A workflow to assemble plant mitochondrial genomes using long-reads: case study in Pisum sativum and Phaseolus vulgaris

Plant mitochondrial genomes are generally not used to study evolution within and between species. They are larger than animal mitochondrial genomes and evolve by accumulating rearrangements rather than mutations [1]. These characteristics make it difficult to obtain complete assemblies using short-reads like in mammals. To address this problem, we developed and tested a plant-based assembly workflow using Nanopore and Pacbio long-reads from Pisum sativum and Phaseolus vulgaris, respectively. Nanopore long-reads from Pisum sativum whole genome sequencing and Pacbio long-reads from Phaseolus vulgaris whole genome sequencing were mapped on all mitochondrial genomes available for legumes at NCB…

Beyond the sequencing of the pea genome: opportunities for genomics-based breeding and translational approaches

International audience; The tribe Fabeae comprises more than 300 legume species, including some of the most ancient and important crops like Pisum sativum (pea), Lens culinaris (lentil), and Vicia faba (faba bean) used for food and feed. The genome sequence of pea, released in 2019, is an important milestone for the community working on legumes and especially on Fabeae. It brings into light evidences related to the genome expansion that occurred after the divergence of Fabeae from their sister tribes and highlights different chromosomal rearrangement events specific or not to the Pisum lineage. The pea genome sequence also represents a valuable resource to accelerate our understanding of th…

The Pea genome and after...

GRaSP project Genetics of Rhizobia Selection by Pea

Prod 2019-88aa; National audience; Because of their ability to fix nitrogen in symbiosis with soil bacteria, legumes such as peas have an important role to play in the development of a sustainable agriculture. However, in the field, biological nitrogen fixation (BNF) could be suboptimal as natural Rhizobium leguminosarum viciae (Rlv) populations are quantitatively and qualitatively heterogeneous, with strains varying in their competitiveness and efficiency of BNF [1,2]. There is a general agreement concerning the interest of Rlv inoculation for improving BNF and thus pea yield [3]. However, even when pea seeds are inoculated by efficient Rlv strains these can be outcompeted by indigenous rh…

Taking cool-season grain legume breeding to the next level: the key role of the pea genome sequence

International audience; The transition from a standalone phenotypic selection to a marker-assisted selection has been seen as a great step forward to improve the breeding process and reach the expected goals. More recently, the genomic revolution has also had its great impact on breeding. -omics are now part of the required toolkit for a successful, cost and time-efficient breeding. The genome sequence of pea (Pisum sativum) has been made available in 2019 through a collaborative international effort. This is a great tool for the pea community in general and the Fabeae community in particular. Current challenges facing pea and other Fabeae production are numerous. A large number of traits h…

Complementary approaches towards the discovery of genes controlling yield in pea

International audience; Pea is one of the most important grain legumes in the world. Improving pea yield is a critical breedingtarget in the current context of consumers’ increasing demand for plant proteins for food and feed. Becauseof its polygenic nature and the impact of the environment, breeding for higher yield is challenging. Weinvestigated the genetic determinism of yield (SW), seed number (SN) and thousand seed weight (TSW) usingboth linkage and linkage-disequilibrium approaches.Nine interconnected mapping populations, representing a total of 1,213 recombinant inbred lineswere phenotyped for SW, SN and TSW in six different field environments. These lines were genotyped usingthe Gen…

The pea genome and beyond

International audience; The recently generated pea genome sequence is a significant step for the pea research community towards unravelling functional diversity and establishing genome-enabled breeding. Re-sequencing data reveal the considerable diversity present in the Pisum genus. High-throughput genotyping is now available to explore large collections using the exome capture technology in genome-wide association studies (GWAS) or tackle map-based QTL cloning. Furthermore, genomic selection strategies have been developed in order to tackle complex traits such as yield regularity and improve selection efficiency. We will present snapshots of these results and discuss potential transfer of …