Identification and interest of molecular markers to monitor plant Pi status.

BACKGROUND: Inorganic phosphate (Pi) is the sole source of phosphorus for plants. It is a limiting factor for plant yield in most soils worldwide. Due to economic and environmental constraints, the use of Pi fertilizer is and will be more and more limited. Unfortunately, evaluation of Pi bioavailability or Pi starvation traits remains a tedious task, which often does not inform us about the real Pi plant status. RESULTS: Here, we identified by transcriptomic studies carried out in the plant model Arabidopsis thaliana, early roots- or leaves-conserved molecular markers for Pi starvation, exhibiting fast response to modifications of phosphate nutritional status. We identified their homologues in three crops (wheat, rapeseed, and maize) and demonstrated that they offer a reliable opportunity to monitor the actual plant internal Pi status. They turn out to be very sensitive in the concentration range of 0-50 µM which is the most common case in the vast majority of soils and situations where Pi hardly accumulates in plants. Besides in vitro conditions, they could also be validated for plants growing in the greenhouse or in open field conditions. CONCLUSION: These markers provide valuable physiological tools for plant physiologists and breeders to assess phosphate bio-availability impact on plant growth in their studies. This also offers the opportunity to cope with the rising economical (shortage) and societal problems (pollution) resulting from the management of this critical natural resource.

Marker-based crop model-assisted ideotype design to improve avoidance of abiotic stress in bread wheat.

Wheat phenology allows escape from seasonal abiotic stresses including frosts and high temperatures, the latter being forecast to increase with climate change. The use of marker-based crop models to identify ideotypes has been proposed to select genotypes adapted to specific weather and management conditions and anticipate climate change. In this study, a marker-based crop model for wheat phenology was calibrated and tested. Climate analysis of 30 years of historical weather data in 72 locations representing the main wheat production areas in France was performed. We carried out marker-based crop model simulations for 1019 wheat cultivars and three sowing dates, which allowed calculation of genotypic stress avoidance frequencies of frost and heat stress and identification of ideotypes. The phenology marker-based crop model allowed prediction of large genotypic variations for the beginning of stem elongation (GS30) and heading date (GS55). Prediction accuracy was assessed using untested genotypes and environments, and showed median genotype prediction errors of 8.5 and 4.2 days for GS30 and GS55, respectively. Climate analysis allowed the definition of a low risk period for each location based on the distribution of the last frost and first heat days. Clustering of locations showed three groups with contrasting levels of frost and heat risks. Marker-based crop model simulations showed the need to optimize the genotype depending on sowing date, particularly in high risk environments. An empirical validation of the approach showed that it holds good promises to improve frost and heat stress avoidance.

A saturated SNP linkage map for the orange wheat blossom midge resistance gene Sm1.

KEY MESSAGE: SNP markers were developed for the OWBM resistance gene Sm1 that will be useful for MAS. The wheat Sm1 region is collinear with an inverted syntenic interval in B. distachyon. Orange wheat blossom midge (OWBM, Sitodiplosis mosellana Géhin) is an important insect pest of wheat (Triticum aestivum) in many growing regions. Sm1 is the only described OWBM resistance gene and is the foundation of managing OWBM through host genetics. Sm1 was previously mapped to wheat chromosome arm 2BS relative to simple sequence repeat (SSR) markers and the dominant, sequence characterized amplified region (SCAR) marker WM1. The objectives of this research were to saturate the Sm1 region with markers, develop improved markers for marker-assisted selection (MAS), and examine the synteny between wheat, Brachypodium distachyon, and rice (Oryza sativa) in the Sm1 region. The present study mapped Sm1 in four populations relative to single nucleotide polymorphisms (SNPs), SSRs, Diversity Array Technology (DArT) markers, single strand conformation polymorphisms (SSCPs), and the SCAR WM1. Numerous high quality SNP assays were designed that mapped near Sm1. BLAST delineated the syntenic intervals in B. distachyon and rice using gene-based SNPs as query sequences. The Sm1 region in wheat was inverted relative to B. distachyon and rice, which suggests a chromosomal rearrangement within the Triticeae lineage. Seven SNPs were tested on a collection of wheat lines known to carry Sm1 and not to carry Sm1. Sm1-flanking SNPs were identified that were useful for predicting the presence or absence of Sm1 based upon haplotype. These SNPs will be a major improvement for MAS of Sm1 in wheat breeding programs.

Exploiting the Repetitive Fraction of the Wheat Genome for High-Throughput Single-Nucleotide Polymorphism Discovery and Genotyping.

Transposable elements (TEs) account for more than 80% of the wheat genome. Although they represent a major obstacle for genomic studies, TEs are also a source of polymorphism and consequently of molecular markers such as insertion site-based polymorphism (ISBP) markers. Insertion site-based polymorphisms have been found to be a great source of genome-specific single-nucleotide polymorphism (SNPs) in the hexaploid wheat ( L.) genome. Here, we report on the development of a high-throughput SNP discovery approach based on sequence capture of ISBP markers. By applying this approach to the reference sequence of chromosome 3B from hexaploid wheat, we designed 39,077 SNPs that are evenly distributed along the chromosome. We demonstrate that these SNPs can be efficiently scored with the KASPar (Kompetitive allele-specific polymerase chain reaction) genotyping technology. Finally, through genetic diversity and genome-wide association studies, we also demonstrate that ISBP-derived SNPs can be used in marker-assisted breeding programs.

Control of flowering and cell fate by LIF2, an RNA binding partner of the polycomb complex component LHP1.

Polycomb Repressive Complexes (PRC) modulate the epigenetic status of key cell fate and developmental regulators in eukaryotes. The chromo domain protein like heterochromatin protein1 (LHP1) is a subunit of a plant PRC1-like complex in Arabidopsis thaliana and recognizes histone H3 lysine 27 trimethylation, a silencing epigenetic mark deposited by the PRC2 complex. We have identified and studied an LHP1-Interacting Factor2 (LIF2). LIF2 protein has RNA recognition motifs and belongs to the large hnRNP protein family, which is involved in RNA processing. LIF2 interacts in vivo, in the cell nucleus, with the LHP1 chromo shadow domain. Expression of LIF2 was detected predominantly in vascular and meristematic tissues. Loss-of-function of LIF2 modifies flowering time, floral developmental homeostasis and gynoecium growth determination. lif2 ovaries have indeterminate growth and produce ectopic inflorescences with severely affected flowers showing proliferation of ectopic stigmatic papillae and ovules in short-day conditions. To look at how LIF2 acts relative to LHP1, we conducted transcriptome analyses in lif2 and lhp1 and identified a common set of deregulated genes, which showed significant enrichment in stress-response genes. By comparing expression of LHP1 targets in lif2, lhp1 and lif2 lhp1 mutants we showed that LIF2 can either antagonize or act with LHP1. Interestingly, repression of the FLC floral transcriptional regulator in lif2 mutant is accompanied by an increase in H3K27 trimethylation at the locus, without any change in LHP1 binding, suggesting that LHP1 is targeted independently from LIF2 and that LHP1 binding does not strictly correlate with gene expression. LIF2, involved in cell identity and cell fate decision, may modulate the activity of LHP1 at specific loci, during specific developmental windows or in response to environmental cues that control cell fate determination. These results highlight a novel link between plant RNA processing and Polycomb regulation.

Mapping of a spontaneous mutation for early flowering time in maize highlights contrasting allelic series at two-linked QTL on chromosome 8.

Only a few mutations affecting flowering time have been detected in maize. We analyzed a spontaneous early mutation, vgt-f7p, which appeared during production of the inbred line F7. This mutation shortens the time from planting to flowering by about 100 growing degree days (GDD), and reduces the number of nodes. It therefore seems to affect the timing of meristem differentiation from a vegetative to a reproductive state. It was mapped to a 6 cM confidence interval on chromosome 8, using a QTL mapping approach. QTL analysis of a mapping population generated by crossing the mutant F7 line (F7p) and the Gaspé flint population showed that vgt-f7p is probably allelic to vgt1, a QTL described in previous studies, and affects earliness more strongly than the Gaspé allele at vgt1. Global analysis of the QTL in the region suggested that there may be two consensus QTL, vgt1 and vgt2. These two QTL have contrasting allelic effects: rare alleles conferring extremely early flowering at vgt1 vs. greater diversity and milder effects at locus vgt2. Finally, detailed syntenic analysis showed that the vgt1 region displays a highly conserved duplicated region on chromosome 6, which also plays an important role in maize flowering time variation. The cloning of vgt1 should, therefore, also facilitate the analysis of the molecular basis of variation due to this second region.