Structural and functional analyses of the wheat genomes based on expressed sequence tags (ESTs) related to abiotic stresses

Abstract

To gain insights into the structure and function of the wheat (Triticum aestivum L.) genomes, we identified 278 ESTs related to abiotic stress (cold, heat, drought, salinity, and aluminum) from 7671 ESTs previously mapped to wheat chromosomes. Of the 278 abiotic stress related ESTs, 259 (811 loci) were assigned to chromosome deletion bins and analyzed for their distribution pattern among the 7 homoeologous chromosome groups. Distribution of abiotic stress related EST loci were not uniform throughout the different regions of the chromosomes of the 3 wheat genomes. Both the short and long arms of group 4 chromosomes showed a higher number of loci in their distal regions compared with proximal regions. Of the 811 loci, the number of mapped loci on the A, B, and D genomes were 258, 281, and 272, respectively. The highest number of abiotic stress related loci were found in homoeologous chromosome group 2 (142 loci) and the lowest number were found in group 6 (94 loci). When considering the genome-specific ESTs, the B genome showed the highest number of unique ESTs (7 loci), while none were found in the D genome. Similarly, considering homoeologous group-specific ESTs, group 2 showed the highest number with 16 unique ESTs (58 loci), followed by group 4 with 9 unique ESTs (33 loci). Many of the classified proteins fell into the biological process categories associated with metabolism, cell growth, and cell maintenance. Most of the mapped ESTs fell into the category of enzyme activity (28%), followed by binding activity (27%). Enzymes related to abiotic stress such as beta-galactosidase, peroxidase, glutathione reductase, and trehalose-6-phosphate synthase were identified. The comparison of stress-responsive ESTs with genomic sequences of rice (Oryza sativa L.) chromosomes revealed the complexities of colinearity. This bin map provides insight into the structural and functional details of wheat genomic regions in relation to abiotic stress.

Meta‐Analysis of Wheat QTL Regions Associated with Adaptation to Drought and Heat Stress

“…While QTL number varied between the three hexaploid wheat genomes, it was not significantly different from what would be predicted on the basis of physical size (Gill et al, 1991), suggesting that the contribution of the three genomes to stress tolerance may be similar. This finding is in contrast to Ramalingam et al (2006), who reported a higher gene density of stress‐related expressed sequence tags (ESTs) mapping to the D genome and to reports of Aegilops tauschii , the D genome progenitor of common wheat, being a rich source of stress‐tolerance alleles in synthetic hexaploids (Trethowan and Mujeeb‐Kazi, 2008). The largest number of individual QTL were located on the Group 2 chromosomes (163 QTL), consistent with the physical bin‐mapping of 142 abiotic stress‐related EST loci to the Group 2 chromosomes, the most of any chromosome group (Ramalingam et al, 2006).…”

Regulation of ATG6/Beclin-1 homologs by abiotic stresses and hormones in rice (Oryza sativa L.)

“…Another cis element, MYCCONSENSUSAT, found in the promoter regions, was involved in the dehydration stress response, which further supports our findings that indicated that all the 3 genes were upregulated under drought stress. ARR1AT is a binding element for the cytokinin response regulator ARR1, which is found in Arabidopsis (Ramalingam et al, 2006;Wu et al, 2007); it acts an upregulator of ATG6 genes and was observed in rice leaves treated with cytokinin, thereby indicating the involvement of ATG6 genes in the cytokinin signaling network (GEO dataset GSE6719; data not shown).…”

Identification and characterization of high temperature stress responsive genes in bread wheat (Triticum aestivum L.) and their regulation at various stages of development

“…The complete sequencing of the wheat genome is challenging because of its large genome size (16,000 Mb; Bennett and Leitch 2005). Nevertheless, mapping and characterizing ESTs offers a manageable approach to the complex architecture and functioning of the wheat transcriptome and helps in unravelling the genetics of stress response (Ramalingam et al 2006;Barnabas et al 2008). Through SSH libraries we have generated a collection of heat stress responsive genes critical for various growth stages in wheat.…”