Microsatellite based genetic diversity study in indigenous chicken ecotypes of Karnataka

Abstract

Aim:The current study was the first of its kind taken upon indigenous ecotypes of the Karnataka in order to unravel the diversity details at 20 chicken microsatellite regions.Materials and Methods:210 indigenous chicken belonging to six districts of Bangalore and Mysore division formed the target sample for the present study. The genomic deoxyribonucleic acid was isolated by phenol chloroform isoamyl alcohol method. A panel of 20 microsatellite regions, including 14 recommended by FAO and six identified from published scientific literature became the targeted chicken genomic region. 27-33 samples were successfully genotyped in each of the six ecotypes through simplex or multiplex polymerase chain reactions, polyacrylamide gel electrophoresis and silver staining for the selected microsatellite panel.Results:The chickens of Ramanagara and Chamrajnagara were most distant with a Nei’s genetic distance value of 0.22. The chickens of Bangalore rural and Mysore were least distant with a value of 0.056. The Ramanagara and Chamrajnagara pair had Nei’s genetic identity value of 0.802, which is least among all pairs of ecotypes. There were five main nodes from which the six ecotypes evolved on the basis 20 microsatellite markers used in this study. This study indicates that the four ecotypes Ramnagara, Bangalore Rural, Chickaballapura and Mysore are genetically identical due to their common ancestral evolution while, Mandya and Chamrajnagara ecotypes formed a relatively different cluster due to a separate common ancestral chicken population and less number of generations since drifting from bifurcation node.Conclusion:Twenty microsatellite markers based genetic diversity study on six indigenous ecotypes indicated lower genetic distances as well as lower FST values compared to the distinguished breeds reported. There were two main clusters, which differentiated into six ecotypes. They may differentiate into more distinct varieties if bred in isolation for a longer number of generations.

Genetic diversity and population structure of indigenous chicken of Bangladesh using microsatellite markers

“…Comparing to the present results on Ho and He , Rudresh et al [ 29 ] reported higher values (0.69 to 0.86) in two chicken populations of Karnataka, India while lower estimates (0.44 to 0.58) were found in Thai and Bhutanese native chickens [ 7 ]. It is notable to mention that direct comparison of data from different studies is probably difficult due to the different genetic backgrounds of the chicken populations studied and the different MS markers used [ 26 ].…”

Sinai and Norfa chicken diversity revealed by microsatellite markers

“…Values ranging from 0.00 to 0.05 is considered as slight, 0.05 to 0.15 moderate, 0.15 to 0.25 is strong, and >0.25 is very strong genetic differentiation (Balloux & Lugon-Moulin, 2002). As a matter of fact, the expectation of F ST under complete differentiation will not always be one, so it might be not dealing with all real population differentiation (Rudresh et al, 2015). Therefore, an F ST value as low as 0.05 might reflect substantial genetic differentiation.…”

Development of Microsatellite Marker System to Determine the Genetic Diversity of Experimental Chicken, Duck, Goose, and Pigeon Populations

“…In summary, we selected 37 and 32 microsatellite loci with good polymorphism in the outbred groups and haplotypes of chicken, respectively [ 12 , 16 , 17 ]. In addition, 15 and 23 loci were screened in the outbred groups and haplotypes of duck, respectively [ 14 , 18 , 19 ].…”