Genetic diversity and population structure of muscovy duck (Cairina moschata) from Nigeria

Abstract

The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (F _ST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene.

Keywords: CYP2U1; Cytochrome b; Genetic diversity; Nigerian Muscovy duck; Population structure.

Figure 1. Sampling locations of domesticated Muscovy ducks and the networks of (i) 397 cytochrome b and (ii) 396 CYP2U1 sequences of domesticated Muscovy ducks based on 940 bp of the cytochrome b and 747 bp of CYP2U1 genes respectively.

(A) Map of 378 domesticated Muscovy duck sampling locations in Nigeria (Sokoto, n = 16 from North West; Kano, n = 62 from North West; Taraba, n = 9 from North East; Oyo, n = 73 from the West; Ekiti, n = 60 from South West; Bayelsa, n = 67 from South South; Kwara, n = 73 from North Central; Niger, n = 18 from North Central) and India, n = 80. Maps of sampling areas shown in color filled circles with the names denoting states and country. The maps were generated using QGIS 3.16.7; (QGIS Development Team, 2021). The shapefiles were downloaded from free online DIVA GIS country shapefiles (https://www.diva-gis.org/gdata). (B) Median-joining networks of (i) 397 cytochrome b and (ii) 396 CYP2U1 sequences of domesticated Muscovy duck samples constructed using NETWORK version 4.6 (Bandelt, Forster & Röhl, 1999). Reference sequences used for haplotype network analysis included: (i) 397 cytochrome b sequences consisting of Nigeria, n = 248 (de novo); Niger, n = 14 (Sola-Ojo et al., 2021); Kwara, n = 57 (Sola-Ojo et al., 2021) and India, n = 78 (Kameshpandian, Thomas & Nagarajan, 2018). (ii) 396 CYP2U1 consisting of Nigeria, n = 237 (de novo); Niger, n = 15 (Sola-Ojo et al., 2021); Kwara, n = 64 (Sola-Ojo et al., 2021) and India, n = 80 (Kameshpandian, Thomas & Nagarajan, 2018). Sizes of the circles are proportional to haplotype frequencies. m, refers to number of mutation steps and those not indicated are just one step mutation. Colours indicate the geographical distribution of the sampling locations across Nigeria and India as shown by the legend in (A).

Figure 2. Linear association between genetic distance (F_ST) and geographical distance (*100 km) in two genes; (A) Cytochrome b, (B) CYP2U1.

The regression line shows negative correlation in both genes (Cytochrome b: Multiple R-squared: 0.2268, Adjusted R-squared: 0.197, p-value: 0.01042 at P < 0.05 and CYP2U1: Multiple R-squared: 0.2666, Adjusted R-squared: 0.2383, p-value: 0.004915 at P < 0.005).