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Sukhija N, Malik AA, Devadasan JM, Dash A, Bidyalaxmi K, Ravi Kumar D, Kousalaya Devi M, Choudhary A, Kanaka KK, Sharma R, Tripathi SB, Niranjan SK, Sivalingam J, Verma A. Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India. Anim Biotechnol 2024; 35:2290521. [PMID: 38088885 DOI: 10.1080/10495398.2023.2290521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.
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Affiliation(s)
- Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, India
| | - Anoop Anand Malik
- TERI School of Advanced Studies, Delhi, India
- The Energy and Resources Institute, North Eastern Regional Centre, Guwahati, India
| | | | | | - Kangabam Bidyalaxmi
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - K K Kanaka
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | | | | | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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Li X, Lan F, Chen X, Yan Y, Li G, Wu G, Sun C, Yang N. Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding. BMC Genomics 2024; 25:638. [PMID: 38926812 PMCID: PMC11210043 DOI: 10.1186/s12864-024-10551-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding. RESULTS In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight. CONCLUSIONS In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.
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Affiliation(s)
- Xiaochang Li
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Fangren Lan
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoman Chen
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Yiyuan Yan
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Guangqi Li
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Guiqin Wu
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
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Gomez Proto G, Mancin E, Sartori C, Mantovani R. Unraveling inbreeding patterns and selection signals in Alpine Grey cattle. Animal 2024; 18:101159. [PMID: 38718700 DOI: 10.1016/j.animal.2024.101159] [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: 11/14/2023] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.
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Affiliation(s)
- G Gomez Proto
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy.
| | - E Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - C Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - R Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environmet, University of Padua, Viale dell'Università, 16, 35020 Legnaro, Italy
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Romanov MN, Shakhin AV, Abdelmanova AS, Volkova NA, Efimov DN, Fisinin VI, Korshunova LG, Anshakov DV, Dotsev AV, Griffin DK, Zinovieva NA. Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka. Genes (Basel) 2024; 15:524. [PMID: 38674458 PMCID: PMC11050503 DOI: 10.3390/genes15040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.
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Affiliation(s)
- Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | - Dmitry N. Efimov
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Vladimir I. Fisinin
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Liudmila G. Korshunova
- Federal State Budget Scientific Institution Federal Scientific Center “All-Russian Research and Technological Poultry Institute”, Sergiev Posad 141311, Moscow Oblast, Russia; (D.N.E.); (V.I.F.); (L.G.K.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center “Zagorsk Experimental Breeding Farm”—Branch of the Federal Research Center “All-Russian Poultry Research and Technological Institute”, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Arsen V. Dotsev
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
| | | | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (A.V.S.); (A.S.A.); (N.A.V.); (A.V.D.)
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Zhao Q, Huang C, Chen Q, Su Y, Zhang Y, Wang R, Su R, Xu H, Liu S, Ma Y, Zhao Q, Ye S. Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat. Animals (Basel) 2024; 14:1246. [PMID: 38672394 PMCID: PMC11047310 DOI: 10.3390/ani14081246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
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Affiliation(s)
- Qian Zhao
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Chang Huang
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yingxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Huijuan Xu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Shucai Liu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
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Sudrajad P, Hartati H, Soewandi BDP, Anwar S, Hapsari AAR, Widi TSM, Bintara S, Maharani D. Population diversity, admixture, and demographic trend of the Sumba Ongole cattle based on genomic data. Anim Biosci 2024; 37:591-599. [PMID: 37946418 PMCID: PMC10915215 DOI: 10.5713/ab.23.0289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/18/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE Sumba Ongole (SO) cattle are valuable breed due to their important role in the development of Indonesian cattle. Despite rapid advances in molecular technology, no genomic studies on SO cattle have been conducted to date. The aim of this study is to provide genomic profile related to the population diversity, admixture, and demographic trends of SO cattle. METHODS Genomic information was gathered from 79 SO cattle using the Illumina Bovine SNP50 v3 Beadchip, and for comparative purposes, additional genotypes from 209 cattle populations worldwide were included. The expected and observed heterozygosity, inbreeding coefficient, pairwise fixation indices between-population, and Nei's genetic distance were examined. Multidimensional scaling, admixture, and treemix analyses were used to investigate the population structure. Based on linkage disequilibrium and effective population size calculations, the demographic trend was observed. RESULTS The findings indicated that the genetic diversity of SO cattle was similar to that of other indicine breeds. SO cattle were genetically related to indicines but not to taurines or Bali cattle. The study further confirmed the close relationship between SO, Ongole, and Nellore cattle. Additionally, a small portion of the Ongole mixture were identified dominant in the SO population at the moment. The study also discovered that SO and Bali cattle (Bos javanicus) could have been ancestors in the development of Ongole Grade cattle, which corresponds to the documented history of Ongolization. Our finding indicate that SO cattle have maintained stability and possess unique traits separate from their ancestors. CONCLUSION In conclusion, the genetic diversity of the SO cattle has been conserved as a result of the growing significance of the present demographic trend. Consistent endeavors are necessary to uphold the fitness of the breed.
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Affiliation(s)
- Pita Sudrajad
- Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, 55281,
Indonesia
- Research Center for Animal Husbandry, Research Organization for Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, 16911,
Indonesia
| | - Hartati Hartati
- Research Center for Animal Husbandry, Research Organization for Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, 16911,
Indonesia
| | - Bayu Dewantoro Putro Soewandi
- Research Center for Animal Husbandry, Research Organization for Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, 16911,
Indonesia
| | - Saiful Anwar
- Research Center for Applied Zoology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911,
Indonesia
| | - Angga Ardhati Rani Hapsari
- Indonesian Research Institute for Animal Production, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Bogor, 16002,
Indonesia
| | | | - Sigit Bintara
- Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, 55281,
Indonesia
| | - Dyah Maharani
- Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta, 55281,
Indonesia
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Barragan AC, Collenberg M, Schwab R, Kersten S, Kerstens MHL, Požárová D, Bezrukov I, Bemm F, Kolár F, Weigel D. Deleterious phenotypes in wild Arabidopsis arenosa populations are common and linked to runs of homozygosity. G3 (BETHESDA, MD.) 2024; 14:jkad290. [PMID: 38124484 PMCID: PMC10917499 DOI: 10.1093/g3journal/jkad290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
In this study, we aimed to systematically assess the frequency at which potentially deleterious phenotypes appear in natural populations of the outcrossing model plant Arabidopsis arenosa, and to establish their underlying genetics. For this purpose, we collected seeds from wild A. arenosa populations and screened over 2,500 plants for unusual phenotypes in the greenhouse. We repeatedly found plants with obvious phenotypic defects, such as small stature and necrotic or chlorotic leaves, among first-generation progeny of wild A. arenosa plants. Such abnormal plants were present in about 10% of maternal sibships, with multiple plants with similar phenotypes in each of these sibships, pointing to a genetic basis of the observed defects. A combination of transcriptome profiling, linkage mapping and genome-wide runs of homozygosity patterns using a newly assembled reference genome indicated a range of underlying genetic architectures associated with phenotypic abnormalities. This included evidence for homozygosity of certain genomic regions, consistent with alleles that are identical by descent being responsible for these defects. Our observations suggest that deleterious alleles with different genetic architectures are segregating at appreciable frequencies in wild A. arenosa populations.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- The Sainsbury Laboratory, Norwich NR4 7UH, UK
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Catalent, 73614 Schorndorf, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Institute of Plant Breeding, University of Hohenheim, 70599 Stuttgart, Germany
| | - Merijn H L Kerstens
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Department of Plant Developmental Biology, Wageningen University and Research, 6708 PB, Wageningen, Netherlands
| | - Doubravka Požárová
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
- The MAMA AI, 100 00 Prague, Czech Republic
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- KWS Saat, 37574 Einbeck, Germany
| | - Filip Kolár
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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Santos MF, Silva MC, Freitas TMS, Dias JM, Moura MI, Juliano RS, Fioravanti CS, Carmo AS. Identification of runs of homozygosity (ROHs) in Curraleiro Pé-Duro and Pantaneiro cattle breeds. Trop Anim Health Prod 2024; 56:92. [PMID: 38430430 DOI: 10.1007/s11250-024-03933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024]
Abstract
This study aimed to identify and characterize runs of homozygosis (ROHs), genes involved in production characteristics and adaptation to tropical systems and to estimate the inbreeding coefficient of Curraleiro Pé-Duro (CPD) and Pantaneiro (PANT), two brazilian locally adapted cattle breeds. The results demonstrated that 79.25% and 54.29% of ROH segments were bigger than 8 Mb in CPD and PANT, respectively, indicating recent inbred matings in the studied population. Six homozygosis islands were identified simultaneously in both breeds, where 175 QTLs and 1072 genes previously described as associated with production traits are located. The inbreeding coefficient (FROH) estimated based on ROHs (FROH) showed that inbreeding is low (2 to 4%), which is different from expected for small populations such as locally adapted ones.
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Affiliation(s)
- M F Santos
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - M C Silva
- Federal University of Grande Dourados, Grande Dourados, Dourados, MS, Brazil
| | - T M S Freitas
- Brasilia University Center of Goiás, São Luís dos Montes Belos, GO, Brazil
- Goiás State University - West Campus, São Luís de Montes Belos, GO, Brazil
| | - J M Dias
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - M I Moura
- Veterinary Medicine Department, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil
| | - R S Juliano
- EMBRAPA - Brazilian Agricultural Research Corporation, Pantanal, MS, Brazil
| | - C S Fioravanti
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - A S Carmo
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil.
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Kar D, Ganguly I, Singh S, Bhatia AK, Dixit SP. Genome-wide runs of homozygosity signatures in diverse Indian goat breeds. 3 Biotech 2024; 14:81. [PMID: 38375512 PMCID: PMC10874352 DOI: 10.1007/s13205-024-03921-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/05/2024] [Indexed: 02/21/2024] Open
Abstract
The present study analyzed ROH and consensus ROH regions in 102 animals of eleven diverse Indian goat (Capra hircus) breeds using whole genome sequencing. A total of 51,705 ROH and 21,271 consensus regions were identified. The mean number of ROH per animal was highest in the meat breed, Jharkhand Black (2693) and lowest in the pashmina breed, Changthangi (60). The average length of ROH (ALROH) was maximum in Kanniadu (974.11 Kb) and minimum in Tellicherry (146.98 Kb). Long ROH is typically associated with more recent inbreeding, whereas short ROH is connected to more ancient inbreeding. The overall ROH-based genomic inbreeding (FROH) was highest for Jharkhand Black (0.602) followed by Kanniadu (0.120) and Sangamneri (0.108) among all breeds. FROH of Jharkhand Black was higher than Kanniadu up to 5 Mb ROH length category. However, in > 20 Mb ROH length category, Kanniadu (0.98) exhibited significantly higher FROH than Jharkhand Black (0.46). This implies that Kanniadu had higher levels of recent inbreeding than Jharkhand Black. Despite this, due to the presence of both recent and ancient inbreeding, Jharkhand Black demonstrated higher overall FROH compared to Kanniadu. ROH patterns revealed dual purpose (meat and dairy) and pashmina breeds as less consanguineous while recent inbreeding was apparent in meat breeds. Analysis of ROH consensus regions identified selection sweeps in key genes governing intramuscular fat deposition, meat tenderisation, lean meat production and carcass weight (CDK4, ALOX15, CASP9, PRDM16, DVL1) in meat breeds; milk fat percentage and mammary gland development (POLD1, NOTCH2, ARHGAP35) in dual purpose (meat and dairy) breeds; while cold adaptation and hair follicle development (APOBEC1, DNAJC3, F2RL1, FGF9) in pashmina breed. MAPK, RAS, BMP and Wnt signaling pathways associated with hair follicle morphogenesis in Changthangi were also identified. PCA analysis based on ROH consensus regions revealed that meat breeds are more diverse than other goat breeds/populations. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03921-y.
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Affiliation(s)
- Dibyasha Kar
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Indrajit Ganguly
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Sanjeev Singh
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Avnish Kumar Bhatia
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - S. P. Dixit
- Division of Animal Genetics, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
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Huang C, Zhao Q, Chen Q, Su Y, Ma Y, Ye S, Zhao Q. Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China. Genes (Basel) 2024; 15:313. [PMID: 38540373 PMCID: PMC10970279 DOI: 10.3390/genes15030313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/25/2024] [Accepted: 02/25/2024] [Indexed: 06/14/2024] Open
Abstract
Runs of Homozygosity (ROH) are continuous homozygous DNA segments in diploid genomes, which have been used to estimate the genetic diversity, inbreeding levels, and genes associated with specific traits in livestock. In this study, we analyzed the resequencing data from 10 local goat breeds in Yunnan province of China and five additional goat populations obtained from a public database. The ROH analysis revealed 21,029 ROH segments across the 15 populations, with an average length of 1.27 Mb, a pattern of ROH, and the assessment of the inbreeding coefficient indicating genetic diversity and varying levels of inbreeding. iHS (integrated haplotype score) was used to analyze high-frequency Single-Nucleotide Polymorphisms (SNPs) in ROH regions, specific genes related to economic traits such as coat color and weight variation. These candidate genes include OCA2 (OCA2 melanosomal transmembrane protein) and MLPH (melanophilin) associated with coat color, EPHA6 (EPH receptor A6) involved in litter size, CDKAL1 (CDK5 regulatory subunit associated protein 1 like 1) and POMC (proopiomelanocortin) linked to weight variation and some putative genes associated with high-altitude adaptability and immune. This study uncovers genetic diversity and inbreeding levels within local goat breeds in Yunnan province, China. The identification of specific genes associated with economic traits and adaptability provides actionable insights for utilization and conservation efforts.
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Affiliation(s)
- Chang Huang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yinxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (C.H.); (Q.Z.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
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11
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Li W, Wu X, Xiang D, Zhang W, Wu L, Meng X, Huo J, Yin Z, Fu G, Zhao G. Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing. Genes (Basel) 2024; 15:233. [PMID: 38397222 PMCID: PMC10887577 DOI: 10.3390/genes15020233] [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: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.
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Affiliation(s)
- Wenjun Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xudong Wu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Decai Xiang
- Institute of Pig and Animal Research, Yunnan Academy of Animal Husbandry and Veterinary Science, Kunming 650201, China;
| | - Wei Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Lingxiang Wu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xintong Meng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Guowen Fu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
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12
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Rajawat D, Panigrahi M, Nayak SS, Bhushan B, Mishra BP, Dutt T. Dissecting the genomic regions of selection on the X chromosome in different cattle breeds. 3 Biotech 2024; 14:50. [PMID: 38268984 PMCID: PMC10803714 DOI: 10.1007/s13205-023-03905-4] [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: 02/09/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024] Open
Abstract
Mammalian X and Y chromosomes independently evolved from various autosomes approximately 300 million years ago (MYA). To fully understand the relationship between genomic composition and phenotypic diversity arising due to the course of evolution, we have scanned regions of selection signatures on the X chromosome in different cattle breeds. In this study, we have prepared the datasets of 184 individuals of different cattle breeds and explored the complete X chromosome by utilizing four within-population and two between-population methods. There were 23, 25, 30, 17, 17, and 12 outlier regions identified in Tajima's D, CLR, iHS, ROH, FST, and XP-EHH. Bioinformatics analysis showed that these regions harbor important candidate genes like AKAP4 for reproduction in Brown Swiss, MBTS2 for production traits in Brown Swiss and Guernsey, CXCR3 and CITED1 for health traits in Jersey and Nelore, and BMX and CD40LG for regulation of X chromosome inactivation in Nelore and Gir. We identified genes shared among multiple methods, such as TRNAC-GCA and IL1RAPL1, which appeared in Tajima's D, ROH, and iHS analyses. The gene TRNAW-CCA was found in ROH, CLR and iHS analyses. The X chromosome exhibits a distinctive interaction between demographic factors and genetic variations, and these findings may provide new insight into the X-linked selection in different cattle breeds.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - B. P. Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Karnal, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
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13
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Illa SK, Mumtaz S, Nath S, Mukherjee S, Mukherjee A. Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle. J Appl Genet 2024; 65:167-180. [PMID: 38110827 DOI: 10.1007/s13353-023-00816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023]
Abstract
Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average FPED (Pedigree based inbreeding coefficient), FROH (Genomic inbreeding coefficient), FHOM (Inbreeding estimated as the ratio of observed and expected homozygous genotypes), FGRM (Inbreeding estimated on genomic relationship method) and FGRM0.5 (Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.
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Affiliation(s)
- Satish Kumar Illa
- Livestock Research Station, Garividi, Sri Venkateswara Veterinary University, Tirupati, Andhra Pradesh State, India
| | - Shabahat Mumtaz
- Animal Husbandry Department, Kolkata, West Bengal State, India
| | - Sapna Nath
- College of Veterinary Science, Garividi, Sri Venkateswara Veterinary University, Tirupati, Andhra Pradesh State, India
| | - Sabyasachi Mukherjee
- Animal Genetics & Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana State, India.
| | - Anupama Mukherjee
- Animal Genetics & Breeding Division, Indian Council of Agricultural Research (ICAR)-National Dairy Research Institute (NDRI), Karnal, Haryana State, India.
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14
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Chessari G, Criscione A, Marletta D, Crepaldi P, Portolano B, Manunza A, Cesarani A, Biscarini F, Mastrangelo S. Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds. Sci Rep 2024; 14:3. [PMID: 38168531 PMCID: PMC10762050 DOI: 10.1038/s41598-023-49125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.
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Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy.
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Paola Crepaldi
- Dipartimento Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, University of Milan, Via Giovanni Celoria 2, 20133, Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Arianna Manunza
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
- Animal and Dairy Science Department, University of Georgia, 425 River Road, 30602, Athens, GA, USA
| | - Filippo Biscarini
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
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Singh VK, Singh S, Nandhini PB, Bhatia AK, Dixit SP, Ganguly I. Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent. Anim Biotechnol 2023; 34:3483-3494. [PMID: 36592947 DOI: 10.1080/10495398.2022.2162910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1-13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.
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Affiliation(s)
- V K Singh
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Singh
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - P B Nandhini
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - A K Bhatia
- Animal Genetic Resources Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - S P Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - I Ganguly
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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16
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Zhang L, Zhang S, Yuan M, Zhan F, Song M, Shang P, Yang F, Li X, Qiao R, Han X, Li X, Fang M, Wang K. Genome-Wide Association Studies and Runs of Homozygosity to Identify Reproduction-Related Genes in Yorkshire Pig Population. Genes (Basel) 2023; 14:2133. [PMID: 38136955 PMCID: PMC10742578 DOI: 10.3390/genes14122133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Reproductive traits hold considerable economic importance in pig breeding and production. However, candidate genes underpinning the reproductive traits are still poorly identified. In the present study, we executed a genome-wide association study (GWAS) and runs of homozygosity (ROH) analysis using the PorcineSNP50 BeadChip array for 585 Yorkshire pigs. Results from the GWAS identified two genome-wide significant and eighteen suggestive significant single nucleotide polymorphisms (SNPs) associated with seven reproductive traits. Furthermore, we identified candidate genes, including ELMO1, AOAH, INSIG2, NUP205, LYPLAL1, RPL34, LIPH, RNF7, GRK7, ETV5, FYN, and SLC30A5, which were chosen due to adjoining significant SNPs and their functions in immunity, fertilization, embryonic development, and sperm quality. Several genes were found in ROH islands associated with spermatozoa, development of the fetus, mature eggs, and litter size, including INSL6, TAF4B, E2F7, RTL1, CDKN1C, and GDF9. This study will provide insight into the genetic basis for pig reproductive traits, facilitating reproduction improvement using the marker-based selection methods.
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Affiliation(s)
- Lige Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Songyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Meng Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Fengting Zhan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Mingkun Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China;
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (L.Z.); (S.Z.); (M.Y.); (F.Z.); (M.S.); (F.Y.); (X.L.); (R.Q.); (X.H.); (X.L.)
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Chakraborty A, Bisht MS, Saxena R, Mahajan S, Pulikkan J, Sharma VK. Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds. Genes Genomics 2023; 45:1399-1408. [PMID: 37231295 DOI: 10.1007/s13258-023-01401-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Indian cattle breeds (Bos indicus) are known for their remarkable adaptability to hot and humid climates, higher nutritious quality of milk, better disease tolerance, and greater ability to perform in poor feed compared to taurine cattle (Bos taurus). Distinct phenotypic differences are observed among the B. indicus breeds; however, the whole genome sequences were unavailable for these indigenous breeds. OBJECTIVE We aimed to perform whole genome sequencing to construct the draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur (the smallest cattle of the world). METHODS We sequenced the whole genomes using Illumina short-read technology, and constructed de novo and reference-based genome assemblies of these native B. indicus breeds for the first time. RESULTS The draft de novo genome assemblies of B. indicus breeds ranged from 1.98 to 3.42 Gbp. We also constructed the mitochondrial genome assemblies (~ 16.3 Kbp), and yet unavailable 18S rRNA marker gene sequences of these B. indicus breeds. The genome assemblies helped to identify the bovine genes related to distinct phenotypic characteristics and other biological processes for this species compared to B. taurus, which are plausibly responsible for providing better adaptive traits. We also identified the genes that showed sequence variation in dwarf and non-dwarf breeds of B. indicus compared to B. taurus. CONCLUSIONS The genome assemblies of these Indian cattle breeds, the 18S rRNA marker genes, and identification of the distinct genes in B. indicus breeds compared to B. taurus will help in future studies on these cattle species.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Manohar S Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Joby Pulikkan
- Department of Genomic Science, Central University of Kerala, Kasaragod, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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Saif-Ur-Rehman M, Hassan FU, Reecy J, Deng T. Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan. Anim Biotechnol 2023; 34:1384-1396. [PMID: 35044288 DOI: 10.1080/10495398.2022.2026369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.
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Affiliation(s)
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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Saravanan KA, Panigrahi M, Kumar H, Nayak SS, Rajawat D, Bhushan B, Dutt T. Progress and future perspectives of livestock genomics in India: a mini review. Anim Biotechnol 2023; 34:1979-1987. [PMID: 35369840 DOI: 10.1080/10495398.2022.2056046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, UP, India
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20
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Bordonaro S, Chessari G, Mastrangelo S, Senczuk G, Chessa S, Castiglioni B, Tumino S, Marletta D, Criscione A. Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds. Anim Genet 2023; 54:591-605. [PMID: 37381662 DOI: 10.1111/age.13344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023]
Abstract
Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.
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Affiliation(s)
- Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, Università del Molise, Campobasso, Italy
| | - Stefania Chessa
- Dipartimento di Scienze Veterinarie, Università di Torino, Torino, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, National Research Council, Lodi, Italy
| | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
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21
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Sallam AM, Reyer H, Wimmers K, Bertolini F, Aboul-Naga A, Braz CU, Rabee AE. Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds. BMC Genomics 2023; 24:573. [PMID: 37752425 PMCID: PMC10521497 DOI: 10.1186/s12864-023-09679-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
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Affiliation(s)
- Ahmed M Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt.
| | - Henry Reyer
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6b, 18059, Rostock, Germany
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Adel Aboul-Naga
- Animal Production Research Institute, Agricultural Research Center, Dokki, Cairo, Egypt
| | - Camila U Braz
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Alaa Emara Rabee
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 Gregory Dr, Urbana, 61801, USA
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22
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Abdoli R, Mirhoseini SZ, Ghavi Hossein-Zadeh N, Zamani P, Moradi MH, Ferdosi MH, Sargolzaei M, Gondro C. Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep. Heredity (Edinb) 2023; 130:358-367. [PMID: 37016136 PMCID: PMC10238534 DOI: 10.1038/s41437-023-00611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.
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Affiliation(s)
- Ramin Abdoli
- Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Gilan, Iran.
| | - Seyed Ziaeddin Mirhoseini
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran.
| | - Navid Ghavi Hossein-Zadeh
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran
| | - Pouya Zamani
- Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, 65178-33131, Iran
| | - Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arāk, 38156-8-8349, Iran
| | - Mohammad Hossein Ferdosi
- AGBU, a joint venture of NSW Department of Primary Industries and University of New England, University of New England, Armidale, NSW, 2351, Australia
| | - Mehdi Sargolzaei
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada
| | - Cedric Gondro
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA
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23
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Dash S, Singh A, Dixit SP, Kumar A, Behera R. Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India. Trop Anim Health Prod 2023; 55:129. [PMID: 36952060 DOI: 10.1007/s11250-023-03534-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
Abstract
The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (n = 19), Tharparkar (n = 17), and Gir (n = 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (FROH) revealed that Gir had the highest FROH (0.099) proposing more inbreeding rate in this population. Effective population size (Ne) decreased slowly over the last 60 generations and at 13 generations ago; Ne was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (r = 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.
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Affiliation(s)
- Soumya Dash
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India.
- School of Crop Health Policy Support Research, ICAR-National Institute of Biotic Stress Management, Raipur, 493225, Chhattisgarh, India.
| | - Avtar Singh
- Animal Genetics and Breeding Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - S P Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Avnish Kumar
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Rajalaxmi Behera
- Regional Centre, ICAR-Directorate of Poultry Research, Bhubaneswar, 751003, Odisha, India
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Visser C, Lashmar SF, Reding J, Berry DP, van Marle-Köster E. Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds. Front Genet 2023; 14:1136078. [PMID: 37007942 PMCID: PMC10063850 DOI: 10.3389/fgene.2023.1136078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8 Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on Bos taurus autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (FPED) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (FSNP) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (FROH), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and FROH calculated for ROH <4Mb in size) to moderate (HST: 0.584 between FPED and FSNP). Correlations strengthened between FPED and FROH as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.
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Affiliation(s)
- Carina Visser
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Carina Visser,
| | - Simon Frederick Lashmar
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Jason Reding
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Donagh P. Berry
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
- Animal and Grassland Research and Innovation Centre, Teagasc, Co. Cork, Ireland
| | - Esté van Marle-Köster
- Department of Animal Science, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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Bhardwaj S, Singh S, Ganguly I, Bhatia AK, Dixit SP. Deciphering local adaptation of native Indian cattle ( Bos indicus) breeds using landscape genomics and in-silico prediction of deleterious SNP effects on protein structure and function. 3 Biotech 2023; 13:86. [PMID: 36816754 PMCID: PMC9931982 DOI: 10.1007/s13205-023-03493-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023] Open
Abstract
India has 50 registered breeds of native cattle (Bos indicus) which are locally adapted to diverse environmental conditions. This study aimed to investigate the genomic basis of adaptation of native Indian cattle and to predict the impact of key SNPs on the amino acid changes that affect protein function. The Illumina 777 K BovineHD BeadChip was used to genotype 178 native cattle belonging to contrasting landscapes and agro-climatic conditions. The genotype-environment association was investigated with R. SamBada, using 5,74,382 QC passed SNPs and 11 predictor variables (10 multi-collinearity controlled environmental variables and 1 variable as "score of PCA" on ancestry coefficients of individuals). In total, 1,12,780 models were selected as significant (q < 0.05) based on G score. The pathway ontology of the annotated genes revealed many important pathways and genes having a direct and indirect role in cold and hot adaptation. Only ten SNP variants had a SIFT score of < 0.05 (deleterious), and only two of them, each lying in the genes CRYBA1 and USP18, were predicted to be deleterious with high confidence. RaptorX predicted the tertiary structures of proteins encoded by wild and mutant variants of these genes. The quality of the models was determined using Ramachandran plots and RaptorX parameters, indicating that they are accurate. RaptorX and I-Mutant 2.0 softwares revealed significant differences among wild and mutant proteins. Adaptive alleles identified in the present investigation might be responsible for the local adaptation of these cattle breeds. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03493-3.
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Affiliation(s)
- Shivam Bhardwaj
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, 132001 India
| | - Sanjeev Singh
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Indrajit Ganguly
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - Avnish Kumar Bhatia
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
| | - S. P. Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132001 India
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The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India. Genes Genomics 2023; 45:813-825. [PMID: 36807878 DOI: 10.1007/s13258-023-01367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. OBJECTIVE The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. METHODS For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). RESULTS A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. CONCLUSIONS This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.
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Tohidi R, Cue RI, Nazari BM, Pahlavan R. The effect of new and ancestral inbreeding on milk production traits in Iranian Holstein cattle. J Anim Breed Genet 2023; 140:276-286. [PMID: 36637050 DOI: 10.1111/jbg.12755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 12/24/2022] [Indexed: 01/14/2023]
Abstract
Inbreeding depression, the reduction of fitness and performance, is due to an increase in the mating of related individuals. Based on the purge hypothesis, inbreeding and breeding over generations reduce the effect of deleterious alleles responsible for inbreeding depression. Thus, recent inbreeding is assumed to be more harmful than ancestral inbreeding. This study aimed at evaluating the effects of new and ancestral inbreeding on milk, fat and protein production in Iranian Holstein cattle. The secondary objective was to examine the changes in predicted breeding values when the inbreeding effect was included in the model's analysis. To this end, inbreeding coefficients were calculated using the pedigree of 2,394,517 Holstein cattle to achieve these goals. In addition, 419,132 records of milk, fat and protein yields of first parity cows were collected to assess inbreeding depression and breeding values. The average inbreeding coefficients were 0.83% and 1.68% for the whole population and the inbred animals, respectively. A 1% increase in classical pedigree-based inbreeding coefficient was associated with a decrease of 11.99 kg in milk, 0.39 kg in fat and 0.29 kg in protein. The effect of ancestral inbreeding was more detrimental to performance traits than the effect of new inbreeding. This result contradicted the hypothesis of purging. By including the inbreeding coefficient in the model, the rank of animals remained unchanged, but the average predicted breeding values increased. In general, inbreeding depression was observed in Iranian Holstein cows; however, no evidence of purging was observed. The average of inbreeding coefficients was not high in this population, although accounting for inbreeding coefficients in the analytical model did significantly increase the predicted breeding values. It is recommended that the analytical model incorporate the inbreeding coefficient to improve the accuracy of genetic evaluation. In future studies, inbreeding depression should be assessed using genomic data for performance and reproduction traits.
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Affiliation(s)
- Reza Tohidi
- Department of Animal Science, Faculty of Agriculture and Animal Science, University of Torbat-e Jam, Torbat-e Jam, Iran
| | - Roger I Cue
- Animal Science Department, McGill University, Montreal, Québec, Canada
| | | | - Rostam Pahlavan
- Animal Breeding Center and Production Improvement of Iran, Karaj, Iran
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Al Kalaldeh M, Swaminathan M, Podtar V, Jadhav S, Dhanikachalam V, Joshi A, Gibson JP. Detection of genomic regions that differentiate Bos indicus from Bos taurus ancestral breeds for milk yield in Indian crossbred cows. Front Genet 2023; 13:1082802. [PMID: 36699459 PMCID: PMC9868639 DOI: 10.3389/fgene.2022.1082802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction: In India, crossbred cows incorporate the high production of B. taurus dairy breeds and the environmental adaptation of local B. indicus cattle. Adaptation to different environments and selection in milk production have shaped the genetic differences between B. indicus and B. taurus cattle. The aim of this paper was to detect, for milk yield of crossbred cows, quantitative trait loci (QTL) that differentiate B. indicus from B. taurus ancestry, as well as QTL that are segregating within the ancestral breeds. Methods: A total of 123,042 test-day milk records for 4,968 crossbred cows, genotyped with real and imputed 770 K SNP, were used. Breed origins were assigned to haplotypes of crossbred cows, and from that, were assigned to SNP alleles. Results: At a false discovery rate (FDR) of 30%, a large number of genomic regions showed significant effects of B. indicus versus B. taurus origin on milk yield, with positive effects coming from both ancestors. No significant regions were detected for Holstein Friesian (HF) versus Jersey effects on milk yield. Additionally, no regions for SNP alleles segregating within indigenous, within HF, and within Jersey were detected. The most significant effects, at FDR 5%, were found in a region on BTA5 (43.98-49.44 Mbp) that differentiates B. indicus from B. taurus, with an estimated difference between homozygotes of approximately 10% of average yield, in favour of B. indicus origin. Discussion: Our results indicate that evolutionary differences between B. indicus and B. taurus cattle for milk yield, as expressed in crossbred cows, occur at many causative loci across the genome. Although subject to the usual first estimation bias, some of the loci appear to have large effects that might make them useful for genomic selection in crossbreds, if confirmed in subsequent studies.
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Affiliation(s)
- Mohammad Al Kalaldeh
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia,*Correspondence: Mohammad Al Kalaldeh, ; John P. Gibson,
| | - Marimuthu Swaminathan
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Vinod Podtar
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Santoshkumar Jadhav
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Velu Dhanikachalam
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Akshay Joshi
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - John P. Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia,*Correspondence: Mohammad Al Kalaldeh, ; John P. Gibson,
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Neumann GB, Korkuć P, Arends D, Wolf MJ, May K, König S, Brockmann GA. Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing. Front Genet 2023; 13:993959. [PMID: 36712857 PMCID: PMC9875303 DOI: 10.3389/fgene.2022.993959] [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: 07/14/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.
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Affiliation(s)
- Guilherme B. Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Danny Arends
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | - Manuel J. Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A. Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Gudrun A. Brockmann,
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Atmore LM, Martínez-García L, Makowiecki D, André C, Lõugas L, Barrett JH, Star B. Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics. Proc Natl Acad Sci U S A 2022; 119:e2208703119. [PMID: 36282902 PMCID: PMC9659336 DOI: 10.1073/pnas.2208703119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/30/2022] [Indexed: 10/14/2023] Open
Abstract
The world's oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first "industrial" fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies.
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Affiliation(s)
- Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Lourdes Martínez-García
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Carl André
- Department of Marine Sciences–Tjärnö, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, 10120 Tallinn, Estonia
| | - James H. Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7012 Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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Panigrahi M, Kumar H, Saravanan KA, Rajawat D, Sonejita Nayak S, Ghildiyal K, Kaisa K, Parida S, Bhushan B, Dutt T. Trajectory of livestock genomics in South Asia: A comprehensive review. Gene 2022; 843:146808. [PMID: 35973570 DOI: 10.1016/j.gene.2022.146808] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kaiho Kaisa
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Li G, Tang J, Huang J, Jiang Y, Fan Y, Wang X, Ren J. Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds. Front Genet 2022; 13:774196. [PMID: 35559012 PMCID: PMC9086400 DOI: 10.3389/fgene.2022.774196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.
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Affiliation(s)
- Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.,Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Jinyan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang, China
| | - Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
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Liu SH, Ma XY, Hassan FU, Gao TY, Deng TX. Genome-wide analysis of runs of homozygosity in Italian Mediterranean buffalo. J Dairy Sci 2022; 105:4324-4334. [PMID: 35307184 DOI: 10.3168/jds.2021-21543] [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: 11/07/2021] [Accepted: 02/07/2022] [Indexed: 11/19/2022]
Abstract
Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, and distribution of ROH islands using the SNP data sets from 899 Mediterranean buffaloes. A total of 42,433 ROH segments were identified, with an average of 47.20 segments per individual. The ROH comprising mostly shorter segments (1-4 Mb) accounted for approximately 72.29% of all ROH. In contrast, the larger ROH (>8 Mb) class accounted for only 7.97% of all ROH segments. Estimated inbreeding coefficients from ROH (FROH) ranged from 0.0201 to 0.0371. Pearson correlations between FROH and genomic relationship matrix increased with the increase of ROH length. We identified ROH hotspots in 12 genomic regions, located on chromosomes 1, 2, 3, 5, 17, and 19, harboring a total of 122 genes. Protein-protein interaction (PPI) analysis revealed the clustering of these genes into 7 PPI networks. Many genes located in these regions were associated with different production traits. In addition, 5 ROH islands overlapped with cattle quantitative trait loci that were mainly associated with milk traits. These findings revealed the genome-wide autozygosity patterns and inbreeding levels in Mediterranean buffalo. Our study identified many candidate genes related to production traits that could be used to assist in selective breeding for genetic improvement of buffalo.
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Affiliation(s)
- Shen-He Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xiao-Ya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Teng-Yun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ting-Xian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
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Kim YM, Seong HS, Kim YS, Hong JK, Sa SJ, Lee J, Lee JH, Cho KH, Chung WH, Choi JW, Cho ES. Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon. Front Genet 2022; 13:779152. [PMID: 35186025 PMCID: PMC8847790 DOI: 10.3389/fgene.2022.779152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/07/2022] [Indexed: 02/03/2023] Open
Abstract
A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.
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Affiliation(s)
- Yong-Min Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea.,Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Ha-Seung Seong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea.,Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Young-Sin Kim
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Joon-Ki Hong
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Soo-Jin Sa
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, South Korea
| | - Jun-Hee Lee
- Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Kyu-Ho Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju, South Korea
| | - Jung-Woo Choi
- Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Eun-Seok Cho
- Swine Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
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Tsartsianidou V, Sánchez-Molano E, Kapsona VV, Basdagianni Z, Chatziplis D, Arsenos G, Triantafyllidis A, Banos G. A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep. Genet Sel Evol 2021; 53:90. [PMID: 34856922 PMCID: PMC8641236 DOI: 10.1186/s12711-021-00682-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023] Open
Abstract
Background The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change. Results We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response. Conclusions Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00682-7.
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Affiliation(s)
- Valentina Tsartsianidou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - Enrique Sánchez-Molano
- Division of Genetics and Genomics, School of Veterinary Studies, The Roslin Institute and Royal (Dick), University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Vanessa Varvara Kapsona
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK
| | - Zoitsa Basdagianni
- Department of Animal Production, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitrios Chatziplis
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agriculture, International Hellenic University, Alexander Campus, 57400, Sindos, Greece
| | - Georgios Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Georgios Banos
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK.,Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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Dixit SP, Bhatia AK, Ganguly I, Singh S, Dash S, Sharma A, Anandkumar N, Dang AK, Jayakumar S. Genome analyses revealed genetic admixture and selection signatures in Bos indicus. Sci Rep 2021; 11:21924. [PMID: 34753978 PMCID: PMC8578574 DOI: 10.1038/s41598-021-01144-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.
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Affiliation(s)
- S P Dixit
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
| | - A K Bhatia
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Indrajit Ganguly
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Sanjeev Singh
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Soumya Dash
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Anurodh Sharma
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - N Anandkumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - A K Dang
- ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - S Jayakumar
- ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
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Fabbri MC, Dadousis C, Tiezzi F, Maltecca C, Lozada-Soto E, Biffani S, Bozzi R. Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity. PLoS One 2021; 16:e0248087. [PMID: 34695128 PMCID: PMC8544844 DOI: 10.1371/journal.pone.0248087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.
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Affiliation(s)
- Maria Chiara Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
- * E-mail:
| | - Christos Dadousis
- Dipartimento di Scienze Medico‐Veterinarie, Università di Parma, Parma, Italy
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Emmanuel Lozada-Soto
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Stefano Biffani
- Institute of Agricultural Biology and Biotechnology (CNR), Milano, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
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Liu D, Chen Z, Zhao W, Guo L, Sun H, Zhu K, Liu G, Shen X, Zhao X, Wang Q, Ma P, Pan Y. Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits. BMC Genomics 2021; 22:747. [PMID: 34654366 PMCID: PMC8520274 DOI: 10.1186/s12864-021-08042-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Background Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows. Results In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits. Conclusions We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08042-x.
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Affiliation(s)
- Dengying Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Zhenliang Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Wei Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Longyu Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Kai Zhu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Guanglei Liu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Xiuping Shen
- Shanghai Agricultural Development Promotion Center, 200335, Shanghai, PR China
| | - Xiaoduo Zhao
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China.
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China.
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Xu Z, Mei S, Zhou J, Zhang Y, Qiao M, Sun H, Li Z, Li L, Dong B, Oyelami FO, Wu J, Peng X. Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed. Front Genet 2021; 12:720081. [PMID: 34539748 PMCID: PMC8440853 DOI: 10.3389/fgene.2021.720081] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/06/2021] [Indexed: 01/31/2023] Open
Abstract
The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (FROH) and homozygosity (FHOM). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, Sus scrofa chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as TRAF7, IGFBP7, XPO1, SLC26A8, PPARD, and OR1F1. These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.
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Affiliation(s)
- Zhong Xu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Shuqi Mei
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Jiawei Zhou
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Yu Zhang
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Mu Qiao
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Hua Sun
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Zipeng Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Lianghua Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Binke Dong
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Favour Oluwapelumi Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Junjing Wu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
| | - Xianwen Peng
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China
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Terán E, Azcona F, Ramón M, Molina A, Dorado J, Hidalgo M, Ross P, Goszczynski D, Demyda-Peyrás S. Sperm morphometry is affected by increased inbreeding in the Retinta cattle breed: A molecular approach. Mol Reprod Dev 2021; 88:416-426. [PMID: 34009693 DOI: 10.1002/mrd.23475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/02/2021] [Accepted: 04/14/2021] [Indexed: 12/11/2022]
Abstract
The effect of inbreeding depression on sperm motility is well documented, but its influence on sperm morphometry has been scarcely examined to date. Here, we combined the use of computer-assisted sperm morphometry analysis (CASMA) with a SNP-based genomic approach to determine and characterize the effect of inbreeding on the sperm shape of a highly inbred cattle population. We determined seven morphometric parameters on frozen-thawed sperm samples of 57 Retinta bulls: length (L, µm), width (W, µm), area (A, µm2 ), perimeter (P, µm), ellipticity (ELI; L/W), elongation (L-W)/(L + W) and perimeter-to-area shape factor (p2a; P2 /4 × π × A). The comparison of highly inbred (HI) and lowly inbreed (LI) individuals based on runs of homozygosity (ROH) inbreeding values (F ROH ) showed no differences between groups. An additional two-step unsupervised sperm subpopulation analysis based on morphometric parameters showed significant differences in the abundance of different sperm subpopulations between groups (p < 0.05). This analysis revealed that HI bulls harbored a higher percentage of narrow-head sperm as opposed to the higher percentage of large- and round-headed sperm detected in LI. A further genomic characterization revealed 23 regions differentially affected by inbreeding in both groups, detecting six genes (SPAG6, ARMC3, PARK7, VAMP3, DYNLRB2, and PHF7) previously related to different spermatogenesis-associated processes.
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Affiliation(s)
- Ester Terán
- IGEVET - Instituto de Genética Veterinaria, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina.,Departamento de Producción Animal, Facultad de Ciencias Veterinarias, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
| | - Florencia Azcona
- IGEVET - Instituto de Genética Veterinaria, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
| | - Manuel Ramón
- CERSYRA-Centro Regional de Selección y Reproducción Animal de Castilla-La Mancha, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Valdepeñas, España
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
| | - Jesús Dorado
- Grupo de Reproducción Veterinaria, Departamento de Medicina y Cirugía animal, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, España
| | - Manuel Hidalgo
- Grupo de Reproducción Veterinaria, Departamento de Medicina y Cirugía animal, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, España
| | - Pablo Ross
- Department of Animal Science, University of California at Davis, Davis, California, USA
| | - Daniel Goszczynski
- Department of Animal Science, University of California at Davis, Davis, California, USA
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, UNLP - CONICET, Facultad de Ciencias Veterinarias Universidad Nacional de la Plata, La Plata, Buenos Aires, Argentina
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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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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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication. Sci Rep 2020; 10:9992. [PMID: 32561783 PMCID: PMC7305206 DOI: 10.1038/s41598-020-66133-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/11/2020] [Indexed: 02/08/2023] Open
Abstract
Y-chromosome genetic diversity in and around its domestication origin and a better understanding of indicine-specific microsatellite alleles are imperative concerns but less -targeted. We analysed Y-chromosome markers in 301 bulls representing 19 native Indian cattle (Bos indicus) and identified new alleles and haplotypes. Compared to other indicine studies, the high Y-haplotype diversity found in Indian cattle supports the hypothesis of greater genetic variability across the centre of origin decreasing along migratory routes with increasing distance. Hence, a considerable paternal genetic diversity of Indian cattle appears to have been lost in transboundary commercial indicine breeds. The Khillar and Gir are the most diversified populations where the first tends to be the well-differentiated traditional breed carrying strikingly distinct Y-lineages with typical BM861-158 bp allele, characteristics of taurine cattle, while retaining standard indicine lineages for all other markers. Geographical distribution found to be an unreliable predictor of parental variation, and Y-lineages seemed closely related to Indian breed function/utility. The comprehensive Y-chromosome information will be useful to examine the demographic expansion/spread of Bos indicus lineages from close proximity to the domestication centre across different countries worldwide and such diversity should be preserved through effective management and conservation programs.
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