Biology subjects

Pidon, H.

Publications and source records attributed to Pidon, H..

10 recordsLinked to original sources

bioRxiv2026

Epistatic interaction of the genes Raw1 and Raw7 controls barb size and frequency in barley awn roughness

Awns of wild barley (Hordeum vulgare ssp. spontaneum L.) are rough by default due to silicified upward-oriented trichomes on the awns epidermis, forming a ratcheted surface, which is advantageous for seed dispersal and burial. Cultivated barley, however, may carry smooth awns covered by smaller barbs or lacking barbs completely. The gene Raw1 on chromosome 5H is a major factor controlling barley awn roughness and was shown to encode a LONG AND BARBED AWN1 (LABA1) homolog. Here we report, by using quantitative analysis of the barb trait, map-based cloning and Cas9-mediated gene knock-out, a second gene Raw7, located on barley chromosome 7H, encoding a putative two-component response regulator. We propose that Raw7 acts downstream of Raw1 in a cytokinin signaling pathway underlying cell cycle control in epidermal barb primordia cells. Raw1 and Raw7 show epistatic interaction, suggesting that Raw1 acts as the primary driver of barb initiation, while Raw7 modulates barb size and frequency. Our findings provide the foundation to study the selection and domestication history of the awn roughness trait in barley, and thus to dissect if awn roughness is providing an advantage in cultivated barley or if the trait persisted after domestication due to linkage drag. SummaryO_LIThe presence of silicified upward-oriented trichomes or barbs arising from the epidermis of barley awns is a prominent trait. They form a ratcheted surface which is advantageous for seed dispersal and burial and defense against herbivory. C_LIO_LIPrevious work identified Raw1 on chromosome 5H as a major determinant of awn roughness in barley. Here, we identify a second awn roughness gene, Raw7 on chromosome 7H, combining quantitative phenotyping of barb traits, map-based cloning and Cas9-mediated targeted mutagenesis for functional analyses. C_LIO_LIGenetic and functional evidence suggests a complex epistatic interaction in which Raw1 primarily drives barb formation and Raw7 fine-tunes endoreduplication-dependent epidermal cell expansion and patterning in barb primordia cells. Raw1 and Raw7 likely act in a cytokinin-dependent two-component signaling pathway, where Raw1 promotes local cytokinin activation and Raw7, a type-B response regulator, mediates downstream transcriptional responses. C_LIO_LIThe proposed pathway suggests additional undetected loci may contribute to awn roughness, and emerging barley pangenome and pan-transcriptome resources provide a framework to identify and functionally validate new candidates. C_LI

plant biology↗

bioRxiv2025

Leaf variegation in a barley EMS mutant is controlled by two epistatic mutations

Variegation mutants provide valuable insights into chloroplast biogenesis. We characterized a newly identified variegated barley mutant, in which the phenotype is controlled by duplicate dominant epistasis--representing, to our knowledge, the first reported case of digenic control in chloroplast-deficient mutants. The causal loci, Var4 and Var5, were mapped on chromosomes 2H and 3H. We used whole-genome resequencing to identify candidate genes. Our two top candidate genes are an NBR1-like selective autophagy receptor gene and a DNAJ-domain containing gene, respectively. Based on their homology-based functional annotation, both candidates could be implicated in chloroplast proteostasis, regulating protein import, folding, and/or degradation. We propose that mild, independent defects in proteostasis from each mutation act synergistically to surpass a functional threshold, impairing chloroplast development in early leaves while allowing partial recovery in later stages. These findings highlight a novel digenic mechanism underlying variegation and point to proteostasis as a central vulnerability in chloroplast biogenesis. HighlightWe identified digenic control of leaf variegation in a barley mutant. Candidate genes, identified through whole-genome resequencing, suggest roles in chloroplast proteostasis.

plant biology↗

bioRxiv2024

Autoregulation of cluster root and nodule development by white lupin CCR1 receptor-like kinase

Root development is controlled by local and systemic regulatory mechanisms that optimize mineral nutrient uptake and carbon allocation. The Autoregulation of Nodulation (AoN) pathway defines a negative regulation of nodule development in Legumes as a way to regulate the costly production of nitrogen-fixing organs. This pathway is defined as a response to symbiotic interaction and has been shown to also control root formation to some extent. However, it remains unclear if root and nodule development are under coordinated genetic regulation. Here, we identified mutants with altered root development in white lupin, constitutively producing specialized lateral roots called cluster roots. We showed that the CCR1 receptor-kinase negatively regulates cluster root and nodule development and targets common molecular modules such as NIN/LBD16-NFYA, defining a novel pathway that we named Autoregulation of Development (AoDev). AoDev defines a negative systemic pathway controlling several types of root organ development, independently of symbiotic partners and nutrient availability.

plant biology↗

bioRxiv2024

Adaptive diversification through structural variation in barley

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here, we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that have become hot spots of gene copy number variation in evolutionarily recent times. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that rapid evolution at structurally complex loci may have helped crop plants adapt to new selective regimes in agricultural ecosystems.

plant biology↗

bioRxiv2023

High-resolution mapping of Ryd4Hb, a major resistance gene to Barley yellow dwarf virus from Hordeum bulbosum

Virus diseases are causing high yield losses in crops worldwide. The Barley yellow dwarf virus (BYDV) complex is responsible for one of the most widespread and economically important viral diseases of cereals. While no complete resistance gene has been uncovered in the primary genepool of barley, sources of resistance were identified in the wild relative Hordeum bulbosum, representing the secondary genepool of barley. One such locus, Ryd4Hb, has been previously introgressed into barley, and was allocated to chromosome 3H, but is tightly linked to a sublethality factor that prevents the incorporation and utilization of Ryd4Hb in barley varieties. To solve this problem, we fine-mapped Ryd4Hb and separated it from this negative factor. We narrowed the Ryd4Hb locus to a 66.5 kbp physical interval in the barley Morex reference genome. The region comprises one complete and one partial gene from the nucleotide-binding and leucine-rich repeat immune receptor family, typical of dominant virus resistance genes. The closest homolog to these two Ryd4Hb candidate genes is the wheat Sr35 stem rust resistance gene. In addition to the fine mapping, we reduced the sublethality factor interval to 600 kbp in barley. Aphid feeding experiments demonstrated that Ryd4Hb provides a direct resistance to BYDV rather than a resistance to its vector. The presented results, including the high-throughput molecular markers, will permit a more targeted selection of the resistance in breeding, enabling the use of Ryd4Hb in barley varieties. Key messageWe mapped Ryd4Hb in a 66.5 kpb interval in barley and dissociated it from a sublethality factor. These results will enable a targeted selection of the resistance in barley breeding.

plant biology↗

bioRxiv2021

ATP-dependent Clp protease subunit C1, HvClpC1, is a strong candidate gene for barley variegation mutant luteostrians as revealed by genetic mapping and genomic re-sequencing

Implementation of next-generation sequencing in forward genetic screens greatly accelerated gene discovery in species with larger genomes, including many crop plants. In barley, extensive mutant collections are available, however, the causative mutations for many of the genes remains largely unknown. Here we demonstrate how a combination of low-resolution genetic mapping, whole-genome resequencing and comparative functional analyses provides a promising path towards candidate identification of genes involved in plastid biology and / or photosynthesis, even if genes are located in recombination poor regions of the genome. As a proof of concept, we simulated the prediction of a candidate gene for the recently cloned variegation mutant albostrians (HvAST / HvCMF7) and adopted the approach for suggesting HvClpC1 as candidate gene for the yellow-green variegation mutant luteostrians. Author SummaryForward genetics is an approach of identifying a causal gene for a mutant phenotype and has proven to be a powerful tool for dissecting the genetic control of biological processes in many species. A large number of barley mutants was generated in the 1940s to 1970s when mutation breeding programs flourished. Genetic dissection of the causative mutations responsible for the phenotype, however, lagged far behind, limited by lack of molecular markers and high-throughput genotyping platforms. Next-generation sequencing technologies have revolutionized genomics, facilitating the process of identifying mutations underlying a phenotype of interest. Multiple mapping-by-sequencing or cloning-by-sequencing strategies were established towards fast gene discovery. In this study, we used mapping-by-sequencing to identify candidate genes within coarsely delimited genetic intervals, for two variegation mutants in barley - luteostrians and albostrians. After testing the approach using the example of the previously cloned albostrians gene HvAST, the gene HvClpC1 could be delimited as candidate gene for luteostrians. The mapping-by-sequencing strategy implemented here is generally suited for surveying barley mutant collections for phenotypes affecting fundamental processes of plant morphology, physiology and development.

genetics↗

bioRxiv2020

High-resolution mapping of Rym14Hb, a wild relative resistance gene to barley yellow mosaic disease

Barley yellow mosaic disease is caused by Barley yellow mosaic virus and Barley mild mosaic virus, and leads to severe yield losses in barley (Hordeum vulgare) in Central Europe and East-Asia. Several resistance loci are used in barley breeding. However, cases of resistance-breaking viral strains are known, raising concerns about the durability of those genes. Rym14Hb is a dominant major resistance gene on chromosome 6HS, originating from barleys secondary genepool wild relative Hordeum bulbosum. As such, the resistance mechanism may represent a case of non-host resistance, which could enhance its durability. A susceptible barley variety and a resistant H. bulbosum introgression line were crossed to produce a large F2 mapping population (n=7,500), to compensate for a ten-fold reduction in recombination rate compared to intraspecific barley crosses. After high-throughput genotyping, the Rym14Hb locus was assigned to a 2Mbp telomeric interval on chromosome 6HS. The co-segregating markers developed in this study can be used for marker-assisted introgression of this locus into barley elite germplasm with a minimum of linkage drag.

plant biology↗

bioRxiv2020

Allele mining unlocks the identification of RYMV resistance genes and alleles in African cultivated rice.

BackgroundRice yellow mosaic virus (RYMV) is a major rice pathogen in Africa. Three resistance genes, i.e. RYMV1, RYMV2 and RYMV3, have been previously described. RYMV1 encodes the translation initiation factor eIF(iso)4G-1 and the best candidate genes for RYMV2 and RYMV3 encode a homolog of an Arabidopsis nucleoporin (CPR5) and a nucleotide-binding domain and leucine-rich repeat containing domain (NLR) protein, respectively. High resistance is very uncommon in Asian cultivated rice (Oryza sativa), with only two highly resistant accessions identified so far, but it is more frequent in African cultivated rice (Oryza glaberrima). ResultsHere we report the findings of a resistance survey in a reference collection of 268 O. glaberrima accessions. A total of 40 resistant accessions were found, thus confirming the high frequency of resistance to RYMV in this species. We analysed the variability of resistance genes or candidate genes in this collection based on high-depth Illumina data or Sanger sequencing. Alleles previously shown to be associated with resistance were observed in 31 resistant accessions but not in any susceptible ones. Five original alleles with a frameshift or untimely stop codon in the candidate gene for RYMV2 were also identified in resistant accessions. A genetic analysis revealed that these alleles, as well as T-DNA insertions in the candidate gene, were responsible of RYMV resistance. All 40 resistant accessions were ultimately linked to a validated or candidate resistance allele at one of the three resistance genes to RYMV. ConclusionThis study demonstrated that the RYMV2 resistance gene is homologous to the Arabidopsis CPR5 gene and revealed five new resistance alleles at this locus. It also confirmed the close association between resistance and an amino-acid substitution in the leucine-rich repeat of the NLR candidate for RYMV3. We also provide an extensive overview of the genetic diversity of resistance to RYMV in the O. glaberrima species, while underlining the contrasted pattern of diversity between O. glaberrima and O. sativa for this trait. The different resistance genes and alleles will be instrumental in breeding varieties with sustainable field resistance to RYMV.

plant biology↗

bioRxiv2020

Genome wide association study pinpoints key agronomic QTLs in African rice Oryza glaberrima

BackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. ResultsUsing a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we demonstrated that we could successfully retrieve known genes from the rice flowering pathway, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting QTLs and candidate genes (including Rymv1 for resistance and SP1, Ghd7.1, APO1 and OsMADS1 for panicle architecture). Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. ConclusionOur results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

plant biology↗

bioRxiv2019

High resolution mapping of a Hordeum bulbosum-derived powdery mildew resistance locus in barley using distinct homologous introgression lines

Powdery mildew caused by Blumeria graminis f.sp. hordei (Bgh) is one of the main foliar diseases in barley (Hordeum vulgare L.; Hv). Naturally occurring resistance genes used in barley breeding are a cost effective and environmentally sustainable strategy to minimize the impact of pathogens, however, the primary gene pool of H. vulgare contains limited diversity owing to recent domestication bottlenecks. To ensure durable resistance against this pathogen, more genes are required that could be unraveled by investigation of secondary barley gene-pool. A large set of Hordeum bulbosum (Hb) introgression lines (ILs) harboring a diverse set of desirable resistance traits have been developed and are being routinely used as source of novel diversity in gene mapping studies. Nevertheless, this strategy is often compromised by a lack of recombination between the introgressed fragment and the orthologous chromosome of the barley genome. In this study, we fine-mapped a Hb gene conferring resistance to barley powdery mildew. The initial genotyping of two Hb ILs mapping populations with differently sized 2HS introgressions revealed severely reduced interspecific recombination in the region of the introgressed segment, preventing precise localization of the gene. To overcome this difficulty, we developed an alternative strategy, exploiting intraspecific recombination by crossing two Hv/Hb ILs with collinear Hb introgressions, one of which carries a powdery mildew resistance gene, while the other doesnt. The intraspecific recombination rate in the Hb-introgressed fragment of 2HS was approximately 20 times higher than it was in the initial simple ILs mapping populations. Using high-throughput genotyping-by-sequencing (GBS), we allocated the resistance gene to a 1.4 Mb interval, based on an estimate using the Hv genome as reference, in populations of only 103 and 146 individuals respectively, similar to what is expected at this locus in barley. The most likely candidate resistance gene within this interval encodes a legume-type lectin-receptor-like protein (LecRLP). Like other LecRLPs that have been implicated in resistance, this gene could be a good candidate for Hb resistance. The reported strategy can be applied as a general strategic approach for identifying genes underlying traits of interest in crop wild relatives.

plant biology↗