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

Abstract

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 ...

Relationship between water use efficiency (WUE) and production of different wheat genotypes at soil water deficit

“…Obviously, the difference in this aspect exhibited the difference in their alleles of different wheat genotypes [16,19,52,70]. The emerging methodologies including, genomic approaches, system-oriented ways, largescale microarray technology, genome-metabolite profiling analysis and transcriptom profiling precise annotation, in combination with genetic mutant selection, transgenic strategy and plant physiology, will uncover this network regulatory system of wheat genotypes being adaptive to different soil water stresses [64].…”

Multi-environment QTL mixed models for drought stress adaptation in wheat

“…The molecular markers were a combination of 74 SSRs, 249 AFLPs and 264 DArT markers (Wenzl et al 2004). Two lines were removed from the analysis; one contained incorrect markers and was most likely a rogue (data not shown) while the second line contained a high number of missing DArT values (40%) (data not shown).…”

Changes of some anti-oxidative physiological indices under soil water deficits among 10 wheat (Triticum aestivum L.) genotypes at tillering stage

“…These results also imply that systemical, deeper, and comprehensive understanding of physiological mechanism of crops under drought stresses is not enough to manipulate the physiological regulatory mechanism and take advantage of full this potential for productivity, Whose study is the bridge between molecular machinery of drought and anti-drought agriculture, because the performance of genetic potential of crops is expressed by physiological realization in fields [36,53,56,62,65]. Towards this aim, many promising methodologies emerge, but they should also be linked with field practice [6,9,11,14,25,42,54,57].…”