Evaluating the influence of the microsatellite marker set on the genetic structure inferred in pyrus communis L.

PLoS ONE

Volumn 10, Issue 9, 2015, Pages

  Urrestarazu, Jorge ^a,b   Royo, José B ^a   Santesteban, Luis G ^a   Miranda, Carlos ^a  

^a PUBLIC UNIVERSITY OF NAVARRE   (Spain)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC MARKER; GENETIC VARIABILITY; GERMPLASM; MICROSATELLITE MARKER; PEAR; POPULATION STRUCTURE; ALLELE; BAYES THEOREM; GENETIC VARIATION; GENETICS; GENOTYPE; PLANT GENOME; PYRUS;

MICROSATELLITE DNA; PLANT DNA;

ALLELES; BAYES THEOREM; DNA, PLANT; GENETIC VARIATION; GENOME, PLANT; GENOTYPE; MICROSATELLITE REPEATS; PYRUS;

EID: 84946592905     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0138417     Document Type: Article

References (77)

1. van Hintum TLJ. Duplication within and between germplasm collections III. A quantitative model. Genet Resour Crop Evol. 2010; 47: 507-513.
2. Montilla-Bascón G, Sánchez-Martín J, Rispail N, Rubiales D, Mur L, Langdon T, et al. Genetic diversity and population structure among oat cultivars and landraces. Plant Mol Biol Rep. 2013; 31: 1305-1314.
3. Potts SM, Han Y, Awais Khan M, Kushad MM, Rayburn AL, Korban SS. Genetic diversity and characterization of a core collection of Malus germplasm using simple sequence repeats (SSRs). Plant Mol Biol Rep. 2012; 30: 827-837.
4. Urrestarazu J, Miranda C, Santesteban LG, Royo JB. Genetic diversity and structure of local apple cultivars from Northeastern Spain assessed by microsatellite markers. Tree Genet Genomes. 2012; 8: 1163-1180.
5. El Bakkali A, Haouane H, Moukhli A, Costes E, van Damme P, Khadari B. Construction of core collections suitable for association mapping to optimize use of mediterranean olive (Olea europaea L.) genetic resources. PLoS ONE. 2013; 8: e61265. doi: 10.1371/journal.pone.0061265
6. Le Cunff L, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, Adam-Blondon AF, et al. Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. Sativa. BMC Plant Biol. 2008; 8: 31. doi: 10.1186/1471-2229-8-31
7. Roy Choudhury D, Singh N, Kumar Singh A, Kumar S, Srinivasan K, Tyagi RK, et al. Rice germplasm from North-Eastern region of India and development of a core germplasm set. PLoS ONE 2014; 9: e113094. doi: 10.1371/journal.pone.0113094
8. Odong TL, van Heerwaarden J, Jansen J, van Hintum TJL, van Eeuwijk FA. Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data? Theor Appl Genet. 2011; 123: 195-205. doi: 10.1007/s00122-011-1576-x
9. Clarke JB, Tobutt KR. A standard set of accessions, microsatellites and genotypes for harmonising the fingerprinting of cherry collections for the ECPGR. Acta Hortic. 2009; 814: 615-618.
10. Evans KM, Fernández-Fernández F, Govan K. Harmonising fingerprinting protocols to allow camparisons between germplasm collections-Pyrus. Acta Hortic 2009; 814: 103-106.
11. Lateur M, Ordidge M, Engels J, Lipman E (eds.). Report of a Working Group on Malus/Pyrus. Fourth Meeting, 7-9 March 2012, Weggis, Switzerland. Bioversity International, Rome, Italy; 2013.
12. Pikunova A, Madduri M, Sedov E, Noordijk Y, Peil A, Troggio M, et al. 'Schmidt's Antonovka' is identical to 'Common Antonovka', an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses. Tree Genet Genomes. 2014; 10: 261-271.
13. Urrestarazu J, Miranda C, Santesteban LG, Royo JB. Recovery and identification of grapevine varieties cultivated in old vineyards from Navarre (Northeastern Spain). Sci Hortic. 2015; 191: 65-73.
14. Garkava-Gustavsson L, Mujaju C, Sehic J, Zborowska A, Backes GM, Hietaranta T, et al. Genetic diversity in Swedish and Finnish heirloom apple cultivars revealed with SSR markers. Sci Hortic. 2013; 162: 43-48.
15. van Treuren R, Kemp H, Ernsting G, Jongejans B, Houtman H, Visser L. Microsatellite genotyping of apple (Malus x domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification. Genet Resour Crop Evol. 2010; 57: 853-865.
16. Aranzana MJ, Abbassi EK, Howard W, Arús P. Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genet. 2010; 11:69. doi: 10.1186/1471-2156-11-69
17. Blasco M, Naval MM, Zuriaga E, Badenes ML. Genetic variation and diversity among loquat accessions. Tree Genet Genomes 2014; 10: 1387-1398.
18. Bourguiba H, Audergon JM, Krichen L, Trifi-Farah N, Mamouni A, Trabelsi S, et al. Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin. BMC Plant Biol 2012; 12: 49. doi: 10.1186/1471-2229-12-49
19. Mariette S, Tavaud M, Arunyawat U, Capdeville G, Millan M, Salin F. Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus. BMC Genet. 2010; 11: 77. doi: 10.1186/1471-2156-11-77
20. Miranda C, Urrestarazu J, Santesteban LG, Royo JB, Urbina V. Genetic diversity and structure in a collection of ancient Spanish pear cultivars assessed by microsatellite markers. J Am Soc Hortic Sci. 2010; 135: 428-437.
21. Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, et al. Genome-wide SNP detection validation and development of an 8K SNP array for apple. PLoS ONE 2012; 7: e31745. doi: 10.1371/journal.pone.0031745
22. Montanari S, Saeed M, Knäbel M, Kim YK, Troggio M, Malnoy M, et al. Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS ONE 2013; 8: e77022. doi: 10.1371/journal.pone.0077022
23. Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, et al. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS ONE 2012; 7: e48305. doi: 10.1371/journal.pone.0048305
24. Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, et al. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germoplasm. PLoS ONE 2012; 7: e35668. doi: 10.1371/journal.pone.0035668
25. Beaumont MA, Rannala B. The Bayesian revolution in genetics. Nat Rev Genet 2004; 5: 251-261
26. Corander J, Marttinen P. Bayesian identification of admixture events using multilocus molecular markers. Mol Ecol 2006; 15: 2833-2843
27. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000; 155: 945-959
28. Porras-Hurtado L, Ruiz Y, Santos C, Phillips C, Carracedo A, Lareu MV. An overview of Structure: applications, parameter settings and supporting software. Front Genet. 2013; 4: 98. doi: 10.3389/fgene. 2013.00098
29. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 2003; 164: 1567-1587
30. Iketani H, Yamamoto T, Katayama H, Uematsu C, Mase N, Sato Y. Introgression between native and prehistorically naturalized (archaeophytic) wild pear (Pyrus spp.) populations in Northern Tohoku, Northeast Japan. Cons Genet. 2010; 11: 115-126.
31. Iketani H, Katayama H, Uematsu C, Mase N, Sato Y, Yamamoto T. Genetic structure of East Asian cultivated pears (Pyrus spp.) and their reclassification in accordance with the nomenclature of cultivated plants. Plant Syst Evol 2012; 298: 1689-1700.
32. Kato S, Imai A, Rie N, Mukai Y. Population genetic structure in a threatened tree, Pyrus calleryana var. dimorphophylla revealed by chloroplast DNA and nuclear SSR locus polymorphisms. Cons Genet. 2013; 14: 983-996.
33. Ferreira dos Santos AR, Ramos-Cabrer AM, Díaz-Hernández MB, Pereira-Lorenzo S. Genetic variability and diversification process in local pear cultivars from Northwestern Spain using microsatellites. Tree Genet Genomes. 2011; 7: 1041-1056.
34. Gasi F, Kurtovic M, Kalamujic B, Pojskic N, Grahic J, Kaiser C, et al. Assessment of European pear (Pyrus communis L.) genetic resources in Bosnia and Herzegovina using microsatellite markers. Sci Hortic 2013; 157: 74-83.
35. Zong Y, Sun P, Liu J, Yue X, Li K, Teng Y. Genetic diversity and population structure of seedling populations of Pyrus pashia. Plant Mol Biol Rep. 2014; 32: 644-651.
36. Coart E, Van Glabeke S, De Loose M, Larsen A, Roldán Ruiz I. Chloroplast diversity in the genus Malus: new insights into the relationship between the European wild apple (Malus sylvestris (L.) Mill.) and the domesticated apple (Malus domestica Borkh.). Mol Ecol 2006; 15: 2171-2182
37. Gharghani A, Zamani Z, Talaie A, Oraguzie NC, Fatahi R, Hajnajari H, et al. Genetic identity and relationships of Iranian apple (Malus x domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis. Genet Resour Crop Evol. 2009; 56: 829-842.
38. Liang W, Dondini L, De Franceschi P, Paris R, Sansavini S, Tartarini S. Genetic diversity, population structure and construction of a core collection of apple cultivars from Italian germplasm. Pant Mol Biol Rep. 2015; 33: 458-473.
39. Patzak J, PaprŠtein F, Henychová A, Sedlák J. Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus × domestica) genetic resources. Genome. 2012; 55: 647-665. doi: 10.1139/g2012-054
40. Pereira-Lorenzo S, Ramos-Cabrer AM, Gonzalez-Diaz AJ, Diaz-Hernandez MB. Genetic assessment of local apple cultivars from La Palma, Spain, using simple sequence repeats (SSRs). Sci Hortic. 2008; 117: 160-166.
41. Pina A, Urrestarazu J, Errea P. Analysis of the genetic diversity of local apple cultivars from mountainous areas from Aragon (Northeastern Spain). Sci Hort. 2014; 174: 1-9.
42. Reim S, Höltken A, Höfer M. Diversity of the European indigenous wild apple (Malus sylvestris (L.) Mill.) in the East Ore Mountains (Osterzgebirge), Germany: II. Genetic characterization. Gen Res Crop Evol. 2013; 60: 879-892.
43. Richards CM, Volk GM, Reilley AA, Henk AD, Lockwood DR, Reeves PA, et al. Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genet Genomes. 2009; 5: 339-347.
44. Volk GM, Richards CM, Henk AD, Reilley AA, Reeves PA, Forsline PL, et al. Capturing the Diversity of Wild Malus orientalis from Georgia, Armenia, Russia, and Turkey. J Am Soc Hortic Sci. 2009; 134: 453-459.
45. Yang BZ, Zhao H, Kranzler HR, Gelernter J. Practical population group assignment with selected informative markers: Characteristics and properties of Bayesian clustering via STRUCTURE. Genet Epidemiol. 2005; 28: 302-312
46. Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005; 14: 2611-2620
47. Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB. Human population genetic structure and inference of group membership. Am J Hum Genet 2003; 72: 578-589
48. Turakulov R, Easteal S. Number of SNPs loci needed to detect population structure. Human Hered 2003; 55: 505-512.
49. Neophytou C. Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes. Tree Genet Genomes. 2014; 10: 273-285.
50. Food and Agriculture Organization of the United Nations/International Plant Genetic Resources Institute. Multi-crop passport descriptors. FAO/IPGRI, Rome, Italy; 2001.
51. Vinatzer B, Patocchi A, Tartarini S, Gianfranceschi L, Sansavini S, Gessler C. Isolation of two microsatellite markers from BAC clones of the Vf scab resistance. Plant Breed. 2004; 123: 321-326.
52. Yamamoto T, Kimura T, Shoda M, Imai T, Saito T, Sawamura Y, et al. Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet. 2002; 106: 9-18
53. Gianfranceschi L, Seglias N, Tarchini R, Komjanc M, Gessler C. Simple sequence repeats for the genetic analysis of apple. Theor Appl Genet. 1998; 96: 1069-1076.
54. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, van De Weg E, et al. Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.). Mol Breed. 2002; 10: 217-241.
55. Guilford P, Prakash S, Zhu JM, Rikkerink E, Gardiner S, Bassett H, et al. Microsatellites in Malus x domestica (apple): abundance, polymorphism and cultivar identification. Theor Appl Genet. 1997; 94: 249-254.
56. Fernández-Fernández F, Harvey NG, James CM. Isolation and characterization of polymorphic microsatellite markers from European pear (Pyrus communis L.). Mol Ecol Notes. 2006; 6: 1039-1041.
57. Hokanson SC, Szewc-McFadden AK, Lamboy WF, McFerson JR. Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus x domestica Borkh. core subset collection. Theor Appl Genet. 1998; 97: 671-683.
58. Tessier R, David J, This P, Boursiquot JM, Charrier A. Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor Appl Genet. 1999; 98: 171-177.
59. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes. 2007; 7: 574-578
60. Stöck M, Ustinova J, Lamatsch DK, Schartl M, Perrin N, Moritz C. A vertebrate reproductive system involving three ploidy levels: hybrid origin of triploids in a contact zone of diploid and tetraploid palearctic green toads (Bufo viridis subgroup). Evolution 2010; 64: 944-959. doi: 10.1111/j.1558-5646.2009. 00876.x
61. Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Cons Genet Resour. 2012; 4: 359-361.
62. Li XW, Meng XQ, Jia HJ, Yu ML, Ma RJ, Wang LR, et al. Peach genetic resources: diversity, population structure and linkage disequilibrium. BMC Genet. 2013; 14: 84. doi: 10.1186/1471-2156-14-84
63. Jacobs MJ, Smulders MJM, van den Berg RG, Vosman B. What's in a name; genetic structure in Solanum section Petota studied using population-genetic tools. BMC Evol Biol. 2011; 11: 42. doi: 10.1186/1471-2148-11-42
64. Jing RC, Vershinin A, Grzebyta J, Shaw P, Smykal P, Marshall D, et al. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol Biol. 2010; 10: 44. doi: 10.1186/1471-2148-10-44
65. Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007; 23: 801-1806.
66. Rosenberg NA. DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes. 2004; 4: 137-138.
67. Bouchet S, Pot D, Deu M, Rami JF, Billot C, Perrier X, et al. Genetic structure, linkage disequilibrium and signature of selection in sorghum: lessons from physically anchored DArT markers. PLoS One 2012; 7:e33470. doi: 10.1371/journal.pone.0033470
68. Meirmans PG, van Tienderen PH. GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes. 2004; 4: 792-794.
69. Pierantoni L, Cho KH, Shin IS, Chiodini R, Tartarini S, Dondini L, et al. Characterisation and transferability of apple SSRs to two European pear F1 population. Theor Appl Genet. 2004; 109: 1519-1524
70. Garkava-Gustavsson L, Brantestam AK, Sehic J, Nybom H. Molecular characterisation of indigenous Swedish apple cultivars based on SSR and S-Allele analysis. Hereditas 2008; 145: 99-112. doi: 10. 1111/j.0018-0661.2008.02042.x
71. Yamamoto T, Kimura T, Terakami S, Nishitani C, Sawamura Y, Saito T, et al. Integrated reference genetic linkage maps of pear based on SSR and AFLP markers. Breed Sci. 2007; 57: 321-329.
72. Yamamoto T, Terakami S, Moriya S, Hosaka F, Kurita K, Kanomori H, et al. DNA markers developed from genome sequencing analysis in Japanese pear (Pyrus pyrifolia). Acta Hortic. 2013; 976: 477-483.
73. Miller AJ, Gross BL. Forest to field: perennial fruit crop domestication. Am J Bot 2011; 98: 1389-1414. doi: 10.3732/ajb.1000522
74. Zohary D, Spiegel-Roy P. Beginnings of fruit growing in the old world. Science. 1975; 187: 319-327
75. Latch EK, Dharmarajan G, Glaubitz JC, Rhodes OE. Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation. Cons Genet. 20016; 7: 295-302.
76. Gharghani A, Zamani Z, Talaie A, Fattahi R, Hajnajari H, Oraguzie NC, et al. The role of Iran (Persia) in apple (Malus × domestica Borkh.) domestication, evolution and migration via the silk trade route. Acta Hortic 2010; 859: 229-236.
77. Hedrick PW. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution. 1999; 53: 313-318.