Association of diversity in microsatellite genotypes with layer traits in Rhode Island Red chicken
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Keywords:
Association, Layer economic traits, Microsatellites, Polymorphisms, Rhode Island Red chickenAbstract
Development of vast varieties of high-yielding commercial poultry germplasm can be attributed to rapid selection and controlled breeding. However, their maximum genetic production potential has not been achieved so far. The present study was conducted to analyze polymorphisms in egg production associated microsatellite markers in the sampled population of the selected strain of Rhode Island Red (RIR) chicken and to determine the association between various genotypes of polymorphic markers and layer production traits. One hundred and eleven pullets belonging to five hatches of RIR, maintained at the institute’s farm were used and data on body weight at 20 weeks of age (BW20) and layer economic traits. Age at sexual maturity (ASM), egg weight at 28 and 40 weeks of age (EW28, EW40) and egg production up to 40 weeks of age (EP40) were analyzed by least squares analysis of variance taking sire as random and hatch as fixed effects. Average ASM and EP40 were 135.19±1.15 days and 124.55±1.94 eggs, respectively. The BW20 revealed low, but positive genetic as well as phenotypic correlations with EP40 thereby suggested its usefulness as a selection criterion for genetic improvement of egg production. All egg production-associated microsatellite loci revealed polymorphism and exhibited a prevalence of heterozygosity. The studied population demonstrated Hardy-Weinberg disequilibrium. Genotypes at two microsatellite loci ADL0023 and ADL0273 demonstrated significant effects on layer economic traits suggesting the probable usefulness of these microsatellite markers polymorphism in marker-assisted selection for genetic improvement of egg production in RIR chicken.
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References
20th Livestock Census. 2019. Department of Animal Husbandry, Dairying & Fisheries Annual Report, Ministry of Agriculture, Govt. of India, New Delhi.
Abasht B, Dekkers J C M and Lamont S J. 2006b. Review of Quantitative trait loci identified in the chicken. Poultry Science 85: 2079–2096.
Abasht B, Pitel F, Lagarrigue S, Duval E L, Roy P L, Demeure O, Vignoles F, Simon J, Cogburn L, Aggrey S, Vignal A and Douaire M. 2006a. Fatness QTL on chicken chromosome 5 and interaction with sex. Genetics Selection Evolution 38: 297–311.
Ahlawat S P S, Sunder J, Kundu A, Chatterjee R N, Rai R B, Kumar B, Senani S, Saha S K and Yadav S P. 2004. Use of RAPD-PCR for genetic analysis of Nicobari fowl of Andamans. British Poultry Science 45: 1–7.
Anees C, Veeramani P, Narayanankutty K, Jacob A and Riyas M A. 2010. Estimation of genetic and phenotypic parameters of economic traits in White Leghorn. Indian Journal of Poultry Science 45: 14–17.
Arya R. 2012. Short tandem repeats (STR) polymorphism in egg-type chicken and its association with egg production traits. Ph.D. Thesis, Indian Veterinary Research Institute, Izatnagar, Deemed University, India.
Bao W B, Shu J T, Musa H H and Chen G H. 2007. Analysis of pairwise genetic distance and its relation with geographical distance of 15 Chinese chicken breeds. International Journal of Tropical Medicine 2 (3): 107–112.
Barot V N, Savaliya F P, Hirani N D, Patel A B, Vataliya P H, Khanna K, Patel A M and Joshi R S. 2008. Genetic parameters of various economic traits in different generations of synthetic White Leghorn. Indian Journal of Poultry Science 43: 20–24.
Basic Animal Husbandry and Fisheries Statistics. 2019. Department of Animal Husbandry, Dairying and Fisheries, Ministry of Agriculture, Government of India, Krishi Bhawan, New Delhi.
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: 314–331.
Chatterjee R N, Niranjan M, Sharma R P, Dange M and Bhattacharya T K. 2010b. Estimation of genetic heterogeneity of chicken germplasm being used for development of rural varieties utilizing DNA markers. Journal of Genetics 89: 33–37.
Chatterjee R N, Sharma R P, Bhattacharya T K, Niranjan M and Reddy B L. 2010a. Microsatellite variability and its relationship with growth, egg production, and immunocompetence traits in chickens. Biochemical Genetics 48: 71–82.
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 Science 7: 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: 186–191.
Chatterjee R N, Sharma R P, Reddy B L N, Niranjan M and Mishra S K. 2007. Genetic analysis of highly inbred chicken using RAPD-PCR and immunocompetence. International Journal of Poultry Science 6: 967–972.
Cheng H H, Levin I, Vallejo R L, Khatib H, Dodgson J B, Crittenden L B and Hillel J. 1995. Development of a genetic map of the chicken with markers of high utility. Poultry Science 74: 1855–1874.
Das A K. 2013. Microsatellite Polymorphism, Immunocompetence Profile and Performance Evaluation of Rhode Island Red chicken and its crosses. Ph.D. Thesis, Indian Veterinary Research Institute, Izatnagar, Deemed University, India. pp: 1–177.
Das A K, Kumar S and Rahim A. 2015. Estimating microsatellite-based genetic diversity in Rhode Island Red chicken. Iranian Journal of Veterinary Research 16 (3): 274–277.
Debnath J, Kumar S, Bhanja S K, Rahim A and Yadav R. 2015a. Factors influencing early layer economic traits in Rhode Island Red chicken. Journal of Animal Research 5 (4): 915–919.
Debnath J, Kumar S, Yadav R and Rahim A. 2015b. Microsatellite genotypes of sire influence early layer economic traits and mortality in Rhode Island Red chicken. Indian Journal of Poultry Science 50 (3): 248–253.
Debnath J. 2016. Microsatellites profiling and their association with layer economic traits in Rhode Island Red chicken. Ph.D. Thesis, Indian Veterinary Research Institute, Izatnagar, Deemed University, India. pp: 1–142.
Debnath J, Kumar S, Das A K and Rahim A. 2019. Association of microsatellites with pre-housing body weights and age at sexual maturity of Rhode Island Red chicken. Indian Journal of Animal Science 89 (10): 1118–1122.
Debnath J, Kumar S, Rahim A and Yadav R. 2017. Genetic variability in egg production-associated microsatellites in Rhode Island Red chicken. Indian Journal of Animal Science 87 (11): 1379–1384.
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.
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. Proceedings of the 3rd International Conference on Genetic Engineering and Applications. pp: 149–161.
Jayalaxmi P, Gupta R B, Chatterjee R N, Sharma R P and Reddy R V. 2010. Genetic analysis of growth and production traits in IWK strain of White Leghorn. Indian Journal of Poultry Science 45: 123–126.
Jilani M H, Harpal S and Singh C B. 2005. Performance evaluation and selection indices in a strain of Rhode Island Red. Indian Journal of Poultry Science 40: 278–281.
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): 379–384.
King S C and Henderson C R. 1954. Variance components analysis in heritability studies. Poultry Science 33 (1): 147–154.
Madapurada A. 2001. Evaluation for egg production and allied traits in colored broiler breeder dam line. M.V.Sc. Thesis, University of Agricultural Sciences, Bangalore, Karnataka, India.
Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590.
Nwague B I, Olorunju S A S, Oni O O, Eduvie L O, Adeyinka I A, Sekoni A A and Abeke F O. 2007. Response of egg number to selection in Rhode Island chickens selected for part period egg production. International Journal of Poultry Science 6 (1): 18–22.
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-Australasian Journal of Animal Science 18 (7): 915–921.
Qadri F S, Savaliya F P, Patel A B, Joshi R S, Hirani N D and Patil S S. 2013. Genetic study on important economic traits in two strains of White Leghorn chicken. Indian Journal of Poultry Science 48: 149–153.
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.
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, Indian Veterinary Research Institute, Izatnagar, Deemed University, India. pp: 1–250.
Rahim A, Kumar S, Yadav R, Debnath J and Krishnan J. 2017. Genetic variability determination in a long-term selected Rhode Island Red chicken strain using microsatellite markers. Veterinarski Arhiv 8 (4): 511–522.
Rajkumar U, Reddy B L N, Padhi M K, Haunshi S, Niranjan M, Bhattacharya T K and Chatterjee R N. 2011. Inheritance of growth and production traits in sex-linked dwarf chicken of laying cycle in 64 weeks. Indian Journal of Poultry Science 48: 143–147.
Roushdy K, El-Dein A Z, Fathi M M, Ali U M and Assy H M. 2008. Microsatellite genetic differentiation analysis of two local chicken breeds compared with foreign Hy-line strain. International Journal of Poultry Science 7 (11): 1045–1053.
Sambrook J and Russell D W. 2001. Molecular Cloning: A Laboratory Manual. 3rd Ed. Cold Spring Harbor Laboratory Press, New York, NY.
Smith K P and Bohren B B. 1975. Age of pullet effects on hatching time, egg weight, and hatchability. Poultry Science 54 (4): 959–963.
Suh S, Sharma A, Lee S, Cho C Y, Kim J H, Choi S B, Kim H, Seong H H, Yeon S H, Kim D H and Ko Y G. 2014. Genetic diversity and relationships of Korean chicken breeds based on 30 microsatellite markers. Asian-Australasian Journal of Animal Science 27 (10): 1399–1405.
Tautz D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17: 6463–6471.
Vasu Y, Rao N G, Sharma R P, Harary R C, Gupta R B and Satyanarayana A. 2004. Inheritance of important economic traits in IWI and control strains of White Leghorn. Indian Journal of Poultry Science 39: 1–8.
Vijh R K and Tantai M S. 2004. Assignment of individuals to four poultry breeds of India using multilocus genotypes. Indian Journal of Animal Science 74: 73–76.
Vikki J. 2012. QTL for egg quality. Proceedings of the 6th European Poultry Genetics Symposium. pp: 38–41.
Wardecka B, Olszewski R, Jaszczak K, Zieba G, Pierzchala M and Wicinska K. 2002. Relationship between microsatellite marker alleles on chromosomes 1–5 originating from the Rhode Island Red and Green-legged Partrigenous breeds and egg production and quality traits in F2 mapping population. Journal of Applied Genetics 43 (3): 319–329.
Yeh F C, Yang R C and Boyle T. 1999. POPGENE version 1.31: Microsoft Windows-based freeware for population genetic analysis, quick user guide. Centre for International Forestry Research, University of Alberta, Edmonton, Alberta, Canada. Website: [http://ualberta.ca/~fyeh/popgene.html].
Conference on Genetic Engineering and Applications. pp: 149-61.
Jayalaxmi P, Gupta R B, Chatterjee R N, Sharma R P and Reddy R V. 2010. Genetic analysis of growth and production traits in IWK strain of White Leghorn. Indian Journal of Poultry Science 45: 123-26.
Jilani M H, Harpal S and Singh C B. 2005. Performance evaluation and selection indices in a strain of Rhode Island Red. Indian Journal of Poultry Science 40: 278-81.
King S C and Henderson C R. 1954. Variance components analysis in heritability studies. Poultry Science 33(1): 147–154.
Madapurada A. 2001. Evaluation for egg production and allied traits in colored broiler breeder dam line. M.V.Sc. Thesis, University of Agricultural Sciences, Bangalore, Karnataka, India.
Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-90.
Nwague B I, Olorunju S A S, Oni O O, Eduvie L O, Adeyinka I A, Sekoni A A and Abeke F O. 2007. Response of egg number to selection in Rhode Island chickens selected for part period egg production. International Journal of Poultry Science 6(1): 18-22.
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-Australasian Journal of Animal Science 18(7): 915-21.
Qadri F S, Savaliya F P, Patel A B, Joshi R S, Hirani N D and Patil S S. 2013. Genetic study on important economic traits in two strains of White Leghorn chicken. Indian Journal of Poultry Science 48: 149-53.
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.
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, Indian Veterinary Research Institute, Izatnagar, Deemed University, India. pp: 1–250.
Rahim A, Kumar S, Yadav R, Debnath J and Krishnan J. 2017. Genetic variability determination in a long-term selected Rhode Island Red chicken strain using microsatellite markers. Veterinarski Arhiv 8(4): 511-22.
Rahim A, Kumar S, Das A K, Debnath J, Yadav R and Krishnan J. 2023. Association of microsatellite genotypes with layer economic traits in a selected strain of Rhode Island Red chicken. The Indian Journal of Animal Sciences 93(12): 1193-98.
Rajkumar U, Reddy B L N, Padhi M K, Haunshi S, Niranjan M, Bhattacharya T K and Chatterjee R N. 2011. Inheritance of growth and production traits in sex-linked dwarf chicken of laying cycle in 64 weeks. Indian Journal of Poultry Science 48: 143-47.
Ramadan G S, Stino F K, El-Komy E M, El Sabry M I, Rashed O S and Ghaly M M. 2024. Analysis of the genetic diversity in the cairo-mix broiler chicken using microsatellite and start codon targeted markers. Egyptian Journal of Veterinary Sciences 1-12.
Roushdy K, El-Dein A Z, Fathi M M, Ali U M and Assy H M. 2008. Microsatellite genetic differentiation analysis of two local chicken breeds compared with foreign Hy-line strain. International Journal of Poultry Science 7(11): 1045–53.
Sambrook J and Russell D W. 2001. Molecular Cloning: A Laboratory Manual. 3rd Ed. Cold Spring Harbor Laboratory Press, New York, NY.
Smith K P and Bohren B B. 1975. Age of pullet effects on hatching time, egg weight, and hatchability. Poultry Science 54(4): 959–63.
Suh S, Sharma A, Lee S, Cho C Y, Kim J H, Choi S B, Kim H, Seong H H, Yeon S H, Kim D H and Ko Y G. 2014. Genetic diversity and relationships of Korean chicken breeds based on 30 microsatellite markers. Asian-Australasian Journal of Animal Science 27(10): 1399-405.
Tautz D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17: 6463-71.
Thamer M A and Noori A A. 2022. Use of microsatellite marker mcw0330 for evaluating the productive performance of Isa brown egg laying hens. Indian Journal of Ecology 18: 384-87.
Vijh R K and Tantai M S. 2004. Assignment of individuals to four poultry breeds of India using multilocus genotypes. Indian Journal of Animal Science 74: 73–76.
Vikki J. 2012. QTL for egg quality. Proceedings of the 6th European Poultry Genetics Symposium. pp: 38–41.
Yeh F C, Yang R C and Boyle T. 1999. POPGENE version 1.31: Microsoft Windows-based freeware for population genetic analysis, quick user guide. Centre for International Forestry Research, University of Alberta, Edmonton, Alberta, Canada. Website: [http://ualberta.ca/~fyeh/popgene.html].
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