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Advances in Genetic Diversity Analysis in Fruit Tree Crops

  • Nerea Larrañaga
  • José Ignacio HormazaEmail author
Part of the Progress in Botany book series (BOTANY, volume 77)

Abstract

Critical advances in the application of molecular tools to analyze genetic diversity in annual and perennial crops have taken place in the last two decades. Although in most cases the new technologies are first developed in annual crops, some particularities of most fruit crops, such as their perennial nature, long generation time, large individual size, or vegetative propagation, make the advantages of using these new approaches even more relevant in these species. In this work, the information available on the different strategies used to analyze genetic diversity in temperate and tropical fruit tree species using molecular approaches is reviewed. Special attention is given to the potential of next-generation sequencing and the combination of genomic tools with geographic information systems.

Keywords

Geographic Information System Geographic Information System Fruit Tree Plant Genetic Resource Landscape Genetic 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This work was supported by the Spanish Ministerio de Economía y Competitividad—European Regional Development Fund, European Union (AGL2013-43732-R), and INIA (RF2012-00010 and RFP2012-00016). NL was supported by an FPI fellowship from the Spanish Ministerio de Economía y Competitividad.

References

  1. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, DeBarry J, Arondel V, Ohlrogge J, Saie IJ, Suliman-Elmeer KM, Bennetzen JL, Kruegger RR, Malek JA (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29:521–527PubMedCrossRefGoogle Scholar
  2. Amar MH, Biswas MK, Zhang Z, Guo WW (2011) Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection. Sci Hortic 128:220–227CrossRefGoogle Scholar
  3. Amel SH, Mokhtar T, Salwa Z, Jihene H, Messaoud M, Abdelmajid R, Mohamed M (2004) Inter-simple sequence repeat fingerprints to assess genetic diversity in Tunisian fig (Ficus carica L.) germplasm. Genet Resour Crop Evol 51:269–275CrossRefGoogle Scholar
  4. Amel SH, Khaled C, Messaoud M, Mohamed M, Mokhtar T (2005) Comparative analysis of genetic diversity in two Tunisian collections of fig cultivars based on random amplified polymorphic DNA and inter simple sequence repeats fingerprints. Genet Resour Crop Evol 52:563–573CrossRefGoogle Scholar
  5. Ansorge WJ (2009) Next-generation DNA sequencing techniques. New Biotechnol 25:195–203CrossRefGoogle Scholar
  6. Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JSS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D’Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C (2011) The genome of Theobroma cacao. Nat Genet 43:101–108PubMedCrossRefGoogle Scholar
  7. Arias R, Borrone J, Tondo C, Kuhn D, Irish B, Schnell R (2012) Genomics of tropical fruit tree crops. In: Schnell RJ, Priyadarshan PM (eds) Genomics of tree crops. Springer, New York, pp 209–239CrossRefGoogle Scholar
  8. Arus P, Verde I, Sosinski B, Zhebentyayeva T, Abbott AG (2012) The peach genome. Tree Genet Genomes 8:531–547CrossRefGoogle Scholar
  9. Basheer-Salimia R, Lorenzi S, Batarseh F, Moreno-Sanz P, Emanuelli F, Grando MS (2014) Molecular identification and genetic relationships of Palestinian grapevine cultivars. Mol Biotechnol 56:546–556PubMedCrossRefGoogle Scholar
  10. Beghe D, Ganino T, Dall’Asta C, Silvanini A, Cirlini M, Fabbri A (2013) Identification and characterization of ancient Italian chestnut using nuclear microsatellite markers. Sci Hortic 164:50–57CrossRefGoogle Scholar
  11. Birmeta G, Nybom H, Bekele E (2004) Distinction between wild and cultivated enset (Ensete ventricosum) gene pools in Ethiopia using RAPD markers. Hereditas 140:139–148PubMedCrossRefGoogle Scholar
  12. Brake M, Migdadi H, Al-Gharaibeh M, Ayoub S, Haddad N, El Oqlah A (2014) Characterization of Jordanian olive cultivars (Olea europaea L.) using RAPD and ISSR molecular markers. Sci Hortic 176:282–289CrossRefGoogle Scholar
  13. Breto MP, Ruiz C, Pina JA, Asins MJ (2001) The diversification of Citrus clementina Hort. ex Tan., a vegetatively propagated crop species. Mol Phylogenet Evol 21:285–293PubMedCrossRefGoogle Scholar
  14. Brown AHD (1978) Isozymes, plant population genetic structure and genetic conservation. Theor Appl Genet 52:145–157PubMedCrossRefGoogle Scholar
  15. Brown W (1983) Genetic diversity and genetic vulnerability—an appraisal. Econ Bot 37:4–12CrossRefGoogle Scholar
  16. Cassman KG (1999) Ecological intensification of cereal production systems: yield potential, soil quality, and precision agriculture. Proc Natl Acad Sci USA 96:5952–5959PubMedPubMedCentralCrossRefGoogle Scholar
  17. Cho KH, Cho KS, Han JH, Kim HR, Shin IS, Kim SH, Chun JA, Hwang HS (2013) Development of sequence characterized amplified region markers for cultivar identification in persimmon. Korean J Hortic Sci 31:798–806CrossRefGoogle Scholar
  18. Cornille A, Gladieux P, Giraud T (2013) Crop-to-wild gene flow and spatial genetic structure in the closest wild relatives of the cultivated apple. Evol Appl 6:737–748CrossRefGoogle Scholar
  19. Coser SM, da Silva Ferreira MF, Ferreira A, Mitre LK, Carvalho CR, Clarindo WR (2012) Assessment of genetic diversity in Psidium guajava L. using different approaches. Sci Hortic 148:223–229CrossRefGoogle Scholar
  20. Crowhurst RN, Gleave AP, MacRae EA, Ampomah-Dwamena C, Atkinson RG, Beuning LL, Bulley SM, Chagne D, Marsh KB, Matich AJ, Montefiori M, Newcomb RD, Schaffer RJ, Usadel B, Allan AC, Boldingh HL, Bowen JH, Davy MW, Eckloff R, Ferguson AR, Fraser LG, Gera E, Hellens RP, Janssen BJ, Klages K, Lo KR, MacDiarmid RM, Nain B, McNeilage MA, Rassam M, Richardson AC, Rikkerink EHA, Ross GS, Schröder R, Snowden KC, Souleyre EJF, Templeton MD, Walton EF, Wang D, Wang MY, Wang YY, Wood M, Wu R, Yauk YK, Laing WA (2008) Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 9:351PubMedPubMedCentralCrossRefGoogle Scholar
  21. D’Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AG, Weissenbach J, Ruiz M, Glaszmann JC, Quétier F, Yahiaoui N, Wincker P (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–217PubMedCrossRefGoogle Scholar
  22. Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J (2013) A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids. BMC Genomics 14:683PubMedPubMedCentralCrossRefGoogle Scholar
  23. De Vicente MC, López C, Fulton T (eds) (2004) Genetic diversity analysis with molecular marker data: learning module. International Plant Genetic Resources Institute (IPGRI), RomeGoogle Scholar
  24. Deschamps S, Llaca V, May GD (2012) Genotyping-by-sequencing in plants. Biology 1:460–483PubMedPubMedCentralCrossRefGoogle Scholar
  25. Du X, Zhang Q, Luo Z (2009a) Development of retrotransposon primers and their utilization for germplasm identification in Diospyros spp. (Ebenaceae). Tree Genet Genomes 5:235–245CrossRefGoogle Scholar
  26. Du XY, Zhang QL, Luo Z (2009b) Comparison of four molecular markers for genetic analysis in Diospyros L. (Ebenaceae). Plant Syst Evol 281:171–181CrossRefGoogle Scholar
  27. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445PubMedCrossRefGoogle Scholar
  28. Escribano P, Viruel MA, Hormaza JI (2007) Molecular analysis of genetic diversity and geographic origin within an ex situ germplasm collection of cherimoya by using SSRs. J Am Soc Hortic Sci 132:357–367Google Scholar
  29. Escribano P, Viruel MA, Hormaza JI (2008) Comparison of different methods to construct a core germplasm collection in woody perennial species with SSR markers. A case study in cherimoya (Annona cherimola Mill.), an underutilized subtropical fruit tree species. Ann Appl Biol 153:25–32CrossRefGoogle Scholar
  30. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50PubMedCentralGoogle Scholar
  31. FAO (1997) The state of the world’s plant genetic resources for food and agriculture. Food and Agriculture Organization of the United Nations, Rome, p 501Google Scholar
  32. Faostat (2014) FAO statistics database on the World Wide Web. http://faostat.fao.org/site/339/default.aspx. Accessed 12–2014
  33. Ford-Lloyd BV, Schmidt M, Armstrong SJ, Barazani O, Engels J, Hadas R, Hammer K, Kell SP, Kang D, Khoshbakht K, Li Y, Long C, Lu BR, Ma K, Nguyen VT, Qiu L, Ge S, Wei W, Zhang Z, Maxted N (2011) Crop wild relatives-undervalued, underutilized and under threat? Bioscience 61:559–565CrossRefGoogle Scholar
  34. Gajera HP, Bambharolia RP, Domadiya RK, Patel SV, Golakiya BA (2014) Molecular characterization and genetic variability studies associated with fruit quality of indigenous mango (Mangifera indica L.) cultivars. Plant Syst Evol 300:1011–1020CrossRefGoogle Scholar
  35. Garcia-Ruiz MT, Mendoza-Castillo VM, Valadez-Moctezuma E, Muratalla-Lua A (2013) Initial assessment of natural diversity in Mexican fig landraces. Genet Mol Res 12:3931–3943PubMedCrossRefGoogle Scholar
  36. Garvin MR, Saitoh K, Gharrett AJ (2010) Application of single nucleotide polymorphisms to non-model species: a technical review. Mol Ecol Resour 10:915–934PubMedCrossRefGoogle Scholar
  37. Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11:759–769PubMedCrossRefGoogle Scholar
  38. Goudet J (2005) Hierfstat, a package for R to compute and test hierarchical F-statistics. Mol Ecol Notes 5:184–186CrossRefGoogle Scholar
  39. Graham J, Marshall B, Squire GR (2003) Genetic differentiation over a spatial environmental gradient in wild Rubus ideaus populations. New Phytol 157:667–675CrossRefGoogle Scholar
  40. Guarino L, Jarvis A, Hijmans RJ, Maxted N (2002) Geographic information systems (GIS) and the conservation and use of plant genetic resources. In: Engels JEA (ed) Managing plant genetic diversity. CAB International, Wallingford, pp 387–404Google Scholar
  41. Guo L, Palumbo R, Zhang ZS, Wang GL, Tay D, Zhang DL, Shen X, Shu HR (2009) Target Region Amplification Polymorphism (TRAP) for evaluating genetic diversity in Malus Mill. genus. Hortscience 44:1117Google Scholar
  42. Hammer K (2003) A paradigm shift in the discipline of plant genetic resources. Genet Resour Crop Evol 50:3–10CrossRefGoogle Scholar
  43. Harrison N, Kidner CA (2011) Next-generation sequencing and systematics: what can a billion base pairs of DNA sequence data do for you? Taxon 60:1552–1566Google Scholar
  44. Holderegger R, Buehler D, Gugerli F, Manel S (2010) Landscape genetics of plants. Trends Plant Sci 15:675–683PubMedCrossRefGoogle Scholar
  45. Ikegami H, Nogata H, Hirashima K, Awamura M, Nakahara T (2009) Analysis of genetic diversity among European and Asian fig varieties (Ficus carica L.) using ISSR, RAPD, and SSR markers. Genet Resour Crop Evol 56:201–209CrossRefGoogle Scholar
  46. Jaillon O, Aury M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida D, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincke P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–467PubMedCrossRefGoogle Scholar
  47. Jarvis A, Yeaman S, Guarino L, Tohme J (2005) The role of geographic analysis in locating, understanding, and using plant genetic diversity. Methods Enzymol 395:279–298PubMedCrossRefGoogle Scholar
  48. Jeffreys AJ (1979) DNA sequence variants in the G gamma-, A gamma-, delta- and beta-globin genes of man. Cell 18:1–10PubMedCrossRefGoogle Scholar
  49. Jing ZB, Ruan X, Wang R, Yang Y (2013a) Genetic diversity and relationships between and within persimmon (Diospyros L.) wild species and cultivated varieties by SRAP markers. Plant Syst Evol 299:1485–1492CrossRefGoogle Scholar
  50. Jing ZB, Cheng J, Guo CH, Wang XP (2013b) Seed traits, nutrient elements and assessment of genetic diversity for almond (Amygdalus spp.) endangered to China as revealed using SRAP markers. Biochem Syst Ecol 49:51–57CrossRefGoogle Scholar
  51. Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405PubMedCrossRefGoogle Scholar
  52. Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334CrossRefGoogle Scholar
  53. Kaya HB, Cetin O, Kaya H, Sahin M, Sefer F, Kahraman A, Tanyolac B (2013) SNP discovery by illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP, SSR and SNP markers. PLoS One 8(9):e73674PubMedPubMedCentralCrossRefGoogle Scholar
  54. Keenan K, McGinnity P, Cross T, Crozier WW, Prodöhl PA (2013) DiveRsity: an R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol Evol 8:782–788CrossRefGoogle Scholar
  55. Kim H, Terakami S, Nishitani C, Kurita K, Kanamori H, Katayose Y, Sawamura Y, Saito T, Yamamoto T (2012) Development of cultivar-specific DNA markers based on retrotransposon-based insertional polymorphism in Japanese pear. Breed Sci 62:53–62PubMedPubMedCentralCrossRefGoogle Scholar
  56. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER (2013) The next-generation sequencing revolution and its impact on genomics. Cell 155:27–38PubMedPubMedCentralCrossRefGoogle Scholar
  57. Koehmstedt AM, Aradhya MK, Soleri D, Smith JL, Polito VS (2011) Molecular characterization of genetic diversity, structure, and differentiation in the olive (Olea europaea L.) germplasm collection of the United States Department of Agriculture. Genet Resour Crop Evol 58:519–531CrossRefGoogle Scholar
  58. Larrañaga N, Hormaza JI (2015) DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae). Front Plant Sci 6:589PubMedPubMedCentralCrossRefGoogle Scholar
  59. Le Corre V, Kremer A (2003) Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection. Genetics 164:1205–1219PubMedPubMedCentralGoogle Scholar
  60. Leinemann L, Steiner W, Hosius B, Kuchma O, Arenhoevel W, Fussi B, Haase B, Kaetzel R, Rogge M, Finkeldey R (2013) Genetic variation of chloroplast and nuclear markers in natural populations of hazelnut (Corylus avellana L.) in Germany. Plant Syst Evol 299:369–378CrossRefGoogle Scholar
  61. Li TF, Liu JR, Xie YN, Wang QY, Meng FJ (2014a) Analysis of genetic diversity in Prunus mira Koehne ex Sargent populations using AFLP markers. Plant Syst Evol 300:475–482CrossRefGoogle Scholar
  62. Li D, Liu Y, Li X, Rao J, Yao X, Zhong C (2014b) Genetic diversity in kiwifruit polyploid complexes: insights into cultivar evaluation, conservation, and utilization. Tree Genet Genomes 10:1451–1463CrossRefGoogle Scholar
  63. Li M, Zhao Z, Miao X (2014c) Genetic diversity and relationships of apricot cultivars in North China revealed by ISSR and SRAP markers. Sci Hortic 173:20–28CrossRefGoogle Scholar
  64. Litt M, Luly JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401PubMedPubMedCentralGoogle Scholar
  65. Liu K, Muse SV (2005) Power marker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129PubMedCrossRefGoogle Scholar
  66. Luo C, He X, Chen H, Ou S, Gao M, Brown JS, Tondo CT, Schnell RJ (2011) Genetic diversity of mango cultivars estimated using SCoT and ISSR markers. Biochem Syst Ecol 39:676–684CrossRefGoogle Scholar
  67. Madhou M, Normand F, Bahorun T, Hormaza JI (2013) Fingerprinting and analysis of genetic diversity of litchi (Litchi chinensis Sonn.) accessions from different germplasm collections using microsatellite markers. Tree Genet Genomes 9:387–396CrossRefGoogle Scholar
  68. Magi A, Benelli M, Gozzini A, Girolami F, Torricelli F, Brandi ML (2010) Bioinformatics for next generation sequencing data. Genes 1:294–307PubMedPubMedCentralCrossRefGoogle Scholar
  69. Malik SK, Uchoi A, Kumar S, Choudhary R, Pal D, Kole PR, Chaudhury R, Bhat KV (2013) Molecular characterization of Citrus macroptera Montr. (satkara): an endangered wild species from northeast India. Plant Biosyst 147:857–863CrossRefGoogle Scholar
  70. Manel S, Holderegger R (2013) Ten years of landscape genetics. Trends Ecol Evol 28:614–621PubMedCrossRefGoogle Scholar
  71. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197CrossRefGoogle Scholar
  72. Mansour E, Ben Khaled A, Triki T, Abid M, Bachar K, Ferchichi A (2015) Evaluation of genetic diversity among South Tunisian pomegranate (Punica granatum L.) accessions using fruit traits and RAPD markers. J Agric Sci Biotechnol 17:109–119Google Scholar
  73. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402PubMedCrossRefGoogle Scholar
  74. Martin C, Herrero M, Hormaza JI (2011) Molecular characterization of apricot germplasm from an old stone collection. PLoS One 6(8):e23979PubMedPubMedCentralCrossRefGoogle Scholar
  75. Martin M, Mattioni C, Molina JR, Alvarez JB, Cherubini M, Herrera MA, Villani F, Martin LM (2012) Landscape genetic structure of chestnut (Castanea sativa Mill.) in Spain. Tree Genet Genomes 8:127–136CrossRefGoogle Scholar
  76. Maxam AM, Gilbert W (1977) A new method for sequencing DNA. Proc Natl Acad Sci USA 74:560–564PubMedPubMedCentralCrossRefGoogle Scholar
  77. Mba C, Tohme J (2005) Use of AFLP markers in surveys of plant diversity. Methods Enzymol 395:177–201PubMedCrossRefGoogle Scholar
  78. Mba C, Guimaraes E, Ghosh K (2012) Re-orienting crop improvement for the changing climatic conditions of the 21st century. Agric Food Secur 1:1–17CrossRefGoogle Scholar
  79. McClure KA, Sawler J, Gardner KM, Money D, Myles S (2014) Genomics: a potential panacea for the perennial problem. Am J Bot 101:1780–1790PubMedCrossRefGoogle Scholar
  80. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996PubMedPubMedCentralCrossRefGoogle Scholar
  81. Mondini L, Noorani A, Pagnotta MA (2009) Assessing plant genetic diversity by molecular tools. Diversity 1:19–35CrossRefGoogle Scholar
  82. Montanari S, Saeed M, Knaebel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D (2013) Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 8(10):e77022PubMedPubMedCentralCrossRefGoogle Scholar
  83. Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, Livingstone D III, Cornejo O, Findley SD, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao M, Scheffler BE, Stack JC, Feltus FA, Mustiga GM, Amores F, Phillips W, Marelli JP, May GD, Shapiro H, Ma J, Bustamante CD, Schnell RJ, Main D, Gilbert D, Parida L, Kuhn DN (2013) The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol 14:r53PubMedPubMedCentralCrossRefGoogle Scholar
  84. Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51:263–273PubMedCrossRefGoogle Scholar
  85. Munthali CRY, Chirwa PW, Changadeya WJ, Akinnifesi FK (2013) Genetic differentiation and diversity of Adansonia digitata L. (baobab) in Malawi using microsatellite markers. Agrofor Syst 87:117–130CrossRefGoogle Scholar
  86. Nair AS, Teo CH, Schwarzacher T, Harrison PH (2005) Genome classification of banana cultivars from South India using IRAP markers. Euphytica 144:285–290CrossRefGoogle Scholar
  87. Passos MAN, de Oliveira CV, Emediato FL, de Camargo TC, Souza MT, Matsumoto T, Renno Azevedo VC, Ferreira CF, Amorim EP, de Alencar Figueiredo LF, Martins NF, de Jesus Barbosa Cavalcante M, Baurens FC, da Silva OB, GJ P Jr, Pignolet L, Abadie C, Ciampi AY, Piffanelli P, Miller RN (2012) Development of expressed sequence tag and expressed sequence tag-simple sequence repeat marker resources for Musa acuminata. AoB Plants 2012:pls030. doi: 10.1093/aobpla/pls030 PubMedPubMedCentralCrossRefGoogle Scholar
  88. Peakall R, Smouse P (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539PubMedPubMedCentralCrossRefGoogle Scholar
  89. Peterson GW, Dong Y, Horbach C, Fu Y (2014) Genotyping-by-sequencing for plant genetic diversity analysis: a lab guide for SNP genotyping. Diversity 6:665–680CrossRefGoogle Scholar
  90. Pollegioni P, Woeste KE, Chiocchini F, Olimpieri I, Tortolano V, Clark J, Hemery GE, Mapelli S, Malvolti ME (2014) Landscape genetics of Persian walnut (Juglans regia L.) across its Asian range. Tree Genet Genomes 10:1027–1043CrossRefGoogle Scholar
  91. Porth I, El-Kassaby YA (2014) Assessment of the genetic diversity in forest tree populations using molecular markers. Diversity 6:283–295CrossRefGoogle Scholar
  92. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedPubMedCentralGoogle Scholar
  93. Raji R, Jannatizadeh A, Fattahi R, Esfahlani MA (2014) Investigation of variability of apricot (Prunus armeniaca L.) using morphological traits and microsatellite markers. Sci Hortic 176:225–231CrossRefGoogle Scholar
  94. Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249Google Scholar
  95. Rohlf FJ (2008) NTSYSpc: numerical taxonomy system, ver. 2.20. Exeter Publishing, Setauket, NYGoogle Scholar
  96. Russell JR, Hedley PE, Cardle L, Dancey S, Morris J, Booth A, Odee D, Mwaura L, Omondi W, Angaine P, Machua J, Muchugi A, Milne I, Kindt R, Jamnadass R, Dawson IK (2014) TropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. PLoS One 9:e102502PubMedPubMedCentralCrossRefGoogle Scholar
  97. Sabir JSM, Abo-Aba S, Bafeel S, Zari TA, Edris S, Shokry AM, Atef A, Gadalla NO, Ramadan AM, Al-Kordy MA, El-Domyati FM, Jansen RK, Bahieldin A (2014) Characterization of ten date palm (Phoenix dactylifera L.) cultivars from Saudi Arabia using AFLP and ISSR markers. C R Biol 337:6–18PubMedCrossRefGoogle Scholar
  98. Samal KC, Jena RC, Swain SS, Das BK, Chand PK (2012) Evaluation of genetic diversity among commercial cultivars, hybrids and local mango (Mangifera indica L.) genotypes of India using cumulative RAPD and ISSR markers. Euphytica 185:195–213CrossRefGoogle Scholar
  99. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467PubMedPubMedCentralCrossRefGoogle Scholar
  100. Sehic J, Garkava-Gustavsson L, Fernandez-Fernandez F, Nybom H (2012) Genetic diversity in a collection of European pear (Pyrus communis) cultivars determined with SSR markers chosen by ECPGR. Sci Hortic 145:39–45CrossRefGoogle Scholar
  101. Shanjani PS, Mardi M, Pazouki L, Hagidimitriou M, Avanzato D, Pirseyedi SM, Ghaffari MR, Nekoui SMK (2009) Analysis of the molecular variation between and within cultivated and wild Pistacia species using AFLPs. Tree Genet Genomes 5:447–458CrossRefGoogle Scholar
  102. Shen Y, Ding X, Wang F, Cai B, Gao Z, Zhang Z (2011) Analysis of genetic diversity in Japanese apricot (Prunus mume Sieb. et Zucc.) based on REMAP and IRAP molecular markers. Sci Hortic 132:50–58CrossRefGoogle Scholar
  103. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145PubMedCrossRefGoogle Scholar
  104. Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S (2013) Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations. Theor Appl Genet 126:2699–2716PubMedCrossRefGoogle Scholar
  105. Storfer A, Murphy MA, Evans JS, Goldberg CS, Robinson S, Spear SF, Dezzani R, Delmelle E, Vierling L, Waits LP (2007) Putting the ‘landscape’ in landscape genetics. Heredity 98:128–142PubMedCrossRefGoogle Scholar
  106. Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP (2010) Landscape genetics: where are we now? Mol Ecol 19:3496–3514PubMedCrossRefGoogle Scholar
  107. Sun LD, Zhang QX, Xu ZD, Yang WR, Guo Y, Lu JX, Pan HT, Cheng TR, Cai M (2013) Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume Sieb. et Zucc.). BMC Genet 14:98PubMedPubMedCentralCrossRefGoogle Scholar
  108. Syed NH, Sureshsundar S, Wilkinson MJ, Bhau BS, Cavalcanti JJV, Flavell AJ (2005) Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theor Appl Genet 110:1195–1202PubMedCrossRefGoogle Scholar
  109. Takrouni MM, Ali IB, Messaoued C, Boussaid M (2012) Genetic variability of Tunisian wild strawberry tree (Arbutus unedo L.) populations interfered from isozyme markers. Sci Hortic 146:92–98CrossRefGoogle Scholar
  110. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729PubMedPubMedCentralCrossRefGoogle Scholar
  111. Thomas E, van Zonneveld M, Loo J, Hodgkin T, Galluzzi G, van Etten J (2012) Present spatial diversity patterns of Theobroma cacao L. in the neotropics reflect genetic differentiation in Pleistocene refugia followed by human-influenced dispersal. PLoS One 7:e47676PubMedPubMedCentralCrossRefGoogle Scholar
  112. van Droogenbroeck B, Kyndt T, Maertens I, Romeijn-Peeters E, Scheldeman X, Romero-Motochi JP, Van Damme P, Goetghebeur P, Gheysen G (2004) Phylogenetic analysis of the highland papayas (Vasconcellea) and allied genera (Caricaceae) using PCR-RFLP. Theor Appl Genet 108:1473–1486PubMedCrossRefGoogle Scholar
  113. van Droogenbroeck B, Kyndt T, Romeijn-Peeters E, van Thuyne W, Goetghebeur P, Romero-Motochi JP, Gheysen G (2006) Evidence of natural hybridization and introgression between Vasconcellea species (Caricaceae) from southern Ecuador revealed by chloroplast, mitochondrial and nuclear DNA markers. Ann Bot 97:793–805PubMedCrossRefGoogle Scholar
  114. van Hintum T, Brown AHD, Spillane C, Hodgkin T (2000) Core collections of plant genetic resources. IPGRI Technical Bulletin No. 3. International Plant Genetic Resources Institute, RomeGoogle Scholar
  115. van Zonneveld M, Scheldeman X, Escribano P, Viruel MA, Van Damme P, Garcia W, Tapia C, Romero J, Siguenas M, Hormaza JI (2012) Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources. PLoS One 7:e29845PubMedPubMedCentralCrossRefGoogle Scholar
  116. Vandergast AG, Perry WM, Lugo RV, Hathaway SA (2011) Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity. Mol Ecol Resour 11:158–161PubMedCrossRefGoogle Scholar
  117. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42:833–839PubMedCrossRefGoogle Scholar
  118. Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arús P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494PubMedCrossRefGoogle Scholar
  119. Vinceti B, Loo J, Gaisberger H, van Zonneveld M, Schueler S, Konrad H, Kadu CAC, Geburek T (2013) Conservation priorities for Prunus africana defined with the aid of spatial analysis of genetic data and climatic variables. PLoS One 8:e59987PubMedPubMedCentralCrossRefGoogle Scholar
  120. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Fritjters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedPubMedCentralCrossRefGoogle Scholar
  121. Wagner I, Maurer WD, Lemmen P, Schmitt HP, Wagner M, Binder M, Patzak P (2014) Hybridization and genetic diversity in wild apple (Malus sylvestris (L.) Mill) from various regions in Germany and from Luxembourg. Silvae Genet 63:81–94Google Scholar
  122. Warschefsky E, Penmetsa RY, Cook DR, von Wettberg EJB (2014) Back to the wilds: tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives. Am J Bot 101:1791–1800PubMedCrossRefGoogle Scholar
  123. Wijeratnam RSW (2000) Identification of problems in processing of underutilized fruits of the tropics and their solutions. Acta Hortic 518:237–240CrossRefGoogle Scholar
  124. Williams JGK, Kuberik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedPubMedCentralCrossRefGoogle Scholar
  125. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408PubMedPubMedCentralCrossRefGoogle Scholar
  126. Wünsch A, Hormaza JI (2002) Cultivar identification and genetic fingerprinting of temperate fruit tree species using DNA markers. Euphytica 125:59–67CrossRefGoogle Scholar
  127. Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45:59–66PubMedCrossRefGoogle Scholar
  128. Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX (1997) POPGENE, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, EdmontonGoogle Scholar
  129. Yilmaz KU, Paydas-Kargi S, Dogan Y, Kafkas S (2012) Genetic diversity analysis based on ISSR, RAPD and SSR among Turkish apricot germplasms in Iran Caucasian eco-geographical group. Sci Hortic 138:138–143CrossRefGoogle Scholar
  130. Zhang Q, Chen W, Sun L, Zhao F, Huang B, Yang W, Tao Y, Wang J, Yuan Z, Fan G, Xing Z, Han C, Pan H, Zhong X, Shi W, Liang X, Du D, Sun F, Xu Z, Hao R, Lv T, Lv Y, Zheng Z, Sun M, Luo L, Cai M, Gao Y, Wang J, Yin Y, Xu X, Cheng T, Wang J (2012) The genome of Prunus mume. Nat Commun 3:1318PubMedPubMedCentralCrossRefGoogle Scholar

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© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Estación Experimental La MayoraMálagaSpain

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