Molecular genetic diversity and origin of Chinese domestic duck breeds

The 667 bp control region of mitochondrial DNA from 8 representative domestic duck breeds in China, which were all native preserved duck breeds, and a mallard (6 Anas zonorhyncha individuals) were sequenced. The genetic polymorphism and the origin of the 8 domestic ducks were analysed. The result showed that the haplotype diversity (Hd) and average nucleotide diversity (Pi) were 0.67136 and 0.19 %, respectively. Hd and Pi of Youxian Sheldrake were the highest in the 8 domestic duck breeds. Kimura-2 parameter genetic distance between the breeds ranged from 0.00056 to 0.00414. The NJ phylogenetic tree and reduced median-joining network chart were constructed by the total 38 haplotypes and 96 sequences, which included 12 sequences of Anas platyrhynchos from GenBank, 6 sequences of Anas zonorhyncha from GenBank and 78 sequences of this study (72 domestic ducks and 6 Anas zonorhyncha). The maternal origin of the 8 domestic ducks all originated from Anas platyrhynchos.


Introduction
Taxonomically, the duck species (domestic duck) belongs to the Anseriformes, Anatidae, Anas platyrhynchos domestic.There were two views about the origin and evolution of Chinese domestic ducks in academia.The monadism view affirmed by overseas scholars was that Chinese domestic ducks were originated from wide Anas platyrhynchos.The dualism view was that Chinese domestic ducks were originated from archaic Anas platyrhynchos and Anas zonorhyncha, domesticated in different areas respectively, or from the generations crossed by Anas platyrhynchos and Anas zonorhyncha (QIU 1998, CHANG 1995).
The mitochondrial DNA (mtDNA) was considered to be the effect genetic marker for the genetic structure among populations and species and the phylogenetic evolution, because of the characters of classical maternal inheritance, less recombinant, rapid evolution, less selection pressure, great genetic variance and so on, and the displacement region (D-loop) especially.Recently, this molecule marker was extensively used on the animal phylogenetic evolution and genetic diversity (RANDI et al. 1998, SACCONE et al. 2000, NIU et al. 2002, LI et al. 2008).
The Chinese domestic duck in particular is one of the earliest domesticated fowls in the world (CASS 1979).China is particularly rich in Waterfowl genetic resources; in 2002, the state identified 27 domestic duck breeds.But, there were only a few studies on the origin of these domestic ducks.The 8 representative breeds including various breed types in China were selected in our study.In this survey, combined with the sequences of Anas platyrhynchos and Anas zonorhyncha, the mtDNA D-loop sequences from 8 representative domestic duck breeds were amplified, sequenced, and analysed to reveal the diversity, origin and evolution of these breeds.The conclusion could provide theoretic basis for the reasonable taxon, protection, development and utilization of the local ducks and offered basic material for the origin and genetic differentiations of the domestic ducks.

PCR amplification and DNA sequencing
Polymerase chain reaction (PCR) was performed to amplify part of the mtDNA control region.The primers reported by SORENSON et al. (1999) were used to amplify the target region.The corresponding sequences were L78 5'-GTT ATT TGG TTA TG CAT ATC GTG-3', and H774 5'-CCA TAT ACG CCA ACC GTC TC-3'.

Data analysis
Electropherograms were obtained using the program Chromas and manually checked insuring the veracity of the DNA sequences.Sequence alignments were performed using DNAman (6.0.40).Haplotype numbers, nucleotide variable sites, haplotype diversity, nucleotide diversity (NEI 1982) were calculated using DnaSP V.4.10.7 (ROZAS 2003).Ignoring the insertion/deletion mutations, the same sequences were considered to be one haplotype.
The same mtDNA D-loop control region sequences of Anas platyrhynchos and Anas zonorhyncha were acquired from GenBank.Kimura 2-parameter distances between breeds were estimated in Mega v. 3.1 (KUMAR et al. 2004) and a neighbour-joining tree was then constructed.The haplotype network was constructed using the software NETWORK 4.5.0.1.

Genetic diversity and distance among 8 domestic duck breeds
Table 2 showed that the largest number of haplotype was found in YX (7) with the haplotype proportion of 58.3 %, the second in GY (4), 33.3 %, and then in the JC, PT, JD and LC (3), 37.5 %, respectively, the lowest in BJ and SX (2), 25.0 %, respectively.The average haplotype diversity (Hd), nucleotide diversity (Pi) and nucleotide difference (K) of the 8 domestic duck populations was 0.67136, 0.00192 and 1.27856, respectively, of which YX was the highest (Hd=0.83333,Pi=0.00322,K=13 636).Kimura 2-parameter distances of mtDNA D-loop in 8 duck breeds were showed as table 3. The genetic distances between the 8 duck breeds were ranged from 0.00056 to 0.00414, the largest was between LC and YX, followed by LC and JD, and the lowest was between SX and JC.
Hd and Pi of 8 domestic duck breeds (0.67136, 0.19 %) were lower than Anas platyrhynchos of that region (0.987, 0.83 %) (KULIKOVA et al. 2005).Compared to other animals, this result was similar to swine (0.122 %) (LAN et al. 1995), significantly less than yak (1.231 %) (LAI et al. 2005) and scalper (2.16 %) (LIU et al. 2006) and significantly higher than chicken (<0.001 %) (WAKANA et al. 1986).Haplotype diversity (Hd) and nucleotide diversity (Pi) of populations were main indexes for evaluating the mtDNA variation and genetic diversity of breed or population.The greater Hd and Pi, the more rich the genetic diversity.Hd and Pi were lower in BJ and SX, and highest in YX.The genetic diversity was mainly affected by the selection period and pressure.The selection period and pressure of BJ and SX were earlier and bigger than YX's.In general, we considered that the nucleotide diversity of Chinese domestic ducks was low, and average nucleotide difference (K) was greater compared to nucleotide diversity.It indicated that the genetic diversity of Chinese domestic ducks was low, the interspecies of which was less than within-species.
In recent years, genetic distance and genetic differentiation of Chinese domestic ducks were analysed by SSR marker (LI et al. 2006 a,b and2007), and some valuable conclusions were obtained.In our investigation, the genetic distances were 0.00056-0.00414.The greatest genetic distance in our test was between LC and other breeds, which was consistent with the report of YAN et al. (2005).LC with a dual purpose for medicine and egg, which was bred for the medicinal trait and laying performance for a long time, differed from other domestic ducks in phenotype and genome.
Most of Chinese duck breeds were formed in Ming and Qing dynasty, such as Pekin duck, Shaoxing duck, Gaoyou duck, the domesticated history was less than one thousand years.At present, there are lots of reports about the origin of Chinese domestic duck, but the origin dispute still existed.Based on mtDNA molecular marker, 8 representative domestic duck breeds were analysed to reveal the diversity, origin and evolution of Chinese domestic duck breeds.
Parts of domestic ducks genetic diversity and the genetic relationship among domestic ducks, Anas platyrhynchos and Anas zonorhyncha were analysed by CHEN et al. (2001) and the results showed that both of Anas platyrhynchos and Anas zonorhyncha contributed to domestic duck evolution.Genomic DNA polymorphism among eight domestic ducks and two wild ducks by using AFLP technique was estimated.The eight domestic duck breeds were originated from both Anas platyrhynchos and Anas zonorhyncha by genetic distance and variance analysis (YAN et al. 2005).The analysis of Genomic DNA polymorphism among three famous duck breeds of domestic ducks (Jinding duck, Liancheng white duck, Shanma duck) and two wild ducks (Anas platyrhynchos and Anas zonorhyncha) in Fujian province by SSR indicated that Anas platyrhynchos contributed more to domestic duck evolution than Anas zonorhyncha (CHEN et al. 2006).In general, the three reports showed that the Chinese domestic ducks were originated from Anas platyrhynchos and Anas zonorhyncha which supported the dualism of duck origin.
The mtDNA phylogeny of the duck comprises two divergent haplotype groups, group A and group B (AVISE et al. 1990).Group A haplotypes are most common and are found worldwide.
B haplotypes occur at high frequencies throughout North America and in frequently in North Asia.Mallards from Asia are attributed to the Group A haplotype clade; spot-billed ducks are attributed to group A or B haplotype clades.The B haplotype from North Asia, however, differs from all other group B haplotypes, forming a separate subclade (SB) nested within the group B clade (accession nos.AY506873, AY506874, and AY506904).Actually, the spotbilled duck was not closely related to Asian Mallards but instead is more closely related to the Mottled Duck (JOHNSON and SORENSON 1999).DNA sequencing revealed clades that correspond to AVISE et al. (1990) group A and group B mtDNA.In this study, 20 haplotypes of domestic ducks were only clustered to group A and also no evidence of contribution of Anas zonorhyncha to the maternal origin of domestic duck breeds.The study conclusion is that Chinese domestic ducks were only originated from Anas platyrhynchos based on mitochondrial DNA analysis.

Table 1
Conservation status and characteristics of the 8 domestic duck breeds Erhaltung und Eigenschaften der 8 Hausentenrassen