knox genes encode homeodomain-containing transcription factors that are required for meristem maintenance and proper patterning of organ initiation. In plants with simple leaves, knox genes are expressed exclusively in the meristem and stem, but in dissected leaves, they are also expressed in leaf primordia, suggesting that they may play a role in the diversity of leaf form. This hypothesis is supported by the intriguing phenotypes found in gain-of-function mutations where knox gene misexpression affects leaf and petal shape. Similar phenotypes are also found in recessive mutations of genes that function to negatively regulate knox genes. KNOX proteins function as heterodimers with other homeodomains in the TALE superclass. The gibberellin and lignin biosynthetic pathways are known to be negatively regulated by KNOX proteins, which results in indeterminate cell fates.

Members of the KNOX gene family have important roles in plant meristems by regulating cell division and differentiation. BREVIPEDICELLUS (BP), one of seven KNOX genes in Arabidopsis, has a primary role in internode patterning. We carried out a comparison of RNA expression profiles between wild-type seedlings and bp mutants at a developmental stage prior to a visible phenotypic difference. Transcript differences were found for a number of genes in cell wall biosynthesis, especially genes in the lignin pathway. The regulation of lignin biosynthesis by BP was demonstrated by observing increased lignin deposition in bp mutants following bolting, decreased lignification in plants overexpressing BP, and aberrant lignin deposition in discrete regions of the bp stem. Furthermore, we showed that BP binds promoters of some genes in the lignin pathway. Our results provide a metabolic fingerprint for BP and identify the lignin pathway as one of the coordinate processes that BP regulates.Supplemental material is available at http://www. genesdev.org. Received June 6, 2003; revised version accepted July 9, 2003. In species with simple leaves, class I members of the KNOX gene family are expressed in shoot meristems and stems, but not leaves or roots. Loss-of-function phenotypes have been described for a few KNOX genes, and demonstrate a role in meristem maintenance (Long et al. 1996;Byrne et al. 2002;Vollbrecht et al. 2000) and stem elongation (Sato et al. 1999;Douglas et al. 2002;Venglat et al. 2002). Mutations in the KNOX gene BREVIPEDI-CELLUS (BP), result in plants with shorter internodes, downward pointing siliques, and an epidermal stripe of disorganized cells along the stem (Douglas et al. 2002;Venglat et al. 2002). BP overexpression results in changes in leaf shape and increased cytokinin levels in several species (Lincoln et al. 1994;Chuck et al. 1996;Ori et al. 2000;Frugis et al. 2001). Results and DiscussionWe compared gene expression profiles between the bp-9 loss-of-function mutant (in the Columbia ecotype, Col) and Col wild-type plants using a high-density Affymetrix oligonucleotide array representing ∼ 8,200 Arabidopsis genes. Two-week-old seedlings grown in short-day conditions were used as starting material. Under these conditions, bp and Col plants had no apparent phenotypic differences. We reasoned that using this approach may uncover early differences in gene expression stemming directly from loss of BP function rather than downstream secondary effects. Two independent RNA extractions and in vitro transcriptions were conducted for each genotype. Each of the two repetitions for the mutant was compared against both repetitions of the wild type to obtain a matrix of four comparisons. A set of filtering parameters (see Supplemental Material) was used to identify significant expression changes and eliminate genes exhibiting erratic patterns. Our analysis revealed a difference in expression of 64 genes (see Supplementry Table 1).Genes identified from the oligo array analysis were divided into functional groups...

Endives (Cichorium endivia L.) are popular vegetables, diversified into curly/frisée- and smooth/broad-leafed (escaroles) cultivar types (cultigroups), and consumed as fresh and bagged salads. They are rich in sesquiterpene lactones (STL) that exert proven function on bitter taste and human health. The assembly of a reference transcriptome of 77,022 unigenes and RNA-sequencing experiments were carried out to characterize the differences between endives and escaroles at the gene structural and expression levels. A set of 3177 SNPs distinguished smooth from curly cultivars, and an SNP-supported phylogenetic tree separated the cultigroups into two distinct clades, consistently with the botanical varieties of origin (crispum and latifolium, respectively). A pool of 699 genes maintained differential expression pattern (core-DEGs) in pairwise comparisons between curly vs smooth cultivars grown in the same environment. Accurate annotation allowed the identification of 26 genes in the sesquiterpenoid biosynthesis pathway, which included several germacrene A synthase, germacrene A oxidase and costunolide synthase members (GAS/GAO/COS module), required for the synthesis of costunolide, a key precursor of lactucopicrin- and lactucin-like sesquiterpene lactones. The core-DEGs contained a GAS gene (contig83192) that was positively correlated with STL levels and recurrently more expressed in curly than smooth endives, suggesting a cultigroup-specific behavior. The significant positive correlation of GAS/GAO/COS transcription and STL abundance (2.4-fold higher in frisée endives) suggested that sesquiterpenoid pathway control occurs at the transcriptional level. Based on correlation analyses, five transcription factors (MYB, MYB-related and WRKY) were inferred to act on contig83192/GAS and specific STL, suggesting the occurrence of two distinct routes in STL biosynthesis.

In addition to the full-length transcript , a splice variant () of the auxin response factor gene has been reported. Here, we identified an intron-retaining variant of, , whose translated product is imported into the nucleus and has tissue-specific localization in By inducibly expressing each variant in flowers, we show that fully complements the short-stamen phenotype of the mutant and restores the expression of , encoding a key regulator of stamen elongation. By contrast, the expression of and had minor or no effects on stamen elongation and expression. Coexpression of and in both the wild type and caused premature anther dehiscence: We show that is responsible for increased expression of the jasmonic acid biosynthetic gene and that is responsible for premature endothecium lignification due to precocious expression of transcription factor gene Finally, we show that ARF8.4 binds to specific auxin-related sequences in both the and promoters and activates their transcription more efficiently than ARF8.2. Our data suggest that ARF8.4 is a tissue-specific functional splice variant that controls filament elongation and endothecium lignification by directly regulating key genes involved in these processes.