BackgroundMaize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation. New tools that improve our understanding of the genetic basis of quantitative traits are needed to guide predictive crop breeding. We have produced the first balanced multi-parental population in maize, a tool that provides high diversity and dense recombination events to allow routine quantitative trait loci (QTL) mapping in maize.ResultsWe produced 1,636 MAGIC maize recombinant inbred lines derived from eight genetically diverse founder lines. The characterization of 529 MAGIC maize lines shows that the population is a balanced, evenly differentiated mosaic of the eight founders, with mapping power and resolution strengthened by high minor allele frequencies and a fast decay of linkage disequilibrium. We show how MAGIC maize may find strong candidate genes by incorporating genome sequencing and transcriptomics data. We discuss three QTL for grain yield and three for flowering time, reporting candidate genes. Power simulations show that subsets of MAGIC maize might achieve high-power and high-definition QTL mapping.ConclusionsWe demonstrate MAGIC maize’s value in identifying the genetic bases of complex traits of agronomic relevance. The design of MAGIC maize allows the accumulation of sequencing and transcriptomics layers to guide the identification of candidate genes for a number of maize traits at different developmental stages. The characterization of the full MAGIC maize population will lead to higher power and definition in QTL mapping, and lay the basis for improved understanding of maize phenotypes, heterosis included. MAGIC maize is available to researchers.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0716-z) contains supplementary material, which is available to authorized users.

BackgroundTo sustain the global requirements for food and renewable resources, unraveling the molecular networks underlying plant growth is becoming pivotal. Although several approaches to identify genes and networks involved in final organ size have been proven successful, our understanding remains fragmentary.ResultsHere, we assessed variation in 103 lines of the Zea mays B73xH99 RIL population for a set of final leaf size and whole shoot traits at the seedling stage, complemented with measurements capturing growth dynamics, and cellular measurements. Most traits correlated well with the size of the division zone, implying that the molecular basis of final leaf size is already defined in dividing cells of growing leaves. Therefore, we searched for association between the transcriptional variation in dividing cells of the growing leaf and final leaf size and seedling biomass, allowing us to identify genes and processes correlated with the specific traits. A number of these genes have a known function in leaf development. Additionally, we illustrated that two independent mechanisms contribute to final leaf size, maximal growth rate and the duration of growth.ConclusionsUntangling complex traits such as leaf size by applying in-depth phenotyping allows us to define the relative contributions of the components and their mutual associations, facilitating dissection of the biological processes and regulatory networks underneath.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0735-9) contains supplementary material, which is available to authorized users.

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Leaves are vital organs for biomass and seed production because of their role in the generation of metabolic energy and organic compounds. A better understanding of the molecular networks underlying leaf development is crucial to sustain global requirements for food and renewable energy. Here, we combined transcriptome profiling of proliferative leaf tissue with indepth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations. Previously, correlation analysis in a classical biparental mapping population identified 1,740 genes correlated with at least one of 14 traits. Here, we extended these results with data from a multiparent advanced generation intercross population. As expected, the phenotypic variability was found to be larger in the latter population than in the biparental population, although general conclusions on the correlations among the traits are comparable. Data integration from the two diverse populations allowed us to identify a set of 226 genes that are robustly associated with diverse leaf traits. This set of genes is enriched for transcriptional regulators and genes involved in protein synthesis and cell wall metabolism. In order to investigate the molecular network context of the candidate gene set, we integrated our data with publicly available functional genomics data and identified a growth regulatory network of 185 genes. Our results illustrate the power of combining in-depth phenotyping with transcriptomics in mapping populations to dissect the genetic control of complex traits and present a set of candidate genes for use in biomass improvement

F-box proteins are part of one of the largest families of regulatory proteins that play important roles in protein degradation. In plants, F-box proteins are functionally very diverse, and only a small subset has been characterized in detail. Here, we identified a novel F-box protein FBX92 as a repressor of leaf growth in Arabidopsis. Overexpression of AtFBX92 resulted in plants with smaller leaves than the wild type, whereas plants with reduced levels of AtFBX92 showed, in contrast, increased leaf growth by stimulating cell proliferation. Detailed cellular analysis suggested that AtFBX92 specifically affects the rate of cell division during early leaf development. This is supported by the increased expression levels of several cell cycle genes in plants with reduced AtFBX92 levels. Surprisingly, overexpression of the maize homologous gene ZmFBX92 in maize had no effect on plant growth, whereas ectopic expression in Arabidopsis increased leaf growth. Expression of a truncated form of AtFBX92 showed that the contrasting effects of ZmFBX92 and AtFBX92 gain of function in Arabidopsis are due to the absence of the F-box-associated domain in the ZmFBX92 gene. Our work reveals an additional player in the complex network that determines leaf size and lays the foundation for identifying putative substrates.

We report on the development of five missense mutants and one recombination substrate of the b-glucuronidase (GUS)-encoding gene of Escherichia coli and their use for detecting mutation and recombination events in transgenic Arabidopsis (Arabidopsis thaliana) plants by reactivation of GUS activity in clonal sectors. The missense mutants were designed to find C:Gto-T:A transitions in a symmetrical sequence context and are in that respect complementary to previously published GUS point mutants. Small peptide tags (hemagglutinin tag and Strep tag II) and green fluorescent protein were translationally fused to GUS, which offers possibilities to check for mutant GUS production levels. We show that spontaneous mutation and recombination events took place. Mutagenic treatment of the plants with ethyl methanesulfonate and ultraviolet-C increased the number of mutations, validating the use of these constructs to measure mutation and recombination frequencies in plants exposed to biotic or abiotic stress conditions, or in response to different genetic backgrounds. Plants were also subjected to heavy metals, methyl jasmonate, salicylic acid, and heat stress, for which no effect could be seen. Together with an ethyl methanesulfonate mutation induction level much higher than previously described, the need is illustrated for many available scoring systems in parallel. Because all GUS missense mutants were cloned in a bacterial expression vector, they can also be used to score mutation events in E. coli.

Plant production is essential for the maintenance of human activity on Earth, and as seeds are the main tool for plant propagation, obtaining high-quality seeds is essential for successful planting. Forest species are applied in diff erent areas, such as timber, the pharmaceutical industry, landscaping projects, and degraded area recovery. The search for seedlings of forest species has increased due to the intense exploitation of ecosystems and the need to recover degraded areas. Therefore, it is necessary to use high-quality seeds that are composed of a complex set of attributes, including genetic, physical, physiological, and sanitary factors that directly infl uence the performance of seeds in the fi eld and their longevity in storage. Forest seeds have peculiarities, such as variable size and shape, nonuniform water content and germination speed, as well as diff erent drying and storage capacities. In addition, they have high genetic variability, which implies diffi culties in their management, such as the presence of dormancy, which can aff ect seed quality and seedling production. Seed germination and vigor are critical factors for the quality of forest seeds, but many species have not yet identifi ed their germination requirements. The lack of information about the peculiarities of each forest species and the high genetic variability among them makes it diffi cult to standardize methods for analyzing the physiological quality of seeds, in addition to becoming an obstacle to their use in reforestation projects, since the lack of diversity in the use of native species is a concern, as it reduces variety and endangers biodiversity

During maturation in seeds, metabolic processes dependent on gene expression are controlled by hormones, including abscisic acid and gibberellin. These hormones determine dormancy or the capacity for germination in seeds and may have different expression levels in the endosperm and embryo of coffee seeds. We quantified gene expression in the biosynthetic pathway of gibberellin and abscisic acid in different parts of Coffea arabica L. seeds in pre and post physiological maturity, in order to better understand the germination mechanisms of this species. Coffee fruits were harvested at green, yellowish-green, cherry, over-ripe and dry stages. For studies of gene expression, intact seeds were used in addition to endosperm and isolated embryos. The RNA from different tissues was extracted and treated with DNAse to synthesize cDNA. Transition levels of CaGA 3 (gibberellin) and CaABI 3 (abscisic acid) genes were quantified with qRT-PCR, using specific primers for coffee. Intact seeds at each phenological stage were submitted to germination tests, to evaluate the physiological quality of the seeds. Seed harvested at green and dry stages showed lower physiological ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 18 (3): gmr18264 S.D.V.F. Rosa et al. 2 quality when compared to the other maturation stages, and germination at the green stage was close to zero. Greatest expression of CaGA 3 and CaABI 3 occurs in the endosperm of coffee seeds in cherry and over-ripe stages, with better physiological performance. There are differences in CaABI 3 and CaGA 3 gene expression in embryos and endosperm of the coffee seeds.