High quality genome sequence reveals important events during domestication of White Lupin

Prod 2019-88m BAP GEAPSI INRA; International audience; White lupin (Lupinus albus; 2n=50) is the only crop producing cluster roots, an outstanding developmental adaptation to low phosphate soils. We report a high-quality chromosome-scale assembly of white lupin genome, together with an extensive transcriptome data from ten different organs. We used singlemolecule real-time technology, in combination with short-reads sequencing and optical and genetic maps to have a successful assembly. The final assembly size is 443 Mb with a N50 of 17 Mb. About 98% of the assembled genome is included on the 25 pseudo-chromosomes. The structural annotation identified 38258 coding genes and 3,129 ncRNA, bein…

Use of translational genomics to identify genes important for legume seed filling

International audience; Translational genomics, i.e., the transfer of genetic information from model species to cultivated crops, is on the brink of revolutionizing plant breeding. The recent publication of genomic sequences for several cultivated legumes is also accelerating this process. For pea, recent highthroughput RNA sequencing, and the prospect of a genome sequencing project, will further accelerate the transfer of information from the Medicago truncatula model to the cultivated crop. We have been using genomics approaches with Medicago as a tool to identify key genes determining seed yield and composition in closely related legumes. Analyses of the proteome and transcriptome of the…

A transcriptomics-based approach enables the first identification of candidate genes involved in non-target-site-based resistance to herbicides in a grass weed (Alopecurus myosuroides)

International audience; Herbicides are the most effective way to control weeds. Yet, the evolution of resistance in many weed species is a considerable threat to herbicide efficacy. Non-target-site-based resistance (NTSR) is the most threatening facet of herbicide resistance. NTSR is widespread, involves a variety of mechanisms, and can confer unpredictable resistance to herbicides, regardless of the herbicide mode of action. Because NTSR is endowed by differences in the expression of a number of genes in resistant and sensitive weed plants, few genes governing NTSR are currently known. This renders NTSR diagnosis and management tricky. The rise of next-generation sequencing technologies no…

Pea in the genomic era

Characterisation of rye-grass (Lolium sp.) transcriptome-wide response to ALS-inhibiting herbicides

International audience; Non-target-site-resistance (NTSR) to herbicides is a major cause for failure in the chemical control of a number of weeds, and is especially widespread and important in grass weeds. Although several gene families have been shown to be involved in NTSR (cytochromes p450, glutathione-S-transferases, glycosyl-transferases, ABC transporters, esterases…), the genetic determinants of NTSR are still poorly known to date. NTSR is part of the response of weeds to herbicides. To unravel NTSR, it is thus of interest to firstly characterise the processes involved in herbicide stress response in grasses. For this purpose, we implemented a comparative whole-transcriptome sequencin…

Use of translational genomics to identify genes important for legume seed development

BAP Pôle GEAPSI; International audience; We have exploited the extensive synteny between the model legume Medicago truncatula and the cultivated garden pea, Pisumsativum, to identify loci controlling seed filling and seedcomposition in the crop species. QTLs for these traits are mapped by analyzing variation with in collections of recombinant inbred lines. Candidate genes with in the QTL intervals are identified by reference to the M.truncatula genomic sequence. This approach was used to uncover an endosperm subtilase that is associated with syntenic seed weight QTLs in Medicago and pea, and we discuss the possible role played by this enzyme in contributing to final seed weight.

Identification de mécanismes de résistance non liée à la cible grâce à la transcriptomique

We have witnessed a dramatic increase in the number of weeds showing herbicide resistance during the past three decades. The potentially most dangerous mechanisms of resistance endows Non-Target-Site based Resistance (NTSR): NTSR is polygenic, unpredictable and can confer cross-resistance to herbicides with different modes of action. High throughput sequencing methods, like RNA sequencing (RNA-seq), are particularly effective to identify genes differentially expressed between two experimental modalities. Therefore, RNA sequencing was implemented to identify genes involved in NTSR to clodinafop (an ACCase inhibitor) in black-grass. Black-grass transcriptome was sequenced from 4 sensitive pla…

A whole-transcriptome approach to unravel non-target-site-based resistance to ALS inhibitors in Ambrosia artemisiifolia

International audience; Non-target-site-resistance (NTSR) to herbicides is a major cause for chemical control failure in a number of weeds. Studies investigating NTSR essentially considered grass weeds. Here, we investigated the transcriptomic bases of NTSR to ALS inhibitors in the global, allergenic weed Ambrosia artemisiifolia. Our objectives were to establish a transcriptome resource for A. artemisiifolia and to use a comparative, quantitative transcriptome sequencing approach (RNA-Seq) to identify candidate NTSR genes in this species. Using the PacBio sequencing technology that generate long sequence reads, a transcriptome resource was obtained from the apical part of one 4-leaf plant, …

Pea in the genomic era

Pea in the genomic era. Séminaire IFR AIB (Agrobiosciences, Interactions & Biodiversité)

Diagnosis of non target site based resistance within rye grass(Lolium sp): development of quick and reliable tests

Non target site resistance (NTSR) is the major threat for effective herbicide-based control of grass weeds. NTSR, still largely unknown, is endowed by the regulation of a subset of the genes involved in the response of the weed to herbicide treatment. This study aims at identifying NTSR genes in rye-grass to develop resistance diagnosis tests. The transcriptome of plants resistant or sensitive to ALS inhibitors collected before and after herbicide application was sequenced using a deep sequencing technology. We identified genes differentially expressed between resistant and sensitive plants. We developed a RT-qPCR test to measure gene expression levels in individual plants from several popu…