Anthony Klein

Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high‐density, high‐resolution consensus genetic map

Single nucleotide polymorphism (SNP) arrays represent important genotyping tools for innovative strategies in both basic research and applied breeding. Pea is an important food, feed and sustainable crop with a large (about 4.45 Gbp) but not yet available genome sequence. In the present study, 12 pea recombinant inbred line populations were genotyped using the newly developed GenoPea 13.2K SNP Array. Individual and consensus genetic maps were built providing insights into the structure and organization of the pea genome. Largely collinear genetic maps of 3918-8503 SNPs were obtained from all mapping populations, and only two of these exhibited putative chromosomal rearrangement signatures. Similar distortion patterns in different populations were noted. A total of 12 802 transcript-derived SNP markers placed on a 15 079-marker high-density, high-resolution consensus map allowed the identification of ohnologue-rich regions within the pea genome and the localization of local duplicates. Dense syntenic networks with sequenced legume genomes were further established, paving the way for the identification of the molecular bases of important agronomic traits segregating in the mapping populations. The information gained on the structure and organization of the genome from this research will undoubtedly contribute to the understanding of the evolution of the pea genome and to its assembly. The GenoPea 13.2K SNP Array and individual and consensus genetic maps are valuable genomic tools for plant scientists to strengthen pea as a model for genetics and physiology and enhance breeding.

Genomic Prediction in Pea: Effect of Marker Density and Training Population Size and Composition on Prediction Accuracy

Pea is an important food and feed crop and a valuable component of low-input farming systems. Improving resistance to biotic and abiotic stresses is a major breeding target to enhance yield potential and regularity. Genomic selection (GS) has lately emerged as a promising technique to increase the accuracy and gain of marker-based selection. It uses genome-wide molecular marker data to predict the breeding values of candidate lines to selection. A collection of 339 genetic resource accessions (CRB339) was subjected to high-density genotyping using the GenoPea 13.2K SNP Array. Genomic prediction accuracy was evaluated for thousand seed weight (TSW), the number of seeds per plant (NSeed), and the date of flowering (BegFlo). Mean cross-environment prediction accuracies reached 0.83 for TSW, 0.68 for NSeed, and 0.65 for BegFlo. For each trait, the statistical method, the marker density, and/or the training population size and composition used for prediction were varied to investigate their effects on prediction accuracy: the effect was large for the size and composition of the training population but limited for the statistical method and marker density. Maximizing the relatedness between individuals in the training and test sets, through the CDmean-based method, significantly improved prediction accuracies. A cross-population cross-validation experiment was further conducted using the CRB339 collection as a training population set and nine recombinant inbred lines populations as test set. Prediction quality was high with mean Q2 of 0.44 for TSW and 0.59 for BegFlo. Results are discussed in the light of current efforts to develop GS strategies in pea.

Single-Transverse-Spin-Asymmetry studies with a fixed-target experiment using the LHC beams (AFTER@LHC)

We discuss the potential of AFTER@LHC to measure single-transverse-spin asymmetries in open-charm and bottomonium production. With a HERMES-like hydrogen polarised target, such measurements over a year can reach precisions close to the per cent level. This is particularly remarkable since these analyses can probably not be carried out anywhere else

A Fixed-Target Programme at the LHC: Physics Case and Projected Performances for Heavy-Ion, Hadron, Spin and Astroparticle Studies

The lower hybrid current drive (LHCD) plays an important role in the long pulse and high performance experiments on the EAST Tokamak, using LHW systems with frequencies of 2.45 GHz and 4.6 GHz. With the initial parallel refractive index mostly peaking at n∥∼1.8−2.1, it is difficult to have on-axis LHCD due to the accessibility conditions which prevents the LHW from propagating into the plasma core. However, according to the investigation of HXR diagnostics, LHW did provide an on-axis current drive in an EAST experiment. To interpret this on-axis LHCD phenomenon, various physics effects that give rise to variations in parallel wave numbers, thus influencing the propagation and the absorption of the LHW, have been taken into account, such as toroidal effects, full wave effects with focusing and diffraction, and scattering effects due to density fluctuations. Numerical tools including ray-tracing and full wave codes that contain one or two of the above physics effects have been used to model the heating and ...

Unleashing meiotic crossovers in crops

Improved plant varieties are hugely significant in our attempts to face the challenges of a growing human population and limited planet resources. Plant breeding relies on meiotic crossovers to combine favorable alleles into elite varieties (1). However, meiotic crossovers are relatively rare, typically one to three per chromosome (2), limiting the efficiency of the breeding process and related activities such as genetic mapping. Several genes that limit meiotic recombination were identified in the model species Arabidopsis (2). Mutation of these genes in Arabidopsis induces a large increase in crossover frequency. However, it remained to be demonstrated whether crossovers could also be increased in crop species hybrids. Here, we explored the effects of mutating the orthologs of FANCM3, RECQ44 or FIGL15 on recombination in three distant crop species, rice (Oryza sativa), pea (Pisum sativum) and tomato (Solanum lycopersium). We found that the single recq4 mutation increases crossovers ~three-fold in these crops, suggesting that manipulating RECQ4 may be a universal tool for increasing recombination in plants. Enhanced recombination could be used in combination with other state-of-the-art technologies such as genomic selection, genome editing or speed breeding to enhance the pace and efficiency of plant improvement.

Physics opportunities with a fixed target experiment at the LHC (AFTER@LHC)

By extracting the beam with a bent crystal or by using an internal gas target, the multi-TeV proton and lead LHC beams allow one to perform the most energetic fixed-target experiments (AFTER@LHC) and to study

Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species.

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QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance

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A fixed-target programme at the LHC for heavy-ion, hadron, spin and astroparticle physics: AFTER@LHC

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Stand grand public à la gare de Dijon : "5 légumineuses par jour"; dans le cardre des journées portes ouvertes du Centre de Dijon, France, 14-15-16 octobre 2016

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