Exploiting a wheat EST database to assess genetic diversity

Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01

IDENTIFICATION OF GENETIC POLYMORPHISM AND DNA METHYLATION PATTERN IN WHEAT (Triticum aestivum L.)

ABSTRACT SSR, RAPD, ISSR and SRAP markers have been used to examine the genetic and epigenetic diversity of wheat (Triticum aestivum L.) germplasm. PCR amplification of the DNA isolated from six wheat genotypes yielded a total of 2118 amplified products, of which 1105 were polymorphic and 1013 were monomorphic. The average PIC value for all molecular marker data was 0.8704 and average percentage of polymorphism was 40.86%. All primers used for RAPD analysis, were also tested by CRED-RA analysis, a method to detect DNA methylation. There were differences between genetic and methylation polymorphism in the studied cultivars. Dendrogram created based on genetic polymorphism showed that PI178383 and Sonmez2001 (0.30) were genetically very different from each other, but in the dendrogram constructed by methylation polymorphism Sonmez2001 and ES14 (0.44) were grouped in one subcluster. Similar to this, in the dendrogram created based on epimarker data Izgi2001 and Harmankaya99 (0.59) were grouped in one subcluster as well as Sonmez2001 and ES14 (0.57) as in the second subcluster. The present study has provided the genetic data that diagnose the level of polymorphisms and epigenetic data which present natural variations of DNA methylation

Data mining of ests for genetic improvement of salt tolerance in wheat

A total of 4,131 expressed sequence tags (ESTs) were selected from wheat EST database (http://wheat.pw.usda.gov/cgi-bin/westsql/est_lib.cgi.) to identify genic regions differing at structural and functional level between durum wheat (tetraploid genome, AABB) and bread wheat (hexaploid genome, AABBDD) cultivars in response to salt stress. Selected ESTs from salt stressed Triticum aestivum cDNA libraries (922 seedling, 2055 root, 1154 sheat ESTs) were used for construction of contig tags. Using contigs assembled (136 seedling, 268 root, 152 sheat) sense and antisense primers were designed to investigate the sequence and expressional differences in bread and durum wheat cultivars. The genetic information obtained from data mining of ESTs can make huge contribution to the characterization of genes in response to salinity stress, and is strongly expected to aid our understanding of the molecular mechanism of salinity stress tolerance of durum and bread wheat in particular