Abstract
A comprehensive genome profiling study was undertaken based on automated genotyping and analysis of 20 microsatellite markers that involved 155 birds representing eight different populations. The distribution of microsatellite markers in each of these breeds helped us to decipher genetic heterogeneity, population genetic structure and evolutionary relationships of the present day chicken populations in India. All the microsatellite loci utilized for the analysis were polymorphic and reasonably informative. A total of 285 alleles were documented at 20 loci with a mean of 14.25 alleles/locus. A total of 103 alleles were found to be population/strain specific of which, only 30 per cent had a frequency of more than 10. The mean PIC values ranged from 0.39 for the locus ADL158 to 0.71 for loci MCW005 or ADL267 across the genomes and 0.55 in Dahlem Red to 0.71 in Desi (non-descript), among the populations. The overall mean expected and observed heterozygosity estimates for our populations were 0.68 and 0.64, respectively. The overall mean inbreeding coefficients (F IS ) varied between -0.05 (Babcock) and 0.16 (Rhode Island Red). The pairwise F ST estimates ranged from 0.06 between Aseel and Desi (non-descript) to 0.14 between Dahlem Red and Babcock. The Nei's genetic distance varied from 0.30 (WLH-IWD and WLH-IWF) to 0.80 (Dahlem Red and Babcock. Phylogenetic analysis grouped all the populations into two main clusters, representing i) the pure breeds, Dahlem Red and Rhode Island Red, and ii) the remaining six populations/strains. All the chicken populations studied were in the state of mild to moderate inbreeding except for commercial birds. A planned breeding is advised for purebreds to revive their genetic potential. High genetic diversity exists in Desi (non-descript), local birds, which can be exploited to genetically improve the birds suitable for backyard poultry.
Highlights
Poultry farming is an important livestock industry sector in India contributing to animal protein needs of the population through meat and eggs
All the microsatellite loci utilized in the present study were found to be polymorphic and reasonably informative according to Botstein et al (1980) criteria
All 20 chromosomal loci studied were successfully amplified through genomes of all the populations studied without exception, wherein all the loci revealed varying number of alleles in all the populations (Figure 1)
Summary
Poultry farming is an important livestock industry sector in India contributing to animal protein needs of the population through meat and eggs. Microsatellites have been already validated as reliable markers in tracking chicken lineages and assessment of gene pool diversity (Vanhala et al, 1998; Romanov and Weigend, 2001). The information on chicken genome sequence and Twenty mono/di/tri-nucleotide microsatellite marker more than 2.8 million single nucleotide polymorphisms loci mapped either in Compton or East Lansing reference (SNPs) greatly enhanced the ability to understand chicken populations were utilized in the present study. High molecular weight analyze genetic relatedness and heterogeneity of a selective genomic DNA was isolated from blood samples as per the population of farmed chicken. This population represented standard protocol (Phenol-chloroform-isoamyl alcohol all the available chicken varieties such as Dahlem Red and extraction).
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