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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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2
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Ghavi Hossein-Zadeh N. An overview of recent technological developments in bovine genomics. Vet Anim Sci 2024; 25:100382. [PMID: 39166173 PMCID: PMC11334705 DOI: 10.1016/j.vas.2024.100382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
Cattle are regarded as highly valuable animals because of their milk, beef, dung, fur, and ability to draft. The scientific community has tried a number of strategies to improve the genetic makeup of bovine germplasm. To ensure higher returns for the dairy and beef industries, researchers face their greatest challenge in improving commercially important traits. One of the biggest developments in the last few decades in the creation of instruments for cattle genetic improvement is the discovery of the genome. Breeding livestock is being revolutionized by genomic selection made possible by the availability of medium- and high-density single nucleotide polymorphism (SNP) arrays coupled with sophisticated statistical techniques. It is becoming easier to access high-dimensional genomic data in cattle. Continuously declining genotyping costs and an increase in services that use genomic data to increase return on investment have both made a significant contribution to this. The field of genomics has come a long way thanks to groundbreaking discoveries such as radiation-hybrid mapping, in situ hybridization, synteny analysis, somatic cell genetics, cytogenetic maps, molecular markers, association studies for quantitative trait loci, high-throughput SNP genotyping, whole-genome shotgun sequencing to whole-genome mapping, and genome editing. These advancements have had a significant positive impact on the field of cattle genomics. This manuscript aimed to review recent advances in genomic technologies for cattle breeding and future prospects in this field.
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Affiliation(s)
- Navid Ghavi Hossein-Zadeh
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran
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3
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Rajawat D, Ghildiyal K, Sonejita Nayak S, Sharma A, Parida S, Kumar S, Ghosh AK, Singh U, Sivalingam J, Bhushan B, Dutt T, Panigrahi M. Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle. Gene 2024; 901:148178. [PMID: 38242377 DOI: 10.1016/j.gene.2024.148178] [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: 09/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from -0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075-35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.
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Affiliation(s)
- Divya Rajawat
- 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
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Pharmacology & Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Shive Kumar
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - A K Ghosh
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Umesh Singh
- ICAR Central Institute for Research on Cattle, Meerut, 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
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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Rahman JU, Kumar D, Singh SP, Shahi BN, Ghosh AK, Kumar A, Dar AH, Ahmad SF, Pathak A, Verma MK. Genetic diversity, population structure analysis and codon substitutions of Indicine Badri cattle using ddRAD sequencing. 3 Biotech 2024; 14:46. [PMID: 38261939 PMCID: PMC10798937 DOI: 10.1007/s13205-023-03894-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
The present study was carried out on 96 animals representing three distinct colour variants of Badri cattle to investigate the genetic diversity, population structure and substitution mutations in the genetic codons due to single nucleotide variations. The DNA samples of 96 Badri cows were genotyped using a double digestion restriction associated DNA (ddRAD) sequencing approach. A standardized bioinformatics pipeline was employed to identify single nucleotide polymorphisms (SNPs), initially detecting 7,168,552 SNPs through alignment with the Bos indicus reference genome assembly. Subsequent stringent quality filtration yielded 65,483 high-confidence SNPs for downstream analysis. Genetic diversity analysis of the Badri cattle population resulted in average values of 0.145, 0.088, and 0.091 for Shannon's diversity Index (I), Simpson's Diversity (h), and Simpson's Unbiased Diversity (uh), respectively. Genetic similarities between the black and brown, black and grey, and brown and grey Badri variants were found to be 0.9972, 0.9980 and 0.9970, respectively. Tajima's D diversity value was observed to be significant and positive for 99.29% of high-confidence SNPs (65,483). STRUCTURE analysis showed admixture among the three Badri colour variants, suggesting a lack of genetic differentiation. Annotation of high-confidence SNPs regarding genetic codon changes indicated maximum substitutions in the GGC with GGT (22 occurrences), followed by AAC to AGC (20 occurrences), GAA to TAA (19 occurrences) and CAA to CAG (19 occurrences). The study concludes there are genetic similarities among colour variants, lack of rare alleles, balancing selection, sudden population contraction and genetic codon substitutions within the Badri cattle population. Insights derived from SNP data analysis hold potential significance for conservation initiatives and breed improvement programs for indicine cattle.
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Affiliation(s)
- Javid Ur Rahman
- Department of Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Silkworm Breeding & Genetics, Centre Sericultural Research and Training Institute, Berhampore, West Bengal 742101 India
| | - Devendra Kumar
- Department of Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Satya Pal Singh
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Bijendra Narayan Shahi
- Department of Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Ashis Kumar Ghosh
- Department of Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Aashaq Hussain Dar
- Department of Livestock Production and Management, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122 India
| | - Abhishek Pathak
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Manish Kumar Verma
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
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5
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Sudhakar A, Nayee N, Saha S, Donthula SK, Poojara HV, Gohil T, Patel AC, Maurya BK. Role of genetic introgression in introducing mutant alleles in Bos indicus cattle and prevalence of lethal genetic disorders in Bos taurus × Bos indicus and Bos indicus cattle in India. Trop Anim Health Prod 2023; 55:399. [PMID: 37940810 DOI: 10.1007/s11250-023-03798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
Fertility is an important trait associated with reproductive performance and animal welfare concern. Lethal alleles affect fertility through early embryonic death, abortions, and stillbirth depending on the genetic expression of the allele. Holstein Friesian and Jersey are two major Bos taurus breeds used widely for increasing milk yield along with purebreds of Bos indicus breeds like Gir, Kankrej, Sahiwal, and Tharparkar. In the present study, prevalence of lethal mutants in crossbred Holstein Friesian (CBHF, n = 2435), crossbred Jersey (CBJY, n = 2874), Gir (n = 3288), Kankrej (n = 593), Sahiwal (n = 965), and Tharparkar (n = 18) were studied. Heterozygous carrier animals were identified for bovine leukocyte adhesion deficiency (BLAD), Citrullinemia, complex vertebral malformation (CVM), Brachyspina, Holstein Haplotype 1 (HH1), Holstein Haplotype 3 (HH3),Holstein Haplotype 4 (HH4) and Jersey Haplotype 1 (JH1). Breed purity analysis confirmed inheritance of Bos taurus genes contributing to the presence of lethal mutant alleles like BLAD, Citrullinemia, HH1, and JH1 in apparently phenotypic Bos indicus animals. Screening and elimination of heterozygous carrier bulls/cows is essential to control fertility loss associated with lethal alleles.
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Affiliation(s)
- A Sudhakar
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India.
| | - Nilesh Nayee
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | - Sujit Saha
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | | | - Hardik V Poojara
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | - Tejas Gohil
- Sabarmati Ashram Gaushala ( Genomics lab), Anand, 388001, Gujarat, India
| | - Aashish C Patel
- College of Veterinary Science and Animal Husbandry, KU, Anand, 388001, Gujarat, India
| | - Brijesh K Maurya
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
- NDDB CALF Ltd., Anand, 388001, Gujarat, India
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6
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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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7
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Masharing N, Sodhi M, Chanda D, Singh I, Vivek P, Tiwari M, Kumari P, Mukesh M. ddRAD sequencing based genotyping of six indigenous dairy cattle breeds of India to infer existing genetic diversity and population structure. Sci Rep 2023; 13:9379. [PMID: 37296129 PMCID: PMC10256769 DOI: 10.1038/s41598-023-32418-6] [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: 09/02/2022] [Accepted: 03/27/2023] [Indexed: 06/12/2023] Open
Abstract
The present investigation aimed to identify genome wide SNPs and to carry out diversity and population structure study using ddRAD-seq based genotyping of 58 individuals of six indigenous milch cattle breeds (Bos indicus) such as Sahiwal, Gir, Rathi, Tharparkar, Red Sindhi and Kankrej of India. A high percentage of reads (94.53%) were mapped to the Bos taurus (ARS-UCD1.2) reference genome assembly. Following filtration criteria, a total of 84,027 high quality SNPs were identified across the genome of 6 cattle breeds with the highest number of SNPs observed in Gir (34,743), followed by Red Sindhi (13,092), Kankrej (12,812), Sahiwal (8956), Tharparkar (7356) and Rathi (7068). Most of these SNPs were distributed in the intronic regions (53.87%) followed by intergenic regions (34.94%) while only 1.23% were located in the exonic regions. Together with analysis of nucleotide diversity (π = 0.373), Tajima's D (D value ranging from - 0.295 to 0.214), observed heterozygosity (HO ranging from 0.464 to 0.551), inbreeding coefficient (FIS ranging from - 0.253 to 0.0513) suggested for the presence of sufficient within breed diversity in the 6 major milch breeds of India. The phylogenetic based structuring, principal component and admixture analysis revealed genetic distinctness as well as purity of almost all of the 6 cattle breeds. Overall, our strategy has successfully identified thousands of high-quality genome wide SNPs that will further enrich the Bos indicus representation basic information about genetic diversity and structure of 6 major Indian milch cattle breeds which should have implications for better management and conservation of valuable indicine cattle diversity.
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Affiliation(s)
- Nampher Masharing
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Monika Sodhi
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Divya Chanda
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Inderpal Singh
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Prince Vivek
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manish Tiwari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Parvesh Kumari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manishi Mukesh
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India.
- ICAR-NBAGR, Karnal, Haryana, 132001, India.
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8
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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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9
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Rodriguez Neira JD, Peripolli E, de Negreiros MPM, Espigolan R, López-Correa R, Aguilar I, Lobo RB, Baldi F. Prediction ability for growth and maternal traits using SNP arrays based on different marker densities in Nellore cattle using the ssGBLUP. J Appl Genet 2022; 63:389-400. [PMID: 35133621 DOI: 10.1007/s13353-022-00685-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/25/2022] [Accepted: 02/02/2022] [Indexed: 11/25/2022]
Abstract
This study aimed to investigate the prediction ability for growth and maternal traits using different low-density customized SNP arrays selected by informativeness and distribution of markers across the genome employing single-step genomic BLUP (ssGBLUP). Phenotypic records for adjusted weight at 210 and 450 days of age were utilized. A total of 945 animals were genotyped with high-density chip, and 267 individuals born after 2008 were selected as validation population. We evaluated 11 scenarios using five customized density arrays (40 k, 20 k, 10 k, 5 k and 2 k) and the HD array was used as desirable scenario. The GEBV predictions and BIF (Beef Improvement Federation) accuracy were obtained with BLUPF90 family programs. Linear regression was used to evaluate the prediction ability, inflation, and bias of GEBV of each customized array. An overestimation of partial GEBVs in contrast with complete GEBVs and increase of BIF accuracy with the density arrays diminished were observed. For all traits, the prediction ability was higher as the array density increased and it was similar with customized arrays higher than 10 k SNPs. Level of inflation was lower as the density array increased of and was higher for MW210 effect. The bias was susceptible to overestimation of GEBVs when the density customized arrays decreased. These results revealed that the BIF accuracy is sensible to overestimation using low-density customized arrays while the prediction ability with least 10,000 informative SNPs obtained from the Illumina BovineHD BeadChip shows accurate and less biased predictions. Low-density customized arrays under ssGBLUP method could be feasible and cost-effective in genomic selection.
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Affiliation(s)
- Juan Diego Rodriguez Neira
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, 14884-900, Brazil.
| | - Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, 14884-900, Brazil
| | - Maria Paula Marinho de Negreiros
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo (Usp), Pirassununga, 13535-900, Brazil
| | - Rafael Espigolan
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo (Usp), Pirassununga, 13535-900, Brazil
| | - Rodrigo López-Correa
- Departamento de Genética y Mejoramiento Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Ignacio Aguilar
- Instituto Nacional de Investigación Agropecuaria (INIA), Montevideo, Uruguay
| | - Raysildo B Lobo
- Associação Nacional de Criadores e Pesquisadores (ANCP), Ribeirão Preto, Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrarias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, 14884-900, Brazil
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10
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Strucken EM, Gebrehiwot NZ, Swaminathan M, Joshi S, Al Kalaldeh M, Gibson JP. Genetic diversity and effective population sizes of thirteen Indian cattle breeds. Genet Sel Evol 2021; 53:47. [PMID: 34074236 PMCID: PMC8170732 DOI: 10.1186/s12711-021-00640-3] [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: 12/02/2020] [Accepted: 05/19/2021] [Indexed: 11/25/2022] Open
Abstract
Background The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. Results Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. Conclusions The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00640-3.
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Affiliation(s)
- Eva M Strucken
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia.
| | - Netsanet Z Gebrehiwot
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | | | - Sachin Joshi
- BAIF Development Research Foundation, Pune, India
| | - Mohammad Al Kalaldeh
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - John P Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, Australia.
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SAHA SUJIT, NAYEE NILESH, SUDHAKAR A, GAJJAR SWAPNIL, TRIVEDI KR, GUPTA RO, KISHORE G. Evaluating efficiency of customized medium density INDUSCHIP for genotyping of Indicine cattle breeds. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2021. [DOI: 10.56093/ijans.v90i11.111492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To initiate genomic selection programme for indicine cattle breeds and their crosses in India, National Dairy Development Board designed a medium-density (52K) customized chip on Illumina platform named as “INDUSCHIP”. The present study was conducted to examine the efficiency of INDUSCHIP SNP panel for genotyping indicine cattle breeds. Total of 500 animals belonging to 14 different indicine breeds were genotyped with Illumina Bovine HD chip. A subset of SNPs was taken for evaluating the performance of selected SNPs in different indicine breeds. The average minor allele frequency (MAF) was found to vary between 0.20–0.29 for different indicine breeds. However, for important milk breeds like Sahiwal, Gir, Red Sindhi and Kankrej the average MAF was found to be 0.27 and above. Mean Linkage Disequilibrium (LD) at 50–60 kbp distance was found to be around 0.21. There was considerable LD decay with increasing distance between SNPs. Around 0.06% SNPs were found to be significantly deviating from Hardy-Weinberg equilibrium. From the Principal component analysis (PCA) it was found that the first three Principal Components i.e. PC1, PC2 and PC3) could separate different indicine breeds. The present study indicated that due to the presence of highly polymorphic SNPs for the breeds of indicine origin, INDUSCHIP panel was found to be effective and informative in genotyping indicine breeds.
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12
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Devadasan MJ, Kumar DR, Vineeth MR, Choudhary A, Surya T, Niranjan SK, Verma A, Sivalingam J. Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle. 3 Biotech 2020; 10:309. [PMID: 32582506 DOI: 10.1007/s13205-020-02297-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
The present study was carried out in Tharparkar cattle for identification of genome-wide SNPs and microsatellites, and then annotate the identified high-quality SNPs to milk production, fertility, carcass, adaptability and immune response of economically important traits. A total of 146,011 SNPs were identified with respect to Bos taurus reference genome which are indicus specific, out of which 10,519 SNPs were found to be novel. Similarly, a total of 87,047 SNPs were identified with respect to Bos indicus reference genome. After final annotation of SNPs identified with respect to Bos indicus reference genome, 2871 SNPs were found to be associated in 383 candidate genes having to do with milk production, fertility, carcass, immune response and adaptability traits. Following that, 2571 microsatellites were identified. The information mined from the data might be of importance for the future breed improvement programs, conservation efforts and for enhancing the SNPs density of the existing bovine SNP chips.
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Affiliation(s)
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | - M R Vineeth
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - T Surya
- ICAR-National Dairy Research Institute, Karnal, India
| | - S K Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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13
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Bickhart DM, McClure JC, Schnabel RD, Rosen BD, Medrano JF, Smith TPL. Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection. J Dairy Sci 2020; 103:5278-5290. [PMID: 32331872 DOI: 10.3168/jds.2019-17693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/03/2019] [Indexed: 11/19/2022]
Abstract
The cattle reference genome assembly has underpinned major innovations in beef and dairy genetics through genome-enabled selection, including removal of deleterious recessive variants and selection for favorable alleles affecting quantitative production traits. The initial reference assemblies, up to and including UMD3.1 and Btau4.1, were based on a combination of clone-by-clone sequencing of bacterial artificial chromosome clones generated from blood DNA of a Hereford bull and whole-genome shotgun sequencing of blood DNA from his inbred daughter/granddaughter named L1 Dominette 01449 (Dominette). The approach introduced assembly gaps, misassemblies, and errors, and it limited the ability to assemble regions that undergo rearrangement in blood cells, such as immune gene clusters. Nonetheless, the reference supported the creation of genotyping tools and provided a basis for many studies of gene expression. Recently, long-read sequencing technologies have emerged that facilitated a re-assembly of the reference genome, using lung tissue from Dominette to resolve many of the problems and providing a bridge to place historical studies in common context. The new reference, ARS-UCD1.2, successfully assembled germline immune gene clusters and improved overall continuity (i.e., reduction of gaps and inversions) by over 250-fold. This reference properly places nearly all of the legacy genetic markers used for over a decade in the industry. In this review, we discuss the improvements made to the cattle reference; remaining issues present in the assembly; tools developed to support genome-based studies in beef and dairy cattle; and the emergence of newer genome assembly methods that are producing even higher-quality assemblies for other breeds of cattle at a fraction of the cost. The new frontier for cattle genomics research will likely include a transition from the individual Hereford reference genome, to a "pan-genome" reference, representing all the DNA segments existing in commonly used cattle breeds, bringing the cattle reference into line with the current direction of human genome research.
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Affiliation(s)
- D M Bickhart
- US Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53705.
| | - J C McClure
- US Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53705
| | - R D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, 65211; MU Institute for Data Science and Informatics, University of Missouri, Columbia, 65211
| | - B D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - J F Medrano
- Department of Animal Science, University of California Davis, 95616
| | - T P L Smith
- Meat Animal Research Center, Agricultural Research Service, USDA, Clay Center, NE 68933
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Gowane GR, Kumar A, Nimbkar C. Challenges and opportunities to livestock breeding programmes in India. J Anim Breed Genet 2019; 136:329-338. [DOI: 10.1111/jbg.12391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Gopal R. Gowane
- ICAR‐Central Sheep and Wool Research Institute Avikanagar Rajasthan India
| | - Arun Kumar
- ICAR‐Central Sheep and Wool Research Institute Avikanagar Rajasthan India
| | - Chanda Nimbkar
- Nimbkar Agricultural Research Institute Phaltan Maharashtra India
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15
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Hanif Q, Farooq M, Amin I, Mansoor S, Zhang Y, Khan QM. In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. PLoS One 2018; 13:e0206154. [PMID: 30365525 PMCID: PMC6203363 DOI: 10.1371/journal.pone.0206154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/08/2018] [Indexed: 12/28/2022] Open
Abstract
The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes' miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome.
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Affiliation(s)
- Quratulain Hanif
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, PK
| | - Muhammad Farooq
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Imran Amin
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Shahid Mansoor
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Yi Zhang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qaiser Mahmood Khan
- Environmental Toxicology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
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