Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

详细信息    查看全文

• 作者：Nahla Bassil (1)
  Paolo Boccacci (2)
  Roberto Botta (3)
  Joseph Postman (1)
  Shawn Mehlenbacher (4)
  
• 关键词：Corylus ; Filbert ; Simple sequence repeat (SSR) markers ; Universal chloroplast SSRs
• 刊名：Genetic Resources and Crop Evolution
• 出版年：2013
• 出版时间：February 2013
• 年：2013
• 卷：60
• 期：2
• 页码：543-568
• 全文大小：650KB
• 参考文献：1. Arroyo-Garc铆a R, Ruiz-Garc铆a L, Bolling L, Ocete R, L贸pez MA, Arnold C, Ergul A, S枚ylemezo臒lu G, Uzun HI, Cabello F, Ib谩帽ez J, Aradhya MK, Atanassov A, Atanassov I, Balint S, Cenis JL, Costantini L, Gorislavets S, Grando MS, Klein BY, McGovern PE, Merdinoglu D, Pejic I, Pelsy F, Primikirios N, Risovannaya V, Roubelakis-Angelakis KA, Snoussi H, Sotiri P, Tamhankar S, This P, Troshin L, Malpica JM, Lefort F, Mart铆nez-Zapater JM (2006) Multiple origins of cultivated grapevine ( / Vitis vinifera L. ssp. / sativa) based on chloroplast DNA polymorphisms. Mol Ecol 15:3707鈥?714 CrossRef
  2. Bandelt HJ, Foster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37鈥?8 CrossRef
  3. Bassil NV, Botta R, Mehlenbacher SA (2005a) Microsatellite markers in hazelnut: isolation, characterization and cross-species amplification. J Am Soc Hort Sci 130:543鈥?49
  4. Bassil NV, Botta R, Mehlenbacher SA (2005b) Additional microsatellite markers of the European hazelnut. Acta Hort 686:105鈥?10
  5. Bassil NV, Postman J, Hummer K, Botu M, Sezer A (2009) SSR fingerprinting panel verifies identities of clones in backup hazelnut collection at USDA genebank. Acta Hort 845:95鈥?02
  6. Boccacci P, Botta R (2009) Investigating the origin of hazelnut ( / Corylus avellana L.) cultivars using chloroplast microsatellites. Genet Resour Crop Evol 56:851鈥?59 CrossRef
  7. Boccacci P, Botta R (2010) Microsatellite variability and genetic structure in hazelnut ( / Corylus avellana L.) cultivars from different growing regions. Sci Hortic 124:128鈥?33 CrossRef
  8. Boccacci P, Akkak A, Bassil NV, Mehlenbacher SA, Botta R (2005) Characterization and evaluation of microsatellite loci in european hazelnut ( / Corylus avellana L.) and their transferability to other / Corylus species. Mol Ecol Notes 5:934鈥?37 CrossRef
  9. Boccacci P, Akkak A, Botta R (2006) DNA-typing and genetic relationships among European hazelnut ( / Corylus avellana L.) cultivars using microsatellite markers. Genome 49:598鈥?11 CrossRef
  10. Boccacci P, Botta R, Rovira M (2008) Genetic diversity of hazelnut ( / Corylus / avellana L.) germplasm in northeastern Spain. HortSci 43:667鈥?72
  11. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314鈥?31
  12. Botta R, Akkak A, Boccacci P (2005) DNA-typing of hazelnut: a universal methodology for describing cultivars and evaluating genetic relatedness. Acta Hort 686:117鈥?24
  13. Chen ZD, Manchester SR, Sun HY (1999) Phylogeny and evolution of the Betulaceae as inferred from DNA sequences, morphology, and paleobotany. Am J Bot 86:1168鈥?181 CrossRef
  14. Crane PR (1989) Early fossil history and evolution of the Betulaceae. In: Crane PR, Blackmore S (eds) Evolution, systematics and fossil history of the Hamamelidae, vol 2, 鈥楬igher鈥?Hamame- lidae. Clarendon Press, Oxford, pp 87鈥?16
  15. Cronquist A (1981) An integrated system of classification of flowering plants. Columbia University Press, London
  16. Cuenca A, Escalante AE, Pi帽ero D (2003) Long-distance colonization, isolation by distance, and historical demography in a relictual Mexican pinyon pine ( / Pinus nelsonii Shaw) as revealed by paternally inherited genetic markers (cpSSRs) M. Mol Ecol 12:2087鈥?097 CrossRef
  17. De Candolle A (1864) / Corylus. In: Prodromus systemnatis naturalis regni vegetabilis, vol 16, part 2. Treuttel & Wurtz, Paris, pp 128鈥?33
  18. Erdo臒an V, Mehlenbacher SA (2000a) Phylogenetic relationships of / Corylus species (Betulaceae) based on nuclear ribosomal DNA ITS region and chloroplast matK gene sequences. Syst Bot 25:727 CrossRef
  19. Erdo臒an V, Mehlenbacher SA (2000b) Interspecific hybridization in hazelnut. J Am Soc Hort Sci 125(4):489鈥?97
  20. Forest F, Bruneau A (2000) Phylogenetic analysis, organization and molecular evolution of the nontranscribed spacer of 5S ribosomal RNA genes in / Corylus (Betulaceae). Int J Plant Sci 161:793鈥?06 CrossRef
  21. Forest F, Savolainen V, Chase MW, Lupia R, Bruneau A, Crane PR (2005) Teasing apart molecular- versus fossil-based error estimates when dating phylogenetic trees: a case study in the Birch family (Betulaceae). Syst Bot 30:118鈥?33 CrossRef
  22. Gastier JM, Pulido JC, Sunden S, Brody T, Buetow KH, Murray JC, Weber JL, Hudson TJ, Sheffield VC, Duyk GM (1995) Survey of trinucleotide repeats in the human genome: assessment of their utility as genetic markers. Hum Mol Genet 4:1829鈥?836 CrossRef
  23. Ghanbari A, Akkak A, Boccacci P, Talaie A, Vezvaie A, Botta A (2005) Characterization of hazelnut ( / Corylus avellana L.) cultivars using microsatellite markers. Acta Hort 686:111鈥?15
  24. G枚kirmak T, Mehlenbacher SA, Bassil NV (2009) Characterization of European hazelnut ( / Corylus avellana) cultivars using SSR markers. Genet Resour Crop Evol 56:147鈥?72 CrossRef
  25. G眉rcan K, Mehlenbacher SA (2010a) Transferability of microsatellite markers in the Betulaceae. J Am Soc Hort Sci 135(2):159鈥?73
  26. G眉rcan K, Mehlenbacher SA (2010b) Development of microsatellite marker loci for European hazelnut ( / Corylus avellana L.) from ISSR fragments. Mol Breed 26:551鈥?59 CrossRef
  27. G眉rcan K, Mehlenbacher SA, Bassil NV, Boccacci P, Akkak A, Botta R (2010a) New microsatellite markers for / Corylus avellana from enriched libraries. Tree Genet Gen 6:513鈥?31 CrossRef
  28. G眉rcan K, Mehlenbacher SA, Erdo臒an V (2010b) Genetic diversity in hazelnut cultivars from Black Sea countries assessed using SSR markers. Plant Breed 129:422鈥?34. doi:10.1111/j.1439-0523.2009.01753.x
  29. Ishii T, McCouch SR (2000) Microsatellites and microsynteny in the chloroplast genomes of / Oryza and eight other Graminae species. Theor Appl Genet 100:1257鈥?266 CrossRef
  30. Ishii T, Mori N, Ogihara Y (2001) Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species. Theor Appl Genet 103:896鈥?04 CrossRef
  31. Kasapligil B (1972) A bibliography on / Corylus (Betulaceae) with annotations. Annu Rpt Northern Nut Growers Assn 63:107鈥?62
  32. Kutil BL, Williams CJ (2001) Triplet repeat microsatellites shared among hard and soft pines. J Heredity 92:327鈥?32 CrossRef
  33. Li PC, Cheng SX (1979) Betulaceae. In: Kuang K-Z, Li P-C (eds) Flora republicae popularis sinicae, vol 21. Science Press, Beijing, pp 44鈥?37 (In Chinese)
  34. Liang WJ, Zhang YM (1988) Investigation and study of filbert resources in China. In: Proceedings of the international symposium on horticultural germplasm, Cultivated and Wild. Beijing, China. 5鈥? Sept. 1988
  35. Liewlaksaneeyanawin C, Ritland CE, El-Kassaby YA, Ritland K (2004) Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. Theor Appl Genet 109:361鈥?69 CrossRef
  36. Liu K, Muse SV (2005) Powermarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128鈥?129 CrossRef
  37. Malus脿 E (1994) Interspecific relationships among / Corylus species. Acta Hort 51:335鈥?40
  38. Mehlenbacher SA (1991) Hazelnuts ( / Corylus). Genetic resources of temperate fruit and nut crops. Acta Hort 290:791鈥?36
  39. Mehlenbacher SA (2009) Genetic resources for hazelnut: state of the art and future perspectives. Acta Hort 845:33鈥?8
  40. Mehlenbacher SA, Brown RN, Nouhra ER, G枚kirmak T, Bassil NV, Kubisiak TL (2006) A genetic linkage map for hazelnut ( / Corylus avellana L.) based on RAPD and SSR markers. Genome 49:122鈥?33
  41. Minch E (1997) MICROSAT version 1.5b. Stanford University Medical Center, Stanford, CA. http://hpgl.stanford.edu/projects/microsat/ Accessed 02 January 2012
  42. Molnar TJ, Goffreda JC, Funk CR (2005) Developing hazelnuts for the eastern United States. Acta Hort 68:609鈥?17
  43. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194鈥?00 CrossRef
  44. Navascu茅s M, Emerson BC (2005) Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy. Mol Ecol 14:1333鈥?341 CrossRef
  45. Nei M (1987) Molecular evolutionay genetics. Columbia University Press, New York
  46. Palm茅 AE, Vendramin GG (2002) Chloroplast DNA variation, postglacial recolonization and hybridization in hazel, / Corylus avellana. Mol Ecol 11:1769鈥?779 CrossRef
  47. Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, M眉ller-Starck G, Demesure-Musch B, Palm茅 A, Mart铆n JP, Rendell S, Vendramin GG (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300:1563鈥?565 CrossRef
  48. Pigg KB, Manchester SR, Wehr WC (2003) / Corylus, / Carpinus, and / Palaeocarpinus (Betulaceae) from the middle Eocene Klondike Mountain and Allenby Formations of northwestern North America. Int J Plant Sci 164:807鈥?22 CrossRef
  49. Pritchard J, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945鈥?59
  50. Provan J, Powell W, Hollingsworth PH (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142鈥?47 CrossRef
  51. Rajora OP, Rahman MH, Dayanandan S, Mosseler A (2001) Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce ( / Picea glauca) and their usefulness in other spruce species. Mol Gen Genet 264:871鈥?82 CrossRef
  52. Rovira M (1997) Genetic variability among hazelnut ( / C. avellana L.) cultivars. Acta Hort 445:45鈥?0
  53. Sathuvalli SR, Mehlenbacher SA (2011) Characterization of American hazelnut ( / Corylus americana) accessions and / Corylus americana聽脳聽 / Corylus avellana hybrids using microsatellite markers. Genet Resour Crop Evol. doi:10.1007/s10722-011-9743-0
  54. Schneider C (1916) Betulaceae. In: ed., Sargent CS (ed) Plantae wilsonianae: an enumeration of the woody plants collected in western China for the Arnold Arboretum of Harvard University during the years 1907, 1908, and 1910, vol. 2. Publications of the Arnold Arboretum, no. 4, pp 423鈥?08
  55. Scotti I, Magni F, Fink R, Powell W, Binnelli G, Hedley PE (2000) Microsatellite repeats are not randomly distributed within Norway spruce ( / Picea abies L.) expressed sequences. Genome 43:41鈥?6
  56. Sheffield VC, Weber JL, Buetow KH, Murray JC, Even DA, Wiles K, Gastier JM, Pulido JC, Yandava C, Sunden SL et al (1995) A collection of tri- and tetra-nucleotide repeat markers used to generate high quality, high resolution human genome-wide linkage maps. Hum Mol Genet 4:1837鈥?844 CrossRef
  57. Shepherd M, Cross M, Maguire TL, Dieters MJ, Williams CG, Henry RJ (2002) Transpecific microsatellites for hard pines. Theor Appl Genet 104:819鈥?27 CrossRef
  58. Slate GL (1947) Some results with filbert breeding at Geneva, New York. Annu Rep North Nut Grow Assoc 38:94鈥?00
  59. St脿gel A, Portis E, Toppino L, Rotino GL, Lanteri S (2008) Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics 9:357鈥?70 CrossRef
  60. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. doi:10.1093/molbev/msr121
  61. Terrab A, Paun O, Talavera S, Tremetsberger K, Arista MF, Stuessy TF (2006) Genetic diversity and population structure in natural populations of Moroccan Atlas cedar ( / Cedrus atlantica, / Pinaceae) determined with cpSSR markers. Am J Bot 93(9):1274鈥?280 CrossRef
  62. Testolin R, Cipriani G (2010) Molecular markers for germplasm identification and characterization. Acta Hort 859:59鈥?2
  63. The Plant List (2010) Version 1. Published on the Internet; http://www.theplantlist.org/. Accessed April 23, 2012
  64. Thompson MM, Lagerstedt HB, Mehlenbacher SA (1996) Hazelnuts. In: Janick J, Moore JN (eds) Fruit breeding: nuts, vol 3. Wiley, New York, pp 125鈥?84
  65. Tozaki T, Inoue S, Mashima S, Ohta M, Miura N, Tomita M (2000) Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome. Genome 43:354鈥?65 CrossRef
  66. Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1鈥?
  67. Weising K, Gardner R (1999) A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 42:9鈥?9 CrossRef
  68. Wendel JF, Doyle JJ (1998) Phylogenetic incongruence: window into genome history and molecular evolution. In: Soltis D, Soltis P, Doyle J (eds) Molecular systematics of plants, 2nd edn. Chapman & Hall, New York
  69. Whitcher IN, Wen J (2001) Phylogeny and biogeography of / Corylus (Betulaceae): inference from ITS sequences. Syst Bot 26:283鈥?98
  70. Yoo K-O, Wen J (2002) Phylogeny and biogeography of / Carpinus and subfamily Coryloideae (Betulaceae). Int J Plant Sci 163:641鈥?50 CrossRef
  71. Yoo K-O, Wen J (2007) Phylogeny of / Carpinus and subfamily Coryloideae (Betulaceae) based on chloroplast and nuclear ribosomal sequence data. Plant Syst Evol 267:25鈥?5 CrossRef
  72. Young ET, Sloan JS, Van Riper K (2000) Trinucleotide repeats are clustered in regulatory genes in / Saccaromyces cerevisae. Genetics 154:1053鈥?068
  
• 作者单位：Nahla Bassil (1)
  Paolo Boccacci (2)
  Roberto Botta (3)
  Joseph Postman (1)
  Shawn Mehlenbacher (4)
  
  1. United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Clonal Germplasm Repository (NCGR), 33447 Peoria Road, Corvallis, OR, 97333, USA
  2. Plant Virology Institute, National Research Council (IVV-CNR), UOS of Grugliasco, Via Leonardo da Vinci, 44, 10095, Grugliasco, TO, Italy
  3. Dipartimento di Colture Arboree, Universit脿 degli Studi di Torino, Via Leonardo da Vinci, 44, 10095, Grugliasco, TO, Italy
  4. Department of Horticulture, Oregon State University, Agricultural and Life Sciences Bldg., 4017, Corvallis, OR, 97331, USA
  
• ISSN：1573-5109

文摘

The US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus), including C. avellana cultivars and representatives of 10 other recognized shrub and tree species. Characterization and study of genetic diversity in this collection require cross-transferable markers, such as trinucleotide microsatellite or simple sequence repeat (SSR) markers and universal chloroplast SSR markers. We developed new SSR markers and evaluated 114 Corylus accessions representing 11 species and 44 interspecific hybrids. Eight of 23 SSRs generated easy-to-score alleles in all species and seven were highly polymorphic. For those seven, the average heterozygosity was moderate at 0.49, and mean allele number, genetic diversity and polymorphism information index were high at 11.71, 0.79 and 0.76, respectively. The three most polymorphic SSRs were CaC-C008, CaC-C040 and CaC-C118. Neighbor-joining (NJ) clustering and structure analysis agreed with classical taxonomic analysis and supported inclusion of C. maxima within the large polymorphic species, C. avellana. Analysis also indicated that C. californica is a distinct species rather than a botanical variety of C. cornuta. Six universal cpSSRs were polymorphic in Corylus and generated 21 distinct chlorotypes with an average of 3 alleles per locus. Diversity at these cpSSRs was high and ranged from 0.33 to 0.64, with an average of 0.54. Incongruence in NJ topologies between the nuclear and chloroplast markers could be attributed to chloroplast capture related to hybridization during the ancestral diversification of the genus, or to homoplasy. The phylogeographical relationships among the 21 chlorotypes in the 11 Corylus species support Asia as a refugium where several hazelnut lineages survived during glaciation and from which they continued to evolve after dispersal from Asia through the Mediterranean to Europe, and across the Atlantic and/or the Bering land bridge to North America.