Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies.
Abstract: The unique horse and pony breeds of India are declining at an alarming rate. These horses have been integral to the Indian culture and customs for centuries and represent a valuable genetic resource. It is imperative to harness the potential of this equine genetic resource that urgently needs conservation. The study highlights the design and development of a high density SNP array, the Axiom_Ashwa to aid in the genetic analysis and conservation efforts for Indian horse and pony breeds. With 613,950 SNPs, this chip offers extensive genome coverage having an average inter-marker distance of 4 kb. The Axiom_Ashwa has been validated on a larger set of diverse indigenous samples as well as Thoroughbreds, demonstrating a high call rate of 99.4% and robustness for genotyping indigenous breeds. Linkage disequilibrium (LD) analysis showed higher average LD in Indian breeds compared to exotic breeds, suggesting a limited effective population size and recent bottlenecks. Phylogenetic and population stratification analyses using PCA and DAPC clearly distinguished horses, ponies and Thoroughbreds, confirming the efficacy of the Axiom_Ashwa chip. These findings underscore the urgent need for conservation efforts for Indian horse breeds, which have experienced significant drop in population size. The Axiom_Ashwa SNP chip offers advantages such as cost-effectiveness and high throughput, providing a more accurate genetic representation of Indian horses.
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Publication Date: 2024-10-23 PubMed ID: 39441226PubMed Central: 4367434DOI: 10.1007/s10142-024-01482-0Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
Summary
This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.
This research undertakes the development of a high-density SNP chip, coined Axiom_Ashwa, to assist in genetic analysis and conservation of indigenous horse and pony breeds in India. These unique breeds are dwindling at an alarming rate despite their cultural significance and genetic value.
Study Purpose and Approach
- The purpose of the study was to create a platform for understanding the genetic makeup of the Indian horse and pony breeds and to aid in conservation efforts.
- The approach used involved designing a high-density SNP (Single Nucleotide Polymorphisms) array known as the Axiom_Ashwa chip, which was used to profile these genetic markers within the breeds’ genomes.
SNP Chip Exhibit and Validation
- This SNP chip contains 613,950 SNPs and delivers comprehensive genome coverage with an average inter-marker distance of 4kb.
- Validation was achieved through trials on a diverse grouping of indigenous samples as well as Thoroughbreds.
- The Axiom_Ashwa chip demonstrated a strong performance with a high call rate of 99.4% and proved robust for genotyping local breeds.
Linkage Disequilibrium Analysis
- Analysis of linkage disequilibrium (LD), the non-random association of alleles at different loci, showed a higher average LD in Indian breeds compared to exotic breeds.
- This indicates a limited effective population size and recent bottleneck events, where a significant percentage of the population has been wiped out.
Phylogenetic and Population Stratification Analyses
- Phylogenetic and population stratification analyses were conducted using PCA (Principal Component Analysis) and DAPC (Discriminant Analysis of Principal Components).
- The results clearly differentiated horses, ponies and Thoroughbreds, which confirm the efficacy of the Axiom_Ashwa chip in genetic analysis.
Significance of the Study
- The study emphasizes the need for urgent conservation efforts for Indian horse breeds, considering their declining population size.
- It introduces a cost-effective and high throughput Axiom_Ashwa SNP chip that provides a more accurate genetic representation of Indian horses.
- This tool can be instrumental in guiding breeding programs aimed at preserving the genetic diversity of Indian horse and pony populations.
Cite This Article
APA
Ahlawat S, Niranjan SK, Arora R, Vijh RK, Kumar A, Sharma U, Raheja M, Popli K, Yadav S, Mehta SC.
(2024).
Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies.
Funct Integr Genomics, 24(6), 195.
https://doi.org/10.1007/s10142-024-01482-0 Publication
Researcher Affiliations
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India. rejagati@gmail.com.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
- Equine Production Campus, ICAR-National Research Centre on Equines, Bikaner, Rajasthan, 334 001, India.
MeSH Terms
- Animals
- Horses / genetics
- Polymorphism, Single Nucleotide
- Linkage Disequilibrium
- Genomics / methods
- India
- Oligonucleotide Array Sequence Analysis
- Phylogeny
- Breeding
References
This article includes 41 references
- Al Abri MA, Brooks SA, Al-Saqri N, Alkharousi K, Johnson EH, Alqaisi O, Al-Rawahi A, Al Marzooqi W. Investigating the population structure and genetic diversity of arabian horses in Oman using SNP markers. Anim Genet 52(3):304–310.
- Andrews S. FastQC A Quality Control tool for High Throughput Sequence Data. .
- Avise JC. Evolutionary Pathways in Nature: A Phylogenetic Approach. (Cambridge University Press, Cambridge, UK, 2006).
- Barbato M, Orozco-ter Wengel P, Tapio M, Bruford MW. SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front Genet 6:109.
- . Basic Animal Husbandry Statistics BAHS. Government of India, Ministry of Fisheries, Animal Husbandry and Dairying. Department of Animal Husbandry and Dairying, Krishi Bhavan, New Delhi, pp 1–172.
- Beeson SK, Schaefer RJ, Mason VC, McCue ME. Robust remapping of equine SNP array coordinates to Eq쪳. Anim Genet Feb 50(1):114–115.
- Behl R, Pundir RK, Behl J, Gupta N, Gupta SK, Singh G, Katoch S, Dogra PK, Ahlawat SPS. Horse genetic resources of India-Spiti ponies. Monograph 19, NBAGR (ICAR), Karnal, India. pp.1–16.
- Behl R, Behl J, Gupta N, Gupta SC. Genetic relationships of five Indian horse breeds using microsatellite markers. Animal 1(4):483–488.
- Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 19:2633–2635.
- Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation plink: rising to the challenge of larger andricher datasets. GigaScience 4(1).
- Corbin LJ, Blott SC, Swinburne JE, Vaudin M, Bishop SC, Woolliams JA. Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Anim Genet 41:8–15.
- Criscione A, Mastrangelo S, D’Alessandro E, Tumino S, Di Gerlando R, Zumbo A, Marletta D, Bordonaro S. Genome-wide survey on three local horse populations with a focus on runs of homozygosity pattern. J Anim Breed Genet 139(5):540–555.
- Devi KM, Ghosh SK. Molecular phylogeny of Indian horse breeds with special reference to Manipuri pony based on mitochondrial D-loop. Mol Biol Rep 40(10):5861–5867.
- Forest G, Eder D. Dedupe. .
- Gupta AK, Tandon SN, Pal Y, Bhardwaj A, Chauhan M. Phenotypic characterization of Indian equine breeds: a comparative study. Anim Genetic Resour Inform (FAO) 50:49–58.
- Gupta AK, Chauhan M, Bhardwaj A, Gupta N, Gupta SC, Pal Y, Tandon SN, Vijh RK. Comparative genetic diversity analysis among six Indian breeds and English Thoroughbred horses. Livest Sci 163:1–11.
- Hellwege JN, Keaton JM, Giri A, Gao X, Velez Edwards DR, Edwards TL. Population Stratification in Genetic Association studies. Curr Protoc Hum Genet 95(1221–).
- Jasielczuk I, Gurgul A, Szmatoła T, Semik-Gurgul E, Pawlina-Tyszko K, Stefaniuk-Szmukier M, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M. Linkage disequilibrium, haplotype blocks and historical effective population size in arabian horses and selected Polish native horse breeds. Livest Sci 239:104095.
- Jombart T, Ahmed I. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics .
- Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94.
- Kendig KI, Baheti S, Bockol MA, Drucker TM, Hart SN, Heldenbrand JR. Sentieon DNASeq variant calling Workflow demonstrates strong computational performance and accuracy. Front Genet 10:736.
- Kusliy MA, Yurlova AA, Neumestova AI, Vorobieva NV, Gutorova NV, Molodtseva AS, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK, Semibratov VP, Iderkhangai TO, Kovalev AA, Erdenebaatar D, Graphodatsky AS, Tishkin AA. Genetic history of the Altai Breed horses: from Ancient Times to Modernity. Genes (Basel) 14(8):1523.
- Lachance J, Tishkoff SA. SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it. BioEssays 35(9):780–786.
- Marletta D, Tupac-Yupanqui I, Bordonaro S, García D, Guastella AM, Criscione A, Cañón J, Dunner S. Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers. J Anim Breed Genet 123(5):315–325.
- Munoz M, Bozzi R, Garcia-Casco J, Nunez Y, Ribani A, Franci O, Garcia F, Škrlep M, Schiavo G, Bovo S, Utzeri VJ. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. Sci Rep 9(1):13546.
- Pacheco S, Kaminsky JC, Kochnev IK, Durrant JD. PCAViz: an Open-Source Python/JavaScript Toolkit for visualizing molecular dynamics simulations in the web browser. J Chem Inf Model 59(10):4087–4092, 1–360.
- Pal Y, Legha RA, Bhardwaj A, Tripathi BN. Status and conservation of equine biodiversity in India. Indian J Comp Microbiol Immunol Infect Dis Equine Prod 41(2):174–184.
- Patterson NJ, Price AL, Reich D. Population structure and Eigen analysis. PLoS Genet 2(12):2074–2093.
- Porto-Neto LR, Kijas JW, Reverter A. The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genet Selection Evol 46(1):22.
- Price A, Patterson NJ, Plenge R, Weinblatt M, Shadick N. Principal component analysis corrects for stratification in genome wide association studies. Nat Genet 38:904–909.
- Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575.
- R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
- Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual. Cold Spring Harbour Lab Press 9(14):23 Cold Spring Harbour, NY.
- Schaefer RJ, McCue ME. Equine genotyping arrays. Vet Clin North Am Equine Pract 36(2):183–193.
- Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. Developing a 670k genotyping array to tag ~ 2 M SNPs across 24 horse breeds. BMC Genomics 18(1):565.
- Sharma RS. The aryan problem and the horse. Social Sci 21(7/8):3.
- Tian C, Plenge RM, Ransom M, Lee A, Villoslada P, Selmi C, Klareskog L, Pulver AE, Qi L, Gregersen PK, Seldin MF. Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet 4(1):e4.
- Vijh RK, Sharma U, Kapoor P, Raheja M, Arora R, Ahlawat S, Dureja V. Design and validation of high-density SNP array of goats and population stratification of Indian goat breeds. Gene 885:147691.
- Vijh RK, Sharma U, Arora R, Kapoor P, Raheja M, Sharma R, Ahlawat S, Dureja V. Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids. Gene 921:148541.
- Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326(5954):865–867.
- Wang J, Santiago E, Caballero A. Prediction and estimation of effective population size. Heredity 117:193–206.
Citations
This article has been cited 0 times.Use Nutrition Calculator
Check if your horse's diet meets their nutrition requirements with our easy-to-use tool Check your horse's diet with our easy-to-use tool
Talk to a Nutritionist
Discuss your horse's feeding plan with our experts over a free phone consultation Discuss your horse's diet over a phone consultation
Submit Diet Evaluation
Get a customized feeding plan for your horse formulated by our equine nutritionists Get a custom feeding plan formulated by our nutritionists
