Skip to main content
SpringerLink
Log in

EST-SSR markers reveal synonymies, homonymies and relationships inconsistent with putative pedigrees in chestnut cultivars

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Over the last two centuries, chestnut breeding programs in Europe and Asia have generated an array of chestnut interspecific hybrids, primarily of European (Castanea sativa), Japanese (C. crenata) and Chinese (C. mollissima) ancestry. During this same period, Europeans colonizing North America imported hybrid chestnuts and made interspecific hybrids with native chestnuts, primarily American chestnut (C. dentata). The importation of Chinese chestnut into the United States in the late 19th century also introduced chestnut blight, which triggered an additional interspecific hybridization effort in an attempt to develop blight resistant American chestnuts. Chestnut cultivars used for nut production in the United States and Canada have arisen against this background of non-native introductions and extensive hybridizing. The development of regionally adapted nut producing trees with dependable crops of high quality nuts requires sorting out the identities of existing cultivars. We chose 11 EST-SSR markers from C. mollissima for the initial task of genotyping 65 chestnut cultivars that grow well in the central United States. Many of these cultivars have interspecific pedigrees involving two or more species. We found extensive homonymies and synonymies, genetic groups inconsistent with published pedigrees, contradictory pedigrees and evidence for incorrect species assignments. Accurate inference of the interspecific ancestries of cultivars grown in the United States and Canada will require genotyping of species reference sets for C. sativa, C. crenata, C. mollissima, C. dentata and possibly C. pumila (the Ozark and Allegheny chinquapins).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Anagnostakis SL (1982) Biological control of chestnut blight. Science 215(4532):466–471. doi:10.1126/science.215.4532.466

    Article  PubMed  CAS  Google Scholar 

  • Anagnostakis SL (1987) Chestnut blight: the classical problem of an introduced pathogen. Mycologia 79:23–27

    Article  Google Scholar 

  • Anagnostakis SL (2007) Chestnut breeding in the United States. The connecticut agricultural experiment station. http://www.ct.gov/caes/cwp/view.asp?a=2815&q=376752. Accessed 22 April 2012

  • Bailey LH (1900) Chestnut. In: Bailey LH, Miller W (eds) Cyclopedia of American horticulture, vol C. MacMillian Co., New York, pp 294–297

  • Bassil N, Boccacci P, Botta R, Postman J, Mehlenbacher S (2012) Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars. Genet Resour Crop Evol. doi:10.1007/s10722-012-9857-z

  • Celton J-M, Chagné D, Tustin S, Terakami S, Nishitani C, Yamamoto T, Gardiner S (2009) Update on comparative genome mapping between Malus and Pyrus. BMC Res Notes 2(1):1–7. doi:10.1186/1756-0500-2-182

    Article  Google Scholar 

  • Cipriani G, Spadotto A, Jurman I, Di Gaspero G, Crespan M, Meneghetti S, Frare E, Vignani R, Cresti M, Morgante M, Pezzotti M, Pe E, Policriti A, Testolin R (2010) The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin. TAG Theor Appl Genet 121(8):1569–1585. doi:10.1007/s00122-010-1411-9

    Article  Google Scholar 

  • Clapper R (1954) Chestnut breeding, techniques and results. J Hered 45(4):201–208

    Google Scholar 

  • Conedera M, Krebs P, Tinner W, Pradella M, Torriani D (2004) The cultivation of Castanea sativa (Mill.) in Europe, from its origin to its diffusion on a continental scale. Veg Hist Archaeobotany 13(3):161–179. doi:10.1007/s00334-004-0038-7

    Google Scholar 

  • Dane F, Lang P, Huang H, Fu Y (2003) Intercontinental genetic divergence of Castanea species in eastern Asia and eastern North America. Heredity 91(3):314–321

    Article  PubMed  CAS  Google Scholar 

  • Decroocq V, Favé MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106(5):912–922. doi:10.1007/s00122-002-1158-z

    PubMed  CAS  Google Scholar 

  • Detlefsen JA, Ruth WA (1922) An orchard of chestnut hybrids. J Hered 13(7):305–314

    Google Scholar 

  • Dinis L-TJ, Peixoto F, Costa R, Gomes-Laranjo J (2010) Molecular characterization of ‘Judia’ (Castanea sativa Mill.) from several Trás-os-Montes regions by nuclear microsatellite markers. Acta Hort (ISHS) 866:225–232

    CAS  Google Scholar 

  • Durand J, Bodenes C, Chancerel E, Frigerio J-M, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn H-P, Villani F, Mattioni C, Cherubini M, Goicoechea P, Herran A, Ikaran Z, Cabane C, Ueno S, Alberto F, Dumoulin P-Y, Guichoux E, de Daruvar A, Kremer A, Plomion C (2010) A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 11(1):570

    Article  PubMed  Google Scholar 

  • Ellis J, Burke J (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99(2):125–132

    Article  PubMed  CAS  Google Scholar 

  • Feng S, Li W, Huang H, Wang J, Wu Y (2009) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23(1):85–97. doi:10.1007/s11032-008-9216-0

    Article  CAS  Google Scholar 

  • Fraser LG, Harvey CF, Crowhurst RN, De Silva HN (2004) EST-derived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 108:1010–1016

    Article  PubMed  CAS  Google Scholar 

  • Fulbright DW, Mandujano M, Stadt S (2010) Chestnut production in Michigan. Acta Horticulturae 866:531–553

    Google Scholar 

  • Gadaleta A, Giancaspro A, Zacheo S, Nigro D, Giove SL, Colasuonno P, Blanco A (2011) Comparison of genomic and EST-derived SSR markers in phylogenetic analysis of wheat. Plant Genet Res 9(02):243–246. doi:10.1017/S147926211100030X

    Article  CAS  Google Scholar 

  • Gasic K, Han Y, Kertbundit S, Shulaev V, Iezzoni A, Stover E, Bell R, Wisniewski M, Korban S (2009) Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Mol Breed 23(3):397–411. doi:10.1007/s11032-008-9243-x

    Article  CAS  Google Scholar 

  • Glover JD, Reganold JP, Bell LW, Borevitz J, Brummer EC, Buckler ES, Cox CM, Cox TS, Crews TE, Culman SW, DeHaan LR, Eriksson D, Gill BS, Holland J, Hu F, Hulke BS, Ibrahim AMH, Jackson W, Jones SS, Murray SC, Paterson AH, Ploschuk E, Sacks EJ, Snapp S, Tao D, Van Tassel DL, Wade LJ, Wyse DL, Xu Y (2010) Increased food and ecosystem security via perennial grains. Science 328(5986):1638–1639. doi:10.1126/science.1188761

    Article  PubMed  CAS  Google Scholar 

  • Gobbin D, Hohl L, Conza L, Jermini M, Gessler C, Conedera M (2007) Microsatellite-based characterization of the Castanea sativa cultivar heritage of southern Switzerland. Genome 50(12):1089–1103. doi:10.1139/g07-086

    Article  PubMed  CAS  Google Scholar 

  • Gökirmak T, Mehlenbacher S, Bassil N (2009) Characterization of European hazelnut (Corylus avellana) cultivars using SSR markers. Genet Resour Crop Evol 56(2):147–172. doi:10.1007/s10722-008-9352-8

    Article  Google Scholar 

  • Hoban S, Romero-Severson J (2011) Homonymy, synonymy and hybrid misassignments in butternut (Juglans cinerea) and Japanese walnut (Juglans ailantifolia) nut cultivars. Genet Resour Crop Evol 1–9. doi:10.1007/s10722-011-9767-5

  • Hoban SM, McCleary TS, Schlarbaum SE, Romero-Severson J (2009) Geographically extensive hybridization between the forest trees American butternut and Japanese walnut. Biol Lett 5(3):324–327

    Article  PubMed  Google Scholar 

  • Hoban SM, McCleary TS, Schlarbaum SE, Anagnostakis SL, Romero-Severson J (2012) Human-impacted landscapes facilitate hybridization between a native and an introduced tree. Evol Appl 5(7):720–731. doi:10.1111/j.1752-4571.2012.00250.x

    Google Scholar 

  • Huang H, Dane F, Norton JD (1994) Allozyme diversity in Chinese, Seguin and American chestnut (Castanea spp.). Theor Appl Genet 88(8):981–985. doi:10.1007/bf00220805

    Article  Google Scholar 

  • Hunt KL, Gold MA, Warmund MR (2005) Chinese chestnut cultivar performance in Missouri. Acta Hortic (ISHS) 693:145–148

    Google Scholar 

  • Jaillon O, Aury J-M, Characterization TFIPCfGG (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467. http://www.nature.com/nature/journal/v449/n7161/suppinfo/nature06148_S1.html

    Google Scholar 

  • Jaynes RA (1970) Chestnuts. In: Jaynes RA (ed) Nut tree culture in North America. Northern Nut Growers Association, Camden, pp 111–127

    Google Scholar 

  • Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16(5):1099–1106

    Article  PubMed  Google Scholar 

  • Li X, Zhou X, Zhou J, Dodson J, Zhang H, Shang X (2007) The earliest archaeobiological evidence of the broadening agriculture in China recorded at Xishanping site in Gansu Province. Sci China, Ser D Earth Sci 50(11):1707–1714. doi:10.1007/s11430-007-0066-0

    Article  Google Scholar 

  • Martin M, Mattioni C, Cherubini M, Taurchini D, Villani F (2010) Genetic diversity in European chestnut populations by means of genomic and genic microsatellite markers. Tree Genet Genomes 6(5):735–744. doi:10.1007/s11295-010-0287-9

    Article  Google Scholar 

  • Martín MA, Mattioni C, Cherubini M, Taurchini D, Villani F (2010) Genetic characterisation of traditional chestnut varieties in Italy using microsatellites (simple sequence repeats) markers. Annals of Applied Biology 157(1):37–44. doi:10.1111/j.1744-7348.2010.00407.x

    Article  Google Scholar 

  • Masaki N (1983) The emergence of food production in Neolithic Japan. J Anthropol Archaeol 2(4):305–322. doi:10.1016/0278-4165(83)90012-0

    Article  Google Scholar 

  • Mattioni C, Cherubini M, Taurchini D, Villani F, Martin MA (2010) Genetic diversity in European chestnut populations. Acta Hortic 866:163–167

    CAS  Google Scholar 

  • Maynard CA, Powell WA, Polin-McGuigan LD, Viéitez AM, Ballester A, Corredoira E, Merkle SA, Andrade GM (2009) Chestnut. In: Kole C, Hall TC (eds) Compendium of transgenic crop plants, vol 4. Wiley, Hoboken. doi:10.1002/9781405181099.k0905

  • Mellano M, Beccaro G, Donno D, Marinoni D, Boccacci P, Canterino S, Cerutti A, Bounous G (2012) Castanea spp. biodiversity conservation: collection and characterization of the genetic diversity of an endangered species. Genet Resour Crop Evol 1–15. doi:10.1007/s10722-012-9794-x

  • Paillet FL (2002) Chestnut: history and ecology of a transformed species. J Biogeogr 29(10–11):1517–1530

    Article  Google Scholar 

  • Payne J, Jaynes R, Kays S (1983) Chinese chestnut production in the United States: practice, problems, and possible solutions. Econ Bot 37(2):187–200. doi:10.1007/bf02858784

    Article  Google Scholar 

  • Pereira-Lorenzo S, Costa R, Ramos-Cabrer A, Ribeiro C, da Silva M, Manzano G, Barreneche T (2010) Variation in grafted European chestnut and hybrids by microsatellites reveals two main origins in the Iberian Peninsula. Tree Genet Genomes 6(5):701–715. doi:10.1007/s11295-010-0285-y

    Article  Google Scholar 

  • Powell GH (1899) The European and Japanese chestnuts in the Eastern United States. Bulletin XLII, Newark

    Google Scholar 

  • Preston JC, Hileman LC, Cubas P (2011) Reduce, reuse, and recycle: developmental evolution of trait diversification. Am J Bot 98(3):397–403. doi:10.3732/ajb.1000279

    Article  PubMed  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959

    PubMed  CAS  Google Scholar 

  • Qin L, Feng YQ, Xu HM, Dong QH, Gao XH (2005) The diversity of Castanea resources and cultivars improvement in China. Acta Hortic 693:421–430

    CAS  Google Scholar 

  • Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386

    Google Scholar 

  • Russell EWB (1987) Pre-blight distribution of Castanea dentata (Marsh.) Borkh. Bull Torrey Bot Club 114(2):183–190

    Article  Google Scholar 

  • Rutter PA, Miller G, Payne JA (1991) Chestnuts (Castanea). Genetic Resources of Temperate Fruit and Nut Crops. ISHS Acta Horticulturae, Leuven

    Google Scholar 

  • Smith J, Pearce BD, Wolfe MS (2012) A European perspective for developing modern multifunctional agroforestry systems for sustainable intensification. Renew Agric Food Syst 27(4):323–332. doi:10.1017/S1742170511000597

  • Studer B, Kolliker R, Muylle H, Asp T, Frei U, Roldan-Ruiz I, Barre P, Tomaszewski C, Meally H, Barth S, Skot L, Armstead I, Dolstra O, Lubberstedt T (2010) EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.). BMC Plant Biol 10(1):177

    Article  PubMed  Google Scholar 

  • Tanaka T, Yamamoto T, Suzuki M (2005) Genetic diversity of Castanea crenata in Northern Japan assessed by SSR markers. Breed Sci 55:271–277

    Article  CAS  Google Scholar 

  • Warmund MR (2011) Chinese chestnut (Castanea mollissima) as a Niche crop in the Central Region of the United States. HortScience 46(3):345–347

    Google Scholar 

  • Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W (2010) Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha curcas L. BMC Res Notes 3(1):42

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

The authors thank Rory Carmichael (Notre Dame Bioinformatics Core Facility) for assistance with bioinformatics and Brent Harker (Notre Dame Genomics Core Facility) for ABI3730xl services. This work was funded through the University of Missouri Center for Agroforestry under cooperative agreement 58-6227-9-059 with the USDA Agricultural Research Service (ARS). Any opinions, findings, conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the view of the United States Department of Agriculture.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA

    Tim McCleary, Mary McAllister & Jeanne Romero-Severson

  2. Center for Agroforestry, University of Missouri, 203 ABNR Building, Columbia, MO, 65211, USA

    Mark Coggeshall

Authors
  1. Tim McCleary
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mary McAllister
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mark Coggeshall
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jeanne Romero-Severson
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jeanne Romero-Severson.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 575 kb)

Supplementary material 2 (DOCX 48 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

McCleary, T., McAllister, M., Coggeshall, M. et al. EST-SSR markers reveal synonymies, homonymies and relationships inconsistent with putative pedigrees in chestnut cultivars. Genet Resour Crop Evol 60, 1209–1222 (2013). https://doi.org/10.1007/s10722-012-9912-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-012-9912-9

Keywords

Search

Navigation