Single-nucleotide polymorphism-based genetic diversity analysis of the Kilakarsal and Vembur sheep breeds

Research (Published online: 26-05-2017)

14. Single-nucleotide polymorphism-based genetic diversity analysis of the Kilakarsal and Vembur sheep breeds

Rathinasamy Selvam, Nagarajan Murali, A. Kannan Thiruvenkadan, Ramesh Saravanakumar, Gurusamy Ponnudurai and Thilak Pon Jawahar

Veterinary World, 10(5): 549-555

Rathinasamy Selvam: Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India.

Nagarajan Murali: Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India.

A. Kannan Thiruvenkadan: Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India.

Ramesh Saravanakumar: Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India.

Gurusamy Ponnudurai: Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India.

Thilak Pon Jawahar: Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tirunelveli - 627 358, Tamil Nadu, India.

doi: 10.14202/vetworld.2017.549-555

Share this article on [Facebook] [LinkedIn]

Article history: Received: 21-12-2016, Accepted: 04-04-2017, Published online: 26-05-2017

Corresponding author: Rathinasamy Selvam

E-mail: selvam.r@tanuvas.ac.in

Citation: Selvam R, Murali N, Thiruvenkadan AK, Saravanakumar R, Ponnudurai G, Jawahar TP (2017) Single-nucleotide polymorphism-based genetic diversity analysis of the Kilakarsal and Vembur sheep breeds, Veterinary World, 10(5): 549-555.

Abstract

Aim: The present study was thus undertaken to analyze the genetic diversity of Kilakarsal and Vembur sheep breeds using single-nucleotide polymorphism (SNP) markers within Toll-like receptor (TLR) 3, 5, 6, 9, and 10 genes.

Materials and Methods: Competitive allele-specific polymerase chain reaction (PCR)-based end-point genotyping was performed using real-time PCR to type the SNPs. Allele discrimination module implemented in real-time PCR was utilized to call the genotypes based on fluorescence intensity recorded for each of the two alleles. Basic diversity indices, namely, gene frequencies, observed heterozygosity, expected heterozygosity, and inbreeding coefficient (F_IS), and testing for Hardy- Weinberg equilibrium (HWE) were estimated using package for elementary analysis of SNP data software program.

Results: Of the 25 SNPs, 22 were found to be polymorphic, whereas two SNPs, namely, TLR3_1081_AC and TLR9_2036_CT, were monomorphic in both Kilakarsal and Vembur sheep populations. The SNP TLR10_1180_AG was monomorphic in Kilakarsal but polymorphic in Vembur sheep. The observed heterozygosities were estimated as 0.289 and 0.309 in Kilakarsal and Vembur sheep, respectively, whereas the expected heterozygosity values were 0.305 and 0.309 in the two breeds, respectively. The overall mean F_IS was 0.107 ranging from -0.005 to 0.241 in Kilakarsal sheep and -0.047 ranging from -0.005 to 0.255 in Vembur sheep. In Kilakarsal sheep, the test for HWE revealed TLR9_1308_GC SNP locus with significant deviation (p<0.05) due to heterozygosity deficit. In Vembur sheep, TLR10_82_CT and TLR10_292_CG loci showed significant deviation (p<0.05) due to heterozygosity excess. Other SNP loci did not deviate from HWE (p>0.05) revealing that the population was in HWE proportions.

Conclusion: The SNP markers within five TLR genes (TLR3, TLR5, TLR6, TLR9, and TLR10) utilized for genotyping in this study were highly polymorphic in Kilakarsal and Vembur breeds of sheep. This study on the genetic diversity analysis of the Kilakarsal and Vembur sheep breeds revealed considerable genetic variation within the breeds and it can be utilized to improve desirable traits.

Keywords: allele discrimination module, competitive allele-specific polymerase chain reaction, Kilakarsal, single-nucleotide polymorphism, Toll-like receptor genes, Vembur.

References

1. Acharya, R.M. (1982) Sheep and Goat Breeds of India. FAO Animal Production and Health Paper 30. Food and Agriculture Organization of the United Nations, Rome, Italy. p190.

2. Hailu, A. and Getu, A. (2015) Breed characterization: Tools and their applications. Open Access. Lib. J., 2: 1-9. [Crossref]

3. Lin, B.Z., Sasazaki, S. and Mannen, H. (2010) Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers. Anim. Sci. J., 81: 281-289. [Crossref] [PubMed]

4. Koopaee, H.K. and Koshkoiyeh, A.E. (2014) SNPs genotyping technologies and their applications in farm animals breeding programs: Review. Braz. Arch. Biol. Technol., 57: 1. [Crossref]

5. Semagn, K., Babu, R., Hearne, S. and Olsen, M. (2013) Single nucleotide polymorphism genotyping using Kompetitive allele specific PCR (KASP): Overview of the technology and its application in crop improvement. Mol. Breed, 33: 1-14. [Crossref]

6. Uenishi, H. and Hiroki, S. (2009) Porcine toll-like receptors: The front line of pathogen monitoring and possible implications for disease resistance. Dev. Comp. Immunol., 33: 353-361. [Crossref]

7. Miller, S.A., Dykes, D.D. and Polesky, H.F. (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res., 16: 12-15. [Crossref]

8. Xu, S., Gupta, S. and Jin, L. (2010) PEAS V1.0: A package for elementary analysis of SNP data. Mol. Ecol. Resour., 10: 1085-1088. [Crossref] [PubMed]

9. Hedrick, P.W. (2000) Genetics of Populations. 2nd ed. Jones and Bartlett, Sudbury, MA.

10. Lee, C.Y., Qin, J., Munyard, K.A., Subramaniam, N.S., Wetherall, J.D., Stear, M.J. and Groth, D.M. (2012) Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion. Anim. Genet., 43: 429-437. [Crossref] [PubMed]

11. Kathiravan, P., Rudolf, P., Mario, P., Silvina, C., Bibiana, C., Daniel, M., Muladno, B., Thiruvenkadan, A.K., Saravanan, R., Masroor, B.E., Faruque, M., Atanaska, T., Mohammed, S., Mario, G.P. and Adama, D. (2014) Candidate gene approach for parasite resistance in sheep variation in immune pathway genes and association with faecal egg count. PLoS One, 9: e88337. [Crossref] [PubMed] [PMC]

12. Wendy, J.M., Smith, K., Yutao, L., Aaron, I., Eliza, C., Sean, M., Tom, D., Belinda, N., Suzanne, M., Robert, M. and Antonio, R. (2010) A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep. BMC Vet. Res., 6: 27. [Crossref] [PubMed] [PMC]

13. Kotze, A. and Muller, G.H. (1994) Genetic relationship in South African cattle breeds. In: Proceedings of the 5th World Congress on Genetics Applied to Livestock Production, Guelph, Canada. University of Guelph, Guelph, Ontario, Canada. 21: 413-416.

14. Rudolf, P., Tanveer, H., Wu, X., Anam, A., Masroor, B., Thiruvenkadan, K., Atanaska, T., Kiala, S., Moumouni, S., Amadou, T., Adama, D. and Kathiravan P. (2016) Short tandem repeat (STR) based genetic diversity and relationship of domestic sheep breeds with primitive wild Punjab Urial sheep. Small Rumin. Res., 148: 11-21.

15. Handley, L.L.J., Byrne, K., Santucci, F., Townsend, S., Taylor, M., Bruford, M.W. and Hewitt, G.M. (2007) Genetic structure of European sheep breeds. Heredity, 99: 620-631. [Crossref] [PubMed]

16. Agaviezor, B.O., Peters, S.O., Adefenwa, M.A., Yakubu, A., Adebambo, O.A., Ozoje, M., Ikeobi, C. and Wheto, M. (2012) Morphological and DNA diversity of Nigerian indigenous sheep. J. Anim. Sci. Biotechnol., 3: 38-53. [Crossref] [PubMed] [PMC]

17. Kusza, S., Dimov, D., Nagy, I., Bosze, Z., Javor, A. and Kukovics, S. (2010) Microsatellite analysis to estimate genetic relationships among five Bulgarian sheep breeds. Genet. Mol. Biol., 33: 51-56. [Crossref] [PubMed] [PMC]

18. Zhong, T., Han, J.L., Guo, J., Zhao, Q.J., Fu, B.L., He, X.H., Jeon, J.T., Guan, W.J. and Ma, Y.H. (2010) Genetic diversity of Chinese indigenous sheep breeds inferred from microsatellite markers. Small Rumin. Res., 90: 88-94. [Crossref]

19. Hedrick, P.W. (2013) High inbreeding in sheep erroneous estimation. J. Hered., 104: 298-299. [Crossref] [PubMed]

20. Barker, J.S., Tan, S.G., Moore, S.S., Mukherjee, T.K., Matheson, J.L. and Selvaraj, O.S. (2001) Genetic variation within and relationships among populations of Asian goats (Capra hircus). J. Anim. Breed. Genet., 118: 213-233. [Crossref]