GENETICS. Two maternal origins of Chinese domestic goose

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1 GENETICS Two maternal origins of Chinese domestic goose H. F. Li,* 1 W. Q. Zhu, K. W. Chen, Y. H,* W. J. Xu,* and W. Song * Institute of Poultry Science, Chinese Academy of Agricultural Science, Sangyuan Road 46, Yangzhou, , Jiangsu, People s Republic of China; and Poultry Genetics and Breeding Department, Institute of Poultry Science, Chinese Academy of Agricultural Science, , People s Republic of China ABSTRACT China is particularly rich in goose genetic resources. Systematic study of the genetic diversity and origin of Chinese domestic geese will provide an important scientific basis for the conservation and utilization of these resources and for human history. The 521-bp control region (D-loop) of mitochondrial DNA from 26 goose breeds and 6 Landaise geese were sequenced. The results showed that the average haplotype diversity and nucleotide diversity of Chinese domestic geese were and , respectively. Shared haplotype Key words: domestic goose, evolution, genetic diversity analysis and systematic evolution analysis revealed that Chinese domestic geese had 2 maternal origins. The Yili goose breed originated from the Greylag goose (Anser anser), and the other 25 domestic goose breeds originated from the swan goose (Anser cygnoides). An interesting finding was that 1 Linxian white goose and 1 Wanxi white goose shared the same H4 haplotype with the Rhine goose and the Landaise goose, which originated from the Greylag goose (A. anser). Further research on this finding is planned Poultry Science 90 : doi: /ps INTRODUCTION 2011 Poultry Science Association Inc. Received February 14, Accepted April 22, Corresponding author: lhfxf_002@yahoo.com.cn For thousands of years of goose domestication, the goose has been considerably differentiated by natural and artificial selection (Romanov and Weigend, 2001). Because of China s long history of animal husbandry and diverse geographical conditions, it has an abundant variety of native goose resources. Twenty-six Chinese domestic goose breeds, identified by state, play a very important role in the agricultural and human history of China. Chinese domestic goose breeds have better adaptability to extensive management, better immunity to diseases, a higher reproduction rate, and better meat quality, which are natural gene pools and are good original materials for crossbreed predominance and high performance. With the increasing demand for goose products, including meat, down feathers, and fatty liver, the goose industry has flourished in China. However, less research has been conducted on the biological and systematic evolution of geese than on other domestic animals. Li et al. (2007) evaluated the genetic diversity of 26 Chinese native goose breeds by using microsatellite markers. They found that Chinese geese had strong genetic potential and that the genetic relationships among the populations had obvious, significant associations with their historical relationships and geographical distributions. Shi et al. (1998), Liu (2003), and Wang et al. (2005) studied mitochondrial DNA (mtdna) polymorphisms of some goose breeds by analyzing their different origins and genetic differentiation. To date, only a few systemic studies of goose diversity and origin have been performed at the mtdna level. It is essential to study the genetic diversity and origin of Chinese native breeds systemically by using mtdna markers to provide a more important scientific basis for the conservation and utilization of these resources. In the present study, 521-bp mtdna D-loop sequences from 26 Chinese domestic goose breeds were amplified, sequenced, and analyzed to reveal the diversity, origin, and evolution of these breeds. The results may help researchers understand the origin of these goose breeds. MATERIALS AND METHODS Specimen Collection A total of 206 blood samples from the 26 Chinese domestic goose breeds were collected from conservation farms or conservation zones, as described in Table 1.The geographic distribution of the 26 Chinese domestic goose breeds are shown in Figure 1. Blood samples from 6 Landaise geese were collected from the city of Hangzhou in the Zhejiang Province of China. Sequences from 1 Rhine goose (AY552169), 1 swan 2705

2 2706 Li et al. Table 1. Sample information and haplotype distribution of the 26 domestic goose breeds Breed Sample size Conservation type 1 Haplotype name (amount) Changle goose 8 CF/CZ H1 (8) Youjiang goose 8 CF/CZ H1 (8) Yangjiang goose 8 CF H1 (8) Wuzong goose 8 CF H1 (8) Taihu goose 8 CZ H1 (8) Lianhua white goose 6 CZ H1 (6) Yili goose 8 CZ H4 (8) Huoyan goose 8 CF/CZ H1 (7), H3 (1) Minbei white goose 8 CZ H1 (7), H5 (1) Yongkang gray goose 8 CZ H1 (7), H5 (1) Linxian white goose 8 CZ H1 (7), H4 (1) Baizi goose 8 CZ H1 (8) Xupu goose 8 CZ H1 (8) Sichuan white goose 8 CF/CZ H1 (8) Gang goose 8 CZ H1 (8) Wugang tong goose 8 CZ H1 (8) Shitou goose 8 CF/CZ H1 (8) Wanxi white goose 8 CF/CZ H1 (7), H4 (1) Xingguo gray goose 8 CF/CZ H1 (7), H2 (1) Fengcheng gray goose 8 CF/CZ H1 (7), H2 (1) Yan goose 8 CF H1 (8) Zhijin white goose 8 CZ H1 (8) Magang goose 8 CF/CZ H1 (8) Zhedong white goose 8 CF/CZ H1 (8) Guangfengbailin goose 8 CZ H1 (8) Zi goose 8 CZ H1 (8) 1 CF = conservation farm; CZ = conservation zone. goose (AY552167), and 2 Greylag geese (AF and AF159963) were downloaded from the National Center for Biotechnology Information web site ( ncbi.nlm.nih.gov/). PCR Amplification and DNA Sequencing Polymerase chain reaction was performed to amplify a 521-nt segment of the mtdna control region by using primers L CCTCTGGTTCCTCGGTCA-3 and H CAACTTCAGTGCCATGCTTT-3 (Wang et al., 2005). The PCR reaction was performed in an Eppendorf Mastercycler (Eppendorf, Hamburg, Germany). The reaction mix contained 2.5 μl of 10 buffer, 2.5 μl of deoxynucleotide 5 -triphosphate (2.5 mm), 2.0 μl of Mg 2+ (25 mm), 1 µl of each primer (25 pmol/ µl), 3.0 μl of genomic DNA (50 ng/μl), and 0.2 Taq polymerase (5 U/μL). The thermal cycling profile for mtdna was as follows: preheating for 5 min at 95 C, followed by 35 cycles of 45 s at 94 C, 45 s at 56 C, 1 min at 72 C, a final extension for 10 min at 72 C, and conservation at 4 C. The PCR products were purified on agarose gel and sequenced on an ABI Prism 3730 DNA Analyzer (ABI, Foster City, CA) in both directions by primer walking, using a BigDye Terminator V. 3.1 Cycle Sequencing Kit (ABI). Data Analysis Electropherograms were obtained using the program Chromas ( html) and were manually checked to ensure the veracity of the DNA sequences. Sequence alignments were performed using DNAman (6.0.40; com/). The average nucleotide composition was calculated by Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 (Kumar et al., 2004). Haplotype numbers, nucleotide variable sites, haplotype diversity (Hd), nucleotide diversity (Pi; Nei, 1982), mismatch distributions, and estimations of gene flow (Nm) were calculated using the software DnaSP V (Rozas et al., 2003). Analysis of molecular variance, the fixation index, and Tajima s D-value (Tajima, 1989) were implemented using Arlequin 3.0 software (Excoffier et al., 2005). Kimura 2-parameter distances between breeds were estimated by MEGA version 4.0 software (Kumar et al., 2004), and a neighbor-joining tree was then constructed. A median-joining network of the mtdna control region sequence haplotypes was constructed according to the method of Bandelt et al. (1999) by using the Network program ( RESULTS Genetic Variation of the mtdna D-Loop in 26 Domestic The average nucleotide composition was 23.8% T, 29.0% C, 32.3% A, and 14.9% G in the 521-nucleotide mtdna D-loop region of 206 domestic geese. The average percentage of A + T (56.1%) was higher than that of G + C (43.9%). Five haplotypes were identified in 26 domestic goose breeds. The average Hd and Pi were and , respectively. Five haplotypes (H1

3 MATERNAL ORIGINS OF CHINESE DOMESTIC GOOSE 2707 Figure 1. Geographic distribution of 26 Chinese goose breeds. YL = Yili goose; G = Gang goose; SC = Sichuan white goose; YOUJ = Youjiang goose; ZJ = Zhijin white goose; XP = Xupu goose; YJ = Yangjiang goose; WG = Wugang tong goose; LX = Linxian white goose; MG = Magang goose; WZ = Wuzong goose; ST = Shitou goose; LH = Lianhua white goose; XG = Xingguo gray goose; WX = Wanxi white goose; GF = Guangfengbailin goose; FC = Fengcheng gray goose; Y = Yan goose; BZ = Baizi goose; CL = Changle goose; HY = Huoyan goose; MB = Minbei white goose; TH = Taihu goose; ZD = Zhedong white goose; YK = Yongkang gray goose; ZI = Zi goose. to H5) were found in 206 Chinese native geese of 26 domestic goose breeds. The accession numbers of the 5 haplotype sequences were GU to GU Differentiation and Expansion of the Chinese Domestic Goose Population Analysis of variance indicated that 48.72% of the genetic variation present was among breeds, whereas 51.28% was within breeds (Table 2). The Nm between the Yili goose breed and the other 25 goose breeds ranged from 0 to 0.25, whereas the Nm among the other 25 goose breeds ranged from 0.86 to It can be inferred from Figure 2 that the Yili goose breed formed 1 group alone and the other 25 goose breeds formed the other group (Figure 2). There was a peak in the mismatch distributions of the haplotypes of 26 domestic goose breeds (Figure 3). Tajima s test Table 2. Hierarchical composition analysis of variation in mitochondrial DNA from 26 goose breeds Source of variation df Sum of squares Variance component 1 Variation (%) Fixation index Among populations Va Within populations Vb Total Va = variance components among populations; Vb = variance components within populations.

4 2708 Li et al. geese. Haplotype H5 consisted of 1 Minbei white goose and 1 Yongkang gray goose, haplotype H6 consisted of 1 Landaise goose, haplotype H7 consisted of 1 grey goose, and haplotype H8 consisted of 1 Greylag goose. The H1 haplotype was shared by 191 domestic geese and 1 swan goose, indicating that Chinese domestic geese had the maternal lineage of the swan goose (A. cygnoides). The finding that the H3 haplotype was shared by the 8 Yili goose, 1 Landaise goose, and 1 Rhine goose indicated the Yili goose breed had the maternal lineage of the Greylag goose (Anser anser). Systematic Evolution of Chinese Domestic The neighbor-joining phylogenetic tree (Figure 4) and reduced median-joining network chart (Figure 5) were constructed using the 8 haplotypes. The maternal lineage of H1, H2, H3, and H5 was close to that of the swan goose, and the maternal lineage of H4 and H6 was close to that of the Greylag goose. These indicated that the Chinese domestic goose had 2 maternal origins, the Yili goose originated from the Greylag goose (A. anser), and the other 25 goose breeds originated from the swan goose (A. cygnoides). DISCUSSION Genetic Diversity of Chinese Domestic Figure 2. Neighbor-joining population tree of the Chinese domestic goose. XG = Xingguo gray goose; YK = Yongkang gray goose; WX = Wanxi white goose; MB = Minbei white goose; LX = Linxian white goose; FC = Fengcheng gray goose; BZ = Baizi goose; CL = Changle goose; G = Gang goose; GF = Guangfengbailin goose; LH = Lianhua white goose; MG = Magang goose; SC = Sichuan white goose; ST = Shitou goose; TH = Taihu goose; WG = Wugang tong goose; WZ = Wuzong goose; XP = Xupu goose; YJ = Yangjiang goose; YOUJ = Youjiang goose; ZD = Zhedong white goose; ZI = Zi goose; ZJ = Zhijin white goose; Y = Yan goose; HY = Huoyan goose; YL = Yili goose. revealed that the 26 Chinese goose breeds were in accordance with the standard neutral model (P > 0.10). These revealed that population expansion of the 26 Chinese domestic goose groups did not exist in the past. The Hd and Pi of the populations were the main indices for evaluating the mtdna variation and genetic diversity of the breeds or population. Richer genetic diversity is associated with greater Hd and Pi. The estimates of Hd and Pi found here for 26 domestic goose breeds ( and ) were lower than those for 6 Chinese domestic goose breeds (0.547 and ; Liu, 2003) and were also lower than those for Anas platyrhynchos of that region (0.987 and 0.83%; Kulikova et al., 2005). Compared with other animals, the Pi was similar to that of swine (0.122%; Lan et al., 1995), significantly less than in the yak (1.231%; Lai et al., 2005) and scalper (2.16%; Liu et al., 2006), and signifi- Haplotype Distributions in 26 Domestic Eight haplotypes (H1 to H8) were found in 216 geese, including 206 Chinese native geese, 6 Landaise geese, 1 Rhine goose, 1 swan goose, and 2 Greylag geese. Haplotype H1, the largest shared haplotype, consisted of 191 Chinese domestic geese, covering 25 goose breeds and 1 swan goose (Anser cygnoides). Haplotype H2 consisted of 1 Fengcheng gray goose and 1 Xingguo gray goose. Haplotype H3 consisted of 1 Huoyan goose. Haplotype H4 consisted of 1 Linxian white goose, 1 Wanxi white goose, 1 Rhine goose, 5 Landaise geese, and 8 Yili Figure 3. Mismatch distributions of the haplotypes of 26 Chinese domestic goose breeds. Exp = expected; Obs = observed.

5 Figure 4. A phylogenetic tree based on D-loop sequences constructed with the neighbor-joining method using Kimura s 2-parameter model (Kumar et al. 2004). H = haplotype. cantly higher than in the chicken (<0.001%; Wakana et al., 1986). Wang et al. (2005) reported that the Pi of 15 Chinese domestic goose breeds ranged from 0 to Li and Wang (2007) analyzed the nucleotide variation in a partial sequence (621-bp) of the full mane of the ND4 gene: mitochondrially encoded NADH dehydrogenase 4 in 6 native goose breeds and found an Hd of and a Pi ranging from 0 to In the above-mentioned research, the Hd and Pi were all low on the mtdna level. The same result was found in the present research. From these results, we suggest that the conservation farms and conservation zones should take practical, scientific measures to protect domestic goose resources. Genetic Differentiation of Chinese Domestic A population bottleneck (or genetic bottleneck) is an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing. With a bottleneck effect, the population size may decrease rapidly and genetic diversity may be lost. A mismatch in the distribution of haplotypes and Tajima s test indicated that a bottleneck event had not occurred in the evolutionary progress of the 26 Chinese goose breeds. An Nm value below 0.5 indicated that genetic drift played the main role in genetic differentiation in the population. An Nm value above 0.5 indicated that gene flow played the main role in genetic differentiation in the population. Genetic drift MATERNAL ORIGINS OF CHINESE DOMESTIC GOOSE may have been the main factor affecting the genetic differentiation of the Yili goose breed (Nm = 0 to 0.25). On the other hand, gene flow was the main reason for the lack of clear differentiation among the remaining 25 domestic goose breeds (Nm = 0.86 to 12.56). The neutral test revealed nucleotide variable sites in the 521-bp D-loop region, in accordance with neutral theory. Variations in this D-loop region were mainly affected by neutral mutation, and the sequence in this region had not been changed by artificial selection. From another angle, this indicated that there was no relationship between artificial selection focused on certain production performance goals and the variance in this D-loop region. Bell et al. (1985), Mannen and Morimoto (2003), and Oh and Yoon (2003) reported that sequence variation in bovine mtdna had effects on milk production, meat quality, and rate of backfat accretion, respectively. Further research is needed to determine whether cytoplasmic inheritance has had effects on the production traits of domestic geese. Origin of the Chinese Domestic Goose 2709 Liu (2003) analyzed nucleotide variation of the 1,401- bp mtdna sequence in 6 breeds of Chinese geese and 2 breeds of domestic Europe geese. The Yili goose and the 2 European goose breeds originated from the Greylag goose (A. anser). The remaining 5 Chinese goose breeds originated from the swan goose (A. cygnoides). Shi et al. (1998), who analyzed the polymorphisms of mtdna in 11 Chinese goose breeds by restriction fragment length polymorphism, stated that the maternal lineage of the Yili goose was different from that of the other 10 goose breeds. In the present study, haplotype analysis and systematic evolution analysis revealed that the Chinese domestic goose had 2 maternal origins. The Yili goose originated from the Greylag goose (A. anser), and the other 25 domestic goose breeds originated from the swan goose (A. cygnoides). An interesting finding was that 1 Linxian white goose and 1 Wanxi white goose shared the same H4 haplotype with the Rhine goose and the Landaise goose, which originated from the Greylag goose (A. anser). Based on earlier microsatellite data (Li et al., 2007), the 2 Chinese domestic white goose individuals in haplotype H4 belonged to the Linxian white goose breed and the Wanxi white goose breed, respectively, which was revealed by the Figure 5. Reduced median-joining networks of mitochondrial DNA D-loop haplotypes. H = haplotype.

6 2710 Li et al. analysis using Structure 2.1 software ( bsd.uchicago.edu/structure.html). This raises the question of whether the 2 white Chinese geese might have some Greylag goose lineage, and we further research is planned to investigate this finding. ACKNOWLEDGMENTS This work was supported by the Programs of the National Technological Supporting Project of P. R. China (No. 2008BDAB2B08), Scientific and Technical Supporting Project of Jiangsu Province (No. Be ), and the High Technological Project of Jiangsu Province of P. R. China (No. BG ). REFERENCES Bandelt, H. J., P. Forster, and A. Rohll Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16: Bell, B. R., B. T. McDaniel, and O. W. Robison Effects of cytoplasmic inheritance on production traits of dairy cattle. J. Dairy Sci. 68: Excoffier, L., G. Laval, and S. Schneider Arlequin Version 3.0: An integrated software package for population genetic data analysis. Evol. Bioinform. Online 1: Kulikova, I. V., S. V. Drovetski, D. D. Gibson, R. J. Harrigan, S. Rohwer, K. Winker, Y. N. Zhuravlev, and K. G. McCracken., Phylogeography of the mallard (Anas platyrhynchos): Hybridization, dispersal, and lineage sorting contribute to complex geographic structure. Auk. 122: Kumar, S., K. Tamura, and M. Nei MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: Lai, J. S., L. Wang, and Y. P. Liu Study on mitochondrial DNA genetic polymorphism of some yak breeds in China. Acta Genetica Sinica. 32: Lan, H., W. Wang, and L. M. Shi Genetic diversity of mitochondrial DNA sequences in swine and wild boar in southwest. J. Gene. Genomics 1: Li, H. F., K. W. Chen, N. Yang, W. T. Song, and Q. P. Tang Evaluation of genetic diversity of Chinese native geese revealed by microsatellite markers. World s Poult. Sci. J. 63: Li, J. H., and J. W. Wang Studies on ND4 gene polymorphism and genetic structure among domestic goose breeds. J. Anhui Agric. Sci. 35: Liu, A. F Analysis on the structure of mtdna sequence and genetic diversity in domestic goose. MS Thesis. Sichuan Agricultural University, Ya an City, P. R. China. Liu, R. Y., X. L. Xia, C. Z. Lei, M. Z. Zhang, H. Chen, and G. S. Yang Genetic diversity of mitochondrial DNA D-loop sequences in cattle breeds in Guizhou. Yi Chuan 3: Mannen, H., and M. Morimoto Identification of mitochondrial DNA substitutions related to meat quality in Japanese Black cattle. J. Anim. Sci. 81: Nei, M Evolution of human races at the gene level. Pages in Human Genetics, Part A: The Unfolding Genome. T. B Bonne, T. Cohen, R. M. Goodman, ed. Alan R. Liss, New York, NY. Oh, J. D., and D. H. Yoon Effect of sequence variation in bovine mitochondrial DNA D-loop region on economic traits for Hanwoo. J. Anim. Sci. Technol. 45: Romanov, M. N., and S. Weigend Analysis of genetic relationship between various populations of domestic and jungle fowl using microsatellite markers. Poult. Sci. 77: Rozas, J., J. C. Sánchez-DelBarrio, X. Messeguer, and R. Rozas DnaSP, DNA polymorphism analysis by the coalescent and other methods. Bioinformatics 19: Shi, X. W., F. T. Zeng, X. P. Qiu, and Y. P. Zhang Origin and differentiation of domestic goose breeds in China, inferred from mitochondrial DNA polymorphism. Yi Chuan Xue Bao 25: Tajima, F Statistical method for testing the meutral mutation hypothesis by DNA polymorphism. Genetics 123: Wakana, S., T. Watanabe, Y. Hayashi, and T. Tomita., A variant in the restriction endonuclease cleavage pattern of mitochondrial DNA in the domestic fowl. Gallus gallus domesticus. Anim. Genet. 17: Wang, J. W., X. P. Qiu, F. T. Zeng, X. W. Shi, and Y. P. Zhang Genetic differentiation of domestic goose breeds in China. Yi Chuan Xue Bao 32: