pressures in various environmental conditions. Conclusions Our results shed insights into diverse selection during breed formation in Chinese local cattle. These findings may promote the application of genome-assisted breeding for well-adapted local breeds with economic and ecological importance. Electronic supplementary material The online version of this article (10.1186/s12864-019-5822-y) contains supplementary material, which is available to authorized users.
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Zwane AA, Schnabel RD, Hoff J, Choudhury A, Makgahlela ML, Maiwashe A, Van Marle-Koster E, Taylor JF. Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa. Front Genet 2019; 10:273. [PMID: 30988672 PMCID: PMC6452414 DOI: 10.3389/fgene.2019.00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. The objective of this study was to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger, and Nguni) using whole genome sequencing. DNA was extracted from blood and hair samples, quantified and prepared at 50 ng/μl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. Annotation of the identified variants classified them into functional categories. Within the coding regions, about 30% of the SNPs were non-synonymous substitutions that encode for alternate amino acids. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Gene ontology terms identified genes such as MLANA, SYT10, and CDC42EP5 that have been associated with coat color in mouse, and ADAMS3, DNAJC3, and PAG5 genes have been associated with fertility in cattle. Further analysis of the variants detected 688 candidate selective sweeps (ZHp Z-scores ≤ -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZHp scores ≤-5). We also identified 96 regions with extremely low ZHp Z-scores (≤-6) in Afrikaner and Nguni. Genes such as KIT and MITF that have been associated with skin pigmentation in cattle and CACNA1C, which has been associated with biopolar disorder in human, were identified in these regions. This study provides the first analysis of sequence data to discover SNPs in indigenous South African cattle breeds. The information will play an important role in our efforts to understand the genetic history of our cattle and in designing appropriate breed improvement programmes.
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Affiliation(s)
- Avhashoni A. Zwane
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
- Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jesse Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Ananyo Choudhury
- Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Mahlako Linah Makgahlela
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Azwihangwisi Maiwashe
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Este Van Marle-Koster
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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Weldenegodguad M, Popov R, Pokharel K, Ammosov I, Ming Y, Ivanova Z, Kantanen J. Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions. Front Genet 2019; 9:728. [PMID: 30687392 PMCID: PMC6336893 DOI: 10.3389/fgene.2018.00728] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/22/2018] [Indexed: 12/30/2022] Open
Abstract
Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.
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Affiliation(s)
- Melak Weldenegodguad
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ruslan Popov
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
| | - Kisun Pokharel
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Innokentyi Ammosov
- Board of Agricultural Office of Eveno-Bytantaj Region, Batagay-Alyta, Russia
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zoya Ivanova
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
| | - Juha Kantanen
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
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Fonseca PADS, dos Santos FC, Lam S, Suárez-Vega A, Miglior F, Schenkel FS, Diniz LDAF, Id-Lahoucine S, Carvalho MRS, Cánovas A. Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results. J Anim Sci 2018; 96:4978-4999. [PMID: 30304443 PMCID: PMC6276581 DOI: 10.1093/jas/sky382] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022] Open
Abstract
Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency. Several genome-wide association studies (GWAS) have identified genomic regions associated with these fertility traits. The aims of this study were as follows: 1) to perform a systematic review of GWAS results for spermatic and testicular traits in cattle and 2) to identify key functional candidate genes for these traits. The identification of functional candidate genes was performed using a systems biology approach, where genes shared between traits and studies were evaluated by a guilt by association gene prioritization (GUILDify and ToppGene software) in order to identify the best functional candidates. These candidate genes were integrated and analyzed in order to identify overlapping patterns among traits and breeds. Results showed that GWAS for testicular-related traits have been developed for beef breeds only, whereas the majority of GWAS for spermatic-related traits were conducted using dairy breeds. When comparing traits measured within the same study, the highest number of genes shared between different traits was observed, indicating a high impact of the population genetic structure and environmental effects. Several chromosomal regions were enriched for functional candidate genes associated with fertility traits. Moreover, multiple functional candidate genes were enriched for markers in a species-specific basis, taurine (Bos taurus) or indicine (Bos indicus). For the different candidate regions identified in the GWAS in the literature, functional candidate genes were detected as follows: B. Taurus chromosome X (BTX) (TEX11, IRAK, CDK16, ATP7A, ATRX, HDAC6, FMR1, L1CAM, MECP2, etc.), BTA17 (TRPV4 and DYNLL1), and BTA14 (MOS, FABP5, ZFPM2). These genes are responsible for regulating important metabolic pathways or biological processes associated with fertility, such as progression of spermatogenesis, control of ciliary activity, development of Sertoli cells, DNA integrity in spermatozoa, and homeostasis of testicular cells. This study represents the first systematic review on male fertility traits in cattle using a system biology approach to identify key candidate genes for these traits.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Stephanie Lam
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Aroa Suárez-Vega
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Filippo Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Samir Id-Lahoucine
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
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Fonseca PADS, Id-Lahoucine S, Reverter A, Medrano JF, Fortes MS, Casellas J, Miglior F, Brito L, Carvalho MRS, Schenkel FS, Nguyen LT, Porto-Neto LR, Thomas MG, Cánovas A. Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle. PLoS One 2018; 13:e0205295. [PMID: 30335783 PMCID: PMC6193631 DOI: 10.1371/journal.pone.0205295] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
The identification of biological processes related to the regulation of complex traits is a difficult task. Commonly, complex traits are regulated through a multitude of genes contributing each to a small part of the total genetic variance. Additionally, some loci can simultaneously regulate several complex traits, a phenomenon defined as pleiotropy. The lack of understanding on the biological processes responsible for the regulation of these traits results in the decrease of selection efficiency and the selection of undesirable hitchhiking effects. The identification of pleiotropic key-regulator genes can assist in developing important tools for investigating biological processes underlying complex traits. A multi-breed and multi-OMICs approach was applied to study the pleiotropic effects of key-regulator genes using three independent beef cattle populations evaluated for fertility traits. A pleiotropic map for 32 traits related to growth, feed efficiency, carcass and meat quality, and reproduction was used to identify genes shared among the different populations and breeds in pleiotropic regions. Furthermore, data-mining analyses were performed using the Cattle QTL database (CattleQTLdb) to identify the QTL category annotated in the regions around the genes shared among breeds. This approach allowed the identification of a main gene network (composed of 38 genes) shared among breeds. This gene network was significantly associated with thyroid activity, among other biological processes, and displayed a high regulatory potential. In addition, it was possible to identify genes with pleiotropic effects related to crucial biological processes that regulate economically relevant traits associated with fertility, production and health, such as MYC, PPARG, GSK3B, TG and IYD genes. These genes will be further investigated to better understand the biological processes involved in the expression of complex traits and assist in the identification of functional variants associated with undesirable phenotypes, such as decreased fertility, poor feed efficiency and negative energetic balance.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Samir Id-Lahoucine
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Juan F. Medrano
- University of California-Davis, Department of Animal Science, Davis, California, United States of America
| | - Marina S. Fortes
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Joaquim Casellas
- Universitat Autònoma de Barcelona, Departament de Ciència Animal i dels Aliments, Barcelona, Bellaterra, Barcelona, Spain
| | - Filippo Miglior
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- Canadian Dairy Network, Guelph, Ontario, Canada
| | - Luiz Brito
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Maria Raquel S. Carvalho
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Flávio S. Schenkel
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Loan T. Nguyen
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Laercio R. Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Milton G. Thomas
- Colorado State University, Department of Animal Science, Fort-Colins, Colorado, United States of America
| | - Angela Cánovas
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- * E-mail:
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41
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Rodriguez-Valera Y, Renand G, Naves M, Fonseca-Jiménez Y, Moreno-Probance TI, Ramos-Onsins S, Rocha D, Ramayo-Caldas Y. Genetic diversity and selection signatures of the beef 'Charolais de Cuba' breed. Sci Rep 2018; 8:11005. [PMID: 30030481 PMCID: PMC6054659 DOI: 10.1038/s41598-018-29453-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/12/2018] [Indexed: 01/19/2023] Open
Abstract
In this study, we used BovineSNP50 Genotyping BeadChip data to estimate the structure, putative ancestral origin as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions of the 'Charolais de Cuba' (CHCU) breed. According to a principal component analysis, CHCU samples cluster together with taurine breeds with an estimated 93% of taurus ancestral alleles. Despite the short period since importation, we detected differentiation (Fst = 0.049) between the French Charolaise (CHA) and CHCU. However, CHA breed was the closest breed to CHCU followed by other hybrids breed with a clear CHA origin. Linkage disequilibrium (r2) decay tends to be lower in CHCU compared to CHA probably due to a less intense artificial selection programs of CHCU. Signals of recent adaptation to tropical conditions between CHCU and CHA were identified. Genes mapping within those regions reflect different functions related to immunity, metabolic changes and heat tolerance (CHCU) and muscle development and meat quality (CHA) that may have had an important role in the phenotypic differentiation of these breeds. Further studies will expand our knowledge on the molecular basis of adaptation of cattle to tropical conditions and molecular process associated with meat quality traits.
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Affiliation(s)
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Michel Naves
- UR143, Unité de Recherches Zootechniques, Institut National de la Recherche Agronomique, Guadeloupe, France
| | | | | | - Sebastian Ramos-Onsins
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), Campus UAB, Bellaterra, 08193, Spain
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Yuliaxis Ramayo-Caldas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, 08140, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
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42
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Avila F, Mickelson JR, Schaefer RJ, McCue ME. Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations. Front Genet 2018; 9:249. [PMID: 30105047 PMCID: PMC6060370 DOI: 10.3389/fgene.2018.00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/22/2018] [Indexed: 11/13/2022] Open
Abstract
Selective breeding for athletic performance in various disciplines has resulted in population stratification within the American Quarter Horse (QH) breed. The goals of this study were to utilize high density genotype data to: (1) identify genomic regions undergoing positive selection within and among QH subpopulations; (2) investigate haplotype structure within each QH subpopulation; and (3) identify candidate genes within genomic regions of interest (ROI), as well as biological pathways, predicted to play a role in elite performance in each group. For that, 65K SNP genotyping data on 143 elite individuals from 6 QH subpopulations (cutting, halter, racing, reining, western pleasure, and working cow) were imputed to 2M SNPs. Signatures of selection were identified using FST-based (di ) and haplotype-based (hapFLK) analyses, accompanied by identification of local haplotype structure and sharing within subpopulations (hapQTL). Regions undergoing positive selection were identified on all 31 autosomes, and ROI on 2 chromosomes were identified by all 3 methods combined. Genes within each ROI were retrieved and used to identify pathways and genes that might contribute to performance in each subpopulation. These included, among others, candidate genes associated with skeletal muscle development, metabolism, and central nervous system development. This work improves our understanding of equine breed development, and provides breeders with a better understanding of how selective breeding impacts the performance of QH populations.
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Affiliation(s)
- Felipe Avila
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Robert J Schaefer
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Molly E McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
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Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics 2017; 18:977. [PMID: 29258433 PMCID: PMC5735816 DOI: 10.1186/s12864-017-4318-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/17/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. RESULTS Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. CONCLUSIONS This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Inna S Povolotskaya
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Javier Quilez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Oscar Ramirez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Vetgenomics, 08193, Barcelona, Spain
| | - Gabriel Santpere
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel Gomez-Sanchez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Adam H Freedman
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - John Novembre
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Arcadi Navarro
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain
| | - Adam Boyko
- Cornell University, Department of Biological Statistics and Computational Biology, New York, NY, 14853, USA
| | - Robert Wayne
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Carles Vilà
- Estación Biológica de Doñana EBD-CSIC, Department of Integrative Ecology, 41092, Sevilla, Spain
| | - Belen Lorente-Galdos
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain.
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Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
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Signer-Hasler H, Burren A, Neuditschko M, Frischknecht M, Garrick D, Stricker C, Gredler B, Bapst B, Flury C. Population structure and genomic inbreeding in nine Swiss dairy cattle populations. Genet Sel Evol 2017; 49:83. [PMID: 29115934 PMCID: PMC5674839 DOI: 10.1186/s12711-017-0358-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 10/26/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (F ROH) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). RESULTS The levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on F ST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of F ROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (F ROH: 0.027), OB (F ROH: 0.029), and SI (F ROH: 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (F ROH: 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26. CONCLUSIONS The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service results in more sires having progeny at each generation and thus this breeding practice is likely the major reason for the remarkable levels of genetic diversity retained within these populations. The fact that the EV population is regionally restricted and its small census size of herd-book cows explain its high level of genomic inbreeding.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Alexander Burren
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Mirjam Frischknecht
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
- Qualitas AG, Zug, Switzerland
| | | | | | | | | | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
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46
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Gutiérrez-Gil B, Esteban-Blanco C, Wiener P, Chitneedi PK, Suarez-Vega A, Arranz JJ. High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds. Genet Sel Evol 2017; 49:81. [PMID: 29115919 PMCID: PMC5674817 DOI: 10.1186/s12711-017-0354-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/19/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. RESULTS Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included. CONCLUSIONS Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.
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Affiliation(s)
- Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
- Fundación Centro Supercomputación de Castilla y León, Campus de Vegazana, León, 24071 Spain
| | - Pamela Wiener
- Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - Praveen Krishna Chitneedi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Aroa Suarez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Juan-Jose Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
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47
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Fleming DS, Weigend S, Simianer H, Weigend A, Rothschild M, Schmidt C, Ashwell C, Persia M, Reecy J, Lamont SJ. Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure. G3 (BETHESDA, MD.) 2017; 7:1525-1537. [PMID: 28341699 PMCID: PMC5427493 DOI: 10.1534/g3.117.041228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/15/2017] [Indexed: 01/11/2023]
Abstract
Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST , integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population's indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.
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Affiliation(s)
| | | | | | | | | | | | - Chris Ashwell
- North Carolina State University, Raleigh, North Carolina 27695
| | - Mike Persia
- Virginia Tech University, Blacksburg, Virginia 24061
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48
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Stainton JJ, Charlesworth B, Haley CS, Kranis A, Watson K, Wiener P. Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens. J Anim Breed Genet 2017; 134:87-97. [PMID: 27349343 PMCID: PMC5363361 DOI: 10.1111/jbg.12228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022]
Abstract
The development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high-density SNP data from a broiler chicken line to detect low-diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity increasing asymptotically from a low level. These regions were larger and thus generally included more genes. Several candidate genes for broiler traits were found within these 'regression regions', including IGF1, GPD2 and MTNR1AI. The results suggest that the identification of zero-diversity regions is too restrictive for characterizing regions under selection, but that regions showing patterns of diversity along the chromosome that are consistent with selective sweeps contain a number of genes that are functional candidates for involvement in broiler development. Many regions identified in this study overlap or are close to regions identified in layer chicken populations, possibly due to their shared precommercialization history or to shared selection pressures between broilers and layers.
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Affiliation(s)
- J J Stainton
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - B Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - C S Haley
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - A Kranis
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.,Aviagen Ltd, Edinburgh, UK
| | | | - P Wiener
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
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49
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Brito LF, Kijas JW, Ventura RV, Sargolzaei M, Porto-Neto LR, Cánovas A, Feng Z, Jafarikia M, Schenkel FS. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics 2017; 18:229. [PMID: 28288562 PMCID: PMC5348779 DOI: 10.1186/s12864-017-3610-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. Results The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. Conclusions In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luiz F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
| | - James W Kijas
- CSIRO Agriculture & Food, Brisbane, Queensland, Australia
| | - Ricardo V Ventura
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Beef Improvement Opportunities, Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Canadian Centre for Swine Improvement Inc., Ottawa, Ontario, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
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50
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Seroussi E, Rosov A, Shirak A, Lam A, Gootwine E. Unveiling genomic regions that underlie differences between Afec-Assaf sheep and its parental Awassi breed. Genet Sel Evol 2017; 49:19. [PMID: 28187715 PMCID: PMC5301402 DOI: 10.1186/s12711-017-0296-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Sheep production in Israel has improved by crossing the fat-tailed local Awassi breed with the East Friesian and later, with the Booroola Merino breed, which led to the formation of the highly prolific Afec-Assaf strain. This strain differs from its parental Awassi breed in morphological traits such as tail and horn size, coat pigmentation and wool characteristics, as well as in production, reproductive and health traits. To identify major genes associated with the formation of the Afec-Assaf strain, we genotyped 41 Awassi and 141 Afec-Assaf sheep using the Illumina Ovine SNP50 BeadChip array, and analyzed the results with PLINK and EMMAX software. The detected variable genomic regions that differed between Awassi and Afec-Assaf sheep (variable genomic regions; VGR) were compared to selection signatures that were reported in 48 published genome-wide association studies in sheep. Because the Afec-Assaf strain, but not the Awassi breed, carries the Booroola mutation, association analysis of BMPR1B used as the test gene was performed to evaluate the ability of this study to identify a VGR that includes such a major gene. RESULTS Of the 20 detected VGR, 12 were novel to this study. A ~7-Mb VGR was identified on Ovies aries chromosome OAR6 where the Booroola mutation is located. Similar to other studies, the most significant VGR was detected on OAR10, in a region that contains candidate genes affecting horn type (RXFP2), climate adaptation (ALOX5AP), fiber diameter (KATNAl1), coat pigmentation (FRY) and genes associated with fat distribution. The VGR on OAR2 included BNC2, which is also involved in controlling coat pigmentation in sheep. Six other VGR contained genes that were shown to be involved in coat pigmentation by analyzing their mammalian orthologues. Genes associated with fat distribution in humans, including GRB14 and COBLL1, were located in additional VGR. Sequencing DNA from Awassi and Afec-Assaf individuals revealed non-synonymous mutations in some of these candidate genes. CONCLUSIONS Our results highlight VGR that differentiate the Awassi breed from the Afec-Assaf strain, some of which may include genes that confer an advantage to Afec-Assaf and Assaf over Awassi sheep with respect to intensive sheep production under Mediterranean conditions.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alexander Rosov
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Andrey Shirak
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Alon Lam
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
| | - Elisha Gootwine
- Institute of Animal Science, ARO, The Volcani Center, PO Box 15159, 7528809 Rishon LeZion, Israel
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