Array-based high-throughput DNA markers for crop improvement

Abstract

The last two decades have witnessed a remarkable activity in the development and use of molecular markers both in animal and plant systems. This activity started with lowthroughput restriction fragment length polymorphisms and culminated in recent years with single nucleotide polymorphisms (SNPs), which are abundant and uniformly distributed. Although the latter became the markers of choice for many, their discovery needed previous sequence information. However, with the availability of microarrays, SNP platforms have been developed, which allow genotyping of thousands of markers in parallel. Besides SNPs, some other novel marker systems, including single feature polymorphisms, diversity array technology and restriction site-associated DNA markers, have also been developed, where arraybased assays have been utilized to provide for the desired ultra-high throughput and low cost. These microarray-based markers are the markers of choice for the future and are already being used for construction of high-density maps, quantitative trait loci (QTL) mapping (including expression QTLs) and genetic diversity analysis with a limited expense in terms of time and money. In this study, we briefly describe the characteristics of these array-based marker systems and review the work that has already been done involving development and use of these markers, not only in simple eukaryotes like yeast, but also in a variety of seed plants with simple or complex genomes.

GENETIC DIVERSITY AND POPULATION STRUCTURE AMONG Grewia tenax GENOTYPES IN SUDAN USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS

“…it was found that ISSR-based cluster is more similar to the combined cluster than RAPD-based cluster [39]. Jatropha curcas also showed similar result when RAPD and ISSR dendrogram patterns were combined [40]. The result of this study showed Some private bands were detected within genotypes (Table 4).…”

Molecular Markers for Sweet Sorghum Based on Microarray Expression Data

“…The association of a particular trait of interest with a DNA polymorphism is essential for breeding purposes. Microarrays have been used to identify abundant DNA polymorphisms throughout the genome (Gupta et al 2008;Hazen and Kay 2003). In particular, ELPs and SFPs can be identified from RNA hybridization studies.…”

“…Single-nucleotide polymorphisms (SNPs) have become the marker of choice because of their abundance and uniform distribution throughout the genome (Gupta et al 2008;Varshney et al 2005;Zhu and Salmeron 2007). Around 90% of the genetic variation in any organism is attributed to SNPs (Varshney et al 2005;Zhu and Salmeron 2007).…”

“…Recent studies have described the use of transcript abundance data from RNA hybridizations to Affymetrix microarrays to discover genetic polymorphisms that can be utilized as markers for genotyping in mapping populations (Borevitz and Chory 2004;Gupta et al 2008;Hazen and Kay 2003;Shiu and Borevitz 2008;Zhu and Salmeron 2007). In an Affymetrix chip, each gene is represented by 11 different 25-bp oligonucleotides that cover features of the transcribed region of that gene (exons and 3′ untranslated regions).…”

Biodiversity Measures in Agriculture Using DNA

“…Differently from the previous cited markers, the definition of single nucleotide polymorphism is not dependent on the methodology used for their detection, which can be various. The most efficient are oligonucleotide arrays (Gupta et al, 2008). Similarly, small insertion or deletion (INDEL) have been localized and their frequencies measured (Zhidkov et al, 2011).…”