Genetic variation at marker loci and in quantitative traits in natural populations of Arabidopsis thaliana

Kuittinen, Helmi; Mattila, Anu; Savolainen, Outi

doi:10.1038/sj.hdy.6881910

Cited by 60 publications

(98 citation statements)

References 3 publications

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“…It is expected that due to founder effects the populations towards the periphery of the species distribution are more likely to be fixed for a certain haplotype than more central populations. This has been suggested for Arabidopsis populations from Great Britain, Japan and Scandinavia (Abbott and Gomes 1989;Todokoro et al 1995;Kuittinen et al 1997), and is true in our case for PON populations. Also, the monomorphic populations were found both in the peripheral regions (PON) and within the centre of the species range (SAN).…”

Section: Historical Processessupporting

confidence: 63%

Understanding the genetic structure of Symplocos laurina Wall. Populations using nuclear gene markers

et al. 2009

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To characterize the genetic diversity of present populations of Symplocos laurina, which grow in the montane forests in India, we analyzed the DNA sequences of a nuclear gene. Using the 881 bp sequence of cytosolic Glyceraldehyde-3-phosphate dehydrogenase gene, we detected 24 haplotypes among 195 individuals sampled from 14 populations. Two dominant haplotypes were distributed over the entire range of this species in India and several private haplotypes were found. Low genetic diversity within population, high differentiation, number of population specific haplotypes and deviation from neutral evolution characterized the present populations of S. laurina. An analysis of molecular variance indicated the presence of geographic structure within the haplotype distribution. The occurrence of S. laurina preglaciation in India is the most parsimonious explanation for the current geographic structure observed. The populations are presumably ancient and might have spread across its extant distribution range in India through a recent range expansion event.

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Section: Historical Processessupporting

confidence: 63%

Understanding the genetic structure of Symplocos laurina Wall. Populations using nuclear gene markers

et al. 2009

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“…The fact that the dierent subgroups remain tightly clustered independently of the data set used and the kind of analysis performed is a further indication that the diversity revealed is natural and is not due to contamination of seed stocks. The source of this variation remains unknown, but the existence of genetic diversity among individuals sampled from native populations has been demonstrated before (Kuittinen et al 1997), indicating that it is a natural phenomenon that should be investigated in more detail.…”

Section: Genetic Relationships Among Ecotypesmentioning

confidence: 99%

“…Comparable results were obtained in an analysis based on microsatellite loci (Innan et al 1997). Investigation of the degree of intra-ecotypic diversity using RFLPs (Bergelson et al 1998) or isozymes and microsatellites (Kuittinen et al 1997) has shown that only very little genetic variation exists within natural populations. In these studies, only a limited number of markers was used and the data sets obtained were rather small.…”

Section: Introductionmentioning

confidence: 99%

AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes

Breyne

Rombaut²,

Gysel³

et al. 1999

Mol Gen Genet

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The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent natural populations, this intraecotypic diversity reflects natural genetic variation and diversification within the ecotypes. The source of this diversity remains unclear but is intriguing in view of the predominantly self-fertilizing nature of Arabidopsis. Interrelationships between the different ecotypes were estimated after AFLP fingerprinting using two enzyme combinations (EcoRI/MseI and SacI/MseI) and a number of selective primer pairs. SacI recognition sites are less evenly distributed in the genome than EcoRI sites, and occur more frequently in coding sequences. In most cases, AFLP data from only one enzyme combination are used for genetic diversity analysis. Our results show that the use of two enzyme combinations can result in significantly different classifications of the ecotypes both in cluster and ordination analysis. This difference most probably reflects differences in the genomic distribution of the AFLP fragments generated, depending on the enzymes and selective primers used. For closely related varieties, as in the case of Arabidopsis ecotypes, this can preclude reliable classification.

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“…In predominant self-pollinating species, recombination rates are decreased and the persistence of linkage disequilibrium is increased (Jain 1976;Flint-Garcia et al 2003). Thus, compared with predominant outcrossing species, self-pollinators are expected to exhibit stronger associations between neutral genetic and morphologic variation (Price et al 1984;Hamrick and Godt 1989;Prentice 1992;Kuittinen et al 1997). The non-association of these data sets may be attributed to the independent segregation of neutral molecular markers and the genes underlying the measured traits, perhaps because of some sexual reproduction in populations, phenotypic plasticity, or differential selection (Coates and Byrne 2005).…”

Section: Morphological Variationmentioning

confidence: 96%

“…In addition to molecular markers, morphometric characters were also used to investigate patterns of variation in C. tetrandrum. The use of these characters, in combination with molecular markers, allows a more comprehensive assessment of intraspecific genetic diversity (Prentice 1992), establishes a broader test of mating system predictions (Price et al 1984), and, in some cases, provides increased sensitivity to population differentiation (Kuittinen et al 1997). The genetic and quantitative data produced by these analyses were used to address the following questions: (i) What do contemporary levels of diversity indicate about recurrent patterns of gene flow within western North American C. tetrandrum?…”

Section: Introductionmentioning

confidence: 99%

Inter-simple sequence repeat (ISSR) and morphological variation in the western North American range ofChrysosplenium tetrandrum(Saxifragaceae)

Levsen

Mort

2009

Botany

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The herbaceous perennial Chrysosplenium tetrandrum (Lund ex Malmgr.) Th. Fr. (Saxifragaceae) is a selfpollinating, circumpolar species with a broad latitudinal distribution and a disjunct North American range. The southernmost populations are isolated in the Rocky Mountains of Colorado and Montana, distantly separated from elements of the main range, which is largely coincident with known glacial refugia (e.g., Beringia) and recently deglaciated regions. We employed analyses of inter-simple sequence repeats (ISSRs) and morphology to determine patterns of variation within the western North American range of C. tetrandrum and test hypotheses of glacial population history and reproductive strategy. Analyses revealed very low estimates of range-wide genetic differentiation (q II = 0.085) and diversity (HS = 0.077, HT = 0.084), which are similar to levels found in other arctic plant species and have been primarily attributed to recent population establishment. Low levels of genetic differentiation among populations of Alaska (q II = 0.072), British Columbia (q II = 0.088), and Washington (q II = 0.058) suggest recent bottleneck or range expansion events. Both the Colorado and Alaska regions showed strong differentiation from each of the other regions, suggesting long-term isolation. The non-association between morphological and genetic variation indicates the effects of phenotypic plasticity or sexual reproduction.Résumé : La plante herbacées pérenne Chrysosplenium tetrandrum (Lund ex Malmgr.) Th. Fr. (Saxifragaceae) constitue une espèce circumpolaire autofécondée ayant une large distribution latitudinale avec aires disjointes en Amérique du Nord. Les populations les plus méridionales sont isolées dans les Montagnes Rocheuses du Colorado et du Montana, séparées et éloignées des éléments de l'aire principale, lesquelles coïncident largement avec des refuges glaciaires (e.g. Beringia) et des régions récemment déglaciées. Les auteurs ont utilisé des analyses de répétitions de séquence inter-simples (ISSRs) et de la morphologie, pour déterminer les patrons de variations au sein de l'aire occidentale en Amérique du Nord du C. tetrandrum, et vérifier l'hypothèse sur l'historique des populations glaciaires et la stratégie de reproduction. Les analyses révèlent des valeurs estimées très faibles pour la variation génétique (q II = 0,085) et de la diversité (HS = 0,077; HT = 0,084) sur l'ensemble de l'aire, lesquelles sont similaires aux degrés retrouvés chez d'autres espèces de plantes arctiques et attribuées à l'établissement récent des populations. Les faibles degrés de différenciation génétique entre les populations de l'Alaska (q II = 0,072), de la Colombie Canadienne (q II = 0,088) et de Washington (q II = 0,058) suggèrent l'existence d'un goulot d'étranglement dans les événements d'expansion d'aire. Les deux régions du Colorado et de l'Alaska montrent une forte différenciation par rapport à chacune des autres régions, suggérant un isolement à long terme. L'inexistence d'association entre la variation génétique et morphol...

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Genetic variation at marker loci and in quantitative traits in natural populations of Arabidopsis thaliana

Cited by 60 publications

References 3 publications

Understanding the genetic structure of Symplocos laurina Wall. Populations using nuclear gene markers

Understanding the genetic structure of Symplocos laurina Wall. Populations using nuclear gene markers

AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes

Inter-simple sequence repeat (ISSR) and morphological variation in the western North American range ofChrysosplenium tetrandrum(Saxifragaceae)

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