Animal Production

Current Issue

By Issue

By Author

By Subject

Author Index

Keyword Index

About Journal

Aims and Scope

Editorial Board

Publication Ethics

Indexing and Abstracting

Related Links

FAQ

Peer Review Process

Journal Metrics

News

Study of linkage disequilibrium and identification of haplotype blocks structure in Sarabi breed cows

Document Type : Research Paper

Authors

1 MSc Student, Animal Science, Universtiy of Tehran

2 null

Abstract

This study was conducted to estimate the linkage disequilibrium (LD) and determine haplotype blocks structure in 93 Sarabi cow using SNP-chip 40k of Illumina company. After genotyping and quality control, 27386 SNP markers on autosomal chromosomes remained for analyzing. The LD was measured by r2 and D' statistics. In this study the average of r2 and D' for range less than of 2.5 kb were maximum with 0.505 and 0.927, respectively. The average of r2 and D' were minimum with 0.064 and 0.486, respectively in range of 2-5 Mb. 582 haplotype blocks were observed in the genome of Sarabi cow. 6.73% SNP from all of the SNPs were covered and 0.83% (21.43 Mb) of the autosomal genome were covered by the blocks haplotype. Population effective size was estimated about 40 that refer to four generations ago. The low number of haplotype block and also low LD level in Sarabi cow population showed high variation. In refer to the result and the number of haplotype blocks in this breed, applying the haplotype blocks could be improve results and high precision on genomic selection study so it was recommended that in study of genomic selection applying the haplotype blocks really useful than single SNP study

Keywords

References
حسین زاده م(1386) معرفی نژادهای گاو شیری، گوشتی، دورگ و ایرانی. چاپ دوم، انتشارات پریور، تبریز، ص 93-85.
2.فلاحی م ح (1395)مطالعه  و  شناسایی ساختار هاپلوتیپی گاومیش­های  نژاد  آذربایجانی. پایان‌نامه کارشناسی ارشد. دانشگاه تهران.
3. Ardlie K, Kruglyak L and Seielstad M (2002) Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics. 3(4): 299-309.
4. Barbato M, Orozco-terWengel P, Tapio M and Bruford M (2015) SNeP a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Frontiers in genetics, 6.
5.Barrett J, Fry B, Maller J and Daly M (2004) Haploview analysis and visualization of LD and haplotype maps. Bioinformatics. 21(2):263-265.
6. Bohmanova J, Sargolzaei M and Schenkel F (2010) Characteristics of linkage disequilibrium in North American Holsteins. BMC genomics. 11(1): 421
7. Browning S and Browning B (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics. 81(5): 1084-1097.
8. Corbin L, Liu A, Bishop S and Woolliams J (2012) Estimation of historical effective population size using linkage disequilibria with marker data. Journal of Animal Breeding and Genetics. 129(4):257-270.
9.Espigolan R, Baldi F , Boligon A , Souza F, Gordo D, Tonussi R and Schenkel F (2013) Study of whole genome linkage disequilibrium in Nellore cattle. BMC genomics 14(1): 305.
10.Farnir F, Coppieters W, Arranz J, Berzi P and Cambisano N (2000) Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 10: 220–227
11. Farré M, Micheletti D and Ruiz-Herrera A (2012) Recombination rates and genomic shuffling in human and chimpanzee a new twist in the chromosomal speciation theory. Molecular Biology and Evolution. 30(4): 853-864.
12. Frankham R, Bradshaw C and Brook B (2014) Genetics in conservation management: revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation. 170: 56-63.
13. Gabriel S, Schaffner S, Nguyen H, Moore J, Roy J, Blumenstiel B and Liu-Cordero S (2002). The structure of haplotype blocks in the human genome. Science. 296(5576): 2225-2229
14. Gautier M, Faraut T, Moazami-Goudarzi K, Navratil V, Foglio M, Grohs C and Gut I (2007) Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics. 177(2): 1059-1070
15. Hill W and Robertson A (1968) Linkage disequilibrium in finite populations. TAG Theoretical and Applied Genetics. 38(6): 226-231.
16. Hayes B (2007) QTL mapping MAS and genomic selection A. short-course. Animal Breeding & Genetics Department of Animal Science. Iowa State University. 1(1): 3-4.
17. Khatkar M, Collins A, Cavanagh J, Hawken, R ,Hobbs M, Zenger K and Raadsma H (2006) A first-generation metric linkage disequilibrium map of bovine chromosome 6. Genetics. 174(1): 79-85.
18. Khatkar M, Zenger K, Hobbs M, Hawken R, Cavanagh J, Barris W and Nicholas F (2007) A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in Holstein–Friesian cattle. Genetics. 176(2): 763-772.
19.Mokry F, Buzanskas M, de Alvarenga Mudadu M, do Amaral Grossi, D, Higa R,Ventura, R and da Silva, M (2014) Linkage disequilibrium and haplotype block structure in a composite beef cattle breed. BMC genomic. 15(7): S6
20. Reich D and Lander E (2001) on the allelic spectrum of human disease. TRENDS in Genetics. 17(9): 502-510.
21. Sargolzaei M, Schenkel F, Jansen G and Schaeffer L (2008) Extent of linkage disequilibrium in Holstein cattle in North America. Journal of Dairy Science. 91(5): 2106-2117.
22.Sabeti P, Reich D, Higgins J, Levine H, Richter D, Schaffner S and Ackerman H (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature. 419(6909): 832-837.
23. Sved J (1971) Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theoretical population biology. 2(2): 125-141.
24.Varilo T, Paunio T, Parker A, Perola M, Meyer J, Terwilliger J and Peltonen L (2003) The interval of linkage disequilibrium detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories. Human Molecular Genetics. 12(1): 51-59.
25. Zhao H, Nettleton D, Soller M and Dekkers J (2005) Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL. Genetical research. 86(01): 77-87.
Animal Production
Volume 20, Issue 1
May 2018
Pages 29-41
Files
Share
How to cite
Statistics