Assessing genetic diversity and phylogeographic structure of duck ( Anas platyrhynchos ) in Nigeria using mitochondrial DNA D-loop sequences

In this study, the maternal genetic diversity and phylogenetic relationship of Nigerian duck populations were assessed. A total of 591 base pair fragment of the mitochondrial DNA (mtDNA) D-loop region of 87 indigenous ducks from two populations in Nigeria were analyzed. Seven haplotypes and 70 polymorphic sites were identified. The mean haplotypic and nucleotide diversity were found to be 0.381±0.058 and 0.315±0.155 respectively. The phylogeny revealed two divergent haplotype clades, suggesting two possible maternal lineage in Nigerian duck population, with the most commonly shared haplotype belonging to Mallard ducks (Anas platyrhynchos). Genetic variation within and between populations accounted for 63.32% and 36.68% of the total genetic variation respectively. This study concluded that there was relatively high genetic diversity and differentiation, thus, this information will probably pave way for further evaluation studies, preservation and improvement of Nigerian ducks as genetic resources.


Introduction
existing.Most researches on duck are been Duck is believed to be one of the earliest overshadowed by the superficiality of the research domesticated fowls in the world (CASS, 1979;Li et.work and the limited breeds and populations al., 2010), and known to have resulted from Mallard investigated (He et. al., 2008).The mtDNA sequence (Wild duck) with South-east Asia as its center of origin variation has been used extensively to study the (Wojcik and Smalec, 2007).Duck is one of the genetic structure and maternal origin of farm animals indigenous poultry species in Nigeria and its (Olowofeso et. al., 2005;Adebambo et. al., 2009; production is at rudimentary stage.Nigerian duck Adebambo et. al., 2010;Ajibike et. al., 2015; Ajibike have been phenotypically characterized based on et. al., 2016).However, mtDNA reports about morphological characters which have provided a domestic duck are relatively scarce and especially in reasonable representation of their genetic difference, Nigeria.however, the accuracy of phenotypic characterization The understanding of Nigerian indigenous is often affected by the influence of the environment ducks' genetic diversity and origin is very crucial for its and the underlying genetic complexity (Yakubu et. al., characterization as an animal genetic resources 2011).
(AnGR), thus, the use of molecular tools particularly Overall, molecular studies investigating the mitochondria DNA (mtDNA) because it is maternally duck breeds and populations in Nigeria seems non-inherited in most species, highly polymorphic, high evolutionary rate and do not undergo recombination.D L -A n a s P F _ L 5 6 p r i m e r ( 5 ' -These features mean that each molecule as a whole GTTGCGGGGTTATTTGGTTA -3').Sequencing was usually has a single genealogical history through performed with BDTv3.1 (Applied Biosystems, USA) maternal lineage (Adebambo et. al., 2009) for further analysis.cycle, there was a rapid thermal ramp to 4 C and Genomic DNA was extracted from air dried holding until the purification of the sequence product blood preserved on FTA classic cards (Whatman was done.Biosciences), using the recommended manufacturer protocol.The samples include 47 ducks from the

Data analysis Northern region of Nigeria representing population I
A 591 bp long fragment, including the (North) and 40 ducks from the Southern region hypervariable region 1 (HV1), was subsequently used representing population II (South).

Purified fragments with a DNA concentration
Nucleotide polymorphism of 30 ng/µl, was sequenced to determine the precise nucleotide sequence.Direct sequencing of HV-1 The pattern of 591 bp mtDNA variability segment of the D-loop region was performed using revealed a high variation between nucleotide 10 and  Muscovy breed (Cairina moschata) (Figure 1).The Tajima and Nei (1984) model using bootstrap method (1000 replications) revealed that identified Nigerian haplotype network analysis (Figure 2) further duck haplotypes were clearly differentiated into two confirms the differentiation between the sampled distinct groups; with two haplotypes (IWO3 and Nigerian duck haplotypes, but, it clearly illustrates IWO43) seems more closely related to the domestic that Nigerian duck haplotypes belongs to a single expansion event centered on IWO3.duck (Anas platyrhynchos and Anas zonorhyncha) calculations were performed based on 1000 Analysis of molecular variance permutations.The result revealed that there was a The analysis of molecular variance (Table 4) higher genetic variation within populations (63.32%) shows the variation in percentage of maternal genetic than among populations (36.68%), with a fixation differentiation within and between Nigerian duck index (F ) value of 0.367.population based on sample locations.The ST

:
Theta value based on expected homozygosity; : Theta value based on number of alleles; : Theta value based on number of segregating sites; : Theta value based on the average number of pairwise differences; C: Cytosine; T: Thymine; A: Adenine; G: Guanine while five (OG29, OG35, OG43, YA14 and GWA7) Phylogenetic and Network analysis haplotypes seems more closely related to the The result of the Neighbour-joining analysis based on

Table 1 : Observed nucleotide polymorphism in Nigerian duck population
578 with North duck population having the highest 70 polymorphic sites with no insertion or deletions polymorphism (67) and South duck has the lowest from the 87 sampled Nigerian indigenous duck were polymorphism (4).The two duck populations shared a observed.The identified haplotypes, observed common haplotype (IWO3), while North duck nucleotide polymorphisms in the D-loop HV-1 segment population has the highest unique haplotype of 5 and of the Nigerian duck sequences and frequencies are South duck population has only one unique shown in Table 1.haplotype.A total of 7 haplotypes (Table 1) defined by

Table 3 : Mismatch distribution of Nigerian duck population
T: time of expansion; and : mutation parameters; D: Tajima's neutrality test; Fs: Fu's neutrality test

Table 2 :
Molecular diversity indices of Nigerian duck population