Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers

https://doi.org/10.17221/9/2016-CJASCitation:Di R., Liu Q.Y., Xie F., Hu W.P., Wang X.-Y., Cao X.-H., Pan Z.-Y., Chen G.-H., Chu M.-X.: (2017): Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers. Czech J. Anim. Sci., 62: 219-225.
supplementary materialdownload PDF
China had the largest population of raising donkeys in the world, however the number of Chinese indigenous donkey decreased dramatically due to the increase of agriculture mechanization in the last century. The species has still been important in China because of its edible and medical value, therefore the survey on its genetic diversity in China is necessary for its conservation and utilization. In this study, 15 microsatellite markers were used to evaluate genetic diversity and population structure of five Chinese indigenous donkey breeds. The mean values of expected heterozygosity, allelic richness, and total number of alleles for all the tested Chinese donkeys were 0.70, 6.04, and 6.28 respectively, suggesting that the genetic diversity of Chinese indigenous donkeys is rich. The Bayesian analysis and principal component analysis plot yielded the same clustering result, which revealed that Guanzhong donkey was the most differentiated breed in all detected samples, and Jinnan (JN) and Guangling (GL) were genetically closed together. Additionally, our results indicated that the heterozygote deficit was severe in two Chinese indigenous donkey breeds (GL and JN), and it warned us that animal conservation activities on this species should be considered carefully in near future.
Aranguren-Méndez José, Jordana Jordi, Gomez Mariano (2001): Genetic diversity in Spanish donkey breeds using microsatellite DNA markers. Genetics Selection Evolution, 33, 433- https://doi.org/10.1186/1297-9686-33-4-433
Aranguren-Méndez J, Gómez M, Jordana J (): Hierarchical analysis of genetic structure in Spanish donkey breeds using microsatellite markers. Heredity, 89, 207-211 https://doi.org/10.1038/sj.hdy.6800117
Beja-Pereira A. (2004): African Origins of the Domestic Donkey. Science, 304, 1781-1781 https://doi.org/10.1126/science.1096008
Bordonaro Salvatore, Guastella Anna Maria, Criscione Andrea, Zuccaro Antonio, Marletta Donata (2012): Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers. The Scientific World Journal, 2012, 1-6 https://doi.org/10.1100/2012/648427
Chen S. Y., Zhou F., Xiao H., Sha T., Wu S. F., Zhang Y. P. (2006): Mitochondrial DNA diversity and population structure of four Chinese donkey breeds. Animal Genetics, 37, 427-429 https://doi.org/10.1111/j.1365-2052.2006.01486.x
Colli L., Perrotta G., Negrini R., Bomba L., Bigi D., Zambonelli P., Verini Supplizi A., Liotta L., Ajmone-Marsan P. (2013): Detecting population structure and recent demographic history in endangered livestock breeds: the case of the Italian autochthonous donkeys. Animal Genetics, 44, 69-78 https://doi.org/10.1111/j.1365-2052.2012.02356.x
Eggleston-Stott M.L., DelValle A., Bautista M., Dileanis S., Wictum E., Bowling A.T. (1997): Nine equine dinucleotide repeats at microsatellite loci UCDEQ136, UCDEQ405, UCDEQ412, UCDEQ425, UCDEQ437, UCDEQ467, UCDEQ487, UCDEQ502 and UCDEQ505. Animal Genetics, 28, 370–371.
EVANNO G., REGNAUT S., GOUDET J. (2005): Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology, 14, 2611-2620 https://doi.org/10.1111/j.1365-294X.2005.02553.x
Goudet J. (2001): FSTAT, a program to estimate and test gene diversities and fixation (Version Available at http://www2.unil.ch/popgen/softwares/fstat.htm (accessed Apr 24, 2017).
Gutierrez J.P., Marmi J., Goyache F., Jordana J. (2005): Pedigree information reveals moderate to high levels of inbreeding and a weak population structure in the endangered Catalonian donkey breed. Journal of Animal Breeding and Genetics, 122, 378-386 https://doi.org/10.1111/j.1439-0388.2005.00546.x
Han Lu, Zhu Songbiao, Ning Chao, Cai Dawei, Wang Kai, Chen Quanjia, Hu Songmei, Yang Junkai, Shao Jing, Zhu Hong, Zhou Hui (2014): Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys. BMC Evolutionary Biology, 14, - https://doi.org/10.1186/s12862-014-0246-4
Ivankovic A., Kavar T., Caput P., Mioc B., Pavic V., Dovc P. (2002): Genetic diversity of three donkey populations in the Croatian coastal region. Animal Genetics, 33, 169-177 https://doi.org/10.1046/j.1365-2052.2002.00879.x
Jordana J., Folch P., Aranguren J. A. (2001): Microsatellite analysis of genetic diversity in the Catalonian donkey breed. Journal of Animal Breeding and Genetics, 118, 57-63 https://doi.org/10.1046/j.1439-0388.2001.00266.x
Jordana J., Ferrando A., Miró J., Goyache F., Loarca A., Martínez López O.R., Canelón J.L., Stemmer A., Aguirre L., Lara M.A.C., Álvarez L.A., Llambí S., Gómez N., Gama L.T., Nóvoa M.F., Martínez R.D., Pérez E., Sierra A., Contreras M.A., Guastella A.M., Marletta D., Arsenos G., Curik I., Landi V., Martínez A., Delgado J.V. (2015): Genetic relationships among American donkey populations: insights into the process of colonization. Journal of Animal Breeding and Genetics, , n/a-n/a https://doi.org/10.1111/jbg.12180
Lei Chu-Zhao, Ge Qing-Lan, Zhang Hu-Cai, Liu Ruo-Yu, Zhang Wei, Jiang Yong-Qing, Dang Rui-Hua, Zheng Hui-Ling, Hou Wen-Tong, Chen Hong (2007): African Maternal Origin and Genetic Diversity of Chinese Domestic Donkeys. Asian-Australasian Journal of Animal Sciences, 20, 645-652 https://doi.org/10.5713/ajas.2007.645
Lopez C. Lopez, Alonso R., Aluja A. S. (2005): Study of the Genetic Origin of the Mexican Creole Donkey (Equus asinus) by Means of the Analysis of the D-Loop Region of Mitochondrial DNA. Tropical Animal Health and Production, 37, 173-188 https://doi.org/10.1007/s11250-005-9001-6
Matassino Donato, Cecchi Francesca, Ciani Ferdinando, Incoronato Caterina, Occidente Mariaconsiglia, Santoro Laura, Ciampolini Roberta (2014): Genetic diversity and variability in two Italian autochthonous donkey genetic types assessed by microsatellite markers. Italian Journal of Animal Science, 13, - https://doi.org/10.4081/ijas.2014.3028
Mburu D. N., Ochieng J. W., Kuria S. G., Jianlin H., Kaufmann B., Rege J. E. O., Hanotte O. (2003): Genetic diversity and relationships of indigenous Kenyan camel (Camelus dromedarius) populations: implications for their classification. Animal Genetics, 34, 26-32 https://doi.org/10.1046/j.1365-2052.2003.00937.x
Meyer A.H., Valberg S.J., Hillers K.R., Schweitzer J.K., Mickelson J.R. (1997): Sixteen new polymorphic equine microsatellites. Animal Genetics, 28, 69–70.
Nei Masatoshi (1972): Genetic Distance between Populations. The American Naturalist, 106, 283- https://doi.org/10.1086/282771
Nei Masatoshi, Tajima Fumio, Tateno Yoshio (1983): Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution, 19, 153-170 https://doi.org/10.1007/BF02300753
Pérez-Pardal L., Grizelj J., Traoré A., Cubric-Curik V., Arsenos G., Dovenski T., Marković B., Fernández I., Cuervo M., Álvarez I., Beja-Pereira A., Curik I., Goyache F. (2014): Lack of mitochondrial DNA structure in Balkan donkey is consistent with a quick spread of the species after domestication. Animal Genetics, 45, 144-147 https://doi.org/10.1111/age.12086
Pritchard J.K., Stephens M., Donnelly P. (2000): Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
Raymond M., Rousset F. (1995): GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism. Journal of Heredity, 86, 248-249 https://doi.org/10.1093/oxfordjournals.jhered.a111573
Rosenberg Noah A. (2004): distruct: a program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138 https://doi.org/10.1046/j.1471-8286.2003.00566.x
Rosenbom S., Costa V., Al-Araimi N., Kefena E., Abdel-Moneim A. S., Abdalla M. A., Bakhiet A., Beja-Pereira A. (2015): Genetic diversity of donkey populations from the putative centers of domestication. Animal Genetics, 46, 30-36 https://doi.org/10.1111/age.12256
Swinburne J E, Marti E, Breen M, Binns M M (1997): Characterization of twelve new horse microsatellite loci: AHT12-AHT23. Animal Genetics, 28, 453-454 https://doi.org/10.1111/j.1365-2052.1997.tb03289.x
Tallmadge R.L., Evans K.G., Hopman T.J., Schug M.D., Aquadro C.F., Bowling A.T., Murray J.D., Caetano A.R., Antczak D.F. (1999a): Equine dinucleotide repeat loci COR081–COR100. Animal Genetics, 30, 470–471.
Tallmadge R.L., Hopman T.J., Schug M.D., Aquadro C.F., Bowling A.T., Murray J.D., Caetano A.R., Antczak D.F. (1999b): Equine dinucleotide repeat loci COR061–COR080. Animal Genetics, 30, 462–463.
Xie C. (1987): Horse and Ass Breeds in China. Shanghai Scientific and Technical Publishing House, Shanghai, China.
Zhang Yun-Sheng, Yang Xue-Yi, Wang Xiao-Bin, Zhang Chun-Mei, Qin Fang, Zhou Zhen-Hui, Lan Xian-Yong, Chen Hong, Lei Chu-Zhao (2010): Cytochrome b Genetic Diversity and Maternal Origin of Chinese Domestic Donkey. Biochemical Genetics, 48, 636-646 https://doi.org/10.1007/s10528-010-9345-0
supplementary materialdownload PDF

© 2018 Czech Academy of Agricultural Sciences