Biology subjects

Budak, H.

Publications and source records attributed to Budak, H..

6 recordsLinked to original sources

bioRxiv2023

Genome-wide characterization of MLO family genes in bread wheat shed light on their role in powdery mildew, rusts, blight, abiotic stresses, and development

Powdery mildew (PM) is a notorious disease that causes up to 62% of yield losses in wheat. The 66 PM resistance quantitative trait loci (QTL)/genes (Pm1 - Pm66) break down when new pathogen races interact with plants. The knockout of three wheat Mildew resistance locus o (MLO) has conferred stable resistance against PM. However, only seven MLO genes are known in bread wheat, which has limited the development of PM-resistant cultivars. Taking advantage of IWGSC Ref-seq v2.1, we identified 47 MLO genes in wheat that were distributed on all 21 chromosomes in a non-random fashion. Phylogenetic analysis showed that MLOs are divided into four clades/subfamilies, while clades I, II, III, and IV harbored 6, 28, 6, and 7 MLO genes, respectively. The phylogenetic patterns were strongly supported by gene structure and motif distribution in different clades. Motif analysis found 16 conserved motifs in wheat MLOs. Comparative phylogenetic tree of wheat, Arabidopsis, and rice MLOs classified the genes into four clades. Evolution analysis showed that segmental duplications and purifying selection are prevalent in TaMLOs. Finally, nine MLOs showed in silico expression in different tissues during growth and development. Eight genes (TaMLO3/6-A2, TaMLO7-A1, TaMLO9-D1, TaMLO10-A2, TaMLO10-B1, TaMLO10-B2, TaMLO10-D1, and TaMLO10-D2) showed overlapping expression under cold, drought, heat stress, and phosphate starvation. Several MLOs showed differential in silico expression under PM (TaMLO10-A2, TaMLO3/6-A2, TaMLO7-A1, TaMLO10-D5), stripe rust (TaMLO9-D1), and head blight (TaMLO10-A2, TaMLO4-A1, TaMLO10-B1, TaMLO10-B2, TaMLO10-D1, TaMLO10-D2). The quantitative real-time polymerase chain reaction (qRT-PCR) showed that nine genes (TaMLO3/6-A2, TaMLO3/6-B2, TaMLO3/6-D2, TaMLO8-A1, TaMLO8-B1, TaMLO8-D1, TaMLO9-A1, TaMLO10-A1, and TaMLO10-D1) exhibited significant upregulation in PM-resistant line after 24, 48, and 72 hours of post-inoculation with the pathogen as compared with the susceptible cultivar. Whereas TaMLO9-D1 showed downregulation. Thus, these MLO genes have a potential role in wheat under these conditions. Therefore, we hope that the MLO genes identified in this study will be edited through CRISPR/Cas9 and/or will be overexpressed to develop PM and disease-resistant and abiotic stress-tolerant wheat.

bioinformatics↗

bioRxiv2020

MADS-box genes galore in wheat genome: phylogenomics, evolution and stress associated functions

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. However, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the latest publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies, without a single FLOWERING LOCUS C homolog present in the wheat genome. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more recent evolutionary origin was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that will accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

genomics↗

bioRxiv2020

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

BackgroundPhotoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-of-function mutations in either PHYB or PHYC result in large delays in heading time and in the differential regulation of a large number of genes in wheat plants grown in an inductive long day (LD) photoperiod. ResultsWe found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed later than wild-type plants. Unexpectedly, both mutants flowered earlier in SD than LD, the inverse response to that of wild-type plants. We observed a larger number of differentially expressed genes between mutants and wild-type under SD than under LD, and in both cases, the number was larger for phyB than for phyC. We identified subsets of differentially expressed and alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We observed significantly higher transcript levels of the flowering promoting genes VRN-A1, PPD-B1 and GIGANTEA in the phy-null mutants in SD than in LD, which suggests that they could contribute to the earlier flowering of the phy-null mutants in SD than in LD. ConclusionsOur study revealed an unexpected reversion of the wheat LD plants into SD plants in the phyB-null and phyC-null mutants and identified candidate genes potentially involved in this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive and non-inductive photoperiods and a set of candidate genes to dissect the underlying developmental regulatory networks in wheat.

plant biology↗

bioRxiv2019

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

We present a chromosome-scale annotated assembly of the rye (Secale cereale L. inbred line Lo7) genome, which we use to explore Triticeae genomic evolution, and ryes superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.

genomics↗

bioRxiv2018

Genome sequence of the wheat stem sawfly, Cephus cinctus, a primitive hymenopteran and wheat pest, illuminates evolution of hymenopteran chemoreceptors

The wheat stem sawfly, Cephus cinctus, is a major pest of wheat and key ecological player in the grasslands of western North America. It also represents a distinctive lineage of sawflies that appeared early during the hymenopteran radiation, but after the clade of Eusymphyta sawflies that is the sister lineage of all other Hymenoptera. We present a high-quality draft genome assembly of 162 Mbp in 1,976 scaffolds with a scaffold N50 of 622 kbp. Automated gene annotation identified 11,210 protein-coding gene models and 1,307 non-coding RNA models. Thirteen percent of the assembly consists of ~58,000 transposable elements partitioned equally between Class-I and Class-II elements. Orthology analysis reveals that 86% of Cephus proteins have identifiable orthologs in other insects. Phylogenomic analysis of conserved subsets of these proteins supports the placement of the Cephidae between the Eusymphyta and the parasitic woodwasp superfamily Orussoidea. Manual annotation and phylogenetic analysis of families of odorant, gustatory, and ionotropic receptors, plus odorant binding proteins, shows that Cephus has representatives for most conserved and expanded gene lineages in the Apocrita (wasps, ants, and bees). Cephus has also maintained several insect gene lineages that have been lost from the Apocrita, most prominently the carbon dioxide receptor subfamily. Furthermore, Cephus encodes a few small lineage-specific chemoreceptor gene family expansions that might be involved in adaptations to new grasses including wheat. These comparative analyses identify gene family members likely to have been present in the hymenopteran ancestor and provide a new perspective on the evolution of the chemosensory gene repertoire.

genomics↗

bioRxiv2018

Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat

BackgroundWhole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits.\n\nResultsWe present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and promoter capture.\n\nConclusionsWe show that a capture design employing an island strategy can enable analysis of the large gene/promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations.

genomics↗