Eur.J.Hortic.Sci. 81 (5) 264-272 | DOI: 10.17660/eJHS.2016/81.5.5|
ISSN 1611-4426 print and 1611-4434 online | © ISHS 2016 | European Journal of Horticultural Science | Original article
Retrotransposon-based sequence-specific amplification polymorphism markers reveal that cultivated Pyrus ussuriensis originated from an interspecific hybridization
Peiyuan Yu1, Shuang Jiang2, Xiaoxiang Wang3, Songling Bai1 and Yuanwen Teng1
1Department of Horticulture, The State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development and
Quality Improvement, Zhejiang University, Hangzhou 310058, Zhejiang, China
2Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
3Horticultural Sub-Academy, Heilongjiang Academy of Agricultural Sciences, Harbin 150069, Heilongjiang, China
Pyrus ussuriensis Maxim. cultivars have long been
considered to be directly derived from wild P. ussuriensis, which is distributed in northeastern China. However, recent studies have revealed that P. ussuriensis cultivars are similar to Pyrus pyrifolia, which is extensively cultivated in China. To clarify the origin of cultivated P. ussuriensis, 12 primers of retrotransposon-based sequence-specific amplification polymorphism marker were used to analyze the genetic relationships among 92 Pyrus accessions, including cultivated P. pyrifolia, cultivated and wild P. ussuriensis, and a few Occidental species. We obtained 1,143 scorable fragments using 12 primer combinations, of which 871 were polymorphic (i.e., 76.20%). A dendrogram produced using Dice similarity coefficients and the unweighted pair group method with arithmetic mean indicated that wild and cultivated P. ussuriensis form a group parallel to the P. pyrifolia group, in which a few P. ussuriensis cultivars are scattered and further divided into independent subgroups. A Bayesian model-based analysis of population structures revealed that P. ussuriensis cultivars consist of two major genepools, with one originating from wild P. ussuriensis and the other from cultivated P. pyrifolia. Our results suggest that cultivated P. ussuriensis originated from an interspecific hybridization between P. ussuriensis and P. pyrifolia. Our findings not only provide new insights into the origin of cultivated P. ussuriensis, but may contribute to the improvement of P. ussuriensis cultivars.
hybridization origin, SSAP markers, Ussurian pear, Pyrus pyrifolia, genetic diversity, genetic structure, domestication
Significance of this study
What is already known on this subject?
What are the new findings?
Pyrus ussuriensis cultivars were believed to have been domesticated directly from wild P. ussuriensis. However, recent DNA marker-based studies indicated there is some genetic diversity between wild and cultivated P. ussuriensis, and cultivated Ussurian pears are similar to P. pyrifolia cultivars.
What is the expected impact on horticulture?
A few P. ussuriensis cultivars are scattered in the P. pyrifolia group, and the majority of wild and cultivated P. ussuriensis are clustered independently. Additionally, P. ussuriensis cultivars are composed of two genepools, with one derived from wild P. ussuriensis and the other from P. pyrifolia.
Our results suggest that P. ussuriensis cultivars originated from interspecific hybridizations between wild P. ussuriensis and P. pyrifolia cultivars. Therefore, extra-Ussurian pear germplasm should be used to improve P. ussuriensis cultivars in pear breeding programs.
Bailey, L.H. (1917). Standard Cyclopedia of Horticulture Pyrus, Vol. 5. (New York: Macmillan), pp. 28652878.
Bajpai, P.K., Warghat, A.R., Sharma, R.K., Yadav, A., Thakur, A.K., Srivastava, R.B., and Stobdan, T. (2014). Structure and genetic diversity of natural populations of Morus alba in the Trans-Himalayan Ladakh Region. Biochem. Genet. 52, 137152. https://doi.org/10.1007/s10528-013-9634-5.
Bao, L., Chen, K., Zhang, D., Cao, Y., Yamamoto, T., and Teng, Y. (2007). Genetic diversity and similarity of pear (Pyrus L.) cultivars native to East Asia revealed by SSR (simple sequence repeat) markers. Genet. Resour. Crop. Ev. 54, 959971. https://doi.org/10.1007/s10722-006-9152-y.
Bao, L., Chen, K., Zhang, D., Li, X., and Teng, Y. (2008). An assessment of genetic variability and relationships within Asian pears based on AFLP (amplified fragment length polymorphism) markers. Sci. Hortic. 116, 374380. https://doi.org/10.1016/j.scienta.2008.02.008.
Berenyi, M., Gichuki, S., Schmidt, J., and Burg, K. (2002). Ty1-copia retrotransposon-based S-SAP (sequence-specific amplified polymorphism) for genetic analysis of sweetpotato. Theor. Appl. Genet. 105, 862869. https://doi.org/10.1007/s00122-002-1015-0.
Biswas, M.K., Chai, L., Amar, M.H., Zhang, X., and Deng, X.-X. (2011). Comparative analysis of genetic diversity in citrus germplasm collection using AFLP, SSAP, SAMPL and SSR markers. Sci. Hortic. 129, 798803. https://doi.org/10.1016/j.scienta.2011.06.015.
Boeke, J.D., and Corces, V.G. (1989). Transcription and reverse transcription of retrotransposons. Annu. Rev. Microbiol. 189, 31213129. https://doi.org/10.1146/annurev.mi.43.100189.002155.
Bolibok-Brągoszewska, H., Zabierzewska, N., Hromada-Judycka, A., and Krzewska, L. (2012). S-SAP markers based on a novel Ty1-copia like element are a powerful tool for the assessment of genetic diversity in Rye (Secale cereale L.) inbred lines. Cereal Res. Commun. 40, 204209. https://doi.org/10.1556/CRC.40.2012.2.4.
Cao, Y., Tian, L., Gao, Y., and Liu, F. (2012). Genetic diversity of cultivated and wild Ussurian Pear (Pyrus ussuriensis maxim.) in China evaluated with M13-tailed SSR markers. Genet. Resour. Crop Ev. 59, 917. https://doi.org/10.1007/s10722-011-9661-1.
Doyle, J., and Doyle, J. (1987). Genomic plant DNA preparation from fresh tissue-CTAB method. Phytochem. Bull. 19, 1115.
He, P., Ma, Y., Dai, H., Li, L., Liu, Y., Li, H., Zhao, G., and Zhang, Z. (2012). Development of Ty1-copia retrotransposon-based S-SAP markers in strawberry (Fragaria Χ ananassa Duch.). Sci. Hortic. 137, 4348. https://doi.org/10.1016/j.scienta.2012.01.004.
Iketani, H., Katayama, H., Uematsu, C., Mase, N., Sato, Y., and Yamamoto, T. (2012). Genetic structure of East Asian cultivated pears (Pyrus spp.) and their reclassification in accordance with the nomenclature of cultivated plants. Plant Syst. Evol. 298, 16891700. https://doi.org/10.1007/s00606-012-0670-0.
Jiang, S., Zong, Y., Yue, X., Postman, J., Teng, Y., and Cai, D. (2015). Prediction of retrotransposons and assessment of genetic variability based on developed retrotransposon-based insertion polymorphism (RBIP) markers in Pyrus. Mol. Genet. Genomics 290, 225237. https://doi.org/10.1007/s00438-014-0914-5.
Jiang, S., Zheng, X., Yu, P., Yue, X., Ahmed, M., Cai, D., and Teng, Y. (2016). Primitive genepools of Asian pears and their complex hybrid origins inferred from fluorescent sequence-specific amplification polymorphism (SSAP) markers based on LTR retrotransposons. PloS ONE 11(2): e0149192. https://doi.org/10.1371/journal.pone.0149192.
Kaczmarska, E., Gawronski, J., Dyduch-Sieminska, M., Najda, A., Marecki, W., and Zebrowska, J. (2015). Genetic diversity and chemical characterization of selected Polish and Russian cultivars and clones of blue honeysuckle (Lonicera caerulea). Turk. J. Agric. For. 39, 394402. https://doi.org/10.3906/tar-1404-149.
Katayama, H., Amo, H., Wuyun, T., Uematsu, C., and Iketani, H. (2016). Genetic structure and diversity of the wild Ussurian pear in East Asia. Breeding Sci. 66, 9099. https://doi.org/10.1270/jsbbs.66.90.
Kikuchi, A. (1946). Assessment of Chinese pear species and cultivars. Collected Records Hort. Res. Faculty Agr. Kyoto Univ. Kyoto, pp. 111 (in Japanese).
Kimura, T., Shi, Y.Z., Shoda, M., Kotobuki, K., Matsuta, N., Hayashi, T., Ban, Y., and Yamamoto, T. (2002). Identification of Asian pear varieties by SSR analysis. Breeding Sci. 52, 115121. https://doi.org/10.1270/jsbbs.52.115.
Ko, W.R., Sa, K.J., Roy, N.S., Choi, H.J., and Lee, J.K. (2016). Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers. Genet. Mol. Res. 15(1). https://doi.org/10.4238/gmr.15017392.
Liang, W., Dondini, L., De Franceschi, P., Paris, R., Sansavini, S., and Tartarini, S. (2015). Genetic diversity, population structure and construction of a core collection of apple cultivars from Italian germplasm. Plant Mol. Biol. Rep. 33, 458473. https://doi.org/10.1007/s11105-014-0754-9.
Li, G., Wu, R., Jia, H., and Teng, Y. (2013). Changes in volatile organic compound composition during the ripening of 'Nanguoli' pears (Pyrus ussuriensis Maxim) harvested at different growing locations. J. Hortic. Sci. Biotech. 88, 563570. https://doi.org/10.1080/14620316.2013.11513007.
Liu, Q., Song, Y., Liu, L., Zhang, M., Sun, J., Zhang, S., and Wu, J. (2015). Genetic diversity and population structure of pear (Pyrus spp.) collections revealed by a set of core genome-wide SSR markers. Tree Genet. Genome 11, 122. https://doi.org/10.1007/s11295-015-0953-z.
Pritchard, J.K., Stephens, M., and Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945959.
Potter, D., Eriksson, T., Evans, R.C., Oh, S., Smedmark, J.E.E., Morgan, D.R., Kerr, M., Robertson, K.R., Arsenault, M., and Dickinson, T.A. (2007). Phylogeny and classification of Rosaceae. Plant Syst. Evol. 266, 543. https://doi.org/10.1007/s00606-007-0539-9.
Pu, F., and Wang, Y. (1963). Pomology of China Pears, Vol. 3. (Shanghai: Shanghai Science and Technology Press).
Rohlf, F.J. (1998). Numerical taxonomy and multivariate analysis system version 2.0. (Setauket , NY: Exeter Publishing).
Rubtsov, G.A. (1944). Geographical distribution of the genus Pyrus and trends and factors in its evolution. Lancet 346, 12231224. https://doi.org/10.1086/281206.
Sanz, A.M., Gonzalez, S.G., Syed, N.H., Suso, M.J., Salda-a, C.C., and Flavell, A.J. (2007). Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Mol. Genet. Genomics 278, 433441. https://doi.org/10.1007/s00438-007-0261-x.
Syed, N.H., Sureshsundar, S., Wilkinson, M.J., Bhau, B.S., Cavalcanti, J.J.V., and Flavell, A.J. (2005). Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theor. Appl. Genet. 110, 11951202. https://doi.org/10.1007/s00122-005-1948-1.
Teng, Y., Tanabe, K., Tamura, F., and Itai, A. (2001). Genetic relationships of pear cultivars in Xinjiang, China, as measured by RAPD markers. J. Hortic. Sci. Biotech. 76, 771779. https://doi.org/10.1080/14620316.2001.11511444.
Teng, Y. (2002). Genetic relationships of Pyrus species and cultivars native to East Asia revealed by Randomly Amplified Polymorphic DNA markers. J. Am. Soc. Hortic. Sci. 127, 262270.
Teng, Y. (2004). Reconsideration on the origin of cultivated pears native to East Asia. Acta Hortic. 634, 175182. https://doi.org/10.17660/ActaHortic.2004.634.21.
Tian, L., Gao, Y., Cao, Y., Liu, F., and Yang, J. (2012). Identification of Chinese white pear cultivars using SSR markers. Genet. Resour. Crop Ev. 59, 317326. https://doi.org/10.1007/s10722-011-9785-3.
Waugh, R., McLean, K., Flavell, J.A., Pearce, R.S., Kumar, A., Thomas, T.B.B., and Powell, W. (1997). Genetic distribution of Bare1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol. Gen. Genet. 253, 687694. https://doi.org/10.1007/s004380050372.
Wojnicka-Poltorak, A., Celinski, K., Chudzinska, E., Prus-Glowacki, W., and Niemtur, S. (2015). Genetic resources of Pinus cembra L. marginal populations from the Tatra mountains: Implications for conservation. Biochem. Genet. 53, 4961. https://doi.org/10.1007/s10528-015-9670-4.
Wuyun, T., Ma, T., Uematsu, C., and Katayama, H. (2013). A phylogenetic network of wild ussurian pears (Pyrus ussuriensis Maxim.) in China revealed by hypervariable regions of chloroplast DNA. Tree Genet. Genome 9, 167177. https://doi.org/10.1007/s11295-012-0544-1.
Wuyun, T., Amo, H., Xu, J., Ma, T., Uematsu, C., and Katayama, H. (2015). Population structure of and conservation strategies for wild Pyrus ussuriensis Maxim in China. PloS one 10(8): e0133686. https://doi.org/10.1371/journal.pone.0133686.
Yeh, F.C. (1997). Population genetic analysis of codominant and dominant markers and quantitative traits. Belg. J. Bot. 129.
Yu, T.T., and Ku, T.C. (1974). Pyrus. In Flora Reipublicae Popularis Sinicae, T.T. Yu, ed. (Beijing: Science Press), pp. 354372.
Received: 15 July 2016 | Accepted: 13 June 2016 | Published: 30 October 2016 | Available online: 26 October 2016