Assessing plant genetic diversity by molecular tools

Diversity

Volumn 1, Issue 1, 2009, Pages 19-35

  Mondini, Linda ^a   Noorani, Arshiya ^a   Pagnotta, Mario A ^a  

^a UNIVERSITY OF TUSCIA   (Italy)

Author keywords

Assessment of diversity; Molecular markers; Plant genetics

Indexed keywords

EID: 79952451853     PISSN: None     EISSN: 14242818     Source Type: Journal    
DOI: 10.3390/d1010019     Document Type: Review

References (63)

1. Barcaccia, G.; Alberini, E.; Rosellini, D. Inheritance and mapping of 2n-egg production in diploid alfalfa. Genome 2000, 43, 528-537.
2. Ayad, W.G.; Hodking, A.; Jaradat, A.; Rao, V.R. Molecular genetic techniques for plant genetic resources. IPGRI Workshop: Rome, Italy, October 9-11, 1995.
3. Agarwal, M.; Shrivastava, N.; Padh, H. Advances in molecular marker techniques and their application in plant sciences. Plant Cell Rep. 2008, 27, 617-631.
4. Primmer, R. From conservation genetics to conservation genomics. "The Year in Ecology and Conservation Biology". Ann. N.Y. Acad. Sci. 2009, 1162, 357-368.
5. Reed, D.H.; Frankham, R. Correlation between fitness and genetic diversity. Cons. Biol. 2003, 17, 230-237.
6. Primack, R.B. Essentials of Conservation Biology. Sinauer Associates: Sunderland, MA, USA, 1993.
7. Karp, A.; Seberg, O.; Buiatti, M. Molecular techniques in the assessment of botanical diversity. Ann. Bot. 1996, 78, 143-149.
8. Spooner, D.; van Treuren, R.; de Vicente, M.C. Molecular Markers for Genebank Management. Bioversity International: Rome, Italy, 2005.
9. Guarino, L. Approaches to Measuring Genetic Erosion. In Proceedings of the Technical Meeting on the Methodology of the FAO World Information and Early Warning System on Plant Genetic Resources; Prague, Czech Republic, June 21-23, 1999.
10. Hamrick, J.L.; Godt, M.J.W. Allozyme diversity in cultivated crops. Crop Science 1997, 37, 26-30.
11. Brown, A.H.D. Enzyme polymorphism in plant populations. Theo. Pop. Biol. 1979, 15, 1-42.
12. Gonzalez, A.A.; Wong, A.; Delgado-Salinas, R.; Gepts, P. Assessment of inter simple sequence repeat markers to differentiate sympatric wild and domesticated populations of common bean. Crop Science 2005, 45, 606-615.
13. Volis, S.; Mendlinger, S.; Turuspekov, Y.; Esnazarov, U.; Abugalieva, S.; Orlovsky, N. Allozyme variation in Turkmenistan populations of wild barley Hordeum Spontaneum. Koch. Annals. Botany 2001, 87, 435-446.
14. Southern, E. Detection of specific sequences among DNA fragments separated by gel-electrophoresis. J. Mol. Biol. 1975, 98, 503.
15. Mullis, K.B.; Faloona, F.A.; Scharf, S.J.; Saiki, S.K.; Horn, G.T.; Erlich, H.A. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor. Symp. Quant. Biol. 1986, 51, 263-273.
16. Welsh, J.; McClelland, M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990, 18, 7213-7218.
17. Williams, J.G.K.; Kubelik, A.R.; Livak, K.J.; Rafalski, J.A.; Tingey, S.V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1991, 18, 6531-6535.
18. Bardakci, F. Random amplified polymorphic DNA (RAPD) markers. Turk. J. Biol. 2001, 25, 185-196.
19. Vos, P.; Hogers, R.; Bleeker, M.; Reijans, M.; van de Lee, T.; Hornes, M.; Frijters, A.; Pot, J.; Peleman, J.; Kuiper, M.; Zabeau, M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995, 23, 4407-4414.
20. Zabeau, M.; Vos, P. Selective Restriction Fragment Amplification:a General Method for DNA Fingerprinting. European Patent EP0534858, September 24, 1992.
21. Althoff, D.M.; Gitzendanner, M.A.; Segraves, K.A. The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. Syst. Biol. 2007, 56, 477-484.
22. Goff, S.A.; Ricke, D.; Lan, T.H.; Presting, G.; Wang, R.; Dunn, M.; Glazebrook, J.; Sessions, A.; Oeller, P.; Varma, H. Hadley, D.; Hutchison, D.; Martin, C.; Katagiri, F.; Lange, B.M.; Moughamer, T.; Xia, Y.; Budworth, P.; Zhong, J.; Miguel, T.; Paszkowski, U.; Zhang, S.; Colbert, M.; Sun, W.L.; Chen, L.; Cooper, B.; Park, S.; Wood, T.C.; Mao, L.; Quail, P.; Wing, R.; Dean, R.; Yu, Y.; Zharkikh, A.; Shen, R.; Sahasrabudhe, S.; Thomas, A.; Cannings, R.; Gutin, A.; Pruss, D.; Reid, J.; Tavtigian, S.; Mitchell, J.; Eldredge, G.; Scholl, T.; Miller, R.M.; Bhatnagar, S.; Adey, N.; Rubano, T.; Tusneem, N.; Robinson, R.; Feldhaus, J.; Macalma, T.; Oliphant, A.; Briggs, S. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296, 92-100.
23. Yu, J.; Hu, S.; Wang, J.; Wong, G.K.; Li, S.; Liu, B.; Deng, Y.; Dai, L.; Zhou, Y.; Zhang, X.; Cao, M.; Liu, J.; Sun, J.; Tang, J.; Chen, Y.; Huang, X.; Lin, W.; Ye, C.; Tong, W.; Cong, L.; Geng, J.; Han, Y.; Li, L.; Li, W.; Hu, G.; Huang, X.; Li, W.; Li, J.; Liu, Z.; Li, L.; Liu, J.; Qi, Q.; Liu, J.; Li, L.; Li, T.; Wang, X.; Lu, H.; Wu, T.; Zhu, M.; Ni, P.; Han, H.; Dong, W.; Ren, X.; Feng, X.; Cui, P.; Li, X.; Wang, H.; Xu, X.; Zhai, W.; Xu, Z.; Zhang, J.; He, S.; Zhang, J.; Xu, J.; Zhang, K.; Zheng, X.; Dong, J.; Zeng, W.; Tao, L.; Ye, J.; Tan, J.; Ren, X.; Chen, X.; He, J.; Liu, D.; Tian, W.; Tian, C.; Xia, H.; Bao, Q.; Li, G.; Gao, H.; Cao, T.; Wang, J.; Zhao, W.; Li, P.; Chen, W.; Wang, X.; Zhang, Y.; Hu, J.; Wang, J.; Liu, S.; Yang, J.; Zhang, G.; Xiong, Y.; Li, Z.; Mao, L.; Zhou, C.; Zhu, Z.; Chen, R.; Hao, B.; Zheng, W.; Chen, S.; Guo, W.; Li, G.; Liu, S.; Tao, M.; Wang, J.; Zhu, L.; Yuan, L.; Yang, H. A draft sequence of the rice Genome (Oryza sativa L. ssp. indica). Science 2002, 296, 79-92.
24. Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408, 796-815.
25. Bouck, A.; Vision, T. The molecular ecologist's guide to expressed sequence tags. Mol. Ecol. 2007, 16, 907-924.
26. Cordeiro, G.M.; Casu, R.; McIntyre, C.L.; Manners, J.M.; Henry, R.J. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci. 2001, 160, 1115-1123.
27. Vasemagi, A. Expressed sequence tag (EST) linked microsatellites as a source of gene associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Mol. Biol. Evol. 2005, 22, 1067-1076.
28. Karaiskou, N. High degree of transferability of 86 newly developed zebra finch EST-linked microsatellite markers in 8 bird species. J. Hered. 2008, 99, 688-693.
29. Dietrich, W.; Katz, H.; Lincoln, S.E.; Shin, H.S.; Friedman, J.; Dracopoli, N.C.; Lander, E.S. A genetic map of mouse suitable for typing intraspecific crosses. Genetics 1992, 131, 423-447.
30. Bell, C.J.; Ecker, J.R. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 1994, 19, 137-144.
31. Morgante, M.; Olivieri, A.M. PCR-amplified microsatelites as markers in plant genetics. Plant J. 1993, 3, 175-182.
32. Schlotterer, C.; Tautz, D. Slippage synthesis of simple sequence DNA. Nucleic Acids Res. 1992, 20, 2211-2215.
33. Gupta, P.K.; Varshney, R.K. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 2000, 113, 163-185.
34. Sunyaev, S.; Hanke, J.; Aydin, A.; Wirkner, U.; Zastrow, I.; Reich, J.; Bork, P. Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. J. Mol. Med. 1999, 77, 754-760.
35. Richard, I.; Beckman, J.S. How neutral are synonymous codon mutations? Nat. Genet. 1995, 10, 259.
36. Sobrino, B.; Briona, M.; Carracedoa, A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci. Int. 2005, 154, 181-194.
37. Provan, J.; Russell, J.R.; Booth, A.; Powell, W. Polymorphic chloroplast simple-sequence repeat primers for systematic and population studies in the genus Hordeum. Mol. Ecol. 1999, 8, 505-511.
38. Provan, J.; Soranzo, N.; Wilson, N.J.; Goldstein, D.B.; Powell, W.A. Low mutation rate for chloroplast microsatellites. Genetics 1999, 153, 943-947.
39. Ali, I.F.; Neale, D.B.; Marshall, K.A. Chloroplast DNA restriction fragment length polymorphism in Sequoia sempervirens D. Don Endl., Pseudotsuga menzipsii (Mirb.) Franco, Calocedrus decurrens (Ton), and Pinus taeda. L. Theor. Appl. Genet. 1991, 81, 83-89.
40. McCauley, D.E. Contrasting the distribution of chloroplast DNA and allozyme polymorphisms among local populations of Silene alba: implications for studying gene flow in plants. Proc. Nat. Acad. Sci. 1994, 17, 8127-8131.
41. Bucci, G.; Anzidei, M.; Madaghiele, A.; Vendramin, G.G. Detection of haplotypic variation and natural hybridization in halepensiscomplex pine species using chloroplast simple sequence repeat (SSR) markers. Mol. Ecol. 1998, 7, 1633-1643.
42. Clark, C.M.; Wentworth, T.M.; Malley, D.M.O. Genetic discontinuity revealed by chloroplast microsatellites in eastern North American Abies (Pinaceae). Am. J. Bot. 2000, 87, 774-778.
43. Parducci, L.; Szmidt, A.E.; Madaghiele, A.; Anzidei, M.; Vendramin, G.G. Genetic variation at chloroplast microsatellites (cpSSRs) in Abies nebrodensis (Lojac.) Mattei and three neighboring Abies species. Theor. Appl. Genet. 2001, 102, 733-740.
44. Shaw, J.; Lickey, E.B.; Beck, J.T.; Farmer, S.B.; Liu, W.; Miller, J.; Siripun, K.C.; Winder, C.T.; Schilling, E.E.; Small, R. The tortoise and Hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am. J. Bot. 2005, 92, 142-166.
45. Miller, W.; McDonald, J.; Pinsker, W. Molecular domestication of mobile elements. Genetica 1997, 100, 261-270.
46. Agrawal, A.; Eastmann, Q.; Schatz, D. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998, 394, 744-751.
47. May, B.P.; Dellaporta, S.L. Transposon sequences drive tissue-specific expression of the maize regulatory gene R-s. Plant J. 1998, 13, 241-248.
48. Girard, L.; Freeling, M. Regulatory changes as a consequence of transposon insertion. Dev. Genet. 1999, 25, 291-296.
49. Gray, Y. It takes two transposon to tango. Trends Genet. 2000, 16, 461-468.
50. Gynheung, A.; Dong-Hoon, J.; Ki-Hong, J.; Sichul, L. Reverse genetic approaches for functional genomics of rice. Plant. Mol. Biol. 2005, 59, 111-123.
51. Katsiotis, A.; Schmidt, T.; Heslop-Harrison, J. Chromosomal and genomic organization of Ty1-copia-like retrotransposon sequences in the genus Avena. Genome 1996, 39, 410-417.
52. Suoniemi, A.; Anamthawat-Jonsson, K.; Arna, T.; Schulman, A. Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome. Plant. Mol. Biol. 1996, 30, 1321-1329.
53. Flavell, A.; Smith, D.; Kumar, A. Extreme heterogenity of Ty1-copia group retrotransposons in plants. Mol. Genet. Genom. 1992, 231, 233-242.
54. Voytas, D.F.; Cummings, M.P.; Konieczny, A.; Ausubel, F.M.; Roderme, S.R. Copia-like retrotransposons are ubiquitous among plants. Proc. Natl. Acad. Sci. USA 1992, 89, 7124-7128.
55. Heid, C.A.; Stevens, J.; Livak, K.J.; Williams, P.M. Real time quantitative PCR. Genome Res. 1996, 6, 986-994.
56. Pagnotta, M.A.; Mondini, L.; Porceddu, E. Real-time PCR and IRAP: tools for assessing genetic variability and quantitation of WIS 2-1A and BARE-1 retrotransposons in hulled wheat. Mol. Gen. Genom. 2009, doi: 10.1007/s00438-009-0462-6 (in press).
57. Akbari, M.; Wenzl, P.; Caig, V.; Carling, J.; Xia, L.; Yang, S.; Uszinski, G.; Mohler, V.; Lehmensiek, A.; Kuchel, H.; Hayden, M.J.; Howes, N.; Sharp, P.; Vaughan, P.; Rathmell, B.; Huttner, E.; Kilian, A. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor. Appl. Genet. 2006, 113, 1409-1420.
58. Bentley, D.R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 2006, 16, 545-552.
59. Holt, R.A.; Jones, S.J.M. The new paradigm of flow cell sequencing. Genome Res. 2008, 18, 839-846.
60. Mardis, E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008, 24, 133-141.
61. Margulies, M.; Egholm, M.; Altman, W.E.; Attiya, S.; Bader, J.S.; Bemben, L.A.; Berka, J.; Braverman, M.S.; Chen, Y.J.; Chen, Z.; Dewell, S.B.; Du, L.; Fierro, J.M.; Gomes, X.V.; Godwin, B.C.; He, W.; Helgesen, S; He Ho, C.; Irzyk, G.P.; Jando, S.C.; Alenquer, M.L.I.; Jarvie, T.P.; Jirage, K.B.; Kim, J.B.; Knight, J.R.; Lanza, J.R.; Leamon, J.H.; Lefkowitz, S.M.; Lei, M.; Li, J.; Lohman, K.L.; Lu, H.; Makhijani, V.B.; McDade, K.E.; McKenna, M.P.; Myers, E.W.; Nickerson, E.; Nobile, J.R.; Plant, R.; Puc, B.P.; Ronan, M.T.; Roth, G.T.; Sarkis, G.J.; Simons, J.F.; Simpson, J.W.; Srinivasan, M.; Tartaro, K.R.; Tomasz, A.; Vogt, K.A.; Volkmer, G.A.; Wang, S.H.; Wang, Y.; Weiner, M.P.; Yu, P.; Begley, R.F.; Rothberg, J.M. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437, 376-380.
62. Shendure, J.; Porreca, G.J.; Reppas, N.B.; Lin, X.; McCutcheon, J.P.; Rosenbaum, A.M.; Wang, M.D.; Zhang, K.; Mitra, R.D.; Church, G.M. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309, 1728-1732.
63. Jump, A.S.; Peñuelas, J. Running to stand still: adaptation and the response of plants to rapid climate change. Ecol. Lett. 2005, 8, 1010-1020.