Biology subjects

Wairich, A.

Publications and source records attributed to Wairich, A..

3 recordsLinked to original sources

bioRxiv2021

Structural and molecular characterization of the Rpv3 locus towards the development of KASP markers for downy mildew resistance in grapevine (Vitis spp.)

Plasmopara viticola is the oomycete that causes downy mildew in grapevine. Varying levels of resistance to P. viticola across grape cultivars allowed quantitative trait loci to be identified. The Rpv3 locus is located at chromosome 18, in a region enriched in TIR-NBS-LRR genes, and the phenotype associated is a high hypersensitive response. In this work, we aimed to identify candidate genes associated with resistance to downy mildew on the Rpv3 locus and to evaluate their transcriptional profiles in a susceptible and a resistant grapevine cultivar after challenging with P. viticola. Candidate genes were identified by representational differential analysis and also by functional enrichment tests. Many predicted genes associated with resistance to diseases were found at the Rpv3 locus. In total, seventeen genes were evaluated by RT-qPCR. Differences in the steady-state expression of these genes were observed between the two cultivars. Four genes were found to be expressed only in Villard Blanc, suggesting their association to the hypersensitivity reaction. Concerning marker assisted-selection for downy mildew resistance, we show the efficient use of a haplotype of SSR markers. Furthermore, based on Rpv3-located SNPs between grapevine cultivars contrasting in downy mildew resistance, we developed and tested forty-one new markers for assisted selection. After genotypic and phenotypic evaluations on segregant populations, two markers, Rpv3_15 and Rpv3_33, were considered efficient for downy mildew resistance identification. This study constitutes an in-depth genomic characterization of the Rpv3 locus, confirms its involvement in resistance against P. viticola infection and presents promising biotechnological tools for the selection of young resistant individuals.

molecular biology↗

bioRxiv2020

Introgression from Oryza meridionalis into domesticated rice Oryza sativa results in shoot-based iron tolerance

Iron (Fe) toxicity is one of the most common mineral disorders affecting rice (Oryza sativa) production in flooded lowland fields. Oryza meridionalis is endemic from Northern Australia and grows in regions with Fe rich soils, making it a candidate for use in adaptive breeding. Aiming to understand tolerance mechanisms in rice, we screened a population of interspecific introgression lines (IL) from a cross between O. sativa and O. meridionalis for the identification of QTLs contributing to Fe toxicity tolerance. Six putative QTLs were identified. A line carrying one introgression from O. meridionalis on chromosome 9 associated with one QTL was highly tolerant despite very high shoot Fe concentrations. Physiological, biochemical, ionomic and transcriptomic analyses showed that the IL tolerance could partly be explained by Fe retention in the leaf sheath and culm. We constructed the interspecific hybrid genome in silico for transcriptomic analysis, and identified differentially regulated introgressed genes from O. meridionalis that could be involved in shoot-based Fe tolerance, such as metallothioneins, glutathione S-transferases and transporters from ABC and MFS families. This is the first work to demonstrate that introgressions of O. meridionalis into the O. sativa genome can confer increased tolerance to excess Fe. HighlightWe identified QTLs associated with iron tolerance derived from O. meridionalis, and characterized their physiological basis in O. sativa.

plant biology↗

bioRxiv2019

The Mitochondrial Iron Regulated (MIR) gene is Oryza genus-specific and evolved before the speciation of major AA-genome lineages

Rice (Oryza sativa L.) is both a model species and an economically relevant crop. The Oryza genus comprises 25 species, which constitute a genetic reservoir for cultivated rice breeding. Genomic data is available for several Oryza species, making it a good model for genetics and evolution within closely related species. The Mitochondrial Iron Regulated (MIR) gene was previously implicated in O. sativa Fe deficiency response, and was considered an orphan gene present only in rice. Here we show that MIR is also found in other Oryza species that belong to the AA genome group. We characterized the evolutionary pattern of MIR genes within the Oryza genus. Our data suggest that MIR originated de novo from non-coding sequences present only in AA genome species, but these sequences in turn are derived from an exon fragment of Raffinose Synthase genes, present in several groups of monocots. We also show that all species that have a putative functional MIR conserve their regulation by Fe deficiency, with the exception of Oryza barthii. In O. barthii, the MIR coding sequence was translocated to a different chromosomal position and separated from its regulatory region, which led to a lack of Fe deficiency responsiveness. Moreover, we show that MIR co-expression subnetwork cluster in O. sativa is responsive to Fe deficiency, evidencing the importance of the newly originated gene in Fe uptake. This work establishes that MIR is not an orphan gene as previously proposed, but a de novo originated gene within the Oryza genus. We also showed that MIR is undergoing genomic changes in at least one species (O. barthii), which can impact its role in Fe deficiency.

plant biology↗