Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers

Overview

Journal Asian-Australas J Anim Sci

Specialty Veterinary Medicine

Date 2014 Sep 3

PMID 25178290

Citations 7

Authors

Sangwon Suh

Aditi Sharma

Seunghwan Lee

Chang-Yeon Cho

Jae-Hwan Kim

Seong-Bok Choi

Hyun Kim

Hwan-Hoo Seong

Seong-Hum Yeon

Dong-Hun Kim

Yeoung-Gyu Ko

Affiliations

Soon will be listed here.

Abstract

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (F IT) in native chicken was 0.234±0.025. Over 30.7% of F IT was contributed by within-population deficiency (F IS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds.

Citing Articles

Chromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies.

Shin H, Park W, Chai H, Lee Y, Jung J, Ko B Sci Data. 2025; 12(1):51.

PMID: 39799174 PMC: 11724944. DOI: 10.1038/s41597-024-04287-9.

Characterisation of runs of homozygosity and inbreeding coefficients in the red-brown Korean native chickens.

Macharia J, Kim J, Kim M, Cho E, Munyaneza J, Lee J Anim Biosci. 2024; 37(8):1355-1366.

PMID: 38665087 PMC: 11222857. DOI: 10.5713/ab.23.0514.

Major histocompatibility complex B variability in Korean native chicken breeds.

Manjula P, Fulton J, Seo D, Lee J Poult Sci. 2020; 99(10):4704-4713.

PMID: 32988505 PMC: 7598131. DOI: 10.1016/j.psj.2020.05.049.

Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers.

Roh H, Kim S, Cho C, Lee J, Jeon D, Kim D Asian-Australas J Anim Sci. 2020; 33(12):1896-1904.

PMID: 32299162 PMC: 7649407. DOI: 10.5713/ajas.19.0958.

Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken.

Vargas P, Leon J, Fiallos Ortega L, Martinez A, Villafuerte Gavilanes A, Delgado J Animals (Basel). 2019; 9(9).

PMID: 31514349 PMC: 6770841. DOI: 10.3390/ani9090670.

References

Evanno G, Regnaut S, Goudet J . Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005; 14(8):2611-20. DOI: 10.1111/j.1365-294X.2005.02553.x. View

Vanhala T, Tuiskula-Haavisto M, Elo K, Vilkki J, Maki-Tanila A . Evaluation of genetic variability and genetic distances between eight chicken lines using microsatellite markers. Poult Sci. 1998; 77(6):783-90. DOI: 10.1093/ps/77.6.783. View

Seo D, Hoque M, Choi N, Sultana H, Park H, Heo K . Discrimination of korean native chicken lines using fifteen selected microsatellite markers. Asian-Australas J Anim Sci. 2014; 26(3):316-22. PMC: 4093483. DOI: 10.5713/ajas.2012.12469. View

Kaya M, Yildiz M . Genetic diversity among Turkish native chickens, Denizli and Gerze, estimated by microsatellite markers. Biochem Genet. 2008; 46(7-8):480-91. PMC: 2480610. DOI: 10.1007/s10528-008-9164-8. View

Leroy G, Verrier E, Meriaux J, Rognon X . Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches. Anim Genet. 2009; 40(3):333-43. DOI: 10.1111/j.1365-2052.2008.01843.x. View

Wimmers K, Ponsuksili S, Hardge T, Valle-Zarate A, Mathur P, Horst P . Genetic distinctness of African, Asian and South American local chickens. Anim Genet. 2000; 31(3):159-65. DOI: 10.1046/j.1365-2052.2000.00605.x. View

Muchadeyi F, Eding H, Wollny C, Groeneveld E, Makuza S, Shamseldin R . Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. Anim Genet. 2007; 38(4):332-9. DOI: 10.1111/j.1365-2052.2007.01606.x. View

Wilkinson S, Wiener P, Teverson D, Haley C, Hocking P . Characterization of the genetic diversity, structure and admixture of British chicken breeds. Anim Genet. 2012; 43(5):552-63. DOI: 10.1111/j.1365-2052.2011.02296.x. View

Hillel J, Groenen M, Tixier-Boichard M, Korol A, David L, Kirzhner V . Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet Sel Evol. 2003; 35(5):533-57. PMC: 2697980. DOI: 10.1186/1297-9686-35-6-533. View

10.

Peakall R, Smouse P . GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics. 2012; 28(19):2537-9. PMC: 3463245. DOI: 10.1093/bioinformatics/bts460. View

11.

Dunnington E, Stallard L, Hillel J, Siegel P . Genetic diversity among commercial chicken populations estimated from DNA fingerprints. Poult Sci. 1994; 73(8):1218-25. DOI: 10.3382/ps.0731218. View

12.

Nei M, Tajima F, Tateno Y . Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J Mol Evol. 1983; 19(2):153-70. DOI: 10.1007/BF02300753. View

13.

Kalinowski S, Taper M, Marshall T . Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol. 2007; 16(5):1099-106. DOI: 10.1111/j.1365-294X.2007.03089.x. View

14.

Crooijmans R, van der Poel J, Groenen M . Functional genes mapped on the chicken genome. Anim Genet. 1995; 26(2):73-8. DOI: 10.1111/j.1365-2052.1995.tb02636.x. View

15.

Pritchard J, Stephens M, Donnelly P . Inference of population structure using multilocus genotype data. Genetics. 2000; 155(2):945-59. PMC: 1461096. DOI: 10.1093/genetics/155.2.945. View

16.

Weir B, Cockerham C . ESTIMATING F-STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE. Evolution. 2017; 38(6):1358-1370. DOI: 10.1111/j.1558-5646.1984.tb05657.x. View

17.

Tadano R, Sekino M, Nishibori M, Tsudzuki M . Microsatellite marker analysis for the genetic relationships among Japanese long-tailed chicken breeds. Poult Sci. 2007; 86(3):460-9. DOI: 10.1093/ps/86.3.460. View

18.

Jakobsson M, Rosenberg N . CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007; 23(14):1801-6. DOI: 10.1093/bioinformatics/btm233. View