The chlorophyll a/b abundances in salt stress treated rice.

<p>The concentration of chlorophyll a/b in salt stress treated rice was analyzed at 0 h, 1 h, 3 h, 6 h, 12 h and 24 h following treatment. Significant differences were determined relative to each treatment using a student’s <i>t</i>-test [<i>P</i>-values <0.05 (*) and <0.01 (**)]. Bars: SD.</p

The expression patterns of genes encoding the differentially expressed proteins.

<p>The expression patterns of the genes encoding the differentially expressed proteins were compared. The flex points are indicated by the black lines. Different patterns are indicated by different types of lines. Different genes are indicated with different colors. <i>(A)</i> The similarly down-regulated patterns were compared. <i>(B)</i> The similar up-regulated patterns and down-regulated patterns were compared.</p

The differentially expressed proteins involved in the antioxidant pathway.

<p>Transcript abundances of mRNAs encoding antioxidant-related proteins were analyzed at 0 h, 1 h, 3 h, 6 h, 12 h and 24 h following salt stress treatment. The mRNA levels at 12 h were compared with the iTRAQ data. Red indicates the proteins that were up-regulated and green indicates the proteins that were down-regulated. Significant differences were determined relative to each treatment using a student’s <i>t</i>-test [<i>P</i>-values <0.05 (*) and <0.01 (**)]. Bars: SD. The changes in transcript abundances at 12 h were compared with the iTRAQ data. <i>(A)</i> Overview of differentially expressed proteins involved in antioxidant. <i>(B)</i> Thioredoxin M-like (gi|57899183). <i>(C)</i> TRX x (gi|32487506). <i>(D)</i> Putative thioredoxin peroxidase (gi|46389828). <i>(E)</i> Putative peroxiredoxin Q (gi|51090743). <i>(F)</i> Putative glutathione S-transferase OsGSTF3 (gi|11177845).</p

Ratio distributions for the identified proteins.

<p>The changes in rice protein contents in response to salt stress were analyzed. The horizontal axis displays the base Log2-transformed ratios. The red point indicates that the ratio was greater than 1.5, and the green point indicates that the ratio was less than 0.67.</p

The antioxidant parameters in salt stress treated rice.

<p>Changes to rice antioxidant parameters were analyzed at 0 h, 1 h, 3 h, 6 h, 12 h and 24 h following salt stress treatment. Significant differences were determined relative to each treatment using a student’s <i>t</i>-test [<i>P</i>-values <0.05 (*) and <0.01 (**)]. Bars: SD. <i>(A)</i> The total antioxidant capacity (T-AOC) was analyzed in salt stress treated rice. <i>(B)</i> POD activity was analyzed in salt stress treated rice. <i>(C)</i> GST activity was analyzed in salt stress treated rice. <i>(D)</i> GSH concentrations were analyzed in salt stress treated rice.</p

The ATPase activity assay.

<p>Changes in rice ATPase activity were assessed at 0 h, 1 h, 3 h, 6 h, 12 h and 24 h following salt stress treatment. Significant differences were determined relative to each treatment using a student’s <i>t</i>-test [<i>P</i>-values <0.05 (*) and <0.01 (**)]. Bars: SD.</p

The differentially expressed proteins involved in photosynthesis.

<p>Transcript abundances of mRNAs encoding proteins involved in photosynthesis were analyzed at 0 h, 1 h, 3 h, 6 h, 12 h and 24 h following salt stress treatment. The mRNA levels at 12 h were compared with the iTRAQ data. Red indicates the proteins that were up-regulated while green indicates the proteins that were down-regulated. Significant differences were determined relative to each treatment using a student’s <i>t</i>-test [<i>P</i>-values <0.05 (*) and <0.01 (**)]. Bars: SD. The changes in transcript abundances at 12 h were compared with the iTRAQ data. <i>(A)</i> Putative PSI antenna protein (Lhca2, gi|34393511). <i>(B)</i> Chlorophyll a/b-binding protein precursor (Lhca1, gi|3789954). <i>(C)</i> Chlorophyll a/b-binding protein precursor (Lhca4, gi|3789952). <i>(D)</i> Chloroplast photosystem I reaction center subunit II precursor-like protein (PsaD, gi|29367391). <i>(E)</i> PSI H subunit GOS5 (PsaH, gi|3885894). <i>(F)</i> Overview of the differentially expressed proteins involved in photosynthesis.</p

Combined bulked segregant sequencing and traditional linkage analysis for identification of candidate gene for purple leaf sheath in maize

<div><p>Anthocyanin accumulation in various maize tissues plays important roles in plant growth and development. In addition, some color-related traits can be used as morphological markers in conventional maize breeding processes and purity identification of hybrid seeds. Here, we noticed that the leaf sheath color was controlled by a dominant gene, because purple (PSH) and green leaf sheaths (GSH) were separated at a ratio of 3:1 in an F₂ population. To map the gene, an F₂ and a recombinant inbred line (RIL) population were derived from a cross between inbred line T877 (PSH) and DH1M (GSH). The <i>PSH</i> locus was mapped to the genomic region within 128.8 to 138.4 Mb using a bulked segregant sequencing approach. This position was further validated by linkage mapping using 190 F₂ plants with GSH. Subsequently, the <i>PSH</i> locus was fine-mapped into an interval of 304.2 kb. A maize gene, GRMZM5G822829, was identified in this region, encoding a bHLH transcription factor. The expression level of this gene in T877 was found to be 9-fold higher than that of DH1M. In conclusion, our results suggest that GRMZM5G822829 is the putative candidate gene conferring leaf sheath color in maize.</p></div

The relative expression levels of <i>PSH</i> in different tissues for T877 and DH1M.

<p>Root1 and root2 indicated roots exposed to light and in the dark, respectively. The lowercase letters “a” indicate that the gene is almost non-expressed, “**” indicate that a significant difference was detected between T877 and DH1M in the same tissue sample (<i>p</i><0.01).</p

Candidate genes in <i>PSH</i> region.

<p>Candidate genes in <i>PSH</i> region.</p