Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize

<p>Abstract</p> <p>Background</p> <p>Auxin signaling is vital for plant growth and development, and plays important role in apical dominance, tropic response, lateral root formation, vascular differentiation, embryo patterning and shoot elongation. Auxin Response Factors (ARFs) are the transcription factors that regulate the expression of auxin responsive genes. The <it>ARF </it>genes are represented by a large multigene family in plants. The first draft of full maize genome assembly has recently been released, however, to our knowledge, the <it>ARF </it>gene family from maize (<it>ZmARF </it>genes) has not been characterized in detail.</p> <p>Results</p> <p>In this study, 31 maize (<it>Zea mays </it>L.) genes that encode ARF proteins were identified in maize genome. It was shown that maize <it>ARF </it>genes fall into related sister pairs and chromosomal mapping revealed that duplication of <it>ZmARFs </it>was associated with the chromosomal block duplications. As expected, duplication of some <it>ZmARFs </it>showed a conserved intron/exon structure, whereas some others were more divergent, suggesting the possibility of functional diversification for these genes. Out of these 31 <it>ZmARF </it>genes, 14 possess auxin-responsive element in their promoter region, among which 7 appear to show small or negligible response to exogenous auxin. The 18 <it>ZmARF </it>genes were predicted to be the potential targets of small RNAs. Transgenic analysis revealed that increased miR167 level could cause degradation of transcripts of six potential targets (<it>ZmARF3</it>, <it>9</it>, <it>16</it>, <it>18</it>, <it>22 </it>and <it>30</it>). The expressions of maize <it>ARF </it>genes are responsive to exogenous auxin treatment. Dynamic expression patterns of <it>ZmARF </it>genes were observed in different stages of embryo development.</p> <p>Conclusions</p> <p>Maize <it>ARF </it>gene family is expanded (31 genes) as compared to <it>Arabidopsis </it>(23 genes) and rice (25 genes). The expression of these genes in maize is regulated by auxin and small RNAs. Dynamic expression patterns of <it>ZmARF </it>genes in embryo at different stages were detected which suggest that maize <it>ARF </it>genes may be involved in seed development and germination.</p

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

<p>Abstract</p> <p>Background</p> <p>Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.</p> <p>Results</p> <p>RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed.</p> <p>Conclusions</p> <p>The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.</p

A functional S locus anther gene is not required for the self-incompatibility response in Brassica oleracea.

The self-incompatibility (SI) response in Brassica involves recognition of self-pollen by the papillar cells of the stigma and is mediated by the products of genes localized at the S (self-incompatibility) locus. Two S locus genes, SRK and SLG, are thought to encode components of a receptor complex present in the female partner. The putative gene product of SLA, a third S locus-linked gene that is expressed specifically in anthers, is a candidate for the male component of the SI recognition system. The identification of a mutant SLA allele, interrupted by a large insert resembling a retrotransposon, in self-compatible Brassica napus initially suggested that SLA played an essential role in the SI response. In this study, we have characterized an SLA allele from a self-compatible B. oleracea var acephala line and show that it too is interrupted by a large insert. However, analysis of seven B. oleracea var botrytis lines exhibiting both self-compatible and self-incompatible phenotypes showed that these lines carry an S allele very similar or identical to that of the B. oleracea var acephala line and that the SLA gene is interrupted by an insert in all seven lines. The insertion of the putative retrotransposon was shown to interfere with gene expression, with no SLA transcripts being detected by RNA gel blot analysis in a self-incompatible B. oleracea var botrytis line carrying an interrupted SLA gene. These data indicate that a functional SLA gene is not required for the SI response in Brassica