Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets

Abstract

Abstract.Freezing tolerance in plants is obtained during a period of low nonfreezing temperatures before the winter sets on, through a biological process known as cold acclimation. Cold is one of the major stress factors that limits the growth, productivity and distribution of plants, and understanding the mechanism of cold tolerance is therefore important for crop improvement. Expressed sequence tags (EST) analysis is a powerful, economical and timeefficient way of assembling information on the transcriptome. To date, several EST sets have been generated from cold-induced cDNA libraries from several different plant species. In this study we utilize the variation in the frequency of ESTs sampled from different cold-stressed plant libraries, in order to identify genes preferentially expressed in cold in comparison to a number of control sets. The species included in the comparative study are oat (Avena sativa), barley (Hordeum vulgare), wheat (Triticum aestivum), rice (Oryza sativa) and Arabidopsis thaliana. However, in order to get comparable gene expression estimates across multiple species and data sets, we choose to compare the expression of tentative ortholog groups (TOGs) instead of single genes, as in the normal procedure. We consider TOGs as preferentially expressed if they are detected as differentially expressed by a test statistic and up-regulated in comparison to all control sets, and/or uniquely expressed during cold stress, i.e., not present in any of the control sets. The result of this analysis revealed a diverse representation of genes in the different species. In addition, the derived TOGs mainly represent genes that are long-term highly or moderately expressed in response to cold and/or other stresses.

The alcohol dehydrogenase gene family in sugarcane and its involvement in cold stress regulation

“…ScADH3 is also up-regulated under abiotic stresses (PEG, NaCl, and 4 °C). These results are consistent with studies on other species showing that the expression of AtADH1 is up-regulated by salt, dehydration [ 18 , 36 , 59 ], and cold stress [ 8 , 9 , 60 ]. Based on these results, we believe that ScADH3 may be involved in the abiotic and biotic stress responses of sugarcane, especially under cold stress, since the expression of this gene was continually upregulated by 4 °C stress.…”

“…ADHs are involved in seed development [ 3 , 4 ], fruit development [ 5 ], and aerobic metabolism in pollen grain [ 6 ]. They also help to protect plants from flooding [ 7 ], drought [ 8 ], cold [ 9 ], and salt [ 10 ] stresses.…”

“…Tesniere and Verries et al [ 13 ] found that Vv-ADH1 and Vv-ADH3 transcripts in grapes accumulate briefly in young fruits, while Vv-ADH2 transcripts strongly increase in the mature phase named veraison. Expression of the ADH gene is induced by different environmental stresses [ 14 ], such as low temperature [ 9 , 15 ], osmotic [ 16 ], drought [ 8 ], salt [ 10 ], mechanical damage [ 17 ], and the exogenous hormone abscisic acid (ABA) [ 18 ]. Dolferus et al [ 18 ] found that hypoxia, dehydration, low temperature, and the phytohormone ABA can induce ADH expression in Arabidopsis .…”

“…Salinity stress induces accumulation of ADH mRNA in soybean ( Glycine max ) [ 19 ], grasspea ( Lathyrus sativus L.) [ 20 ], and Arabidopsis [ 21 ]. The ADH gene is one of the most common cold-induced genes in cereal crops and Arabidopsis [ 9 ]. In addition, the ADH levels in octoploid strawberry are highly correlated with cold tolerance [ 15 ].…”

Global Expression Profiling of Low Temperature Induced Genes in the Chilling Tolerant Japonica Rice Jumli Marshi

“…However, the plant species most extensively studied during cold stress and acclimation is a non-crop plant, Arabidopsis thaliana , where global transcriptional profiling experiments have identified several cold responsive genes [12], [13], [14], [15], [16], [17]. The complexity of genetic re-programming upon cold stress has also been demonstrated by various bioinformatics approaches [15], [18], [19], [20], [21].…”