Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis

Theoretical and Applied Genetics

Volumn 117, Issue 3, 2008, Pages 413-424

  Smýkal, Petr ^a   Hýbl, Miroslav ^a   Corander, Jukka ^b   Jarkovský, Jiří ^c   Flavell, Andrew J ^d   Griga, Miroslav ^a  

^a AGRITEC Ltd   (Czech Republic)

^b ÅBO AKADEMI UNIVERSITY   (Finland)

^c MASARYK UNIVERSITY   (Czech Republic)

^d UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADMINISTRATIVE DATA PROCESSING; BAYESIAN NETWORKS; CLUSTER ANALYSIS; FINANCIAL DATA PROCESSING; FLOW OF SOLIDS; LINGUISTICS; MOLECULES; MORPHOLOGY; NUCLEIC ACIDS; ORGANIC ACIDS; POPULATION STATISTICS; PRINCIPAL COMPONENT ANALYSIS; SEMICONDUCTOR RELAYS; SEPARATION;

APPLIED (CO); BAYESIAN ANALYSIS; BAYESIAN METHODS; CORE SELECTION; DATA TYPING; DNA DATA; GENE DIVERSITY; GENETIC DIVERSITIES; INFORMATION CONTENTS; MICRO SATELLITES; MOLECULAR DATA; MOLECULAR MARKERS; MORPHOLOGICAL PARAMETERS; MULTI DIMENSIONAL SCALING; PHENOTYPIC DATA; PISUM SATIVUM; POPULATION STRUCTURES; PRINCIPAL COMPONENTS; RETROTRANSPOSON; SIMPLE SEQUENCE REPEAT (SSR); SPRINGER (CO); SUB-CLUSTERS; THREE-AXIS; TOTAL VARIABILITY;

QUALITY CONTROL;

MICROSATELLITE DNA;

ALLELE; ARTICLE; BAYES THEOREM; GENE FREQUENCY; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; PEA; POPULATION DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; RETROPOSON; VARIABLE NUMBER OF TANDEM REPEAT;

ALLELES; BAYES THEOREM; GENE FREQUENCY; GENETIC MARKERS; MICROSATELLITE REPEATS; MINISATELLITE REPEATS; PEAS; POPULATION DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; RETROELEMENTS; VARIATION (GENETICS);

ANIMALIA; PISUM SATIVUM;

EID: 47249119613     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-008-0785-4     Document Type: Article

References (62)

1. Baranger A, Aubrey G, Aran G, Laine AL, Deniot G, Potier J, Burstin J (2004) Genetic diversity within Pisum sativum using protein and PCR-based markers. Theor Appl Genet 108:1309-1321
2. Beaumont MA, Rannala B (2004) The Bayesian revolution in genetics. Nature Rev 5:251-261
3. Beckmann JS, Soller M (1990) Toward a unified approach to genetic mapping of eukaryotes based on sequence tagged microsatellite sites. Biotechnology 10:930-932
4. Bredemeijer GMM, Cooke RJ, Ganal MW, Peeter R, Isakk P, Noordijk Y, Rendell S, Jackson J, Roder MS, Wendehake K, Dijcks M, Amelaine M, Wickaert V, Bertrand L, Vosman B (2002) Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theor Appl Genet 105:1019-1026
5. Brown AHD, Spillane C (1999) Implementing core collections - principles, procedures, progress, problems and promise. In: Johnson RC, Hodgkin T (eds) Core collections for today and tommorow. IPGRI, Rome
6. Brown AHD, Weir BS (1983) Measuring genetic variability in plant populations. In: Tanksley SD, Orton TJ (eds) Isozymes in plant genetics and breeding, part A. Elsevier, Amsterdam
7. Burstin J, Deniot G, Potier J, Weinachter C, Aubert G, Baranger A (2001) Microsatellite polymorphism in Pisum sativum. Plant Breed 120:311-217
8. Corander J, Martiinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol Ecology 15:2833-2843
9. Corander J, Waldmann P, Marttinen P, Sillanpää MJ (2004) BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 20:2363-2369
10. Corander J, Gyllenberg M, Koski T (2007) Random partition models and exchangeability for Bayesian identification of population structure. Bull Math Biol 69:797-815
11. Donini P, Law JR, Koebner RMD, Reeves JC, Cooke RJ (2000) Temporal trends in the diversity of UK wheat. Theor Appl Genet 100:912-917
12. Ellis THN, Poyser SJ, Knox MR, Vershinin AV, Ambrose MJ (1998) Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol Gen Genet 260:9-19
13. Erskine W, Muehlbauer FJ (1991) Allozyme and morpfological variability, outcrossing rate and core collection formation in lentil germplasm. Theor Appl Genet 83:119-125
14. Esquinas-Alacazar J (2005) Protecting crop genetic diversity for food security: political, ethical and technical challenges. Nature Rev Genet 6:946-953
15. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567-1587
16. Flavell AJ, Knox MR, Pearce SR, Ellis THN (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16:643-650
17. Ford R, LeRoux K, Itman C, Brouwer JB, Tayler PWJ (2002) Diversity analysis and genotyping in Pisum with sequence tagged microsatellite (STSM) primers. Euphytica 124:397-405
18. Flavell AJ, Bolshakov VN, Booth A, Jing R, Russell J, Ellis THN, Isaac P (2003) A microarray-based high throughput molecular marker genotyping method: the tagged microarray marker (TAM) approach. Nucleic Acids Res e31:e115
19. Frankel OH, Brown AHD (1984) Current plant genetic resources - a critical appraisal. In: Genetics: new Frontiers, vol IV. Oxford and IBH Publ. Co., New Delhi
20. Goudet J (1995) FSTAT (ver. 1.2): a computer program to calculate F-statistics. J Heredity 86:485-486
21. Hu J, Zhu J, Xu HM (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet 101:264-268
22. Jing RC, Knox MR, Lee JM, Vershinin AV, Ambrose M, Ellis THN, Flavell AJ (2005) Insertional polymorphism and antiquity of PDR1 retrotransposon insertions in Pisum species. Genetics 171:741-752
23. Jing R, Bolshakov VI, Flavell AJ (2007) The Tagged Microarray Marker (TAM) method for high throughput detection of single nucleotide and indel polymorphisms. Nature Protocols 2:168-177
24. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704-711
25. Kimura M, Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725-738
26. Kruskal JB (1964) Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29:1-27
27. Le Clerc V, Bazante F, Baril C, Guiard J, Zhang D (2005) Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers. Theor Appl Genet 110:294-302
28. Le Clerc V, Cadot V, Canadas M, Lallemand J, Guerin D, Boulineau F (2006) Indicators to assess temporal genetic diversity in the French Catalogue: no losses for maize and peas. Theor Appl Genet 113:1197-1209
29. Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381-398
30. Loridon K, McPhee K, Morin J, Dubreuil P, Pilet-Nayel ML, Aubert G, Rameau C, Baranger A, Coyne C, Lejeune-Henaut I, Burstin J (2005) Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). Theor Appl Genet 111:1022-1031
31. Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15:271-289
32. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209-220
33. Nei M (1973) Analysis of gene diversity in subdivaded populations. Proc Natl Acad Sci USA 70:3321-3323
34. Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590
35. Nersting LG, Andersen SB, von Bothmer R, Gullord M, Jorgensen RB (2006) Morphological and molecular diversity of Nordic oat through one hundred years of breeding. Euphytica 150:327-337
36. Pavelková A, Moravec J, Hájek D, Bareš I, Sehnalová J (1986) Descriptor list genus Pisum L. RICP Prague. Genové zdroje 32:46
37. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945-959
38. Reif JC, Melchinger AE, Frish M (2005) Genetical and mathematical properties of similarity and dissimilarity coefficients applied in plant breeding and seed bank management. Crop Sci 45:1-7
39. Reynolds J, Weir BS, Cockerham C (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105:767-776
40. Rohlf F (2006) NTSYSpc: Numerical Taxonomy System (ver. 2.2). Exeter Publishing, Ltd., Setauket
41. Rousseeuw PJ (1987) Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 20:53-65
42. Roussel V, Leisova L, Exbrayat F, Stehno Z, Balfourier F (2005) SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000. Theor Appl Genet 111:162-170
43. Roussel V, Koenig J, Beckert M, Balfourier F (2006) Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor Appl Genet 108:920-930
44. Shannon CE, Weaver W (1962) The mathematical theory of communication. Univer. of Illinois Press, Urbana
45. Simioniuc D, Uptmoor R, Friedt W, Ordon F (2002) Genetic diversity and relationships among pea cultivars revealed by RAPDs and AFLPs. Plant Breed 121:429-435
46. Smýkal P (2006) Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification. J Appl Genet 47:221-230
47. Smýkal P, Valledor L, Rodríguez R, Griga M (2007) Assessment of genetic and epigenetic stability in long-term in vitro shoot culture of pea (Pisum sativum L.). Plant Cell Rep 26:1985-1998
48. SPSS for Windows, Rel. 12.0.1 (2003) SPSS Inc., Chicago
49. StatSoft Inc (2006) STATISTICA (data analysis software system), version 7.1. http://www.statsoft.com
50. Tanksley SD, McCouch SR (1997) Seed bank and molecular maps: unlocking genetic potential from the wild. Science 277:1063-1066
51. Tar'an B, Zhang C, Wankertin T, Tullu A, Vandenberg A (2005) Genetic diversity among varietis and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters. Genome 48:257-272
52. Tohme J, Jones P, Beebe S, Iwanaga M (1995) The combined use of agroecological and characterization data to establish the CIAT Phaseolus vulgaris core collection. In: Hodgkin T, Brown AHD, van Hintum TJL, Morales EAV (eds) Core collections of plant genetic resources. Wiley, Chichester, pp 95-107
53. Van Hintum TJL (1999) The general methodology for creating a core collection. In: Johnson RC, Hodgkin T (eds) Core collections for today and tomorrow. International Plant Genetic Resources Institute, Rome, pp 10-17
54. Vavilov NI (1926) Studies on the origin of cultivated plants, Bulletin of Applied Botany, vol 26. Leningrad, USSR
55. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
56. Wang JC, Hu J, Xu HM, Zhang S (2007) A strategy on constructing core collections by least distance stepwise sampling. Theor Appl Genet 115:1-8
57. Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58:236
58. Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BT, Powell W (1997) Genetic distribution of BARE-1 retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687-694
59. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphism amplified by arbitrary primers are usefull as genetic markers. Nucleic Acids Res 18:6531-6535
60. Wright S (1965) The interpretation of population structure by F-statistics with special regards to systems of mating. Evolution 19:395-420
61. Yeh FC, Boyle TJB (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg J Bot 129:157
62. Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction. Genomics 20:176-183