Genetic variability in egg production-associated microsatellites in Rhode Island Red chicken

JOWEL DEBNATH; SANJEEV KUMAR; ABDUL RAHIM; RAMJI YADAV

doi:10.56093/ijans.v87i11.75891

Authors

JOWEL DEBNATH ICAR-Central Avian Research Institute, Izatnagar, Uttar Pradesh 243 122 India
SANJEEV KUMAR ICAR-Central Avian Research Institute, Izatnagar, Uttar Pradesh 243 122 India
ABDUL RAHIM ICAR-Central Avian Research Institute, Izatnagar, Uttar Pradesh 243 122 India
RAMJI YADAV ICAR-Central Avian Research Institute, Izatnagar, Uttar Pradesh 243 122 India

https://doi.org/10.56093/ijans.v87i11.75891

Keywords:

Chicken, Egg production, Genetic variability, Heterozygosity, Microsatellites, PIC, Rhode Island Red

Abstract

Present investigation was carried out in 114 birds belonging to selected strains of Rhode Island Red chicken maintained at institute experimental layer farm with the objective to analyze polymorphism in egg production associated microsatellite loci and to determine various population genetics statistics based on allelic polymorphism. Genomic DNA samples were isolated from all experimental birds and PCR was performed using primers for ten microsatellite loci, reported to be associated with egg production traits in chicken. Alleles were separated on 3.4% MetaPhore^TM agarose and their sizes were determined by Quantity One software. Allelic data were analyzed by POPGENE. Allele numbers varied from 2 to 5 and average number of alleles per locus was 4.00±0.37 (Na). Allele sizes ranged from 99-280 bp. Allele frequency per locus ranged from 0.0225-0.8919. Nei's heterozygosity, Botstein's polymorphic information content (PIC) and Wright's fixation indices at each locus were estimated. All studied microsatellite loci were polymorphic and estimated PIC ranged from 0.19 (ADL0273) to 0.72 (MCW0110). Seven loci were moderate to highly polymorphic (PIC>0.50). Nei's heterozygosity per locus ranged from 0.20 (ADL0273) to 0.77 (MCW0110). Averaged effective number of alleles (Ne), Shannon's Information index (I) and Wright's fixation indices were 2.71±0.26, 1.0654±0.1046 and 0.5126±0.0757, respectively. Average observed (Ho) and expected (He) heterozygosities were 0.3036±0.0625 and 0.5930±0.0505, respectively. Study revealed prevalence of heterozygosity as the Ne was lesser than the Na. It further revealed that the population was under Hardy-Weinberg disequilibrium as (He) was more than (Ho).Chi square and G-square estimates were significant, which suggested that the studied microsatellite loci might have some association with ongoing selection for 40-week part-period egg production in RIR chicken.

Downloads

Download data is not yet available.

References

Albers G AA and Van Sambeek F M J P. 2002. Breeding strategies for layers in view of new technologies. Abstracts Proceedings of the 11th European Poultry Conference. p 31.

Alyethodi R R and Kumar S. 2010. Genetic characterization of Moti Indian native duck using microsatellite markers. Journal of Applied Animal Research 38(1): 223–27. DOI: https://doi.org/10.1080/09712119.2010.10539515

Bao W B, Chen G H, Li B C, Wu X S, Shu J T, Wu S L, Xu Q and Steffen W. 2008. Analysis of genetic diversity and phylogenetic relationships among Red jungle fowls and Chinese domestic fowls. Science in China Series C: Life Sciences 51: 560–68. DOI: https://doi.org/10.1007/s11427-008-0076-y

Botstein D, White R L, Skolnick M and Davis R W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–31.

Chatterjee R N, Sharma R P, Mishra A, Dange M and Bhattacharya T K. 2008a.Variability of microsatellites and their association with egg production traits in chicken. International Journal of Poultry Sciences 7: 77–80. DOI: https://doi.org/10.3923/ijps.2008.77.80

Chatterjee R N, Sharma R P, Mishra A, Dange M and Bhattacharya T K. 2008b. Association of microsatellites with growth and immunocompetence traits in crossbred layer chicken. Journal of Poultry Science 45:186–91. DOI: https://doi.org/10.2141/jpsa.45.186

Chatterjee R N, Niranjan M, Sharma R P, Dang M and Bhattacharya T K. 2010. Estimation of genetic heterogeneity of chicken germplasm being used for development of rural varieties utilizing DNA markers. Journal of Genetics 89: 33–37. DOI: https://doi.org/10.1007/s12041-011-0006-9

Das A K. 2013. Microsatellite polymorphism, immunocompetence profile and performance evaluation of Rhode Island Red chicken and its crosses. Ph.D Thesis Submitted to Indian Veterinary Research Institute, Deemed University.

Das A K, Kumar S and Rahim A. 2015a. Microsatellite analysis after long term selection for egg production in Rhode Island Red chicken. Indian Journal of Animal Sciences 85(11): 1220.

Das A K, Kumar S and Rahim. 2015b. Estimating microsatellite based genetic diversity in Rhode Island Red chicken. Iranian Journal of Veterinary Research 16(3): 274–77.

Das A K, Kumar S, Rahim A and Kokate L S. 2016. Association study between microsatellite genotypes and layer performances in Rhode Island Red chicken. Indian Journal of Animal Sciences 86(9): 1021–24.

Deshmukh B, Kumar D, Kashyap N and Sharma D. 2015. Study of genetic polymorphism of various chicken breeds using microsatellite markers. Indian Journal of Animal Research 49:1–7. DOI: https://doi.org/10.5958/0976-0555.2015.00001.1

El-Sayed M A, Roushdy K H, Galal A and EL-Attar A H. 2011. Genetic differentiation of two Egyptian chicken breeds using 15 microsatellite markers. Proceeding of 3rd International Conference of Genetic Engineering and its Application, pp 149–151.

Hu Y D, Zhou Y, Liu X H and Zhu Q. 2010. Correlations between microsatellite loci and growth and carcass traits in Chinese Silkies. Research Journal of Poultry Sciences 3(1): 5–10. DOI: https://doi.org/10.3923/rjpscience.2010.5.10

Kagami H, Nakamura H and Tomita T. 1990. Sex identification in chickens by means of the presence of the W chromosome- specific repetitive DNA units. Japanese Poultry Science 27(5): 379–84. DOI: https://doi.org/10.2141/jpsa.27.379

Keambou T C, Hako B A, Ommeh S, Bembide C, Ngono E P, Manjeli Y, Wamonje K, Wanjala B, Wamalwa M, Cho C Y, Skilton R A and Djikeng A. 2014. Genetic diversity of the Cameroon Indigenous chicken ecotypes. International Journal of Poultry Sciences 13(5): 279–91. DOI: https://doi.org/10.3923/ijps.2014.279.291

Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583– 90. DOI: https://doi.org/10.1093/genetics/89.3.583

Pandey A K, Kumar D, Sharma R, Sharma U, Vijh R K and Ahlawat S P S. 2005. Population structure and genetic bottleneck analysis of ankleshwar poultry breed by microsatellite markers. Asian Australian Journal of Animal Science 18(7): 915–21. DOI: https://doi.org/10.5713/ajas.2005.915

Parmar S N S, Tolenkhomba T C, Thakur M S, Joshi C G, Rank D N, Solanki J V, Srivastava P N and Pillai P V A. 2007. Analysis of genetic relationship among three varieties of indigenous Kadaknath breed using 25 chicken microsatellite markers. Indian Journal of Biotechnology 6: 205–09.

Radwan L M, El-Dlebshany A E and EL- Denary M E. 2014. Microsatellite genetic differentiation analysis and organic matrix of eggshell in the 16th generation of chickens selected for egg production traits. Egyptian Journal of Animal Production 51(1): 41–47. DOI: https://doi.org/10.21608/ejap.2014.93667

Rahim A. 2015. Microsatellite, immunocompetence and candidate gene expression profiling of Rhode Island Red chicken and association of microsatellite alleles and immunocompetence traits with layer economic traits. Ph.D. Thesis Submitted to Indian Veterinary Research Institute, Deemed University.

Sewalem A, Morrice D M, Law A, Windsor D, Haley C S, Ikeobi C O, Burt D W and Hocking P M. 2002. Mapping quantitative trait loci for body weight at three, six and nine weeks of age in a broiler layer cross. Poultry Science 81: 1775–81. DOI: https://doi.org/10.1093/ps/81.12.1775

Suh S, Sharma A, Lee S, Cho C, Kim J, Choi S, Kim H, Seong H, Yeon S, Kim D and Ko Y. 2014. Genetic diversity and relationships of Korean chicken breeds based on 30 microsatellite markers. Asian Australian Journal of Animal Science 27(10): 1399–1405. DOI: https://doi.org/10.5713/ajas.2014.14016

Vijh R K and Tantai M S. 2004. Assignment of individuals to four poultry breeds of India using multilocus genotypes. Indian Journal of Animal Sciences 74: 73–76.

Wimmers K, Ponsuksili S, Hardge T, Valle-Zarate A, Mathur P K and Horst P. 2000. Genetic distinctness of African, Asian and South American local chickens. Animal Genetics 31: 159–65. Yeh F C, Yang R C and Boyle T. 1999. POPGENE version 1.31, DOI: https://doi.org/10.1046/j.1365-2052.2000.00605.x

Microsoft Windows based freeware for population genetic analysis, quick user guide. Center for International Forestry Research, University of Alberta, Edmonton, Alberta, Canada.