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Argun Karsli B, Demir E, Bilginer U, Dogru H, Karsli T, Kaya S. Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq. Sci Rep 2024; 14:20518. [PMID: 39227733 PMCID: PMC11371811 DOI: 10.1038/s41598-024-71617-7] [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: 06/11/2024] [Accepted: 08/29/2024] [Indexed: 09/05/2024] Open
Abstract
High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection.
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Affiliation(s)
- Bahar Argun Karsli
- Department of Agricultural Biotechnology, Faculty of Agriculture, Eskişehir Osmangazi University, Eskişehir, 26160, Türkiye.
| | - Eymen Demir
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Türkiye
| | - Umit Bilginer
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Türkiye
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Huriye Dogru
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, 15100, Türkiye
| | - Taki Karsli
- Institution Department of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi University, Eskisehir, 26160, Türkiye
| | - Sarp Kaya
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, 15100, Türkiye
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2
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Becker GM, Thorne JW, Burke JM, Lewis RM, Notter DR, Morgan JLM, Schauer CS, Stewart WC, Redden RR, Murdoch BM. Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep. Genet Sel Evol 2024; 56:56. [PMID: 39080565 PMCID: PMC11290166 DOI: 10.1186/s12711-024-00905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 04/23/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs). RESULTS Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms. CONCLUSIONS In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.
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Affiliation(s)
- Gabrielle M Becker
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
| | - Jacob W Thorne
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Joan M Burke
- USDA, ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, USA
| | - Ronald M Lewis
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - David R Notter
- School of Animal Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Christopher S Schauer
- Hettinger Research Extension Center, North Dakota State University, Hettinger, ND, USA
| | - Whit C Stewart
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - R R Redden
- Texas A&M AgriLife Extension, Texas A&M University, San Angelo, TX, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Science, University of Idaho, Moscow, ID, USA.
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3
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Luo X, Zhang J, Guo J, Zhao W, Tian Y, Xiang H, Kang H, Ye F, Chen S, Li H, Ma Z. Transcriptomic Analysis Reveals the Effects of miR-122 Overexpression in the Liver of Qingyuan Partridge Chickens. Animals (Basel) 2024; 14:2132. [PMID: 39061594 PMCID: PMC11274173 DOI: 10.3390/ani14142132] [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: 07/05/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
The liver of chickens is essential for maintaining physiological activities and homeostasis. This study aims to investigate the specific function and molecular regulatory mechanism of microRNA-122 (miR-122), which is highly expressed in chicken liver. A lentivirus-mediated overexpression vector of miR-122 was constructed and used to infect 12-day-old female Qingyuan Partridge chickens. Transcriptome sequencing analysis was performed to identify differentially expressed genes in the liver. Overexpression of miR-122 resulted in 776 differentially expressed genes (DEGs). Enrichment analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) revealed associations with lipid metabolism, cellular senescence, cell adhesion molecules, and the MAPK signaling pathway. Eight potential target genes of miR-122 (ARHGAP32, CTSD, LBH, PLEKHB2, SEC14L1, SLC2A1, SLC6A14, and SP8) were identified through miRNA target prediction platforms and literature integration. This study provides novel insights into the molecular regulatory mechanisms of miR-122 in chicken liver, highlighting its role in key biological processes and signaling pathways. These discoveries enhance our understanding of miR-122's impact on chicken liver function and offer valuable information for improving chicken production performance and health.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zheng Ma
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.); (J.Z.); (J.G.); (W.Z.); (Y.T.); (H.X.); (H.K.); (F.Y.); (S.C.); (H.L.)
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4
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Zhang X, Yang L, Xie Z, Gan J, Zhu P, Song J, Kang H, Zhang Z, Liu L, Xiang H, Li H. Genetic assessment and candidate genes identification for breed-specific characteristics of Qingyuan partridge chicken based on runs of homozygosity. BMC Genomics 2024; 25:577. [PMID: 38858651 PMCID: PMC11163754 DOI: 10.1186/s12864-024-10492-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH. RESULTS The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands. CONCLUSIONS These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.
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Affiliation(s)
- Xing Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Liu Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Key Laboratory of National Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant, China Conservation and Research Centre for the Giant Panda, Panda National Park, Chengdu, 611830, China
| | - Zhuojun Xie
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Jiankang Gan
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China
| | - Piao Zhu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Jiani Song
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Huimin Kang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Zhengfen Zhang
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Chongqing, 400715, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- Guangdong Tinoo's Foods Group Co., Ltd, Qingyuan, 511827, China.
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5
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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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Nayak SS, Panigrahi M, Rajawat D, Jain K, Sharma A, Bhushan B, Dutt T. Unique footprints of balancing selection in bovine genome. 3 Biotech 2024; 14:55. [PMID: 38282911 PMCID: PMC10817884 DOI: 10.1007/s13205-024-03914-x] [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: 02/17/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
Balancing selection is the process of selection that preserves various alleles within a population. Studying the areas undergoing balancing selection is essential, because it preserves genetic diversity in a population. Finding genes that exhibit signs of balancing selection during the domestication of cattle is the goal of this study. To identify regions where polymorphism has persisted in the cattle population for millions of years, we examined the genome of cattle. In this study, we used bovine SNP 50 k data to conduct a detailed genome-wide assessment of selection signatures for balancing selection. We have included the genotyped data from 427 animals, including five taurines, two crossbreds, and eight Indian cattle breeds. For this study, we employed Tajima's D approach to identify signature regions undergoing balancing selection. Using the NCBI database, PANTHER 17.0, and CattleQTL database, the annotation was carried out after finding the relevant areas under balancing selection. The number of genomic regions undergoing balancing selection in Ayrshire, Brown-Swiss, Frieswal, Gir, Guernsey, Hariana, Holstein Friesian, Jersey, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, Tharparkar, and Vrindavani was 11, 13, 13, 19, 18, 11, 17, 14, 14, 12, 10, 12, 13, 13, and 11, respectively. We have observed multiple immune system-related genes going through balancing selection, including KIT, NFATC2, GBP4, LRRC32, SYT7, RAG1, RAG2, LOC513659, and ZBTB17. In our study, we found that the majority of the immune-related genes and a few genes associated with growth, reproduction, production, and adaptation are undergoing balancing selection.
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Affiliation(s)
- Sonali Sonejita Nayak
- 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
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
| | - Anurodh Sharma
- 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
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122 India
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Sun X, Guo J, Li R, Zhang H, Zhang Y, Liu GE, Emu Q, Zhang H. Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals (Basel) 2024; 14:444. [PMID: 38338087 PMCID: PMC10854784 DOI: 10.3390/ani14030444] [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: 12/02/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.
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Affiliation(s)
- Xueliang Sun
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Huanhuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yifei Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Quzhe Emu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, No. 7, Niusha Road, Chengdu 610066, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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8
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Panigrahi M, Rajawat D, Nayak SS, Ghildiyal K, Sharma A, Jain K, Lei C, Bhushan B, Mishra BP, Dutt T. Landmarks in the history of selective sweeps. Anim Genet 2023; 54:667-688. [PMID: 37710403 DOI: 10.1111/age.13355] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
Abstract
Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next-generation sequencing, high-density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large-scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu Prasad Mishra
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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9
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Nayak SS, Panigrahi M, Kumar H, Rajawat D, Sharma A, Bhushan B, Dutt T. Evidence for selective sweeps in the MHC gene repertoire of various cattle breeds. Anim Biotechnol 2023; 34:4167-4173. [PMID: 37039747 DOI: 10.1080/10495398.2023.2196317] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle.
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Affiliation(s)
- Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
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10
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Saravanan KA, Rajawat D, Kumar H, Nayak SS, Bhushan B, Dutt T, Panigrahi M. Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data. Anim Biotechnol 2023; 34:3343-3354. [PMID: 36384399 DOI: 10.1080/10495398.2022.2145292] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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11
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Rajawat D, Panigrahi M, Nayak SS, Ghildiyal K, Sharma A, Kumar H, Parida S, Bhushan B, Gaur GK, Mishra BP, Dutt T. Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection. Anim Biotechnol 2023; 34:3920-3933. [PMID: 37493405 DOI: 10.1080/10495398.2023.2240387] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Subhashree Parida
- Pharmacology and Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - B P Mishra
- Animal Biotechnology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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12
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Lukic B, Curik I, Drzaic I, Galić V, Shihabi M, Vostry L, Cubric-Curik V. Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds. J Anim Sci Biotechnol 2023; 14:142. [PMID: 37932811 PMCID: PMC10626677 DOI: 10.1186/s40104-023-00936-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. RESULTS We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. CONCLUSIONS Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.
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Affiliation(s)
- Boris Lukic
- Faculty of Agrobiotechnical Sciences Osijek, J.J, Strossmayer University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia.
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia.
| | - Ivana Drzaic
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Vlatko Galić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Južno predgrađe 17, 31000, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Luboš Vostry
- Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praque, Czech Republic
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
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13
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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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14
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Mousavi SF, Razmkabir M, Rostamzadeh J, Seyedabadi HR, Naboulsi R, Petersen JL, Lindgren G. Genetic diversity and signatures of selection in four indigenous horse breeds of Iran. Heredity (Edinb) 2023:10.1038/s41437-023-00624-7. [PMID: 37308718 PMCID: PMC10382556 DOI: 10.1038/s41437-023-00624-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 06/14/2023] Open
Abstract
Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Arabian, and Kurdish breeds, respectively. By analysis of the population genetic structure, we classified the north breeds (Caspian and Turkmen) and west/southwest breeds (Persian Arabian and Kurdish) into two phylogeographic clades reflecting their geographic origin. Using the de-correlated composite of multiple selection signal statistics based on pairwise comparisons, we detected a different number of significant SNPs under putative selection from 13 to 28 for the six pairwise comparisons (FDR < 0.05). The identified SNPs under putative selection coincided with genes previously associated with known QTLs for morphological, adaptation, and fitness traits. Our results showed HMGA2 and LLPH as strong candidate genes for height variation between Caspian horses with a small size and the other studied breeds with a medium size. Using the results of studies on human height retrieved from the GWAS catalog, we suggested 38 new putative candidate genes under selection. These results provide a genomewide map of selection signatures in the studied breeds, which represent valuable information for formulating genetic conservation and improved breeding strategies for the breeds.
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Affiliation(s)
- Seyedeh Fatemeh Mousavi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mohammad Razmkabir
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Jalal Rostamzadeh
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Hamid-Reza Seyedabadi
- Animal Science Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Rakan Naboulsi
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, Tomtebodavägen 18A, 17177, Stockholm, Sweden
| | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium.
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15
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Machová K, Marina H, Arranz JJ, Pelayo R, Rychtářová J, Milerski M, Vostrý L, Suárez-Vega A. Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms. Animal 2023; 17:100690. [PMID: 36566708 DOI: 10.1016/j.animal.2022.100690] [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: 08/31/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Wallachian and Sumava sheep are autochthonous breeds that have undergone a significant bottleneck effect and subsequent restoration efforts. The first objective of this study was to evaluate the degree of genetic variability of both breeds and, therefore, the current management of the breeding. The second was to determine whether these two breeds still retain their genetic uniqueness in relation to each other and other breeds, despite regenerative interventions. Our data consisted of 48 individuals of Sumava and 37 individuals of Wallachian sheep. The comparison data contained 25 other breeds (primarily European) from the HapMap dataset generated by the International Sheep Genomics Consortium. When comparing all 27 breeds, the Czech breeds clustered with 15 other breeds and formed a single branch with them according to Nei's distances. At the same time, however, the clusters of both breeds were integral and easily distinguishable from the others when displayed with principal component analysis (PCA). Population substructure analysis did not show any common genetic ancestry of the Czech national breeds and breeds used for regeneration or, eventually, breeds whose ancestral population was used for regeneration. The average values of FST were higher in Wallachian sheep (FST = 0.14) than in Sumava sheep (FST = 0.08). The linkage disequilibrium (LD) extension per autosome was higher in Wallachian than in Sumava sheep. Consequently, the Ne estimates five generations ago were 68 for Sumava versus 34 for Wallachian sheep. Both native Czech breeds exhibit a wide range of inbreeding based on the excess of homozygosity (FHOM) among individuals, from -0.04 to 0.16 in Sumava and from -0.13 to 0.12 in Wallachian. Average inbreeding based on runs of homozygosity was 0.21 in Sumava and 0.27 in Wallachian. Most detected runs of homozygosity (ROH) were less than 5 Mb long for both breeds. ROH segments longer than 15 Mb were absent in Wallachian sheep. Concerning putative selection signatures, a total of 471 candidate genes in Wallachian sheep within 11 hotspots and 653 genes within 13 hotspots in Sumava sheep were identified. Czech breeds appear to be well differentiated from each other and other European breeds. Their genetic diversity is low, especially in the case of the Wallachian breed. Sumava is not so threatened by low diversity but has a larger share of the non-native gene pool.
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Affiliation(s)
- Karolína Machová
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic.
| | - Héctor Marina
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Juan Jose Arranz
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Rocío Pelayo
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
| | - Jana Rychtářová
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Michal Milerski
- Institute of Animal Science, Prague, Czech republic, Přátelství 815, 104 00 Praha, Uhříněves, Czech Republic
| | - Luboš Vostrý
- Department of Genetics and Breeding, Czech University of Life Sciences (CZU), Prague, Czech Republic, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, 165 00 Praha, Suchdol, Czech Republic
| | - Aroa Suárez-Vega
- Department of Animal Production, University of Leon, Leon, Spain, Veterinary Faculty, Campus de Vegazana, s/n, 24071 Leon, Spain
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16
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Wanjala G, Kusuma Astuti P, Bagi Z, Kichamu N, Strausz P, Kusza S. A review on the potential effects of environmental and economic factors on sheep genetic diversity: Consequences of climate change. Saudi J Biol Sci 2022; 30:103505. [DOI: 10.1016/j.sjbs.2022.103505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/17/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
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17
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de Souza TC, de Souza TC, da Cruz VAR, Mourão GB, Pedrosa VB, Rovadoscki GA, Coutinho LL, de Camargo GMF, Costa RB, de Carvalho GGP, Pinto LFB. Estimates of heritability and candidate genes for primal cuts and dressing percentage in Santa Ines sheep. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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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: 20] [Impact Index Per Article: 10.0] [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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19
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Kumar H, Panigrahi M, Panwar A, Rajawat D, Nayak SS, Saravanan KA, Kaisa K, Parida S, Bhushan B, Dutt T. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. J Comput Biol 2022; 29:943-960. [PMID: 35639362 DOI: 10.1089/cmb.2021.0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.
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Affiliation(s)
- Harshit Kumar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Anuradha Panwar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Divya Rajawat
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Sonali Sonejita Nayak
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - K A Saravanan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Kaiho Kaisa
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Subhashree Parida
- Divisions of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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20
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Mészárosová M, Mészáros G, Moravčíková N, Pavlík I, Margetín M, Kasarda R. Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep. Animals (Basel) 2022; 12:ani12111346. [PMID: 35681809 PMCID: PMC9179888 DOI: 10.3390/ani12111346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.
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Affiliation(s)
- Mária Mészárosová
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180 Vienna, Austria;
| | - Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
- Correspondence:
| | - Ivan Pavlík
- Research Institute of Animal Production—NPPC Slovakia, Hlohovecká 2, 95141 Nitra—Lužianky, Slovakia;
| | - Milan Margetín
- Faculty of Agrobiology and Food Resources, Institute of Animal Science, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
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21
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Genomic Population Structure of the Main Historical Genetic Lines of Spanish Merino Sheep. Animals (Basel) 2022; 12:ani12101327. [PMID: 35625173 PMCID: PMC9138057 DOI: 10.3390/ani12101327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Historical documentation shows that the Spanish Merino sheep was selected over many centuries due to the quality of wool, following which it was used to originate all other Merino breeds around the world, mainly by crossbreeding with local breeds. Today, the historical genetic lines that originated the Spanish Merino are still preserved in several closed herds in which they have been bred for nearly 200 years, maintaining their original genetic purity. Our study demonstrates, using a genomic approach, the exceptional genetic richness and variability of these lines, which are clearly differentiated from modern Merino breeds, and must therefore be protected to safeguard the large genetic pool they represent. Abstract According to historiographical documentation, the Romans first began to select Merino sheep in the Iberian Peninsula during the first century, with the aim of obtaining a breed appreciated for the quality of its wool. This process continued locally during the Middle Ages, when Spanish sheep were protected, and their export to foreign countries was banned. It was during the 16th century when individual Merino sheep were allowed to spread around the world to be used to improve the wool quality of local breeds. However, the wool crisis of the 1960s shifted the selection criteria of the Merino breed towards meat production at the expenses of wool. Consequently, individuals that display the genetic and phenotypic characteristics of those sheep originally bred in the kingdom of Spain in the Middle Ages are extremely difficult to find in commercial herds. In this study, we characterized the genetic basis of 403 individuals from the main historical Spanish Merino genetic lines (Granda, Hidalgo, Lopez-Montenegro, Maeso, Donoso and Egea), which were bred in isolation over the last 200 years, using a genomic approach based on genotyping data from the Axiom™ Ovine 50K SNP Genotyping Array. Our analysis included measuring population structure, genomic differentiation indexes, runs of homozygosity (ROH) patterns, and an analysis of molecular variance (AMOVA). The results showed large genetic differences between the historical lines, even though they belong to the same breed. In addition, ROH analysis showed differences due to increased inbreeding among the ancient generations compared with the modern Merino lines, confirming the breed’s ancestral and closed origin. However, our results also showed a high variability and richness within the Spanish historical Merino lines from a genetic viewpoint. This fact, together with their great ability to produce high-quality wool, suggests that ancestral Merino lines from Spain should be considered a valuable genetic population to be maintained as a resource for the improvement of wool-producing sheep breeds all around the world.
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Waineina RW, Okeno TO, Ilatsia ED, Ngeno K. Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya. Front Genet 2022; 13:858923. [PMID: 35528543 PMCID: PMC9068939 DOI: 10.3389/fgene.2022.858923] [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: 01/20/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Artificial and natural selection in livestock is expected to leave unique footprints on their genomes. Goat breeds in Kenya have evolved for survival, breeding, and production in various harsh ecological areas, and their genomes are likely to have acquired unique alleles for adaptation to such diverse production environments and other traits of economic importance. To investigate signals of selection for some selected goat breeds in Kenya, Alpine (n = 29), Galla (n = 12), Saanen (n = 24), and Toggenburg (n = 31) were considered. A total of 53,347 single-nucleotide polymorphisms (SNPs) generated using the Illumina GoatSNP50 BeadChip were analyzed. After quality control, 47,663 autosomal single-nucleotide polymorphisms remained for downstream analyses. Several complementary approaches were applied for the following analyses: integrated Haplotype Score (iHS), cross-population-extended haplotype homozygosity (XP-EHH), hapFLK, and FLK. A total of 404 top genomic regions were identified across all the four breeds, based on the four complementary analyses. Out of the 16 identified putative selection signature regions by the intersection of multiple-selective signal analyses, most of the putative regions were found to overlap significantly with the iHS and XP-EHH analyses on chromosomes 3, 4, 10, 15, 22, and 26. These regions were enriched with some genes involved in pathways associated directly or indirectly with environmental adaptation regulating immune responses (e.g., HYAL1 and HYAL3), milk production (e.g., LEPR and PDE4B), and adaptability (e.g., MST1 and PCK). The results revealed few intersect between breeds in genomic selection signature regions. In general, this did not present the typical classic selection signatures as predicted due to the complex nature of the traits. The results support that some various selection pressures (e.g., environmental challenges, artificial selection, and genome admixture challenges) have molded the genome of goat breeds in Kenya. Therefore, the research provides new knowledge on the conservation and utilization of these goat genetic resources in Kenya. In-depth research is needed to detect precise genes connected with adaptation and production in goat breeds in Kenya.
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Affiliation(s)
- Ruth W Waineina
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya.,Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Tobias O Okeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
| | - Evans D Ilatsia
- Dairy Research Institute, Kenya Agricultural and Livestock Organization, Naivasha, Kenya
| | - Kiplangat Ngeno
- Department of Animal Sciences, Animal Breeding and Genomics Group, Egerton University, Egerton, Kenya
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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Goyache F, Fernández I, Tapsoba ASR, Traoré A, Menéndez-Arias NA, Álvarez I. Functional characterization of Copy Number Variations regions in Djallonké sheep. J Anim Breed Genet 2021; 138:600-612. [PMID: 33682236 DOI: 10.1111/jbg.12542] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/04/2021] [Accepted: 02/12/2021] [Indexed: 12/22/2022]
Abstract
A total of 184 Djallonké (West African Dwarf) sheep of Burkina Faso were analysed for Copy Number Variations (CNV) using Ovine 50 K SNP BeadChip genotyping data and two different CNV calling platforms: PennCNV and QuantiSNP. Analyses allowed to identify a total of 63 candidate Copy Number Variations Regions (CNVR) on 11 different ovine chromosomes covering about 82.5 Mb of the sheep genome. Gene-annotation enrichment analysis allowed to identify a total of 751 potential candidate ovine genes located in the candidate CNVR bounds. Functional annotation allowed to identify five statistically significant Functional Clusters (FC; enrichment factor > 1.3) involving 61 candidate genes. All genes forming significantly enriched FC were located on ovine chromosome (OAR) 21. FC1 (22 genes including PAG4 and PAG6) and FC5 (three genes: CTSC, CTSW and CTSF), coding proteases (peptidases and cathepsins, respectively), were involved in reproductive performance and modulation of gestation. Both FC3 and FC4 were involved in inflammatory and immunologic response through coding serum amyloid A and B-box-type zinc finger proteins, respectively. Finally, FC2 consisted of 27 genes (including OR10G6 and OR8B8) involved in olfactory receptor activity, key for animals adapting to new food resources. CNVR identified on at least 15% of individuals were considered CNVR hotspots and further overlapped with previously reported quantitative trait loci (QTL). CNVR hotspots spanning genes putatively involved with lipid metabolism (SKP1, TCF7, JADE2, UBE2B and SAR1B) and differential expression in mammary gland (SEC24A and CDKN2AIPNL) on OAR5 and dairy traits (CCDC198 and SLC35F4) on OAR7 overlapped with QTL associated with lipid metabolism, milk protein yield and milk fat percentage. Information obtained from local sheep populations naturally adapted to harsh environments contributes to increase our understanding of the genomic importance of CNV.
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Affiliation(s)
- Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
| | | | | | | | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
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