MADS-box genes controlling inflorescence morphogenesis in sunflower

MADS-box genes play an important role in plant ontogeny, particularly, in the regulation of floral organ induction and development. Eight full-length cDNAs of HAM genes (Helianthus annuus MADS) have been isolated from sunflower. They encode MADS-box transcription factors expressed in inflorescence tissues. In the frames of the ABCDE model, the HAM proteins were classified according to their structural homology to known MADS-box transcription factors. The HAM45 and HAM59 genes encode the homeotic C function and are involved in the control of the identity of pistil and stamens, while the HAM75 and HAM92 genes determine the A function and identity of floral and inflorescence meristems and petal identity. The HAM31, HAM2, HAM63, and HAM91 genes encode the B function and are involved in the formation of petals and stamens; and the HAM137 gene encodes the E function. Analysis of the expression of HAM genes in sunflower has demonstrated that the structural and functional differences between the ray and tubular flowers in the inflorescence could be a consequence of the lack of HAM59 expression during ray flower initiation

Tomato yield heterosis is triggered by a dosage sensitivity of the florigen pathway that fine-tunes shoot architecture

The superiority of hybrids has long been exploited in agriculture, and although many models explaining "heterosis" have been put forth, direct empirical support is limited. Particularly elusive have been cases of heterozygosity for single gene mutations causing heterosis under a genetic model known as overdominance. In tomato (Solanum lycopersicum), plants carrying mutations in SINGLE FLOWER TRUSS (SFT) encoding the flowering hormone florigen are severely delayed in flowering, become extremely large, and produce few flowers and fruits, but when heterozygous, yields are dramatically increased. Curiously, this overdominance is evident only in the background of "determinate" plants, in which the continuous production of side shoots and inflorescences gradually halts due to a defect in the flowering repressor SELF PRUNING (SP). How sp facilitates sft overdominance is unclear, but is thought to relate to the opposing functions these genes have on flowering time and shoot architecture. We show that sft mutant heterozygosity (sft/+) causes weak semi-dominant delays in flowering of both primary and side shoots. Using transcriptome sequencing of shoot meristems, we demonstrate that this delay begins before seedling meristems become reproductive, followed by delays in subsequent side shoot meristems that, in turn, postpone the arrest of shoot and inflorescence production. Reducing SFT levels in sp plants by artificial microRNAs recapitulates the dose-dependent modification of shoot and inflorescence production of sft/+ heterozygotes, confirming that fine-tuning levels of functional SFT transcripts provides a foundation for higher yields. Finally, we show that although flowering delays by florigen mutant heterozygosity are conserved in Arabidopsis, increased yield is not, likely because cyclical flowering is absent. We suggest sft heterozygosity triggers a yield improvement by optimizing plant architecture via its dosage response in the florigen pathway. Exploiting dosage sensitivity of florigen and its family members therefore provides a path to enhance productivity in other crops, but species-specific tuning will be required

A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification.

Quantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping

Functional Mapping of Plant Growth in Arabidopsis thaliana

Most traits important to agriculture, biology, and biomedicine are complex traits, determined by both genetic and environmental factors. The complex traits that change their phenotypes over different stages of development are called dynamic traits. Traditional quantitative trait loci (QTLs) mapping approaches ignore the dynamic changes of complex traits. Functional mapping, as a powerful statistical tool, can not only map QTLs that control the developmental pattern and process of complex traits, but also describe the dynamic changes of complex traits. In this study, we used functional mapping to identify those QTLs that affect height growth in 10th generation recombinant inbred lines derived from two different Arabidopsis thaliana accessions. Functional mapping identified 48 QTLs that are related to height traits. The growth curves of different genotypes can be drawn for each significant locus. By GO gene function annotations, we found that these QTLs detected are associated with the synthesis of biological macromolecules and the regulation of biological functions. Our findings provide unique insights into the genetic control of height growth of A. thaliana and will provide a theoretical basis for the study of complex traits

How have advances in comparative floral development influenced our understanding of floral evolution?

Evolutionary developmental biology has come to prominence in the past two decades, in both the plant kingdom and the animal kingdom, particularly following the description of homeotic genes linked to key morphological transitions. A primary goal of evolutionary developmental biology (“evo-devo”) is to define how developmental programs are modified to generate novel or labile morphologies. This requires an understanding of the molecular genetic basis of these programs and of the evolutionary changes they have undergone. The past decade has seen the establishment of a common language and common standards, and these changes have greatly improved the integration of evo-devo. Recently, a more comparative approach has been added to mechanistic developmental biology. In this review we attempt to show how, by using this “next-generation evo-devo” approach, insights into both developmental biology and evolutionary biology can be gained. Although the concepts we discuss are more broadly applicable, we have focused our examples on traits of the angiosperm flower, a structure that has undergone enormous morphological and developmental evolution since its relatively recent appearance in the fossil record.Work in the Glover laboratory on these topics is funded by the BBSRC, EU Marie Curie Actions, Isaac Newton Trust, Leverhulme Trust, NERC and the NSF, and we gratefully acknowledge all support.This is the accepted manuscript of a paper published in the International Journal of Plant Sciences (Glover BJ, Airoldi CA, Brockington SF, Fernández-Mazuecos M, Martínez-Pérez C, Mellers G, Moyroud E, Taylor L, International Journal of Plant Sciences, 2015, 176, 4, 307-323, doi:10.1086/681562). The final version is available at http://dx.doi.org/10.1086/68156

<i>Medicago truncatula</i> functional genomics: an invaluable resource for studies on agriculture sustainability

Legume functional genomics has moved many steps forward in the last two decades thanks to the improvement of genomics technologies and to the efforts of the research community. Tools for functional genomics studies are now available in Lotus japonicus, Medicago truncatula and soybean. In this chapter we focus on M.truncatula, as a model species for forage legumes, on the main achievements obtained due to the reported resources and on the future perspectives for the study of gene function in this species

Quantitative Genetics and Functional-Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization

Background and Aims: Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype x environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional-structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods: The GreenLab model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings of the species-specific parameters of the model. The QTL Cartographer software was used to study QTL detection of simulated plant traits. A genetic algorithm was implemented to define the ideotype for yield maximization based on the model parameters and the associated allelic combination. Key Results and Conclusions: By keeping the environmental factors constant and using a virtual population with a large number of individuals generated by a Mendelian genetic model, results for an ideal case could be simulated. Virtual QTL detection was compared in the case of phenotypic traits - such as cob weight - and when traits were model parameters, and was found to be more accurate in the latter case. The practical interest of this approach is illustrated by calculating the parameters (and the corresponding genotype) associated with yield optimization of a GreenLab maize model. The paper discusses the potentials of GreenLab to represent environment x genotype interactions, in particular through its main state variable, the ratio of biomass supply over demand

Embryology of \u3cem\u3eManekia naranjoana\u3c/em\u3e (Piperaceae) and its Implications for the Origin of the Sixteen-nucleate Female Gametophyte in Piperales

Piperaceae is unique among Piperales because it is the only tetrasporic group in the order and a great deal of diversity in the ontogenetic trajectories of the female gametophyte is found in its genera. The evolutionary developmental origin of the sixteen-nucleate female gametophyte remains unclear in the family until now. In Piperaceae, Manekia has been identified as sister to Zippelia, and this clade is sister to core Piperaceae (Piper, Peperomia). This research is the first attempt to understand the development of the female gametophyte of Manekia naranjoana in order to provide critical data on the origin of tetrasporic development in the family. Several aspects of the floral biology and phenological events taking place in the ovary, the flower and the inflorescence were explored. Manekia has a tetrasporic, sixteen nuclei female gametophyte, that is being produced from a single archesporial cell. The egg apparatus is located at the micropylar end of the female gametophyte. It is constituted of three cells, two synergids and an egg. The central cell nuclei consist of two nuclei, one from the micropylar end and the other one from the chalazal one. The eleven remaining nuclei are arranged toward the chalazal pole of the female gametophyte, and sometimes fuse. This description corresponds mostly to the Drusa type. But Penaea type is also occasionally reported for first time in this study for the genus. Manekia and Zippelia share a similar structure of the female gametophyte with a total of 16 nuclei, and two nuclei in a central cell suggesting a triploid endosperm. The transition from monosporic to tetraporic female gametophyte development can be explained through the theory of modular construction and several kind modifications in the ontogenetic trajectories. Heterochronic and heterotopic changes, additions, and deletions in the development of the female gametophytes reflect evolutionary histories of the particular taxa implicated. A great deal of plasticity in terms of lack of polarity and nuclear fusion of antipodals was found in the chalazal module of the female gametophyte of Manekia