Abstract
Characterizations of plant genetic resources based on molecular markers have been increased in the last years. Studies using a broad range of markers applied on hundreds of plant species are the theoretical basis for inferring genetic diversity to propose both breeding and conservation strategies. Despite increased importance of molecular characterization in plant genetic resources, there is scarce information about analysis of this type of data. To fill this gap of information, this review discuss the rationale behind analyses achieved to study genetic relationship among accessions (within and between groups) and to identify accession, and also discuss the adequacy of some analyses and/or parameters for specific purposes. Genetic diversity within groups may be either quantified for the whole group (parameters to choose will depend on type of marker), or quantified and visualized for the relationships among individuals. Quantification parameters will be chosen depending on type of marker, reproduction mode and relatedness of individuals. Visualization is achieved by hierarchical and non-hierarchical methods. Genetic diversity between groups should be quantified either by analysis of molecular variance, or Nei’s parameters, or Wright’s F-statistics. Efficiency of accession identification can be evaluated by maximal probability of identical match by chance and number of resolved genotypes.
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References
Alvarez J, Martín L (2006) Genetic diversity and structure in a natural Hordeum chilense population based on gliadin analysis. Plant Syst Evol 261:11–18. doi:10.1007/s00606-006-0436-7
Archak S, Gaikwad A, Gautam D, Rao EVV, Swamy KR, Kurihaloo J (2003) Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India. Genome 46(3):362–369. doi:10.1139/g03-016
Barcaccia G, Lucchin M, Parrini P (2003) Characterization of a flint maize (Zea mays var. indurata) Italian landrace, II. Genetic diversity and relatedness assessed by SSR and inter-SSR molecular markers. Genet Resour Crop Evol 50:253–271. doi:10.1023/A:1023539901316
Beebe S, Skroch P, Tohme J, Duque M, Pedraza F, Nienhuis J (2000) Structure of genetic diversity among common landraces of middle American origin based on correspondence analysis of RAPD. Crop Sci 40:264–273
Blair M, Giraldo M, Buendía H, Tovar E, Duque M, Beebe S (2006) Microsatellite marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet 113:100–109. doi:10.1007/s00122-006-0276-4
Bolibok H, Rakoczy-Trojanowska M, Hromada A, Pietrzykowski R (2005) Efficiency of different PCR-based marker systems in assessing genetic diversity among winter rye (Secale cereale L.) inbred lines. Euphytica 146:109–116. doi:10.1007/s10681-005-0548-0
Botstein D, White R, Skolnick M, Davis R (1980) Construction of genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331
Branco C, Vieira E, Malone G, Kopp M, Malone E, Bernardes A, Mistura C, Carvalho F, Oliveira C (2007) IRAP and REMAP assessments of genetic similarity in rice. J Appl Genet 48:107–113
Bussel J (1999) The distribution of random amplified polymorphic DNA (RAPD) diversity amongst populations of Isotoma petraea (Lobeliaceae). Mol Ecol 8:775–789. doi:10.1046/j.1365-294X.1999.00627.x
Camacho F, Liston A (2001) Population structure and genetic diversity of Botrychium pumicola (Ophiogossaceae) based on inter-simple sequence repeats (ISSR). Am J Bot 88:1065–1070. doi:10.2307/2657089
Cavallari M, Forzza R, Veasey E, Zucchi M, Oliveira G (2006) Genetic variation in three endangered species of Encholoirium (Bromeliaceae) from Cadeia do Espinhaco, Brazil, detected using RAPD markers. Biodivers Conserv 15:4357–4373. doi:10.1007/s10531-005-3741-5
Chabane K, Abdalla O, Sayed H, Valkoun J (2007) Assessment of EST-microsatellites markers for discrimination and genetic diversity in bread and durum wheat landraces from Afghanistan. Genet Resour Crop Evol 54:1073–1080. doi:10.1007/s10722-006-9193-2
Che Y, Li L (2007) Genetic diversity of prolamines in Agropyron mongolicum Keng indigenous to northern China. Genet Resour Crop Evol 54:1145–1151. doi:10.1007/s10722-006-9006-7
Cheng Y, Hwang S, Chiou W, Lin T (2006) Allozyme variation of populations of Castanopsis carlesii (Fagaceae) revealing the diversity centres and areas of the greatest divergence in Taiwan. Ann Bot (Lond) 98:601–608. doi:10.1093/aob/mcl135
Choudhury P, Tanveer H, Dixit G (2007) Identification and detection of genetic relatedness among important varieties of pea (Pisum sativum L.) grown in India. Genetica 130:183–191. doi:10.1007/s10709-006-9005-9
Chung M, Nason J, Chung M (2005) Spatial genetic structure in populations of the terrestrial orchid Orchis cyclochila (Orchidaceae). Plant Syst Evol 254:209–219. doi:10.1007/s00606-005-0341-5
Cordeiro G, Pan Y, Henry R (2003) Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm. Plant Sci 165:181–189. doi:10.1016/S0168-9452(03)00157-2
Dagher-Kharrat M, Mariette S, Lefevre F, Fady B (2007) Geographical diversity and genetic relationships among Cedrus species estimated by AFLP. Tree Genet Genomes 3:275–285. doi:10.1007/s11295-006-0065-x
Dawson I, Simons A, Waugh R, Powell W (1995) Diversity and genetic differentiation among subpopulations of Gliricidia sepium revealed by PCR-based assays. Heredity 74:10–18. doi:10.1038/hdy.1995.2
De Riek J, Calsyn E, Everaert I, Van Bockstaele E, De Loose M (2001) AFLP based alternatives for the assessment of distinctness, uniformity and stability of sugar beet varieties. Theor Appl Genet 103:1254–1265. doi:10.1007/s001220100710
Diaz L, Blair M (2006) Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers. Theor Appl Genet 114:143–154. doi:10.1007/s00122-006-0417-9
Dice L (1945) Measures of the amount of ecologic association between species. Ecology 26:297–302. doi:10.2307/1932409
Drossou A, Katsiosis A, Leggett J, Loukas M, Tsakas S (2004) Genome and species relationships in genus Avena based on RAPD and AFLP molecular markers. Theor Appl Genet 109:48–54. doi:10.1007/s00122-004-1615-y
Duncan T, Baum B (1981) Numerical phenetics: its uses in botanical systematics. Annu Rev Ecol Syst 12:387–404. doi:10.1146/annurev.es.12.110181.002131
Efron B (1979) Bootstrap methods: another look at the jackknife. Ann Stat 7:1–26. doi:10.1214/aos/1176344552
El Mousadik A, Petit R (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L. Skeels)] endemic to Morocco. Theor Appl Genet 92:832–836. doi:10.1007/BF00221895
Excoffier L, Smouse P, Quattro J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: applicatio to human mitochondrial DNA restriction data. Genetics 131:179–191
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol Int J Org 39:783–791. doi:10.2307/2408678
Fernandez M, Figueiras A, Benito C (2002) The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin. Theor Appl Genet 104:845–851. doi:10.1007/s00122-001-0848-2
Feyissa T, Nybom H, Bartish I, Welander M (2007) Analysis of genetic diversity in the endangered tropical tree species Hagenia abyssinica using ISSR markers. Genet Resour Crop Evol 54:947–958. doi:10.1007/s10722-006-9155-8
Foulley J, Ollivier L (2006) Estimating allelic richness and its diversity. Livest Sci 101:150–158. doi:10.1016/j.livprodsci.2005.10.021
Geleta N, Labuschagne M, Viljoen C (2006) Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers. Biodivers Conserv 15:3251–3265. doi:10.1007/s10531-005-0313-7
Gimenes M, Hoshino A, Barbosa A, Palmieri D, Lopes C (2007) Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea). BMC Plant Biol 7:9. doi:10.1186/1471-2229-7-9
Goudet J (1995) FSTAT, version 1.2: a computer program to calculate F-statistics. J Hered 86:485–486
Goulão L, Oliveira C (2001) Molecular characterization of cultivars of apple (Malus × domestica Borkh.) using microsatellite (SSR and ISSR) markers. Euphytica 122:81–89. doi:10.1023/A:1012691814643
Gower J (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325–338
Gower J (1985) Measure of similarity, dissimilarity and distances. In: Kotz S (ed) Encyclopedia of statistical sciences, vol 5. Wiley, New York, USA
Grünwald N, Goodwin S, Milgroom M, Fry W (2003) Analysis of genotypic diversity data for populations of microorganism. Phytopathology 93:738–746. doi:10.1094/PHYTO.2003.93.6.738
Guo H, Li S, Peng J, Ke W (2007) Genetic diversity of Nelumbo accessions revealed by RAPD. Genet Resour Crop Evol 54:741–748. doi:10.1007/s10722-006-0025-1
Hai L, Wagner C, Friedt W (2007) Quantitative structure analysis of genetic diversity among spring bread wheats (Triticum aestivum L.) from different geographical regions. Genetica 130:213–225. doi:10.1007/s10709-006-9008-6
Hartl D, Clark A (1997) Principles of population genetics. Sinauer, Sunderland, MA
Hayati A, Wickneswari R, Maizura I, Rajanaidu N (2004) Genetic diversity of oil palm (Elaeis quineensis Jacq.) germplasm collections from Africa: implications for improvement and conservation of genetic resources. Theor Appl Genet 108:1274–1284. doi:10.1007/s00122-003-1545-0
Heider B, Andersson M, Shultze-Kraft R (2007) RAPD variation among north Vietnamese Flemingia macrophylla (Willd.) Kuntze ex Merr. accessions. Biodivers Conserv 16:1617–1631. doi:10.1007/s10531-006-9024-y
Hill M (1973) Diversity and evenness: a unifying notation and its consequences. Ecology 54:427–432. doi:10.2307/1934352
Holgersson M (1978) The limited value of cophenetic correlation as a clustering criterion. Pattern Recognit 10:287–295. doi:10.1016/0031-3203(78)90038-9
Islam M, Kloppstech K, Esch E (2005) Population genetic diversity of Curcuma zedoaria (Christm.) Roscoe—a conservation prioritised medicinal plant in Bangladesh. Conserv Genet 6:1027–1033. doi:10.1007/s10592-005-9080-y
Jaccard P (1908) Nouvelles rescherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270
Jakse J, Kindlhofer K, Jarnovik B (2001) Assessment of genetic variation and differentiation of hop genotypes by microsatellite and AFLP markers. Genome 44:773–782. doi:10.1139/gen-44-5-773
Kalinowsky S (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conserv Genet 5:539–543. doi:10.1023/B:COGE.0000041021.91777.1a
Kamala V, Bramel P, Sivaramakrishnan S, Chandra S, Kannan S, Harikrishna S, ManoharRao D (2006) Genetic and phenotypic diversity in downy-mildew-resistant sorghum (Sorghum bicolor (L.) Moench) germplasm. Genet Resour Crop Evol 53:1243–1253. doi:10.1007/s10722-005-5678-7
Karp A, Kresovich S, Bhat K, Ayad W, Hodgkin T (1997) Molecular tools in plant genetic resources conservation: a guide to the technologie. IPGRI Technical Bulletin No. 2. International Plant Genetic Resources Institute, Rome, Italy
Katsiotis A, Hagidimitriou M, Drossou A, Pontikis C, Loukas M (2003) Genetic relationships among species and cultivars of Pistacia using RAPDs and AFLPs. Euphytica 132:279–286. doi:10.1023/A:1025027323184
Kaundun S, Zhyvoloup A, Park Y (2000) Evaluation of the genetic diversity among elite tea (Camellia sinensis var. sinensis) accessions using RAPD markers. Euphytica 115:7–16. doi:10.1023/A:1003939120048
Kim S, Lee C, Santos-Guerra A (2005) Genetic analysis and conservation of the endangered Carary Island woody sow-thistle Sonchus gandogeri (Asteraceae). J Plant Res 118:147–153. doi:10.1007/s10265-005-0203-9
Kolodinska Brantestam A, von Bothmer R, Dayteg C, Rashal I, Tuvesson S, Weibull J (2007) Genetic diversity changes and relationships in spring barley (Hordeum vulgare L.) germplasm of Nordic and Baltic areas as shown by SSR markers. Genet Resour Crop Evol 54:749–758. doi:10.1007/s10722-006-9159-4
Kosman E, Leonard K (2005) Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Mol Ecol 14:415–424. doi:10.1111/j.1365-294X.2005.02416.x
Krauss S (2000) Accurate gene diversity estimates from amplified fragment length polymorphism (AFLP) markers. Mol Ecol 9:1241–1245. doi:10.1046/j.1365-294x.2000.01001.x
Kreike C, Van Eck H, Lebot V (2004) Genetic diverstiy of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific. Theor Appl Genet 109:761–768. doi:10.1007/s00122-004-1691-z
Kruskal J (1964a) Nonmetric multidimensional scaling: a numerical method. Psychometrika 29:28–42
Kruskal J (1964b) Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29:1–27. doi:10.1007/BF02289565
Lamboy W (1994) Computing genetic similarity coefficients from RAPD data: the effects of PCR artifacts. PCR Methods Appl 4:31–37
Larionova A, Yakhneva N, Abaimov A (2004) Genetic diversity and differentiation of gmelin larch Larix gmelinii populations from Evenkia (Central Siberia). Russ J Genet 40:1127–1133. doi:10.1023/B:RUGE.0000044756.55722.d8
Laurentin H, Karlovsky P (2006) Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment lenght polymorphism (AFLP). BMC Genet 7:10
Laurentin H, Karlovsky P (2007) AFLP fingerprinting of sesame (Sesamum indicum L.) cultivars: identification, genetic relationship and comparison of AFLP informativeness parameters. Genet Resour Crop Evol 54:1437–1446. doi:10.1007/s10722-006-9128-y
Li S, Qian Z, Cai Y, Zhao G (2006) A comparison of the genetic diversity in Dipteronia sinensis Oliv. and Dipteronia dyeriana Henry. Front Biol China 4:381–388. doi:10.1007/s11515-006-0050-7
Link W, Dixkens C, Singh M, Schwall M, Melchinger A (1995) Genetic diversity in European and Mediterranean faba bean germplasm revealed by RAPD markers. Theor Appl Genet 90:27–32. doi:10.1007/BF00220992
Lynch M, Milligan B (1994) Analysis of population genetic structure with RAPD markers. Mol Ecol 3:91–99. doi:10.1111/j.1365-294X.1994.tb00109.x
Mace E, Phong D, Upadhyaya H, Chandra S, Crouch J (2006) SSR analysis of cultivated groundut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases. Euphytica 152:317–330. doi:10.1007/s10681-006-9218-0
Maguire T, Peakall R, Saenger P (2002) Comparative analysis of genetic diversity in the mangrove species Avicennia marina (Forsk.) Vierh. (Avicenniaceae) detected by AFLPs and SSRs. Theor Appl Genet 104:388–398. doi:10.1007/s001220100724
Magurran A (1988) Ecological diversity and its measurement. Princenton University Press, Princenton, New Jersey, USA
Manimekalai R, Nagarajan P (2006) Interrelationships among coconut (Cocos nucifera L.) accessions using RAPD technique. Genet Resour Crop Evol 53:1137–1144. doi:10.1007/s10722-005-1303-z
Marghali S, Panaud O, Lamy F, Ghariani S, Sarr A, Harrakchi M, Trifi-Farah N (2005) Exploration of intra- and inter-population genetic diversity in Hedysarum coronarium L. By AFLP markers. Genet Resour Crop Evol 52:277–284. doi:10.1007/s10722-005-5459-3
Martínez L, Cavagnaro P, Masuelli R, Zuñiga M (2006) SSR-based assessment of genetic diversity in South American Vitis vinifera varieties. Plant Sci 170:1036–1044. doi:10.1016/j.plantsci.2005.12.006
McGrath J, Derrico C, Yu Y (1999) Genetic diversity in selected, historical US sugarbeet germplasm and Beta vulgaris ssp. maritima. Theor Appl Genet 98:968–976. doi:10.1007/s001220051157
Melchinger A (1993) Use of RFLP markers for analysies of genetic relationships among breeding materials and prediction of hybrid performance. In: Buxton D (ed) First international crop sciences congress. Crop Science Society of America, Madison, Wis, pp 621–628
Mengistu L, Mueller-Warrant G, Barker R (2000) Genetic diversity of Poa annua in western Oregon grass seed crops. Theor Appl Genet 101:70–79. doi:10.1007/s001220051451
Menkir A, Kling J, Badu-Apraku B, Ingelbrecht I (2005) Molecular marker-based genetic diversity assessment of Striga-resistant maize inbred lines. Theor Appl Genet 110:1145–1153. doi:10.1007/s00122-005-1946-3
Moss W (1979) Phenetic approaches to classification. Am Zool 19:1217–1223
Naydenov K, Tremblay F, Alexandrov A, Fenton N (2005) Structure of Pinus sylvestris L. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: provenance tests. Biochem Syst Ecol 33:1226–1245. doi:10.1016/j.bse.2005.07.011
Nei M (1972) Genetic distance between populations. Am Nat 106:283–292. doi:10.1086/282771
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Nat Acad Aci USA 70:3321–3323. doi:10.1073/pnas.70.12.3321
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590
Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273. doi:10.1073/pnas.76.10.5269
Omrani-Sabbaghi A, Shahriari M, Falahati-Anbaran M, Mohammadi S, Nankali A, Mardi M, Ghareyazie B (2007) Microsatellite markers based assessment of genetic diversity in Iranian olive (Olea europea L.) collections. Sci Hortic (Amsterdam) 112:439–447. doi:10.1016/j.scienta.2006.12.051
Ott J (1992) Strategies for characterizing highly polymorphic markers in human gene map**. Am J Hum Genet 51:283–290
Ovesná J, Poláková K, Leisová L (2002) DNA analyses and their applications in plant breeding. Czech J Genet Plant Breed. 38:29–40
Owen C, Bita E, Banilas G, Hajjar S, Sellianakis V, Aksoy U, Hepaksoy S, Chamoun R, Talhook S, Metzidakis I, Hatzopoulos P, Kalaitzis P (2005) AFLP reveals structural details of genetic diversity within cultivated olive germplasm from the Eastern Mediterraneas. Theor Appl Genet 110:1169–1176. doi:10.1007/s00122-004-1861-z
Oyama K, Hernández-Vergugo S, Sánchez C, González-Rodríguez A, Sánchez-Peña P, Garzón-Tiznado J, Casas A (2006) Genetic structure of wild and domesticated populations of Capsicum annuum (Solanaceae) from northwestern Mexico analyzed by RAPDs. Genet Resour Crop Evol 53:553–562. doi:10.1007/s10722-004-2363-1
Peakall R, Smouse P, Huff D (1995) Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchoe dactyloides. Mol Ecol 4:135–147. doi:10.1111/j.1365-294X.1995.tb00203.x
Pinto L, Oliveira K, Marconi T, Garcia A, Ulian E, de Souza A (2006) Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs. Plant Breed 125:378–384. doi:10.1111/j.1439-0523.2006.01227.x
Pomper K, Crabtree S, Brown S, Jones S, Bonney T (2003) Assessment of genetic diversity of pawpaw (Asimina triloba) cultivars with intersimple sequence repeat markers. J Am Soc Hortic Sci 128:521–525
Portis E, Barchi L, Acquadro A, Macua J, Lanteri S (2005) Genetic diversity assessment in cultivated cardoon by AFLP (amplified fragment lenght polymorphism) and microsatellite markers. Plant Breed 124:299–304. doi:10.1111/j.1439-0523.2005.01098.x
Powell W, Margenta M, Andre C, Hanfrey M, Vogel J, Tingey S, Rafalsky A (1996) The utility of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238. doi:10.1007/BF00564200
Prevost A, Wilkinson M (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112. doi:10.1007/s001220051046
Rajora O, Rahman M (2003) Microsatellite DNA and RAPD fingerprinting, identification and genetic relationships of hybrid poplar (Populus × canadensis) cultivars. Theor Appl Genet 106:470–477
Ramakrishna W, Lagu M, Gupta V, Ranjekar P (1994) DNA fingerprinting in rice using oligonucleotide probes specific for simple repetitive DNA sequences. Theor Appl Genet 88:402–406
Ramanatha R, Hodgkin T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult 68:1–19. doi:10.1023/A:1013359015812
Rao N (2004) Plant genetic resources: advancing conservation and use through biotechnology. Afr J Biotechnol 3(2):136–145
Reif J, Melchinger E, Frisch M (2005) Genetical and mathematical properties of similarity and dissimilarity coefficients applied in plant breeding and seed bank management. Crop Sci 45:1–7
Roldán-Ruiz I, Dendauw J, van Bockstaele E, Depicker A, De Loose M (2000) AFLP markers reveal high polymorphic rates in ryegrass (Lolium spp.). Mol Breed 6:125–134. doi:10.1023/A:1009680614564
Romeiras M, Cotrim H, Duarte M, Pais M (2007) Genetic diversity of three endangered species of Echium L. (Boraginaceae) endemic to Cape Verde islands. Biodivers Conserv 16:547–566. doi:10.1007/s10531-006-6734-0
Sarkhosh A, Zamani Z, Fatahi R, Ebadi A (2006) RAPD markers reveal polymorphism among some Iranian pomegranate (Punica granatum L.) genotypes. Sci Hortic (Amsterdam) 111:24–29. doi:10.1016/j.scienta.2006.07.033
Shannon C, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana
Sheng H, An L, Chen T, Xu S, Liu G, Zheng X, Pu L, Liu Y, Lian Y (2006) Analysis of the genetic diversity and relationships among and within species of Hippophae (Elaeagnaceae) based on RAPD markers. Plant Syst Evol 260:25–37. doi:10.1007/s00606-006-0413-1
Sica M, Gamba G, Montieri S, Gaudio L, Aceto S (2005) ISSR markers show differentiation among Italian populations of Asparagus acutifolius L. BMC Genet 6:17. doi:10.1186/1471-2156-6-17
Singh R, Sharma R, Singh A, Singh V, Singh N, Tiwari S, Mohapatra T (2004) Suitability of mapped sequence tagged microsatellite site markers for establishing distincntess, uniformity and stability in aromatic rice. Euphytica 135:135–143. doi:10.1023/B:EUPH.0000014905.10397.08
Smith J, Chin E, Shu H, Smith O, Wall S, Senior M, Mitchell S, Kresovich S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theor Appl Genet 95:163–173. doi:10.1007/s001220050544
Smouse P, Peakall R (1999) Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity 82:561–573. doi:10.1038/sj.hdy.6885180
Sonnante G, Pignone D (2007) The major Italian landraces of lentil (Lens culinaris Medik.): their molecular diversity and possible origin. Genet Resour Crop Evol 54:1023–1031. doi:10.1007/s10722-006-9153-x
Spataro G, Taviani P, Negri V (2007) Genetic variation and population structure in a Eurasian collection of Isatis tinctoria L. Genet Resour Crop Evol 54:573–584. doi:10.1007/s10722-006-0014-4
Storme V, VandenBroeck A, Ivens B, Halfmaerten D, VanSlycken J, Castiglione S, Grasse F, Fossati T, Cottrell J, Tabbener H, Levevre F, Saintagne C, Fluch S, Krystufek V, Burg K, Bordács S, Borovics A, Gebhardt K, Vornam B, Pohl A, Alba N, Agúndez D, Maestro C, Notivol E, Bovenschen J, van Dam B, van der Schoot J, Vosman B, Boerjan W, Smulders M (2004) Ex-situ conservation of Black poplar in Europe: genetic diversity in nine gene bank collections and their value for nature development. Theor Appl Genet 108:969–981. doi:10.1007/s00122-003-1523-6
Tams S, Melchinger A, Bauer E (2005) Genetic similarity among European winter triticale elite germplasm assessed with AFLP and comparisons with SSR and pedigree data. Plant Breed 124:154–160. doi:10.1111/j.1439-0523.2004.01047.x
Tara Satyavathi C, Bhat K, Bharadwaj C, Tiwari S, Chaudhury V (2006) AFLP analysis of genetic diversity in Indian soybean [Glycine max (L.) Merr.] varieties. Genet Resour Crop Evol 53:1069–1079. doi:10.1007/s10722-005-0779-x
Teklewold A, Becker H (2006) Geographic pattern of genetic diversity among 43 Ethiopian mustard (Brassica carinata A. Braun) accessions as revealed by RAPD analysis. Genet Resour Crop Evol 53:1173–1185. doi:10.1007/s10722-005-2011-4
Tessier C, David J, This P, Boursiquot J, Charrier A (1999) Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor Appl Genet 98:171–177. doi:10.1007/s001220051054
Ude G, Pillay M, Ogundiwin E, Tenkouano A (2003) Genetic diversity in an African plantain core collection using AFLP and RAPD markers. Theor Appl Genet 107(2):248–255. doi:10.1007/s00122-003-1246-8
Wang L, Guo J, Zhao G (2006) Genetic diversity of the endangered and endemic species Psathyrostachys huashanica natural populations using simple sequence repeats (SSRs) markers. Biochem Syst Ecol 34:310–318. doi:10.1016/j.bse.2005.09.009
Wang X, Chiang T, Roux N, Hao G, Ge X (2007) Genetic diversity of wild banana (Musa balbisiana Colla) in China as revealed by AFLP markers. Genet Resour Crop Evol 54:1125–1132. doi:10.1007/s10722-006-9004-9
Weiguo Z, Zhihua Z, Xuexia M, Yong Z, Sibao W, Jianhua H, Hui X, Yile P, Yong** H (2007) A comparison of genetic variation among wild and cultivated Morus species (Moraceae:Morus) as revealed by ISSR and SSR markers. Biodivers Conserv 16:275–290. doi:10.1007/s10531-005-6973-5
Wetton J, Carter R, Parkin D, Walters D (1987) Demographic study of a wild house sparrow population by DNA fingerprinting. Nature 327:147–149. doi:10.1038/327147a0
Wiesnerová D, Wiesner I (2004) ISSR-based clustering of cultivated flax germplasm is statistically correlated to thousand seed mass. Mol Biotechnol 26:207–214. doi:10.1385/MB:26:3:207
Wright S (1943) Isolation by distance. Genetics 28:114–138
Wright S (1951) The genetical structure of populations. Ann Eugen 15:323–354
Yap I, Nelson R (1996) WinBoot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI, Manila, Philippines
Zeid M, Schön C, Link W (2003) Genetic diversity in recent elite faba bean lines using AFLP markers. Theor Appl Genet 107:1304–1314. doi:10.1007/s00122-003-1350-9
Zhao N, Gao Y, Wang J, Ren A (2006a) Genetic diversity and population differentiation of the dominant species Stipa krylovii in the inner Mongolia steppe. Biochem Genet 44:513–526. doi:10.1007/s10528-006-9054-x
Zhao R, Cheng Z, Lu W, Lu B (2006b) Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers. Chin Sci Bull 51:1219–1227. doi:10.1007/s11434-006-1219-9
Zhyvotovsky L (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Mol Ecol 8:907–913. doi:10.1046/j.1365-294x.1999.00620.x
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Laurentin, H. Data analysis for molecular characterization of plant genetic resources. Genet Resour Crop Evol 56, 277–292 (2009). https://doi.org/10.1007/s10722-008-9397-8
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DOI: https://doi.org/10.1007/s10722-008-9397-8