Rice diversity panel provides accurate genomic predictions for complex traits in the progenies of biparental crosses involving members of the panel

So far, most potential applications of genomic prediction in plant improvement have been explored using cross validation approaches. This is the first empirical study to evaluate the accuracy of genomic prediction of the performances of progenies in a typical rice breeding program. Using a cross validation approach, we first analyzed the effects of marker selection and statistical methods on the accuracy of prediction of three different heritability traits in a reference population (RP) of 284 inbred accessions. Next, we investigated the size and the degree of relatedness with the progeny population (PP) of sub-sets of the RP that maximize the accuracy of prediction of phenotype across generations, i.e., for 97 F5–F7 lines derived from biparental crosses between 31 accessions of the RP. The extent of linkage disequilibrium was high (r2 = 0.2 at 0.80 Mb in RP and at 1.1 Mb in PP). Consequently, average marker density above one per 22 kb did not improve the accuracy of predictions in the RP. The accuracy of progeny prediction varied greatly depending on the composition of the training set, the trait, LD and minor allele frequency. The highest accuracy achieved for each trait exceeded 0.50 and was only slightly below the accuracy achieved by cross validation in the RP. Our results thus show that relatively high accuracy (0.41–0.54) can be achieved using only a rather small share of the RP, most related to the PP, as the training set. The practical implications of these results for rice breeding programs are discussed. (Résumé d'auteur

Identification of SNP and SSR markers in eggplant using RAD tag sequencing

<p>Abstract</p> <p>Background</p> <p>The eggplant (<it>Solanum melongena </it>L.) genome is relatively unexplored, especially compared to those of the other major <it>Solanaceae </it>crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant.</p> <p>Results</p> <p>RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci.</p> <p>Conclusion</p> <p>The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the <it>Solanaceae </it>family.</p

The CC-NB-LRR-Type Rdg2a Resistance Gene Confers Immunity to the Seed-Borne Barley Leaf Stripe Pathogen in the Absence of Hypersensitive Cell Death

BACKGROUND: Leaf stripe disease on barley (Hordeum vulgare) is caused by the seed-transmitted hemi-biotrophic fungus Pyrenophora graminea. Race-specific resistance to leaf stripe is controlled by two known Rdg (Resistance to Drechslera graminea) genes: the H. spontaneum-derived Rdg1a and Rdg2a, identified in H. vulgare. The aim of the present work was to isolate the Rdg2a leaf stripe resistance gene, to characterize the Rdg2a locus organization and evolution and to elucidate the histological bases of Rdg2a-based leaf stripe resistance. PRINCIPLE FINDINGS: We describe here the positional cloning and functional characterization of the leaf stripe resistance gene Rdg2a. At the Rdg2a locus, three sequence-related coiled-coil, nucleotide-binding site, and leucine-rich repeat (CC-NB-LRR) encoding genes were identified. Sequence comparisons suggested that paralogs of this resistance locus evolved through recent gene duplication, and were subjected to frequent sequence exchange. Transformation of the leaf stripe susceptible cv. Golden Promise with two Rdg2a-candidates under the control of their native 5′ regulatory sequences identified a member of the CC-NB-LRR gene family that conferred resistance against the Dg2 leaf stripe isolate, against which the Rdg2a-gene is effective. Histological analysis demonstrated that Rdg2a-mediated leaf stripe resistance involves autofluorescing cells and prevents pathogen colonization in the embryos without any detectable hypersensitive cell death response, supporting a cell wall reinforcement-based resistance mechanism. CONCLUSIONS: This work reports about the cloning of a resistance gene effective against a seed borne disease. We observed that Rdg2a was subjected to diversifying selection which is consistent with a model in which the R gene co-evolves with a pathogen effector(s) gene. We propose that inducible responses giving rise to physical and chemical barriers to infection in the cell walls and intercellular spaces of the barley embryo tissues represent mechanisms by which the CC-NB-LRR-encoding Rdg2a gene mediates resistance to leaf stripe in the absence of hypersensitive cell death.Davide Bulgarelli, Chiara Biselli, Nicholas C. Collins, Gabriella Consonni, Antonio M. Stanca, Paul Schulze-Lefert and Giampiero Val

Genetic bases of barley resistance to the leaf stripe agent Pyrenophora graminea.

Leaf stripe, caused by Pyrenophora graminea, is a serious disease of barley in many productionareas. Genetic mapping of major genes and quantitative trait loci for this disease has revealedresistance loci on the chromosomes 1(7H), 2 (2H) and 3(3H). QTLs for partial resistance have beenidentified in segregating populations derived from the crosses between Proctor and Nudinka, L94and Vada, L94 and C123, Steptoe and Morex. Major genes conferring useful range of activity havebeen identified in the barley cultivars Vada and Thibaut. The Thibaut resistance gene, named asRdg2a, has been subjected to high resolution mapping and a syntenic relationship of the resistancegene locus with rice chromosome 6 has been established. In the course of the mapping of major andquantitative disease resistance loci, molecular markers for resistance breeding for disease controlusing gene technology have been identified and validated for utilization in marker assisted selectionof disease resistance

Investigation of rice blast development in susceptible and resistant rice cultivars using a gfp-expressing Magnaporthe oryzae isolate

In this study, an isolate of Magnaporthe oryzae expressing the green fluorescent protein gene (gfp) was used to monitor early events in the interaction of M. oryzae with resistant rice cultivars harbouring a blast resistance (R) gene. In the resistant cultivars Saber and TeQing (Pib gene), M. oryzae spores germinated normally on the leaf surface but produced morphologically abnormal germ tubes. Germling growth and development were markedly and adversely affected in leaves of these resistant cultivars. Penetration of host cells was never seen, supporting the idea that disruption of germling development on the leaf surface might be one of the resistance mechanisms associated with Pib function. Thus, this particular R gene appeared to function in the absence of host penetration by the fungal pathogen. Confocal laser scanning microscopy of M. oryzae-infected susceptible rice cultivars showed the dimorphic growth pattern that is typically observed during the biotrophic and necrotrophic stages of leaf colonization in susceptible cultivars. The suitability of the gfp-expressing M. oryzae isolate for further research on R-gene function and identification of resistant genotypes in rice germplasm collections is discussed.LCS was a recipient of a predoctoral fellowship from the Generalitat de Catalunya. We are grateful to A. Godó for her collaboration in parts of this work. This work was funded by grant BIO2009-08719 from MINECO and the Proyecto Intramural 200420E613 from CSIC to BSS, the Consolider-Ingenio CSD2007-00036 to CRAG, the VALORYZA project (DM 301/7303/06 Ministero delle Politiche Agricole, Rome, Italy) to EL, and the EU co-funded project EURIGEN (049 AGRI GEN RES). We also thank the Xarxa de Referencia en Biotechnologia and SGR (Support to Research Groups from the Agència de Gestió d'Ajuts Universitaris i de Recerca) from the Generalitat de Catalunya for substantial support. EL acknowledges a CRA grant as visiting scientist at CRAG, Barcelona.Peer reviewe

La coltivazione del riso in regime biologico: i risultati della sperimentazione 2012

Within the frame of an experimental project on organic farming, cultivation trials were performed to characterize rice varietal response on farms with expertise in rice organic farming cultivation. Selected varieties included recently developed and traditional ones belonging to all different merceological classes. For the round rice group, the varieties were Brio, Cerere, Ducato and Selenio. For the long A group, varieties were chosen according to their end use: Loto and Opale, utilized for the production of parboiled rice while Ulisse, Meco and Volano for the national market. For the long B group Arsenal, Ellebi and Salvo were tested. The experimentation revealed an average yield of about 6 t/ ha, therefore lower than those recorded under conventional farming conditions. The highest yield was observed in Mede Lomellina (Pv) with Brio, Opale and Meco, being the best performing varieties with about 7 t/ha, while in Valle Lomellina (PV) average yield was lower (5,9 t/ha) and the varieties with highest yield were Loto, Opale, Ulisse (about 6,5 t/ha) and finally Selenio with about 8 t/ha. Considering also the availability of data derived from the experimentation of the previous years, data highlighted that within the round group the varieties Brio and Selenio were the most adaptable ones to organic farming conditions. Within the long A group, Opale for parboiled rice, and Volano for national market demonstrated to provide good yield levels for the 3 years although the cultivar Volano had serious lodging, while within the long B group, Ellebi was the best performing considering the three years of trials and Arsenal showed good yield and high amylose content

Leaf stripe resistance gene in Barley: marker assisted selection and fine mapping of the resistance gene Rdg2a

A barley gene conferring resistance to the leaf stripe agent has been mapped on the chromosome arm 7HS. This resistance gene, named as Rdg2a, confers resistance towards several isolates having therefore a useful range of activity. To verify the reliability of a PCRbased marker (MWG2018) associated to the resistance gene to assess the leaf stripe resistant phenotype in barley breeding programs, several resistant lines obtained from several crosses were tested for the allelic composition at the MWG2018 locus. The results showed that the resistant phenotype of the lines was always associated with the resistant allele of the molecular marker, evidentiating the reliability of this marker to select for leaf stripe resistance; this marker is routinely used in practical breeding. To saturate the Rdg2a chromosomal region with molecular markers, two approaches have substantially been used: 1) several RGAs have been tested for co-segregation with Rdg2a; 2) by exploiting the syntenic relationships between the telomeric regions of barley chromosome 7H and rice chromosome 6, rice ESTs informations have been used to generate PCR-based markers then mapped in the Rdg2a mapping population. By using these approaches, we have observed tight association of RGAs with Rdg2a and conservation of syntenic relationships between the telomeric regions of barley chromosome 7H and rice chromosome 6 for the Rdg2a chromosomal region