Nuclear DNA content of some important plant species

523

382

Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99. A lthough 50 years have passed since the structure of DNA was deciphered (1), the study of DNA variation emerged as a field of scientific endeavor only in the last 25 years. Two groups of technologies were developing in parallel from the very beginning: DNA sequencing and molecular markers. DNA sequencing technology developed quickly from proof of concept (2, 3) to an automated process (4), enabling the field of genomics. Molecular marker technologies progressed rapidly as well. Based on the Southern blot technique (5), Botstein et al. (6) developed the restriction fragment length polymorphism (RFLP) technique as a method for creating genetic linkage maps.Development of the PCR technique spawned two important molecular marker techniques: amplified fragment length polymorphism (AFLP) (7) and simple sequence repeats (8). Thousands of studies using molecular markers in plants, including hundreds in barley, have been published but are not referenced because of space limitations.DNA sequencing and molecular marker technologies started to merge when the accumulated sequence data began to yield information on sequence variation among different accessions of the same species. It was soon noted that single-nucleotide polymorphism (SNP) is the most abundant marker type, promising nearly unlimited supply of markers (9). Many alternatives were developed for the SNP assay (primer extension, selective ligation) and the platform to type assays in high throughput (DNA chip, printed and self-assembling arrays, matrix-assisted laser desorption ionization͞ time-of-flight mass spectroscopy) (10)(11)(12)(13)(14).For humans and a limited number of model organisms, the throughput of SNP assays has increased impressively, and assay costs have decreased correspondingly. Yet discovering sequence polymorphism in nonmodel species is difficult, which is particularly true for many crops with limited resources and often complex, polyploid genomes. We have developed Diversity Arrays Technology (DArT) to enable whole-genome profiling of such crops without the need of sequence information. DArT is based on microarray hybridizations that detect the presence versus absence of individual fragments in genomic representations as described by Jaccoud et al. (15).For our initial proof-of-concept study, we selected a species with a simple genome (rice) and used AFLP-like complexity reduction methods to generate genomic representations (15). Here we apply a non-AFLP version ...

mentioning

confidence: 96%

Diversity Arrays Technology (DArT) for whole-genome profiling of barley

Wenzl

Carling

Kudrna

et al. 2004

523

382

“…thaliana harbors all of the TE types found in larger plant genomes; however, copy number is generally low, with all TEs accounting for only Ϸ10% of the A. thaliana genome (2). Although A. thaliana and B. oleracea diverged from a common ancestor Ϸ15-20 million years ago (1), the B. oleracea genome at Ϸ600 Mb is almost 5-fold larger (24). Recent studies indicate that the B. oleracea genome has expanded through triplication since its divergence from Arabidopsis (25)(26)(27).…”

mentioning

confidence: 99%

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea

Zhang

Wessler

2004

143

111

Transposable elements (TEs) are the major component of plant genomes where they contribute significantly to the >1,000-fold genome size variation. To understand the dynamics of TE-mediated genome expansion, we have undertaken a comparative analysis of the TEs in two related organisms: the weed Arabidopsis thaliana (125 megabases) and Brassica oleracea (Ϸ600 megabases), a species with many crop plants. Comparison of the whole genome sequence of A. thaliana with a partial draft of B. oleracea has permitted an estimation of the patterns of TE amplification, diversification, and loss that has occurred in related species since their divergence from a common ancestor. Although we find that nearly all TE lineages are shared, the number of elements in each lineage is almost always greater in B. oleracea. Class 1 (retro) elements are the most abundant TE class in both species with LTR and non-LTR elements comprising the largest fraction of each genome. However, several families of class 2 (DNA) elements have amplified to very high copy number in B. oleracea where they have contributed significantly to genome expansion. Taken together, the results of this analysis indicate that amplification of both class 1 and class 2 TEs is responsible, in part, for B. oleracea genome expansion since divergence from a common ancestor with A. thaliana. In addition, the observation that B. oleracea and A. thaliana share virtually all TE lineages makes it unlikely that wholesale removal of TEs is responsible for the compact genome of A. thaliana.

“…T he 145-Mbp genome of Arabidopsis thaliana is one of the smallest known among higher plants (1). Its low, interspersed, repetitive DNA content (2) makes it an ideal model for genomic studies.…”

mentioning

confidence: 99%

Genome organization in dicots: Genome duplication in Arabidopsis and synteny between soybean and Arabidopsis

Grant

Cregan

Shoemaker

2000

232

166

Synteny between soybean and Arabidopsis was studied by using conceptual translations of DNA sequences from loci that map to soybean linkage groups A2, J, and L. Synteny was found between these linkage groups and all four of the Arabidopsis chromosomes, where GenBank contained enough sequence for synteny to be identified confidently. Soybean linkage group A2 (soyA2) and Arabidopsis chromosome I showed significant synteny over almost their entire lengths, with only 2-3 chromosomal rearrangements required to bring the maps into substantial agreement. Smaller blocks of synteny were identified between soyA2 and Arabidopsis chromosomes IV and V (near the RPP5 and RPP8 genes) and between soyA2 and Arabidopsis chromosomes I and V (near the PhyA and PhyC genes). These subchromosomal syntenic regions were themselves homeologous, suggesting that Arabidopsis has undergone a number of segmental duplications or possibly a complete genome duplication during its evolution. Homologies between the homeologous soybean linkage groups J and L and Arabidopsis chromosomes II and IV also revealed evidence of segmental duplication in Arabidopsis. Further support for this hypothesis was provided by the observation of very close linkage in Arabidopsis of homologs of soybean Vsp27 and Bng181 (three locations) and purple acid phosphatase-like sequences and homologs of soybean A256 (five locations). Simulations show that the synteny and duplications we report are unlikely to have arisen by chance during our analysis of the homology reports.