The type B Arabidopsis Response Regulators (ARRs) of Arabidopsis thaliana are transcription factors that act as positive regulators in the two-component cytokinin signaling pathway. We employed a mutant-based approach to perform a detailed characterization of the roles of ARR1, ARR10, and ARR12 in plant growth and development. The most pronounced phenotype was found in the arr1-3 arr10-5 arr12-1 triple loss-of-function mutant, which showed almost complete insensitivity to high levels of exogenously applied cytokinins. The triple mutant exhibited reduced stature due to decreased cell division in the shoot, enhanced seed size, increased sensitivity to light, altered chlorophyll and anthocyanin concentrations, and an aborted primary root with protoxylem but no metaxylem. Microarray analysis revealed that expression of the majority of cytokinin-regulated genes requires the function of ARR1, ARR10, and ARR12. Characterization of double mutants revealed differing contributions of the type B ARRs to mutant phenotypes. Our results support a model in which cytokinin regulates a wide array of downstream responses through the action of a multistep phosphorelay that culminates in transcriptional regulation by ARR1, ARR10, and ARR12.

Iron is essential for photosynthesis and is often a limiting nutrient for plant productivity. Plants respond to conditions of iron deficiency by increasing transcript abundance of key genes involved in iron homeostasis, but only a few regulators of these genes have been identified. Using genome-wide expression analysis, we searched for transcription factors that are induced within 24 hours after transferring plants to iron-deficient growth conditions. Out of nearly 100 transcription factors shown to be up-regulated, we identified MYB10 and MYB72 as the most highly induced transcription factors. Here, we show that MYB10 and MYB72 are functionally redundant and are required for plant survival in alkaline soil where iron availability is greatly restricted. myb10myb72 double mutants fail to induce transcript accumulation of the nicotianamine synthase gene NAS4. Both myb10myb72 mutants and nas4-1 mutants have reduced iron concentrations, chlorophyll levels, and shoot mass under iron-limiting conditions, indicating that these genes are essential for proper plant growth. The double myb10myb72 mutant also showed nickel and zinc sensitivity, similar to the nas4 mutant. Ectopic expression of NAS4 rescues myb10myb72 plants, suggesting that loss of NAS4 is the primary defect in these plants and emphasizes the importance of nicotianamine, an iron chelator, in iron homeostasis. Overall, our results provide evidence that MYB10 and MYB72 act early in the iron-deficiency regulatory cascade to drive gene expression of NAS4 and are essential for plant survival under iron deficiency. Iron deficiency is the most common human nutritional disorder, afflicting more than three billion people worldwide. Most of these people rely on plants for their dietary iron. Iron is also one of the three nutrients that most commonly limit plant growth. Despite progress in tracing how Fe moves throughout the plant, we still do not fully understand how plants sense and respond to Fe availability. Here, we report on two apparently redundant MYB transcription factors that are acting to control one gene that has a major impact on the ability of plants to grow in alkaline soil where iron availability is greatly restricted. In the absence of these transcription factors, plants are unable to survive on this soil. As 1/3 of the world's soils are alkaline, understanding how plants cope may enable the growth of crops on soils currently not suitable for agricultural production. These two transcription factors also extend the iron deficiency network and this work provides insight into the tight control plants exert over iron uptake and distribution.

The most established model of the eukaryotic innate immune system is derived from examples of large effect monogenic quantitative resistance to pathogens. However, many host-pathogen interactions involve many genes of small to medium effect and exhibit quantitative resistance. We used the Arabidopsis-Botrytis pathosystem to explore the quantitative genetic architecture underlying host innate immune system in a population of Arabidopsis thaliana. By infecting a diverse panel of Arabidopsis accessions with four phenotypically and genotypically distinct isolates of the fungal necrotroph B. cinerea, we identified a total of 2,982 genes associated with quantitative resistance using lesion area and 3,354 genes associated with camalexin production as measures of the interaction. Most genes were associated with resistance to a specific Botrytis isolate, which demonstrates the influence of pathogen genetic variation in analyzing host quantitative resistance. While known resistance genes, such as receptor-like kinases (RLKs) and nucleotide-binding site leucine-rich repeat proteins (NLRs), were found to be enriched among associated genes, they only account for a small fraction of the total genes associated with quantitative resistance. Using publically available co-expression data, we condensed the quantitative resistance associated genes into co-expressed gene networks. GO analysis of these networks implicated several biological processes commonly connected to disease resistance, including defense hormone signaling and ROS production, as well as novel processes, such as leaf development. Validation of single gene T-DNA knockouts in a Col-0 background demonstrate a high success rate (60%) when accounting for differences in environmental and Botrytis genetic variation. This study shows that the genetic architecture underlying host innate immune system is extremely complex and is likely able to sense and respond to differential virulence among pathogen genotypes. The innate immune system is an important driver of quantitative resistance among all eukaryotes and is the primary immune system for many multicellular organisms, including plants, fungi, and insects. While some components of the innate immune system are known, many components are still undiscovered. Here we use genome wide association (GWA) mapping in a natural population of the Arabidopsis thaliana host against four phenotypically and genetically distinct isolates of the fungal pathogen Botrytis cinerea to describe and validate components of the plant innate immune system. Using both the induced production of a known defense compound, camalexin, and lesion area as quantified outputs of the plant innate immune system, we found approximately 2,982 and 3,354 genes associated with quantitative resistance respectively. Genes associated with variation in the plant immune system were largely dependent on the pathogen genotype, indicating the presence of specificity in pathogen detection and response by the host. Associated genes, which were filtered into co-expression networks followed by GO enrichment analysis, showed both known and novel biological processes associated with pathogen response. Validation of associated genes using single gene knockouts in a common genetic background indicates an ability to validate causal genes with a 60% validation rate.

Plants respond to neighbor shade by increasing stem and petiole elongation. Shade, sensed by phytochrome photoreceptors, causes stabilization ofPHYTOCHROME INTERACTING FACTORproteins and subsequent induction ofYUCCAauxin biosynthetic genes. To investigate the role ofYUCCAgenes in phytochrome-mediated elongation, we examined auxin signaling kinetics after an end-of-day far-red (EOD-FR) light treatment, and found that an auxin responsive reporter is rapidly induced within 2 hours of far-red exposure.YUCCA2, 5, 8,and9are all induced with similar kinetics suggesting that theycould act redundantly to control shade-mediated elongation. To test this hypothesis we constructed ayucca2, 5, 8, 9quadruple mutant and found that the hypocotyl and petiole EOD-FR and shade avoidance responses are completely disrupted. This work shows thatYUCCAauxin biosynthetic genes are essential for detectable shade avoidance and thatYUCCAgenes are important for petiole shade avoidance.

Demonstration of key methods for high throughput leaf measurements. These methods can be used to accelerate leaf phenotyping when...