An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs

Teulat, Béatrice; Aldam, C.; Trehin, R.; Lebrun, Patricia; Barker, J. H. A.; Arnold, G. M.; Karp, A.; Baudouin, Luc; Rognon, François

doi:10.1007/s001220051350

Cited by 133 publications

(113 citation statements)

References 16 publications

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“…In contrast, Roa et al (2000) reported significant Mantel tests between AFLP and microsatellite genetic similarities calculated across seven species of the Manihot genus. Teulat et al (2000) and Pejic et al (1998) also reported congruent patterns of genetic distances between Cocos nucifera populations and maize inbred lines, respectively. As proposed by Powell et al (1996), the strength of the correlation between genetic distances calculated from AFLPs and microsatellites could increase when the among-taxa genetic divergences themselves increase.…”

Section: Introductionmentioning

confidence: 65%

“…This may be associated with the higher polymorphism of these markers. Previous studies have shown that at the lowest hierarchical level, microsatellites always displayed the lowest values of similarity when compared to other markers, reflecting their high information content (Russell et al, 1997, Pejic et al, 1998, Teulat et al, 2000. As a result, they appear less suitable for assigning individuals on this intermediate spatial scale, but microsatellites could be more efficient than AFLPs for investigating within-population structure and are widely preferred over AFLPs for fine-scale genetic studies (eg Streiff et al, 1998;Ueno et al, 2000;Bonnin et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2004

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Genetic 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 withinpopulation diversity estimates. Genetic differentiation was higher with AFLPs (y ¼ 0.40) than with microsatellites (y ¼ 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.

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Section: Introductionmentioning

confidence: 65%

Section: Discussionmentioning

confidence: 99%

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

et al. 2004

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“…More particularly, DNA profiling studies have already provided some insights. For example, Teulat et al (2000) found that the populations from Tonga and Fiji generally had distinct alleles from those of the rest of the South Pacific. They considered that the high levels of polymorphism revealed by the SSRs indicate that populations could be identified and information on allelic diversity obtained with relatively few loci.…”

Section: Molecular Techniquesmentioning

confidence: 99%

“…RFLP (Restriction fragment length polymorphism) Lebrun et al 1998Lebrun et al , 1999Rohde et al1992 SSR (Simple sequence repeat or microsatellite DNA) Duran et al 1997;Karp 1999;Perera et al 1999Perera et al , 2000Rivera et al 1999;Teulat et al 2000 Mainly dominant markers detected RAPD (Random amplified polymorphic DNA) Anzizar et al 1998;Ashburner & Harries 1999;Ashburner & Rohde 1994;Ashburner et al 1997;Banks 1994;Cardeña et al 1999;Duran et al 1997;Rohde et al 1999;Upadhyay et al 2002;Wadt et al 1999 AFLP (Amplified fragment length polymorphism) Perera et al 1998;Rohde et al 1999;Teulat et al 2000 ISTR (Internal sequence tagged repeat) Anzizar et al 1998;Duran et al 1997;Rohde et al 1995Rohde et al , 1999 STS (Sequence tagged site amplification) Rohde et al 1999 and the Ancestry of Coconut Palm Populations on Pacific Islands.…”

Section: Codominant Markers Detectedmentioning

confidence: 99%

“…Archaeological evidence in support of the domestication theory was subsequently located in Borneo (Harries 1981c) and Society Islands (Lepofsky et al 1992) but efforts to identify shell fragments in Papua New Guinea (Hossfeld 1948, Kirch, personal communication 1987 and Solomon Islands (Spriggs 1984) Despite the small number of publications on coconut molecular genetics it appears to be difficult for research workers to keep up to date. For example Teulat et al (2000) writing as recently as October 1998 say ". .…”

Section: Codominant Markers Detectedmentioning

confidence: 99%

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Floating, Boating and Introgression: Molecular techniques and the ancestry of coconut palm populations on Pacific Islands

Harries¹,

Baudouin²,

Cardeña³

2004

Ethnobot. Res. App.

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SSR‐based DNA fingerprinting of fruit crops

et al. 2023

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The DNA fingerprinting of fruit crops, based on DNA microsatellite markers that are considered to be the key markers for the molecular analysis of germplasm collections, is reviewed. Simple sequence repeats (SSRs) remain the markers of choice for fingerprinting in humans, animals, plants, and other living organisms. This review, that considers 44 fruit species, provides a set of markers that are suitable for profiling accessions and that should make the databases produced in different laboratories more comparable. Every effort has been made to select SSR markers that are robust and easily scorable considering that such analyses are sometimes used in legal cases. The review first describes the basic protocols, procedures, and methods of data analyses; it then describes the fingerprinting of individual species or groups of species, providing a set of SSR markers and appropriate guidance based on the revised literature and on the authors' experience.

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An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs

Cited by 133 publications

References 16 publications

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

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

Floating, Boating and Introgression: Molecular techniques and the ancestry of coconut palm populations on Pacific Islands

SSR‐based DNA fingerprinting of fruit crops

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