Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population

Background: To 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. Results: Here, 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. Conclusions: Untangling 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

Epigenetic regulation of adaptive responses of forest tree species to the environment

Epigenetic variation is likely to contribute to the phenotypic plasticity and adaptative capacity of plant species, and may be especially important for long-lived organisms with complex life cycles, including forest trees. Diverse environmental stresses and hybridization/polyploidization events can create reversible heritable epigenetic marks that can be transmitted to subsequent generations as a form of molecular “memory”. Epigenetic changes might also contribute to the ability of plants to colonize or persist in variable environments. In this review, we provide an overview of recent data on epigenetic mechanisms involved in developmental processes and responses to environmental cues in plant, with a focus on forest tree species. We consider the possible role of forest tree epigenetics as a new source of adaptive traits in plant breeding, biotechnology, and ecosystem conservation under rapid climate chang

A molecular genetic analysis of resistance to poleroviruses in sugar beet and oilseed rape

Beet mild yellowing virus (BMYV) and Turnip yellows virus (TuYV) are both poleroviruses that cause significant reduction in the yields of sugar beet and oilseed rape respectively. Both viruses are transmitted by the aphid vector Myzus persicae. Current control methods rely heavily on the use of insecticides for controlling the aphids which can spread these viruses to a wide range of host plants. Recent EU guidelines have tightened control on the use of some of these pesticides, meaning it is becoming increasingly important to find alternative control methods. It is widely agreed in the scientific community, that the best control method would be to generate durable genetically resistant crop plants. In order to achieve this gene targets, either for active or passive resistance, would need to be identified. This study has built on a project that identified a naturally BMYV resistant A. thaliana ecotype, Sna-1. Crosses of the susceptible ecotype (Col-0) to the resistant ecotype Sna-1 identified the resistance as ‘passive’, where susceptibility was dominant, and conditioned by a monogenic trait. This study began by characterising the gene responsible for susceptibility by bulked segregant analysis and AFLP™. This identified a region of ca. 5Mbp region on A. thaliana chromosome 4. This region contains the Arabidopsis elongation initiation factor 4E (eIF4E) gene which has already been implicated in susceptibility to other viruses. This gene has frequently been shown to be important for viral infection in plants, and naturally occurring mutations can result in resistance to other viruses. Further investigation revealed a 12 bp duplicated sequence in the Sna-1 eIF4E allele, located in a region that encodes the cap-binding pocket of eIF4E. The same region has been shown to be required for virus infection in other species. Infections were therefore carried out using mutants in this gene, using TAS-ELISA. Previously susceptible Col-0 plants containing a T-DNA insert, or EMS point mutations in the eIF4E gene were found to be resistant to BMYV infection. Functional complementation with the Col-0 eIF4E allele into a stock that contained Sna-1 eIF4E resulted in susceptibility to BMYV, confirming its role as a susceptibility factor. As BMYV and TuYV are closely related viruses it was hypothesised they would share a similar infection strategy. The mutation in eIF4E was not enough to prevent virus infection, and the method of infection of the UK-BB TuYV isolate remains to be elucidated as infection studies in mutants with defective components of the eukaryotic translation initiation factors, including eIF(Iso)4E gene, has so far failed to identify any requirements for UK-BB TuYV infection. Several T-DNA insertion lines in the eIF(iso)4E gene were tested but it was not possible to verify that any of these lines were true knock-outs. However, the molelcular tools for future verification have been developed. A recent report has implicated eIF(iso)4G components in TuYV infection of Arabidopsis but this result could not be repeated in this study. Further study is required to fully understand the mode of infection of both viruses. It is expected that the identification of essential host genes required for virus infection will aid in the breeding of genetically resistant crops, and reduce the current dependence on harmful pesticides

Natural variation at XND1 impacts root hydraulics and trade-off for stress responses in Arabidopsis

Soil water uptake by roots is a key component of plant performance and adaptation to adverse environments. Here, we use a genome-wide association analysis to identify the XYLEM NAC DOMAIN 1 (XND1) transcription factor as a negative regulator of Arabidopsis root hydraulic conductivity (Lp). The distinct functionalities of a series of natural XND1 variants and a single nucleotide polymorphism that determines XND1 translation efficiency demonstrate the significance of XND1 natural variation at species-wide level. Phenotyping of xnd1 mutants and natural XND1 variants show that XND1 modulates Lp through action on xylem formation and potential indirect effects on aquaporin function and that it diminishes drought stress tolerance. XND1 also mediates the inhibition of xylem formation by the bacterial elicitor flagellin and counteracts plant infection by the root pathogen Ralstonia solanacearum. Thus, genetic variation at XND1, and xylem differentiation contribute to resolving the major trade-off between abiotic and biotic stress resistance in Arabidopsis

The biochemical basis of plant ATG8 substrate specificity

Autophagy is an essential eukaryotic cellular quality control pathway that involves the degradation of self- and non-self macromolecules , with multiple layers of specificity defining the dynamics of substrate uptake, sub-cellular trafficking, and turnover. ATG8 is a highly-conserved ubiquitin-like protein that is central to the selectivity of the autophagy pathway, directly or indirectly binding desired autophagic cargo. Throughout plant evolution, ATG8 has expanded from a single protein in algae to multiple isoforms in higher plants. However, the degree to which ATG8 isoforms have functionally specialized to bind distinct proteins is unclear. In this thesis, I described the potato ATG8 interactome using in planta immunoprecipitation followed by mass spectrometry, discovering that potato ATG8 isoforms bind distinct sets of plant proteins with varying degrees of overlap. In addition, I defined the biochemical basis of potato ATG8 specialization. I revealed that the ATG8 N-terminal β-strand underpins binding specificity to substrates that contain ATG8-interacting motifs (AIMs), including the ATG8targetting effector from the potato late blight pathogen Phytophthora infestans, PexRD54. To approach the question of ATG8 substrate specificity from the opposing direction, I also explored the evolutionary dynamics of PexRD54 in different host-specific lineages of Phytophthora. I found that the PexRD54 ortholog from P. mirabilis, a closely related species to P. infestans, has a polymorphism in its AIM which nearly abolishes binding to the ATG8s of its host, Mirabilis jalapa. These results provide insights into the requirements of a functional ATG8-interacting motif, as well as raise questions as to whether specific selective pressures of the M. jalapa host environment have shaped the evolution the P. mirabilis PexRD54