AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes

Breyne, Peter; Rombaut, Dries; Gysel, Ann Van; Montagu, Marc Van; Geräts, Tom

doi:10.1007/s004380050005

Cited by 89 publications

(66 citation statements)

References 37 publications

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“…No clear correlation between DNA variation and the geographical origin was seen. Analysis of genetic diversity within and between Arabidopsis thaliana ecotypes resulted in similar findings (Innan et al 1997;Breyne et al 1999). We investigated at a microlevel how SNPs were distributed between the strains; we sequenced, now in a directed fashion, the environment of two regions that seemed highly polymorphic based on the number of SNPs found in shotgun clones (H04J21 for CB4857; W08E3 for AB1).…”

Section: Snps Are Sharedmentioning

confidence: 62%

Single Nucleotide Polymorphisms in Wild Isolates of Caenorhabditis elegans

Koch

Luenen²,

Horst³

et al. 2000

Genome Research

138

131

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Caenorhabditis elegans (isolate N2 from Bristol, UK) is the first animal of which the complete genome sequence was available. We sampled genomic DNA of natural isolates of C. elegans from four different locations (Australia, Germany, California, and Wisconsin) and found single nucleotide polymorphisms (SNPs) by comparing with the Bristol strain. SNPs are under-represented in coding regions, and many were found to be third base silent codon mutations. We tested 19 additional natural isolates for the presence and distribution of SNPs originally found in one of the four strains. Most SNPs are present in isolates from around the globe and thus are older than the latest contact between these strains. An exception is formed by an isolate from an island (Hawaii) that contains many unique SNPs, absent in the tested isolates from the rest of the world. It has been noticed previously that conserved genes (as defined by homology to genes in Saccharomyces cerevisiae) cluster in the chromosome centers. We found that the SNP frequency outside these regions is 4.5 times higher, supporting the notion of a higher rate of evolution of genes on the chromosome arms.Caenorhabditis elegans is the first animal of which the genome was sequenced (The C. elegans Sequencing Consortium 1998). Recently, the genome sequence of Drosophila has also become available (Adams et al. 2000). C. elegans is a sexually-reproducing animal, but the egg-laying animals are actually hermaphrodites: They produce some sperm that they can use to selffertilize. Self-fertilization quickly results in inbred lines. Although the generation time of C. elegans is ∼3-4 days, it is likely that in the wild the average time of clonal expansion without male-female mating is much longer. The strain Bristol N2, of which the genome sequence was determined, was isolated from mushroom compost in Bristol, UK, before 1956(Nicholas et al. 1959Fatt and Dougherty 1963) and frozen by John Sulston in 1969 (Brenner 1974). This animal occurs worldwide; isolates have been found on all continents except Antarctica (Hodgkin and Doniach 1997). Based on restriction fragment length polymorphisms (RFLPs) associated with Tc1 transposons, at least 20 races were defined. Previous research has indicated that spontaneous mutation rates in C. elegans are low (Anderson 1995), except for transposon insertions in strains that show germ-line transposition. Most strains have been stored frozen since their isolation from nature (Hodgkin and Doniach 1997). For this reason we consider it likely that the single nucleotide polymorphism (SNP) pattern we observe in the strains is identical to that of the original isolate. In this paper we sampled the genome of different natural isolates of C. elegans for SNPs. We investigated the nature of the polymorphisms and determined how they are distributed over the chromosomes and whether we could see differences between coding and noncoding regions. We also investigated how SNPS are distributed over natural isolates from over the globe, and we used this to infer relati...

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Section: Snps Are Sharedmentioning

confidence: 62%

Single Nucleotide Polymorphisms in Wild Isolates of Caenorhabditis elegans

Koch

Luenen²,

Horst³

et al. 2000

Genome Research

138

131

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“…In previous studies, the hierarchical AMOVA on the genetic variation of the natural population of A. thaliana revealed different patterns for different populations. In most cases, the observed genetic variation was consistent with its lifestyle: less variation existed within populations and more genetic variation was found among populations (Hanfstingl et al, 1994;Bergelson et al, 1998;Breyne et al, 1999;Miyashita et al, 1999;Jorgensen and Mauricio, 2004;Stenoien et al, 2005). For example, Stenoien et al (2005) found that, on average, only 12% of the genetic variation occurred among individuals within 10 northern European populations of A. thaliana, as screened by microsatellite markers.…”

Section: Genetic Variation Among and Within Populationsmentioning

confidence: 84%

“…The use of this species as a model organism has become increasingly important since the elucidation of its genome sequence (The Arabidopsis Genome Initiative, 2000). In addition to a few well-known ecotypes such as Colombia and Landsberg, which have been cultivated in laboratory conditions for plant physiological, developmental, molecular and functional genomic studies, more and more naturally distributed populations (or ecotypes) have been collected and characterized for their genetic variation (King et al, 1993;Innan et al, 1997;Kuittinen et al, 1997;Ullrich et al, 1997;Bergelson et al, 1998;Loridon et al, 1998;Vos, 1998;Breyne et al, 1999;Miyashita et al, 1999;Erschadi et al, 2000;Sharbel et al, 2000;Barth et al, 2002;Hoffmann et al, 2003;Jorgensen and Mauricio, 2004;Nordborg et al, 2005;Stenoien et al, 2005;Schmid et al, 2006). Understanding the amount and distribution of genetic variation between and among populations is not only crucial for ecological and evolutionary studies, but also serves as a base for functional genomic studies.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of the natural populations of Arabidopsis thaliana in China

Kang

Ren

et al. 2007

Heredity

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Although extensive studies have been conducted on the genetic structure of Arabidopsis thaliana (A. thaliana) populations worldwide, the populations from China have never been studied. In this study, we collected 560 individuals from 19 natural populations of A. thaliana distributed in East China along the lower reaches of the Yangtze River, and two populations from northwest China (Xinjiang Province). We adopted two kinds of molecular marker, inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPDs) to investigate the genetic diversity within and among populations, and the correlation between the genetic and geographic distances. Thirteen ISSR primers produced 165 polymorphic bands (PPB) (96%) and 11 RAPD primers produced 162 polymorphic bands (98%) in about 560 individuals. The two marker systems generated similar patterns of genetic diversity in these natural populations. The AMOVA analysis indicated about 42-45% of the total genetic variation existed within populations, and found possible geographic structure. The Mantel test revealed a significant correlation between the geographic distance and the genetic distance of these populations in general. A close genetic relationship was found among four populations in the Jiangxi Province, and these always appeared clustered together as a monophyletic group in unweighted pair-group method with arithmetic averages dendrograms based on both ISSR and RAPD data sets. Based on the observation of recolonization and extinction of naturally distributed populations of A. thaliana, and the pattern of their genetic differentiation, the distribution of this species in China might be a result of natural dispersal under the strong influence of human activity.

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“…Differing results occurred in the cross C24 3 Aa-0 (140% versus 9%). This difference may be due to the use of different parental lines in the crosses, as Arabidopsis accessions are not always genetically homogeneous (Breyne et al, 1999).…”

Section: Discussionmentioning

confidence: 99%

Heterosis of Biomass Production in Arabidopsis. Establishment during Early Development

et al. 2004

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Heterosis has been widely used in agriculture to increase yield and to broaden adaptability of hybrid varieties and is applied to an increasing number of crop species. We performed a systematic survey of the extent and degree of heterosis for dry biomass in 63 Arabidopsis accessions crossed to three reference lines (Col-0, C24, and Nd). We detected a high heritability (69%) for biomass production in Arabidopsis. Among the 169 crosses analyzed, 29 exhibited significant mid-parent-heterosis for shoot biomass. Furthermore, we analyzed two divergent accessions, C24 and Col-0, the F1 hybrids of which were shown to exhibit hybrid vigor, in more detail. In the combination Col-0/C24, heterosis for biomass was enhanced at higher light intensities; we found 51% to 66% mid-parent-heterosis at low and intermediate light intensities (60 and 120 μmol m−2 s−1), and 161% at high light intensity (240 μmol m−2 s−1). While at the low and intermediate light intensities relative growth rates of the hybrids were higher only in the early developmental phase (0–15 d after sowing [DAS]), at high light intensity the hybrids showed increased relative growth rates over the entire vegetative phase (until 25 DAS). An important finding was the early onset of heterosis for biomass; in the cross Col-0/C24, differences between parental and hybrid lines in leaf size and dry shoot mass could be detected as early as 10 DAS. The widespread occurrence of heterosis in the model plant Arabidopsis opens the possibility to investigate the genetic basis of this phenomenon using the tools of genetical genomics.

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AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes

Cited by 89 publications

References 37 publications

Single Nucleotide Polymorphisms in Wild Isolates of Caenorhabditis elegans

Single Nucleotide Polymorphisms in Wild Isolates of Caenorhabditis elegans

Genetic diversity of the natural populations of Arabidopsis thaliana in China

Heterosis of Biomass Production in Arabidopsis. Establishment during Early Development

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