Analysis generated a total of 41 microsatellite alleles across all studied loci by using 16 microsattelites. The study utilized the same set of primers as reported by
Alyethodi et al., (2010). Highest numbers of alleles 5 (A/B/C/D/E) were recorded at locus CAUD 04 and CAUD 05. The number of alleles at various polymorphic microsatellite loci ranged from 1 to 5 and frequency ranges from 0.04 to 1. The polymorphic patterns were observed in 12 out of 17 microsatellite loci studied in the present study. The average number of alleles per locus is 2.41. Similar studies was reported by
Sankhyan, (2007) on Indian Runner and Moti native ducks, where Moti native duck had higher number of alleles (5) than Indian Runner, whereas
Huang et al., (2005) recorded the highest numbers of alleles (3) at locus CAUD 011. The number of alleles at various polymorphic microsatellite loci ranged from 1 to 3. They used automated DNA sequencer/genotyper and reported higher average allele number with same primer pairs which may be attributed to the sensitivity of instrument/techniques employed in their studies, besides the genetic differences. In the present study, the frequencies of most of alleles were high and 36 out of 43 (83. 72%) polymorphic alleles had a frequency of more than 10 per cent. Another study indicating that Moti native duck can be tagged as a distinct population from other native Indian ducks based on the microsatellites studies
(Rajkumar et al., 2008). Polymorphic patterns were observed in 14 out of 16 microsatellite loci studied. The average number of alleles per locus (2) was in accordance with the report of
Maak et al., 2000. They estimated the same as 2.9 and 3.5 in Muscovy and Pekin ducks, respectively.
Sankhyan (2007) reported an average number of allele as 3.0 in Indian Runner duck. All the loci investigated in the present study were polymorphic in nature. The number of observed alleles (Na) with an over all mean of 1.93± 0.258. However, the effective number of alleles (Ne) with a mean of 1.6933± 0.2712.Shannon’s information index with a mean value of 0.5685±0.1693. The overall means for observed (HO) and expected (He) heterozygosities were 0.2889±0.2477 and 0.5289 ± 0.0853 respectively. Similar findings were reported by
Sankhyan, 2007 with an average heterozygosity of 0.56±0.02 in Indian Runner native duck.
Rajkumar et al., (2008) also reported an average heterozygosity at polymorphic microsatellite loci as 0.52±0.02 in Moti ducks. Whereas,
Huang et al., (2005) recorded average heterozygosity of 0.47±0.01 for the same set of primers. The chi-square (c2) test for Hardy-Weinberg equilibrium revealed that all the loci is in within Hardy-Weinberg equilibrium. The Nei’s genetic identity and genetic distance has been depicted in Fig 1.