Genetic Diversity Of Indigenous Chicken Populations From Cambodia Using 20 Microsatellite DNA Markers

This study analyzed the genetic diversity of five indigenous chicken populations from Cambodia using 20 microsatellite DNA loci in terms of the allele frequencies, heterozygosity and polymorphism information content (PIC) etc. Based on the Nei's DS and DA genetic distances, the UPGMA and NJ phylogenetic trees were constructed. The genetic structures of these populations were estimated using STRUCTURE software. The results showed that there were 214 alleles in 300 samples of the five populations and the average number of observed alleles of per locus was 10.7±8.1, indicating high allelic polymorphism. The genetic diversity was high in all five populations with estimation of average expected heterozygosity (He) was 0.655-0.707. The PIC of 20 loci except for MCW0222, MCW0014 and MCW0081 were higher than 0.5. The UPGMA tree showed that the CKC and CKP populations had a relatively closer genetic relationship, so do for the CSR and COD populations. Five populations had same genetic background based on genetic structure analysis.To understand DNA sequence structural variation and its relationship with allelic distribution pattern obtained from genotyping data of microsatellite markers, PCR products of major alleles at two supposedly simple di-nucleotide chicken microsatellite loci of MCW0330 and LEI0094 were directly sequenced. The results showed that repeat unit at LEI0094 locus was a simple di-nucleotide of (AC)n for most alleles while remaining alleles had their (AC)n being irregularly interrupted by one or two (GA) nucleotides. On the other hand, MCW0330 locus carried a very complicated compound microsatellite consisted of three big structural blocks as its repeat units that were consisted of CACAGACACA, CAGACACA, and CTCAGACA. A few SNPs detected in upstream flanking sequences and specific combinations of basic structural units in repeat sequences of MCW0330 and LEI0094 loci contributed to define not only alleles different in both fragment sizes and sequence structures but also to alleles same in fragment sizes but different in sequence structures that may lead to different peak patterns observed during genotyping exercise. Such'cryptic'alleles same in sequence sizes but different in sequence structures can lead to an underestimated value in diversity and an ascertainment bias in interpreting microsatellite data.