Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP

Genetics and Molecular Biology

Volumn 34, Issue 2, 2011, Pages 252-258

  Khanlou, Khosro Mehdi ^a,b   Vandepitte, Katrien ^c   Asl, Leila Kheibarshekan ^b   van Bockstaele, Erik ^a,b  

^a INSTITUTE FOR AGRICULTURAL AND FISHERIES RESEARCH ILVO   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

^c UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

AFLP; Genetic diversity parameters; Sampling strategy; White clover

Indexed keywords

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANALYSIS OF VARIANCE; ARTICLE; CULTIVAR; GENETIC PARAMETERS; GENETIC SCREENING; GENETIC VARIABILITY; HETEROZYGOSITY; NONHUMAN; PLANT GENETICS; SAMPLE SIZE; SAMPLING; SIMULATION; WHITE CLOVER;

TRIFOLIUM REPENS;

EID: 79957886945     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572011000200015     Document Type: Article

References (44)

1. Annicchiarico P and Piano E (1995) Variation within and among Ladino white clover ecotypes for agronomic traits. Euphytica 86:135-142.
2. Bashalkhanov S, Pandey M and Rajora OP (2009) A simple method for estimating genetic diversity in large populations from finite sample sizes. BMC Genetics 10:e84.
3. Belkhir K, Dawson KJ and Bonhomme F (2006) A comparison of rarefaction and Bayesian methods for predicting the allelic richness of future samples on the basis of currently available samples. J Hered 97:483-492.
4. Berg EE and Hamrick JL (1995) Fine-scale genetic structure of a Turkey oak forest. Evolution 49:110-120.
5. Bonin A, Ehrich D and Manel S (2007) Statistical analysis of amplified fragment length polymorphism data: A toolbox for molecular ecologists and evolutionists. Mol Ecol 16:3737-3758.
6. Bortolini F, Dall'Agnol M and Schifino-Wittmann MT (2006) Molecular characterization of the USDA white clover (Trifolium repens L.) core collection by RAPD markers. Genet Resour Crop Evol 53:1081-1087.
7. Brink GE, Pederson GA, Alison MW, Ball DM, Bouton JH, Rawls RC, Stuedemann JA and Venuto BC (1999) Growth of white clover ecotypes, cultivars, and germplasms in the southeastern USA. Crop Sci 39:1809-1814.
8. Bussell JD (1999) The distribution of random amplified polymorphic DNA (RAPD) diversity amongst populations of Isotoma petraea (Lobeliaceae). Mol Ecol 8:775-789.
9. Cahn MG and Harper JL (1976) The biology of leaf mark polymorphism in Trifolium repens L.1. Distribution of pheno-types at a local scale. Heredity 37:309-325.
10. Chapman DF (1983) Growth and Demography of Trifolium repens Stolons in Grazed Hill Pastures. J Appl Ecol 20:597-608.
11. Doyle JJ and Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13-15.
12. Ewens WJ (1972) Sampling theory of selectively neutral alleles. Theor Pop Biol 3:87-112.
13. Gustine DL and Elwinger GF (2003) Spatiotemporal genetic structure within white clover populations in grazed swards. Crop Sci 43:337-344.
14. Gustine DL and Sanderson MA (2001) Molecular analysis of white clover population structure in grazed swards during two growing seasons. Crop Sci 41:1143-1149.
15. Hamrick JL and Godt MJW (1996) Effects of life history traits on genetic diversity in plant species. Phil Trans R Soc Lond Ser B Biol Sci 351:1291-1298.
16. Harberd DJ (1963) Observations on natural clones of Trifolium repens L. New Phytol 62:198-204.
17. Herrmann D, Boller B, Widmer F and Kölliker R (2005) Optimization of bulked AFLP analysis and its application for exploring diversity of natural and cultivated populations of red clover. Genome 48:474-486.
18. Isabel N, Beaulieu J and Bousquet J (1995) Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified polymorphic DNA loci in black spruce. Proc Natl Acad Sci USA 92:6369-6373.
19. Kölliker R, Jones ES, Jahufer MZZ and Forster JW (2001) Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.). Euphytica 121:305-315.
20. Kongkiatngam P, Waterway MJ, Fortin MG and Coulman BE (1995) Genetic variation within and between two cultivars of red clover (Trifolium pratense L.) - Comparisons of morphological, isozyme, and RAPD markers. Euphytica 84:237-246.
21. Leberg PL (2002) Estimating allelic richness: Effects of sample size and bottlenecks. Mol Ecol 11:2445-2449.
22. Marghali S, Panaud O, Lamy F, Ghariani S, Sarr A, Marrakchi M and 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.
23. Meirmans PG and Van Tienderen PH (2004) GENOTYPE and GENODIVE: Two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792-794.
24. Mohapatra KP, Sehgal RN, Sharma RK and Mohapatra T (2009) Genetic analysis and conservation of endangered medicinal tree species Taxus wallichiana in the Himalayan region. New Forests 37:109-121.
25. Nybom H and Bartish IV (2000) Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspect Plant Ecol Evol Syst 3:93-114.
26. Peakall R, Gilmore S, Keys W, Morgante M and Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: Implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275-1287.
27. Peakall R and Smouse PE (2006) GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288-295.
28. Petit RJ, El Mousadik A and Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844-855.
29. Rizza MD, Real D, Reyno R, Porro V, Burgueño J, Errico E and Quesenberry KH (2007) Genetic diversity and DNA content of three South American and three Eurasiatic Trifolium species. Genet Mol Biol 30:1118-1124.
30. Sardaro MLS, Atallah M, Tavakol E, Russi L and Porceddu E (2008) Diversity for AFLP and SSR in natural populations of Lotus corniculatus L. from Italy. Crop Sci 48:1080-1089.
31. Sedcole JR (1977) Number of plants necessary to recover a trait. Crop Sci 17:667-668.
32. Segovia-Lerma A, Cantrell RG, Conway JM and Ray IM (2003) AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates. Genome 46:51-58.
33. Singh M, Chabane K, Valkoun J and Blake T (2006) Optimum sample size for estimating gene diversity in wild wheat using AFLP markers. Genet Resour Crop Evol 53:23-33.
34. Suzuki JI, Herben T and Maki M (2004) An under-appreciated difficulty: Sampling of plant populations for analysis using molecular markers. Evol Ecol 18:625-646.
35. Van Treuren R, Bas N, Goossens PJ, Jansen J and Van Soest LJM (2005) Genetic diversity in perennial ryegrass and white clover among old Dutch grasslands as compared to cultivars and nature reserves. Mol Ecol 14:39-52.
36. Vandepitte K, Roldan-Ruiz I, Leus L, Jacquemyn H and Honnay O (2009) Canopy closure shapes clonal diversity and fine-scale genetic structure in the dioecious understorey perennial Mercurialis perennis. J Ecol 97:404-414.
37. Vos P, Hogers R, Bleeker M, Reijans M, van de lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al. (1995) AFLP: A new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414.
38. Ward SM and Jasieniuk M (2009) Sampling weedy and invasive plant populations for genetic diversity analysis. Weed Sci 57:593-602.
39. Welham CVJ, Turkington R and Sayre C (2002) Morphological plasticity of white clover (Trifolium repens L.) in response to spatial and temporal resource heterogeneity. Oecologia 130:231-238.
40. Williams WM (1987) Genetics and breeding. In: Baker MJ and Williams WM (eds) White Clover. CAB International, Wallingford, pp 343-419.
41. Wu J, Krutovskii KV and Strauss SH (1999) Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers. Genome 42:893-908.
42. Xu WW, Sleper DA and Krause GF (1994) Genetic diversity of tall fescue germplasm based on RFLPs. Crop Sci 34:246-252.
43. Zhao R, Cheng Z, Lu WF and Lu BR (2006) Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers. Chin Sci Bull 51:1219-1227.
44. Zhu W, Zhou T, Zhong M and Lu B (2007) Sampling strategy for wild soybean (Glycine soja) populations based on their genetic diversity and fine-scale spatial genetic structure. Frontiers Biol China 2:397-402.