Spatially structured genetic diversity of the Amerindian yam (Dioscorea trifida L.) assessed by SSR and ISSR markers in Southern Brazil

Dioscorea trifida L. (Dioscoreaceae) is among the economically most important cultivated Amerindian yam species, whose origin and domestication are still unresolved issues. in order to estimate the genetic diversity maintained by traditional farmers in Brazil, 53 accessions of D. trifida from 11 municipalities in the states of São Paulo, Santa Catarina, Mato Grosso and Amazonas were characterized on the basis of eight Simple Sequence Repeats (SSR) and 16 Inter Simple Sequence Repeats (ISSR) markers. the level of polymorphism among the accessions was high, 95 % for SSR and 75.8 % for ISSR. the SSR marker showed higher discrimination power among accessions compared to ISSR, with D parameter values of 0.79 and 0.44, respectively. Although SSR and ISSR markers led to dendrograms with different topologies, both separated the accessions into three main groups: I-Ubatuba-SP; II-Iguape-SP and Santa Catarina; and III-Mato Grosso. the accessions from Amazonas State were classified in group II with SSR and in a separate group with ISSR. Bayesian and principal coordinate analyzes conducted with both molecular markers corroborated the classification into three main groups. Higher variation was found within groups in the AMOVA analysis for both markers (66.5 and 60.6 % for ISSR and SSR, respectively), and higher Shannon diversity index was found for group II with SSR. Significant but low correlations were found between genetic and geographic distances (r = 0.08; p = 0.0007 for SSR and r = 0.16; p = 0.0002 for ISSR). Therefore, results from both markers showed a slight spatially structured genetic diversity in D. trifida accessions maintained by small traditional farmers in Brazil.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ São Paulo, Luiz de Queiroz Coll Agr, Dept Genet, BR-13400970 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Biol Sci, BR-09972270 São Paulo, BrazilUniv Calif Davis, Dept Plant Sci MS1, Sect Crop & Ecosyst Sci, Davis, CA 95616 USAUniversidade Federal de São Paulo, Dept Biol Sci, BR-09972270 São Paulo, BrazilFAPESP: 2007/04805-2Web of Scienc

Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers

Times Cited: 17 Cited Reference Count: 61International audienceGenetic diversity and structure of 12 populations of Eryngium alpinum L. were investigated using 63 dominant amplified fragment length polymorphism (AFLP) and seven codominant microsatellite (48 alleles) markers. Within-population diversity estimates obtained with both markers were not correlated, but the microsatellite-based fixation index F-IS was correlated with both AFLP diversity indices ( number of polymorphic bands and Nei's expected heterozygosity). Only AFLP diversity indices increased with the size of populations, although they did not significantly differ among them (Kruskall-Wallis test). The discrepancy between AFLPs and microsatellites may be explained by a better coverage of the genome with numerous AFLPs, the higher mutation rates of microsatellites or the absence of significant difference among within-population diversity estimates. Genetic differentiation was higher with AFLPs (theta = 0.40) than with microsatellites (theta = 0.23), probably due to the higher polymorphism of microsatellites. Thus, we considered global qualitative patterns rather than absolute estimates to compare the performance of both types of markers. On a large geographic scale, the Mantel test and multivariate analysis showed that genetic patterns were more congruent with the spatial arrangement of populations when inferred from microsatellites than from AFLPs, suggesting higher homoplasy of AFLP markers. On a small spatial scale, AFLPs managed to discriminate individuals from neighboring populations whereas microsatellites did not ( multivariate analysis), and the percentage of individuals correctly assigned to their population of origin was higher with AFLPs than with microsatellites. However, dominant AFLPs cannot be used to study heterozygosity-related topics. Thus, distinct molecular markers should be used depending on the biological question and the geographical scale investigated