Exploiting a fast neutron mutant genetic resource in Pisum sativum (pea) for functional genomics

Abstract

Abstract.A fast neutron (FN)-mutagenised population was generated in Pisum sativum L. (pea) to enable the identification and isolation of genes underlying traits and processes. Studies of several phenotypic traits have clearly demonstrated the utility of the resource by associating gene deletions with phenotype followed by functional tests exploiting additional mutant sources, from both induced and natural variant germplasm. For forward genetic screens, next generation sequencing methodologies provide an opportunity for identifying genes associated with deletions rapidly and systematically. The application of rapid reverse genetic screens of the fast neutron mutant pea population supports conclusions on the frequency of deletions based on phenotype alone. These studies also suggest that large deletions affecting one or more loci can be non-deleterious to the pea genome, yielding mutants that could not be obtained by other means. Deletion mutants affecting genes associated with seed metabolism and storage are providing unique opportunities to identify the products of complex and related gene families, and to study the downstream consequences of such deletions.

Linking Auxin with Photosynthetic Rate via Leaf Venation

“…The recessive mutant alleles were named crd-1 (Swiecicki, 1989), crd-2 (Berdnikov et al, 2000), crd-3 (FN 1522/1), and crd-4 (UTILLdb L905). To identify the gene affected in the crd mutants, we used a nextgeneration RNA sequencing approach, focusing on the identification of any transcripts missing from the crd-3 allele, as most lesions characterized so far from the JI 2822-derived fast-neutron mutant population have been large, gene-sized deletions (Domoney et al, 2013). We assembled a reference transcriptome from the corresponding wild-type line (WT-3) comprising 79,693 contigs (N50 = 1,191 bp), and used this reference transcriptome to map reads from triplicate crd-3 samples.…”

“…In this paper, two novel crd mutant alleles were identified. The crd-3 mutant was identified as line FN 1522/1 in a fast neutron mutagenesis population of the JI 2822 line (WT-3; Domoney et al, 2013). The crd-4 mutant was observed incidentally in line 905, derived from an ethyl methane sulfonate mutagenesis population of the Caméor line in the UTILLdb program (Dalmais et al, 2008).…”

Grain Legumes

“…The JIC Pisum Genetic Stocks are partially duplicated at the USDA (Ambrose and Coyne 2009), and at Polish (297) and Bulgarian (150 accessions) genebanks. Also maintained by JIC is a fast neutron (FN) population started with 1400 seeds of JI 2822 subjected to 20 Grays FN radiation (Domoney et al 2013;Hofer et al 2009). A very fruitful targeting induced local lesions in genomes (TILLING) reference population from the pea cultivar 'Caméor' and database (UTILLdb) resource is available for forward and reverse genetics from INRA ( urgv.evry.inra.fr/UTILLdb;Dalmais et al 2008).…”

“…It may be expected that novel mutants affecting flowering time, seed composition and yield are in the pipeline and will be in demand by breeders. Equally, the development of high-throughput and rapid screening methodologies for the detection of deletion mutants for seed quality targets (Domoney et al 2013) may be expected to expand the potential for the identification and introduction of novelty by breeders.…”

Translational Genomics in Agriculture: Some Examples in Grain Legumes

“…However, systematic mutant populations have been developed in several species in order to address this issue. TILLING populations are available for L. japonicus, pea, M. truncatula and chickpea (Dalmais et al, 2008;Le-Signor et al, 2009;Perry et al, 2003;Varshney et al, unpublished), Fast Neutron generated deletion mutant populations for M. truncatula, pea and soybean (Bolon et al, 2011;Hofer et al, 2009;Rogers et al, 2009;Smykal et al, 2012) and insertion mutant populations generated using exogenous (Medicago, d 'Erfurth et al, 2003) and endogeneous retrotransposons (Lotus, Urbański et al, 2012) have been generated and have contributed to gene discovery in these species (see Domoney et al, 2013;Domonkos et al, 2013;Urbański et al, 2013).…”