Linkage Disequilibrium and Within-breed Genetic Diversity in Iranian Zandi Sheep

Overview

Journal Arch Anim Breed

Date 2019 Dec 7

PMID 31807624

Citations 11

Authors

Seyed Mohammad Ghoreishifar

Hossein Moradi-Shahrbabak

Nahid Parna

Pourya Davoudi

Majid Khansefid

Affiliations

Soon will be listed here.

Abstract

This research aimed to measure the extent of linkage disequilibrium (LD), effective population size ( ), and runs of homozygosity (ROHs) in one of the major Iranian sheep breeds (Zandi) using 96 samples genotyped with Illumina Ovine SNP50 BeadChip. The amount of LD ( ) for single-nucleotide polymorphism (SNP) pairs in short distances (10-20 kb) was but rapidly decreased to by increasing the distance between SNP pairs (40-60 kb). The of Zandi sheep in past (approximately 3500 generations ago) and recent (five generations ago) populations was estimated to be 6475 and 122, respectively. The ROH-based inbreeding was 0.023. We found 558 ROH regions, of which 37 % were relatively long (  Mb). Compared with the rate of LD reduction in other species (e.g., cattle and pigs), in Zandi, it was reduced more rapidly by increasing the distance between SNP pairs. According to the LD pattern and high genetic diversity of Zandi sheep, we need to use an SNP panel with a higher density than Illumina Ovine SNP50 BeadChip for genomic selection and genome-wide association studies in this breed.

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References

Biegelmeyer P, Gulias-Gomes C, Caetano A, Steibel J, Cardoso F . Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle. BMC Genet. 2016; 17:32. PMC: 4736111. DOI: 10.1186/s12863-016-0339-8. View

Sved J . Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol. 1971; 2(2):125-41. DOI: 10.1016/0040-5809(71)90011-6. View

Leroy G . Inbreeding depression in livestock species: review and meta-analysis. Anim Genet. 2014; 45(5):618-28. DOI: 10.1111/age.12178. View

Browning S, Browning B . Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007; 81(5):1084-97. PMC: 2265661. DOI: 10.1086/521987. View

Lencz T, Lambert C, DeRosse P, Burdick K, Morgan T, Kane J . Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci U S A. 2007; 104(50):19942-7. PMC: 2148402. DOI: 10.1073/pnas.0710021104. View

Mohammadi K, Beigi Nassiri M, Rahmatnejad E, Sheikh M, Fayazi J, Karimi Manesh A . Phenotypic and genetic parameter estimates for reproductive traits in Zandi sheep. Trop Anim Health Prod. 2012; 45(2):671-7. DOI: 10.1007/s11250-012-0276-0. View

Liu S, He S, Chen L, Li W, Di J, Liu M . Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs. Genes Genomics. 2017; 39(7):733-745. PMC: 5486679. DOI: 10.1007/s13258-017-0539-2. View

Carlson C, Eberle M, Kruglyak L, Nickerson D . Mapping complex disease loci in whole-genome association studies. Nature. 2004; 429(6990):446-52. DOI: 10.1038/nature02623. View

Mcquillan R, Leutenegger A, Abdel-Rahman R, Franklin C, Pericic M, Barac-Lauc L . Runs of homozygosity in European populations. Am J Hum Genet. 2008; 83(3):359-72. PMC: 2556426. DOI: 10.1016/j.ajhg.2008.08.007. View

10.

Gusev A, Palamara P, Aponte G, Zhuang Z, Darvasi A, Gregersen P . The architecture of long-range haplotypes shared within and across populations. Mol Biol Evol. 2011; 29(2):473-86. PMC: 3350316. DOI: 10.1093/molbev/msr133. View

11.

Chang C, Chow C, Tellier L, Vattikuti S, Purcell S, Lee J . Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015; 4:7. PMC: 4342193. DOI: 10.1186/s13742-015-0047-8. View

12.

Al-Mamun H, Clark S, Kwan P, Gondro C . Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genet Sel Evol. 2015; 47:90. PMC: 4659207. DOI: 10.1186/s12711-015-0169-6. View

13.

Mastrangelo S, Portolano B, Di Gerlando R, Ciampolini R, Tolone M, Sardina M . Genome-wide analysis in endangered populations: a case study in Barbaresca sheep. Animal. 2017; 11(7):1107-1116. DOI: 10.1017/S1751731116002780. View

14.

Hayes B, Lewin H, Goddard M . The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation. Trends Genet. 2012; 29(4):206-14. DOI: 10.1016/j.tig.2012.11.009. View

15.

Wang J . Estimation of effective population sizes from data on genetic markers. Philos Trans R Soc Lond B Biol Sci. 2005; 360(1459):1395-409. PMC: 1847562. DOI: 10.1098/rstb.2005.1682. View

16.

Ferencakovic M, Solkner J, Curik I . Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. Genet Sel Evol. 2013; 45:42. PMC: 4176748. DOI: 10.1186/1297-9686-45-42. View

17.

Notter D . The importance of genetic diversity in livestock populations of the future. J Anim Sci. 1999; 77(1):61-9. DOI: 10.2527/1999.77161x. View

18.

Grossi D, Jafarikia M, Brito L, Buzanskas M, Sargolzaei M, Schenkel F . Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs. BMC Genet. 2017; 18(1):6. PMC: 5251314. DOI: 10.1186/s12863-017-0473-y. View

19.

Nicolazzi E, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C . SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species. BMC Genomics. 2015; 16:283. PMC: 4399246. DOI: 10.1186/s12864-015-1497-1. View

20.

Kijas J, Lenstra J, Hayes B, Boitard S, Porto Neto L, San Cristobal M . Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol. 2012; 10(2):e1001258. PMC: 3274507. DOI: 10.1371/journal.pbio.1001258. View