Genetic diversity of Muscovy ducks revealed by mtDNA d-loop

Based on geographical location and previous studies, the Muscovy ducks were grouped into six different populations such as India-Manipuri (IM), Wuyi-China (WC), Yuyao-China (YC), Fujian-China (FC) and Unkown-China (UC) and France. In total, 12 haplotypes were observed from six Muscovy population. The India-Manipuri (IM) population contributes 8 haplotypes. The AMOVA test shows high (75.12%) genetic variation within population. The NJ phylogenetic tree shows the intermingled China, India and France Muscovy populations. In order to find the depth of haplotype differences, the median joining network was constructed whereby H1 haplotype were shared by India and China population. Moreover, except H1 haplotype, other seven haplotypes from IM population were not observed to be shared with China population. Most importantly 33 InDel sites were observed, with regard to that another MJ network was constructed based on the InDel (Insertion-Deletion) sites or including alignment gaps. This InDel MJ network shows that India and China haplotypes separation based on H5 and H1 haplotype, and star-like structure also observed in both the networks. The non-metric multidimensional scaling (NMDS) plot and cluster analysis shows that France population was distinct from other populations and the IM shows closeness with Unknown-China (UC) population. Other three China populations FC, WC and YC clustered together and differ from France and IMUC groups. The finding of this study would help to understand the maternal genetic evolution of Muscovy duck.