Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat

Abstract

Expressed sequence tags (ESTs) are a valuable source of molecular markers. To enhance the resolution of an existing linkage map and to identify putative functional polymorphic gene loci in hexaploid wheat (Triticum aestivum L.), over 260,000 ESTs from 5 different grass species were analyzed and 5418 SSR-containing sequences were identified. Using sequence similarity analysis, 156 cross-species superclusters and 138 singletons were used to develop primer pairs, which were then tested on the genomic DNA of barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and wheat. Three-hundred sixty-eight primer pairs produced PCR amplicons from at least one species and 227 primer pairs amplified DNA from two or more species. EST-SSR sequences containing dinucleotide motifs were significantly more polymorphic (74%) than those containing trinucleotides (56%), and polymorphism was similar for markers in both coding and 5' untranslated (UTR) regions. Out of 112 EST-SSR markers, 90 identified 149 loci that were integrated into a reference wheat genetic map. These loci were distributed on 19 of the 21 wheat chromosomes and were clustered in the distal chromosomal regions. Multiple-loci were detected by 39% of the primer pairs. Of the 90 mapped ESTs, putative functions for 22 were identified using BLASTX queries. In addition, 80 EST-SSR markers (104 loci) were located to chromosomes using nullisomic-tetrasomic lines. The enhanced map from this study provides a basis for comparative mapping using orthologous and PCR-based markers and for identification of expressed genes possibly affecting important traits in wheat.

Identification of novel and useful EST-SSR markers from de novo transcriptome sequence of wheat (Triticum aestivum L.)

“…Nulli-tetrasomic lines are widely employed to assign molecular markers and genes due to the precision associated with the line. Yu et al (2004) located 80 EST-SSRs and 104 loci on wheat chromosomes using nulli-tetrasomic lines, and Chen et al (2005) located 93 EST-SSRs (193 loci) on wheat chromosomes. Li et al (2008) located 139 EST-SSRs (240 loci) on the 21 wheat chromosomes.…”

“…Although a number of EST-SSRs have been developed from the published EST database (Yu et al, 2004;Chen et al, 2005;Li et al, 2008), the development and application of EST-SSR markers from transcriptome sequence in wheat are still largely limited compared, with those of EST-SSR markers from other crop species.…”

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers

“…The number of SSR tandem repeats can vary in a sequence, and many such variants (alleles) can exist in a population (Powell et al, 1996). SSR markers tend to be among the most polymorphic genetic marker types and have been introduced into the process of cultivar and variety identification as well as in pedigree reconstruction and genetic mapping (Holton et al, 2002;Yu et al, 2004a;Celucia et al, 2009), to analyze functional diversity (Senior et al, 1998;Leigh et al, 2003;Dreisigacker et al, 2004), and for comparative mapping (Yu et al, 2004b;Varshney et al, 2005a). Although the identification of SSRs in gene sequences of plants started as early as 1993 (Varshney et al, 2005b), full exploitation of this marker during this period was limited by the amount of sequence data available for SSR analysis, and therefore, only a few genomic SSRs were reported.…”

Development of EST-SSR Markers to Assess Genetic Diversity in Elettaria Cardamomum Maton

“…Due to the vast amount of ESTs deposited in public databases, a large number of EST-SSRs have been developed, and the polymorphism and transferability of EST-SSRs were checked in many plant species (Aggarwal et al, 2007;Luro et al,2008;Poncet et al, 2006) including cereals (Kantety et al,2002), wheat (Yu et al, 2004), citrus (Chen et al,2006), coffee (Aggarwal et al, 2007), rubber (Feng et al, 2009), chickpea (Choudhary et al, 2009), peanut (Liang et al,2009) and grape (Huang et al, 2011).…”