Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit

Abstract

Soybean has a wide range of applications in the industry and, due to its crop potential, its improvement is widely desirable. During drought conditions, soybean crops suffer significant losses in productivity. Therefore, understanding the responses of the soybean under this stress is an effective way of targeting crop improvement techniques. In this study, we employed the Suppressive Subtractive Hybridization (SSH) technique to investigate differentially expressed genes under water deficit conditions. Embrapa 48 and BR 16 soybean lines, known as drought-tolerant and -sensitive, respectively, were grown hydroponically and subjected to different short-term periods of stress by withholding the nutrient solution. Using this approach, we have identified genes expressed during the early response to water deficit in roots and leaves. These genes were compared among the lines to assess probable differences in the plant transcriptomes. In general, similar biochemical processes were predominant in both cultivars; however, there were more considerable differences between roots and leaves of Embrapa 48. Moreover, we present here a fast, clean and straightforward method to obtain drought-stressed root tissues and a large enriched collection of transcripts expressed by soybean plants under water deficit that can be useful for further studies towards the understanding of plant responses to stress.

Expression Patterns of GmAP2/EREB-Like Transcription Factors Involved in Soybean Responses to Water Deficit

“…4). This gene was previously identified in forwarded subtractive libraries as being expressed in the leaf tissues of BR 16 plants [24], which corroborated the findings of this study. This contrasting behavior in different tissues should be highlighted because it might indicate that the promoter acts in a tissue-specific manner.…”

“…The gene expression data that was stored in the soybean database [24] was useful for identifying AP2/EREB - and DRIP- family transcripts that were differentially expressed under water-deficit conditions. The differentially expressed transcripts were present in the soybean genome in the Phytozome database v1.0 (http://www.phytozome.net/search.php), which allowed us to examine correlations between the expressed transcripts and the soybean gene models (Glymas).…”

“…The experiments were performed as described by Rodrigues et al [24]. Briefly, leaves and roots from control and stressed plants were obtained from Embrapa 48 and BR 16 soybean cultivars that had been grown hydroponically, as described by Martins et al [25].…”

Achievements and Challenges in Legume Breeding for Pest and Disease Resistance

“…For instance, the combination of SuperSAGE with NGS has already been applied to study the molecular aspects of resistance to ascochyta blight in several legumes Fondevilla et al, 2014a;García et al, 2013;Madrid et al, 2013). The combination of SSH with NGS has also started to be applied in soybean to study the genes involved during the symbiotic interaction (Barros de Carvalho et al, 2013) and in response to drought (Rodrigues et al, 2012;Oliveira-Vidal et al, 2012) to study disease and pest resistance. In addition, RNAseq technique that involves the sequencing of all transcripts expressed in a given situation is not only a powerful tool to develop de novo transcriptomes but also to compare the whole transcriptome expression profiling in two different situations.…”

Transcriptional Analysis of Drought-Induced Genes in the Roots of a Tolerant Genotype of the Common Bean (Phaseolus vulgaris L.)

“…(2012) [24] employed the SSH technique combined with high-throughput sequencing technology to investigate differentially expressed genes from two soybean cultivars, Embrapa 48 (tolerant) and BR16 (susceptible), under water deficit treatments. Twelve libraries were constructed using leaves and roots harvested in different stages of development, resulting in 6051 differentially regulated genes for Embrapa 48, and 4293 for BR16.…”