Assessment of genetic structure among different pear species (Pyrus spp.) using apple-derived SSR and evidence of duplications in the pear genome

References

• Potter D, Eriksson T, Evans RC, et al. Phylogeny and classification of Rosaceae. Plant Syst Evol. 2007;266:5–43.
   Web of Science ®Google Scholar
• Bell RL. Pears (Pyrus). In: Moore JN, Ballington JR, editors. Genetic resources of temperate fruit and nut crops I. Wageningen (Netherlands): International Society for Horticultural Science; 1990. p. 655–697.
   Google Scholar
• Bell RL, Quamme HA, Layne REC, et al. Pears. In: Janick J, Moore.JN. editor. Fruit breeding, Vol 1. Tree and tropical fruits. New York (USA): Wiley; 1996. p. 441–514.
   Google Scholar
• Weeden N, Lamb RC. Genetics and linkage analysis of 19 isozyme loci in apple. J Am Soc Hort Sci. 1987;112:865–872.
   Web of Science ®Google Scholar
• Vavilov NI. Origin and geography of cultivated plants; Vol. 15. Cambridge (UK:): Cambridge University Press; 1992.
   Google Scholar
• Yamamoto T, Kimura T, Sawamura Y, et al. SSRs isolated from apple can identify polymorphism and genetic diversity in pear. Theor Appl Genet. 2001;102:865–870.
   Web of Science ®Google Scholar
• Yamamoto T, Kimura T, Shoda M, et al. Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes. 2002;2:14–16.
   Web of Science ®Google Scholar
• Wunsch A, Hormaza JI. Characterization of variability and genetic similarity of European pear using microsatellite loci developed in apple. Sci Hort. 2007;173:37–43.
   Google Scholar
• Pierantoni L, Cho KH, Shin IS, et al. Characterization and transferability of apple SSRs to two European pear F1 populations. Theor Appl Genet. 2004;109:1519–1524.
   PubMed Web of Science ®Google Scholar
• Volk GM, Richards CM, Henk AD, et al. Diversity of wild Pyrus communis based on microsatellite analysis. J Ame Soc Hort Sci. 2006;131:408–417.
   Web of Science ®Google Scholar
• Brini W, Mars M, Hormaz JI. Genetic diversity in local Tunisian pears (Pyrus communis L.) studied with SSR markers. Sci Hort. 2008;115:337–341.
   Web of Science ®Google Scholar
• Wolko L, Antkowiak W, Lanartowicz E, et al. Genetic diversity of European pear cultivars (Pyrus communis L.) and wild pear (Pyrus pyraster (L.) Burgsd.) inferred from microsatellite markers analysis. Genet Resour Crop Evol. 2010;57:801–806.
   Web of Science ®Google Scholar
• Santos A, Ramos-Cabrer AM, Díaz-Hernández MB, et al. Genetic variability and diversification process in local pear cultivars from northwestern Spain using microsatellites. Tree Genet Genomes. 2011;7:1041–1056.
   Web of Science ®Google Scholar
• Queiroza A, Assunc A, Ramadasb I, et al. Molecular characterization of Portuguese pear landraces (Pyrus communis L.) using SSR markers. Sci Horti. 2015;183:72–76.
   Web of Science ®Google Scholar
• Erfani J, Ebadi A, Abdollahi H, et al. Genetic diversity of some pear cultivars and genotypes using simple sequence repeat (SSR) markers. Plant Mol Biol Rep. 2012;30:1065–1072.
   Web of Science ®Google Scholar
• Liebhard R, Gianfranceschi L, Koller B, et al. Development and characterization of 140 new microsatellites in apple (Malus x domestica Borkh.). Mol Breed. 2002;10:217–241.
   Web of Science ®Google Scholar
• Guilford P, Prakash S, Zhu JM, et al. Microsatellites in Malus x domestica (apple): abundance, polymorphism, and cultivar identification. Theor Appl Genet. 1997;94:249–254.
   Web of Science ®Google Scholar
• Yamamoto T, Iketani H, Ieki H, et al. Transgenic grapevine plants expressing a rice chitinase with enhanced resistance to fungal pathogens. Plant Cell Rep. 2000;19:639–646.
   PubMed Web of Science ®Google Scholar
• Rechinger KH. Flora Iranica, no 66. Graz, Austria: Akademische Druck-und Verlagsanstalt; 1969.
   Google Scholar
• Marshall TC, Slate J, Kruuk LEB, et al. Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol. 1998;7:639–655.
   PubMed Web of Science ®Google Scholar
• Rohlf FJ. NTSYSpc numerical taxonomy and multivariate analysis system version 2.0 user guide. Setauket: Applied Biostatistics Inc.; 1998.
   Google Scholar
• Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research—an update. Bioinformatics. 2012;8(19):2537–2539.
   Google Scholar
• Nei M. Genetic distance between populations. Am Nat. 1972;106:283–292.
   Web of Science ®Google Scholar
• Yeh FC, Yang RC, Boyle TBJ, et al. POPGENE, the user-friendly shareware for population genetic analysis. Edmonton, Alberta (Canada:): Molecular Biology and Biotechnology Center, University of Alberta; 1997.
   Google Scholar
• Tamura K, Peterson D, Peterson N, et al. MEGA6:molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2012;30:2725–2729.
   Web of Science ®Google Scholar
• Pritchard, JK, Stepheens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–959.
   PubMed Web of Science ®Google Scholar
• Evanno G, Regnaut S, Goudet J. Detecting the number of clusters ofindividuals using the software structure, a simulation study. Mol Ecol. 2005;14:2611–2620.
   PubMed Web of Science ®Google Scholar
• Earl DA, VonHoldt BM. STRUCTURE HARVESTER, A website and programfor visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2012;4:359–361.
   Web of Science ®Google Scholar
• Gürcan K, Mehlenbacher S. Transferability of microsatellite markers in the Betulaceae. J Am Soc Hortic Sci. 2010;135:159–173.
   Web of Science ®Google Scholar
• Wang H, Walla JA, Zhong S, et al. Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.). Plant Cell Rep. 2012;31(11):2047–2055.
   PubMed Web of Science ®Google Scholar
• Fan L, Zhang MY, Liu QZ, et al. Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Mol Biol Rep. 2013;31:1271–1282.
   PubMed Web of Science ®Google Scholar
• Drašnarová A, Krak K, Vít P, et al. Cross-amplification and multiplexing of SSR markers for Alnus glutinosa and A. incana. Tree Genet Genomes. 2014; [cited 2017 Nov 13];10:865. DOI:10.1007/s11295-014-0727-z.
   Web of Science ®Google Scholar
• Yamamoto T, Kimura T, Shoda M, et al. Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet. 2002;106:9–18.
   PubMed Web of Science ®Google Scholar
• Yamamoto T, Kimura T, Soejima J, et al. Identification of quince varieties using SSR markers developed from pear and apple. Breeding Sci. 2004;54:239–244.
   Web of Science ®Google Scholar
• Kato S, Imai A, Rie N, et al. Population genetic structure in a threatened tree, Pyrus calleryana var. dimorphophylla revealed by chloroplast DNA and nuclear SSR locus polymorphisms. Conserv Genet. 2013;14:983–996.
   Web of Science ®Google Scholar
• Wolko L, Bocianowski J, Antkowiak W, et al. Genetic diversity and population structure of wild pear (Pyrus pyraster (L.) Burgsd.) in Poland. Open Life Sci. 2015;10:19–29.
   Web of Science ®Google Scholar
• Kumar S, Kirk C, Deng C, et al. Genotyping-by-sequencing of pear (Pyrus spp.) accessions unravels novel patterns of genetic diversity and selection footprints. Hortic Res. 2017; [cited 2017 Nov 13];4:17015. DOI 10.1038/hortres.2017.15.
   PubMed Web of Science ®Google Scholar
• Hennink S, Zeven AC. The interprestation of Nei and Shannon-Weaver within population variation indices. Euphytica. 1991;51:235–240.
   Web of Science ®Google Scholar
• Chamberlain JR, Hubert JD. Molecular analysis of genetic variation. In: Chamberlain JR, editor. Calliandra calothyrsus: an agro-forestry tree for the humid tropics. Tropical Forestry Paper No. 40. Oxford (UK): Oxford Forestry Research Institute; 1998. p. 67–76.
   Google Scholar
• Bell RL, Hough LF. Interspecific and intergeneric hybridization of Pyrus. Hort Sci. 1986;21:62–64.
   Google Scholar
• Milne RI, Abbott RJ, Wolff K, et al. Hybridization among sympatric species of Rhododendron (Ericaceae) in Turkey: morphological and molecular evidence. Am J Bot. 1999;86:1776–1785.
   PubMed Web of Science ®Google Scholar
• Doyle JJ, Egan AN. Dating the origins of polyploidy events. New Phytol. 2010;186:73–85.
   PubMed Web of Science ®Google Scholar
• Zhang J. Evolution by gene duplication: an update. Trends Ecol Evol. 2003;18(6):292–298.
   Web of Science ®Google Scholar
• Taylor JS, Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet. 2004;38:615–643.
   PubMed Web of Science ®Google Scholar
• Messer PW, Arndt PF. The majority of recent short DNA insertions in the human genome are tandem duplications. Mol Biol Evol. 2007;24:1190–1197.
   PubMed Web of Science ®Google Scholar
• Seyfert AL, Cristescu MEA, Frisse L, et al. The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics. 2008;178:2113–2121.
   PubMed Web of Science ®Google Scholar
• Gürcan K. Simple sequence repeat marker development and use in european hazelnut (Corylus avellana L.). [dissertation]. Oregon (USA): Oregon State University; 2009.
   Google Scholar
• Velasco R, Zharkikh A, Affourtit J, et al. The genome of the domesticated apple (Malus domestica Borkh.). Nat Genet. 2010;42:833–839.
   PubMed Web of Science ®Google Scholar
• Chavarriaga-Aguirre P, Maya M, Bonierbale M, et al. Microsatellites in cassava (Manihot esculenta Crantz): discovery, inheritance and variability. Theor Appl Genet. 1998;97:493–501.
   Web of Science ®Google Scholar
• Kim NH, Choi HI, Kim KH. Evidence of genome duplication revealed by sequence analysis of multi-loci expressed sequence tag-simple sequence repeat bands in Panax ginseng Meyer. J Ginseng Res. 2014;38:130–135.
   PubMed Web of Science ®Google Scholar
• Li M, Li L, Dunwell JM, et al. Characterization of the lipoxygenase (LOX) gene family in the Chinese white pear (Pyrus bretschneideri) and comparison with other members of the Rosaceae. BMC Genomics. 2014; [cited 2017 Nov 13];15:444. DOI:10.1186/1471-2164-15-444.
   PubMed Web of Science ®Google Scholar
• Cao Y, Han Y, Li D. MYB transcription factors in Chinese pear (Pyrus bretschneideri Rehd.): genome-wide identification, classification, and expression profiling during fruit development. Front Plant Sci. 2016; [cited 2017 Nov 13];7:577. DOI: 10.3389/fpls.2016.00577.
   PubMed Web of Science ®Google Scholar