Transcript profile of the response of two soybean genotypes to potassium deficiency

Abstract

The macronutrient potassium (K) is essential to plant growth and development. Crop yield potential is often affected by lack of soluble K. The molecular regulation mechanism of physiological and biochemical responses to K starvation in soybean roots and shoots is not fully understood. In the present study, two soybean varieties were subjected to low-K stress conditions: a low-K-tolerant variety (You06-71) and a low-K-sensitive variety (HengChun04-11). Eight libraries were generated for analysis: 2 genotypes ×2 tissues (roots and shoots) ×2 time periods [short term (0.5 to 12 h) and long term (3 to 12 d)]. RNA derived from the roots and shoots of these two varieties across two periods (short term and long term) were sequenced and the transcriptomes were compared using high-throughput tag-sequencing. To this end, a large number of clean tags (tags used for analysis after removal of dirty tags) corresponding to distinct tags (all types of clean tags) were identified in eight libraries (L1, You06-71-root short term; L2, HengChun04-11-root short term; L3, You06-71-shoot short term; L4, HengChun04-11-shoot short term; L5, You06-71-root long term; L6, HengChun04-11-root long term; L7, You06-71-shoot long term; L8, HengChun04-11-shoot long term). All clean tags were mapped to the available soybean (Glycine max) transcript database (http://www.soybase.org). Many genes showed substantial differences in expression across the libraries. In total, 5,440 transcripts involved in 118 KEGG pathways were either up- or down-regulated. Fifteen genes were randomly selected and their expression levels were confirmed using quantitative RT-PCR. Our results provide preliminary information on the molecular mechanism of potassium absorption and transport under low-K stress conditions in different soybean tissues.

Figure 1. Comparison of the morphological changes of different soybean (Glycine max) varieties under low-K stress condition.

You06-71 is the low-K tolerant variety; HengChun is the low-K sensitive variety.

Figure 2. Distribution of total clean tag and distinct tag counts over different tag abundance categories from eight libraries.

The x-axes represent percentage of total clean and distinct tag (%). The y-axes represent the tag copy number. Clean tags (tags used for analysis after removal of dirty tags), distinct tags (all types of clean tags). L1, You06-71-root short term; L2, HengChun04-11-root short term; L3, You06-71-shoot short term; L4, HengChun04-11-shoot short term; L5, You06-71-root long term; L6, HengChun04-11-root long term; L7, You06-71-shoot long term; L8, HengChun04-11-shoot long term.

Figure 3. Histogram presentation of gene ontology classification.

It includes three main categories: biological processes, cellular components, and molecular functions. The y-axes on the left and right indicate the percentage of a specific category of genes in that main category and the number of genes in a category, respectively.

Figure 4. Enrichment analysis of the 26 (A-Z) main pathways.

The x-axes represent the category of each pathway. The y-axes represent the number of genes in pathway analysis.

Figure 5. Number of up-regulated genes and down-regulated genes with significant differential expression among different sample libraries.

L1, You06-71-root short term; L2, HengChun04-11-root short term; L3, You06-71-shoot short term; L4, HengChun04-11-shoot short term; L5, You06-71-root long term; L6, HengChun04-11-root long term; L7, You06-71-shoot long term; L8, HengChun04-11-shoot long term.

Figure 6. Analysis of tag-mapped transcripts (genes) in eight libraries.

L1, You06-71-root short term; L2, HengChun04-11-root short term; L3, You06-71-shoot short term; L4, HengChun04-11-shoot short term; L5, You06-71-root long term; L6, HengChun04-11-root long term; L7, You06-71-shoot long term; L8, HengChun04-11-shoot long term.

Figure 7. Validation of the Solexa results using qRT-PCR method.

The y-axes on the left and right indicate the relative expressed level of tag-mapped genes in qRT-PCR and in Solexa sequencing analysis, respectively. The expression level of fifteen selected genes was measured by qRT-PCR. TUA5, UBQ10 and UKN2 were chosen as an endogenous reference.