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Map-based cloning has been widely used to identify genes responsible for mutant phenotypes in Arabidopsis, especially those mutants generated by EMS or fast neutron mutagenesis. The success of map-based cloning relies on the availability of molecular markers that distinguish the polymorphisms between two Arabidopsis ecotypes. So far, most molecular markers in Arabidopsis have been generated by individual laboratories or the Arabidopsis Information Resource (TAIR). However, the TAIR markers, which are distributed unevenly on the five Arabidopsis chromosomes, only cover approximately 25% of the Arabidopsis BACs. Designing and testing molecular markers is still a time-consuming endeavor. Here we report the construction of a high-resolution BAC-based Arabidopsis mapping platform (AMP), using Col-0 and Ler as model ecotypes. The AMP comprises 1346 markers (1073 INDEL and 273 CAPS/dCAPS markers), of which 971 were newly designed and experimentally confirmed, 179 were from published papers and 196 were TAIR markers. These AMP markers cover 1186 BACs, 1121 of which are in non-centromere regions, representing approximately 75% of the Arabidopsis BACs in non-centromere regions. All the marker information is included on the AMP website (http://amp.genomics.org.cn/) for easy access and download, and sets of standard markers for initial chromosomal localization of a particular gene are recommended. The feasibility of using the AMP to map mutated genes is also discussed.

Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed.

Summary • Auxin is essential for many aspects of plant growth and development, including the determination of lateral organ shapes. • Here, the characterization of a dominant Arabidopsis thaliana mutant spl-D (SPOROCYTELESS dominant), and the roles of SPL in auxin homeostasis and plant development, are reported. • The spl-D mutant displayed a severe up-curling leaf phenotype caused by increased expression of SPOROCYTELESS/NOZZLE (SPL/NZZ), a putative transcription factor gene that was previously linked to sporocyte formation. The spl-D plants also displayed pleiotropic developmental defects including fewer lateral roots, simpler venation patterns, and reduced shoot apical dominance. The leaf and floral phenotypes of spl-D and SPL over-expression lines were reminiscent of yucca (yuc) triple and quadruple mutants, suggesting that SPL may regulate auxin homeostasis. Consistent with this hypothesis, it was found that over-expression of SPL led to down-regulation of the auxin reporter DR5-GUS, and that many auxin-responsive genes were down-regulated in spl-D leaves. Interestingly, the expression of YUC2 and YUC6, two key genes in auxin biosynthesis, was significantly repressed in spl-D plants. • Taken together with the genetic and phenotypic analysis of spl-D/yuc6-D double mutant, these data suggest that SPL may regulate auxin homeostasis by repressing the transcription of YUC2 and YUC6 and participate in lateral organ morphogenesis.

We previously reported that Arabidopsis indole-3-acetic acid (IAA)-methyltransferase-1 (IAMT1) catalyzes the conversion of IAA, an essential phytohormone, to methyl-IAA (MeIAA) and that IAMT1 plays an important role in leaf development. Here, we present the possible mechanisms of action of MeIAA in Arabidopsis. We showed that MeIAA was more potent than IAA in the inhibition of hypocotyl elongation and that MeIAA and naphthalene-acetic acid (NAA), but not IAA, rescued the hypocotyl gravitropic defects in dark-grown aux1. However, MeIAA was less potent than IAA in the inhibition of primary root elongation in light-grown seedlings, and could not rescue the agravitropic root phenotype of aux1. MeIAA had a stronger capacity to induce lateral roots than both IAA and NAA and rescued the defective lateral root phenotype of aux1 seedlings. However, its capacity to induce root hairs was weaker than IAA and NAA and did not rescue the defective root hair phenotype of aux1 seedlings. These data indicate that MeIAA is an inactive form of IAA. The different sensitivities to MeIAA among different organs probably resulted from different expression localization and capacities of a putative MeIAA esterase to convert MeIAA to IAA.

Leaf morphogenesis is strictly controlled not only by intrinsic genetic factors, such as transcriptional factors, but also by environmental cues, such as light, water and pathogens. Nevertheless, the molecular mechanism of how leaf morphogenesis is regulated by genetic programs and environmental cues is far from clear. Numerous series of events demonstrate that plant hormones, mostly small and simple molecules, play crucial roles in plant growth and development, and in responses of plants to environmental cues such as light. With more and more genetics and molecular evidence obtained from the model plant Arabidopsis, several fundamental aspects of leaf morphogenesis including the initiation of leaf primordia, the determination of leaf axes, the regulation of cell division and expansion in leaves have been gradually unveiled. Among these phytohormones, auxin is found to be essential in the regulation of leaf morphogenesis.

Map-based cloning has been widely used to identify genes responsible for mutant phenotypes in Arabidopsis, especially those mutants generated by EMS or fast neutron mutagenesis. The success of map-based cloning relies on the availability of molecular markers that distinguish the polymorphisms between two Arabidopsis ecotypes. So far, most molecular markers in Arabidopsis have been generated by individual laboratories or the Arabidopsis Information Resource (TAIR). However, the TAIR markers, which are distributed unevenly on the five Arabidopsis chromosomes, only cover approximately 25% of the Arabidopsis BACs. Designing and testing molecular markers is still a time-consuming endeavor. Here we report the construction of a high-resolution BAC-based Arabidopsis mapping platform (AMP), using Col-0 and Ler as model ecotypes. The AMP comprises 1346 markers (1073 INDEL and 273 CAPS/dCAPS markers), of which 971 were newly designed and experimentally confirmed, 179 were from published papers and 196 were TAIR markers. These AMP markers cover 1186 BACs, 1121 of which are in non-centromere regions, representing approximately 75% of the Arabidopsis BACs in non-centromere regions. All the marker information is included on the AMP website (http://amp.genomics.org.cn/) for easy access and download, and sets of standard markers for initial chromosomal localization of a particular gene are recommended. The feasibility of using the AMP to map mutated genes is also discussed.

Recently, as part of biosafety assessments, unintended effects have been given much attention. In this study, we applied a proteomics approach to elucidate the unintended effects of random T-DNA insertion in transgenic plants. Separated proteins extracted from 12 trans-genic Arabidopsis thaliana with different T-DNA insertion sites and from wild-type (ecotype Col-o) were analyzed. In the transgenic plants, 102 significantly altered protein spots were detected, in which 59 were up-regulated and 43 down-regulated. MALDI-TOF MS analysis showed that most of these expression level-altered proteins were involved in energy transfer, oxidative respiration and photosynthesis. However, none of these proteins was a toxic protein or allergen. Using plants with or without cold treatment, a natural environmental stress, as controls, we found that the number of the altered proteins was even less in those transgenic plants than those triggered by the cold treatment, suggesting that the transgenic events had a weaker impact on the plants than the environmental stresses. Interestingly, the phosphinothricin acetyl transferase (PAT), the BAR-encoded protein, was detected in nine out of twelve different T-DNA insertion lines at five different insertion sites. These data suggest that the most significant impact of transgenic events on the host plants is from the transgene itself, i.e., from the predictable intended effects, rather than unintended effects. This study also suggests that the proteomics approach has the potential to detect the unintended effects in transgenic plants.