BackgroundZinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum).ResultsIn this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment.ConclusionSystematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4082-y) contains supplementary material, which is available to authorized users.

The actin depolymerizing factor (ADF) proteins have growth, development, defense-related and growth regulatory functions in plants. The present study used genome-wide analysis to investigate ADF family genes in tomato. Eleven tomato ADF genes were identified and differential expression patterns were found in different organs. SlADF6 was preferentially expressed in roots, suggesting its function in root development. SlADF1, SlADF3 and SlADF10 were predominately expressed in the flowers compared to the other organs and specifically in the stamen compared to other flower parts, indicating their potential roles in pollen development. The comparatively higher expression of SlADF3 and SlADF11 at early fruit developmental stages might implicate them in determining final fruit size. SlADF5 and SlADF8 had relatively higher levels of expression five days after the breaker stage of fruit development, suggesting their possible role in fruit ripening. Notably, six genes were induced by cold and heat, seven by drought, five by NaCl, and four each by abscisic acid (ABA), jasmonic acid (JA) and wounding treatments. The differential expression patterns of the SlADF genes under different types of stresses suggested their function in stress tolerance in tomato plants. Our results will be helpful for the functional characterization of ADF genes during organ and fruit development of tomato under different stresses.

Three red rice ecotypes (Oryza spp), including LA 5, MS 5 and TX 4, were evaluated for acetolactate synthase resistance/tolerance to imazethapyr. The red rice ecotypes were compared with a tolerant line (CL-121), a resistant line (CL-161) and a conventional rice variety (Cypress). Based on enzymatic activity, the mean I(50) values were 1.5, 1.1, 1.5, 1.6, 20.8 and 590.6 microM imazethapyr, respectively, for LA 5, MS 5, TX 4, Cypress, CL-121 and CL-161. CL-161 was 32 times more resistant than CL-121 and at least 420 times more resistant than the average of the red rice ecotypes and Cypress. Results from the acetolactate synthase (ALS) assay showed that red rice ecotypes and Cypress had high susceptibility to imazethapyr when compared with the tolerant CL-121 and the resistant CL-161. Measurable enzymatic tolerance to ALS-inhibiting herbicides has not yet developed in these red rice ecotypes.

Clomazone has been successfully used for weed control in rice, but crop injury is a potential problem on light-textured soils. Experiments were conducted to determine the effect of soil characteristics and water potential on plant-available clomazone and rice injury. A centrifugal double-tube technique was used to determine plant-available concentration in soil solution (ACSS), total amount available in soil solution (TASS), and Kdvalues for clomazone on four soils at four water potentials. A rice bioassay was conducted parallel to the plant-available study to correlate biological availability to ACSS, TASS, and Kd. TASS was significantly different in all soils. The order of increasing TASS for the soils studied was Morey < Edna < Nada < Crowley, which correlated well with soil characteristics. The order of increasing TASS after equilibrium was − 90 < − 75 < − 33 < 0 kPa. TASS values at 0 kPa were greater than two times the TASS values at − 90 kPa. It appears that severe rice injury from clomazone on these soils could occur if TASS > 110 ng g−1and Kd< 1.1 ml g−1. We propose that the double-tube technique provides a more accurate estimate of available herbicide because the solution–soil ratios are < 0.33:1 and would be more representative of a plant root–herbicide relationship. This technique or some variation possibly could be further developed such that clomazone rates could be more clearly defined particularly on lighter-textured soils. TASS may be a better predictor of plant-available herbicide than ACSS when evaluating moderately to highly water-soluble herbicides in a nonsaturated soil environment.

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