Biology subjects

Riaz, S.

Publications and source records attributed to Riaz, S..

10 recordsLinked to original sources

bioRxiv2025

Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce's Disease in Vitis arizonica and its hybrids

Previous genetic mapping studies indicate that multiple haplotypes of the Pierces disease (PD) Resistance 1 (PdR1) locus occur in Vitis arizonica and its hybrids. To characterize sequence diversity at this locus, we assembled chromosome-scale diploid genomes for four PD-resistant (PD-R) accessions: b43-17 (PdR1a/PdR1b), the backcross 07744-094 (PdR1c/PdR1-), b46-43 (PdR1e/PdR1f), and b42-26 (PdR1-/PdR1-), which displays quantitative PD resistance not associated with PdR1. Haplotype resolution of PdR1a, PdR1b, PdR1c, and PdR1e revealed substantial variation in intergenic repeat content and gene composition between PdR1 and their alternative haplotype at the PdR1 locus not associated with PD resistance phenotype (PdR1-), as well as among PdR1 haplotypes, demonstrating extensive sequence diversity at the PdR1 locus. Sequence graph analysis uncovered substantial structural divergence concentrated in approximately one quarter of the locus, together with smaller-scale variation across haplotypes. This analysis identified PdR1-specific graph nodes, showing that PdR1a and PdR1b share most of their PdR1-specific features, whereas PdR1c contains the highest number of private nodes, followed by PdR1e. Integration of sequence graph features with gene expression data further refined a set of defense-related candidate genes within PdR1c. Together, these results identify candidate genes for functional validation and indicate that multiple resistance determinants co-localized within the PdR1 locus may contribute to PD resistance, highlighting opportunities for targeted genetic improvement strategies.

genomics↗

bioRxiv2025

The study of differential expressions of MCPH and Seckel syndrome genes and their paralogues

Seckel syndrome and MCPH are single-gene neurodevelopmental disorders, with or without dwarfism. These genes are parts of essential cellular pathways but are regulated differently in both forms of microcephaly. These genes have diverged from single ancestral genes in to related but different gene paralogues during evolution. It is suggested that the paralogues might be redundant in other body organs and might rescue any abnormality in cases of MCPH, but not in Seckel syndrome. This study uncovers the spatio-temporal dynamics of these genes together with their paralogues at the mRNA level where the different tissues of embryos might exhibit different transcript variants or different levels of the various transcript variants to find the complementation in case of the MCPH but divergence in case of the Seckel syndrome. Here, we studied Cdk5Rap2-Pde4dip, Phc1-Phc3 (for MCPH) and Cep63-Ccdc67 (for Seckel) in the embryonic mouse tissues using RT-PCR throughout the peak of neurogenesis from E12.5 to E18.5. We found already known and novel spatio-temporal differential expression suggesting different regulation at the mRNA level. The results of PCR were analyzed on the agarose gel and were quantified by assigning relative intensity percentage scores to each band and plotting the cumulative expression of each gene in to the graphs for spatio-temporal dynamics and plotted each gene separately for temporal dynamics. For MCPH, Cdk5Rap2-Pde4dip had similar profiles and seemed to be redundant whereas Phc1-Phc3 seem to have complementary roles in brain development. The expression profiles of Cep63-Ccdc67 were very different indicating of their divergent and essential roles in development.

genetics↗

bioRxiv2025

Integration of diploid T2T parental genomes with progeny genomes and transcriptomes identifies resistance genes in the grape powdery mildew resistance loci Ren6 and Ren7 of Vitis piazeskii

The Chinese grape accession Vitis piasezkii DVIT2027 carries two loci associated with powdery mildew (PM) resistance loci, Ren6 and Ren7, which differ in timing and strength of response to Erysiphe necator. Both loci are consistent with recognition by intracellular immune receptors. To identify the underlying nucleotide-binding leucine-rich repeat (NLR) genes, we assembled chromosome-scale diploid genomes of DVIT2027 and the susceptible V. vinifera F2-35, parents of a segregating F1 population. We integrated these assemblies with deep resequencing data from eight F1 sib-lines carrying different Ren6/Ren7 combinations and generated trio-binned, parent-phased genomes for six progeny. This resolved both PM-resistant (PMR) and PM-susceptible (PMS) haplotypes at Ren6 and Ren7. Comparative analyses revealed extensive structural variation and complete haplotype specificity among NLRs, with several candidate genes lacking allelic counterparts in PMS haplotypes. Expression profiling across PMR sib-lines identified four and two CC-NBS-LRR genes potentially associated with Ren6 and Ren7, respectively. Sequence graph reconstruction of these loci across multiple V. piasezkii accessions revealed broad intraspecific diversity and DVIT2027-specific nodes, including within candidate NLR genes. These results provide a high-resolution view of Ren6 and Ren7 and support the identification of resistance gene candidates for functional validation and grapevine breeding.

plant biology↗

bioRxiv2022

The grape powdery mildew resistance loci Ren2, Ren3, Ren4D, Ren4U, Run1, Run1.2b, Run2.1, and Run2.2 activate different transcriptional responses to Erysiphe necator

Multiple grape powdery mildew (PM) genetic resistance (R) loci have been found in wild grape species. Little is known about the defense responses associated with each R locus. In this study, we compare the defense mechanisms associated with PM resistance in interspecific crosses segregating for a single R locus from Muscadinia rotundifolia (Run1, Run1.2b, Run2.1, Run2.2), Vitis cinerea (Ren2), V. romanetii (Ren4D and Ren4U), and the interspecific hybrid Villard blanc (Ren3). By combining optical microscopy, visual scoring, and biomass estimation, we show that the eight R loci confer resistance by limiting infection at different stages. We assessed the defense mechanisms triggered in response to PM at 1 and 5 days post inoculation (dpi) via RNA sequencing. To account for the genetic differences between species, we developed for each accession a diploid synthetic reference transcriptome by incorporating into the PN40024 reference homozygous and heterozygous sequence variants and de novo assembled transcripts. Most of the R loci exhibited a higher number of differentially expressed genes (DEGs) associated with PM resistance at 1 dpi compared to 5 dpi, suggesting that PM resistance is mostly associated with an early transcriptional reprogramming. Comparison of the PM resistance-associated DEGs showed a limited overlap between pairs of R loci, and nearly half of the DEGs were specific to a single R locus. The largest overlap of PM resistance-associated DEGs was found between Ren3+, Ren4D+, and Ren4U+ genotypes at 1 dpi, and between Ren4U+ and Run1+ accessions at 5 dpi. The Ren3+, Ren4D+, and Ren4U+ were also found to have the highest number of R locus-specific DEGs in response to PM. Both shared and R locus-specific DEGs included genes from different defense-related categories, indicating that the presence of E. necator triggered distinct transcriptional responses in the eight R loci.

genetics↗

bioRxiv2022

Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Xylella fastidiosa is a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives, causing economically devastating damage. There is, however, little understanding of the genes that contribute to resistance, the genomic architecture of resistance, and the potential role of climate in shaping resistance, in part because major crops like grapevines (V. vinifera) are not resistant to the bacterium. Here we studied a wild grapevine species, Vitis arizonica, that segregates for resistance to X. fastidiosa. Using genome-wide association, we identified candidate genes that mediate the host response to X. fastidiosa infection. We uncovered evidence that resistance requires genes from multiple genomic regions, based on data from breeding populations and from additional Vitis species. We also inferred that resistance evolved more than once in the wild, suggesting that wild Vitis species may be a rich source for resistance alleles and mechanisms. Finally, resistance in V. arizonica was climate dependent, because individuals from low (< 10{degrees}C) temperature locations in the wettest quarter were typically susceptible to infection, likely reflecting a lack of pathogen pressure in these climates. Surprisingly, climate was nearly as effective a predictor of resistance phenotypes as some genetic markers. This work underscores that pathogen pressure is likely to increase with climate, but it also provides genetic insight and tools for breeding and transforming resistant crops.

genetics↗

bioRxiv2021

Characterization of the grape powdery mildew genetic resistance loci in Muscadinia rotundifolia Trayshed

Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew. It carries two powdery mildew resistance-associated genetic loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. In this study, we identified, phased, and reconstructed the two haplotypes of each resistance-associated locus. Haplotype phasing allowed the identification of several structural variation events between haplotypes of both loci. Combined with manual refinement of the gene models, we found that the heterozygous structural variants affected the gene content, with some resulting in duplicated or hemizygous nucleotide-binding leucine-rich repeat (NLR) genes. Structural variations also impacted the domain composition of some NLRs. These findings emphasize the need of generating haplotype-resolved sequences instead of using consensus sequences for identifying haplotype-specific candidate genes. Comparison of the NLRs in the Run1.2 and Run2.2 loci indicated that the two loci are composed of a different number and classes of NLR genes. We provide a list of candidate NLR genes from the Run1.2b and Run2.2 loci, whose expression suggests a role in powdery mildew resistance in Trayshed. These first complete and haplotype-resolved resistance-associated loci, and their candidate NLR genes, represent new resources to develop powdery mildew-resistant grape cultivars.

plant biology↗

bioRxiv2021

Potential therapy for progressive vision loss due to PCDH15-associated Usher syndrome developed in an orthologous Usher mouse

Usher syndrome type I (USH1) is characterized by congenital deafness, vestibular areflexia, and progressive retinal degeneration with age. The protein-truncating p.Arg245* founder variant of PCDH15 has an ~2% carrier frequency among Ashkenazi Jews, accounting for nearly 60% of their USH1 cases. Here, longitudinal ocular phenotyping in thirteen USH1F individuals harboring the p.Arg245* variant revealed progressive retinal degeneration, leading to severe loss of vision with macular atrophy by the sixth decade. Half of the affected individuals met either the visual acuity or visual field loss definition for legal blindness by the middle of their fifth decade of life. Mice homozygous for p.Arg250* (Pcdh15R250X; equivalent to human p.Arg245*) also have early visual deficits evaluated using electroretinography. Light-dependent translocation of phototransduction cascade proteins, arrestin and transducin, was found to be impaired in Pcdh15R250X mice. Retinal pigment epithelium-(RPE) specific visual retinoid cycle proteins, RPE65 which converts all-trans retinoids to 11-cis retinoids and CRALBP that transports retinoids, and key retinoid levels were also reduced in Pcdh15R250X mice, suggesting a dual role for protocadherin-15 in photoreceptors and RPE. Administration of exogenous 9-cis retinal, an analog of the naturally occurring 11-cis retinal, improved ERG amplitudes in these mutant mice, suggesting a basis for a clinical trial of exogenous FDA approved retinoids to preserve vision in USH1F patients. SummaryIn a preclinical setting studying exogenous retinoids using a novel Usher syndrome mouse model, we describe a potential therapy to treat PCDH15-mediated visual dysfunction.

neuroscience↗

bioRxiv2021

Extensive introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation

Introgressive hybridization can introduce adaptive genetic variation into a species or population. To evaluate the evolutionary forces that contribute to introgression, we studied six Vitis species that are native to the Southwestern United States and potentially useful for breeding grapevine (V. vinifera) rootstocks. By creating a reference genome from one wild species, V. arizonica, and by resequencing 130 accessions, we focused on identifying putatively introgressed regions (pIRs) between species. We found that up to ~8% of extant genome is attributable to introgression between species. The pIRs tended to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explored SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierces Disease. pIRs were enriched for SNPs associated with both climate and bacterial levels, suggesting potential drivers of adaptive events. Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the history of economically important wild relatives of a critical crop.

evolutionary biology↗

bioRxiv2019

The genetic basis of sex determination in grapevines (Vitis spp.)

Sex determination in grapevine evolved through a complex succession of switches in sexual systems. Phased genomes built with single molecule real-time sequencing reads were assembled for eleven accessions of cultivated hermaphrodite grapevines and dioecious males and females, including the ancestor of domesticated grapevine and other related wild species. By comparing the phased sex haplotypes, we defined the sex locus of the Vitis genus and identified polymorphisms spanning regulatory and coding sequences that are in perfect association with each sex-type throughout the genus. These findings identified a novel male-fertility candidate gene, INP1, and significantly refined the model of sex determination in Vitis and its evolution.

evolutionary biology↗

bioRxiv2017

Ventral hippocampal CA1 and CA3 differentially mediate learned approach-avoidance conflict processing

The ventral hippocampus is thought to play a key role in the resolution of approach-avoidance conflict, a scenario that arises when stimuli with opposing valences are present simultaneously. Little is known, however, about the contributions of specific hippocampal sub-regions in this process, a critical issue given the functional and anatomical heterogeneity of this structure. Using a non-spatial cue-based paradigm in rats, we found that transient pharmacological inactivation of ventral CA1 produced an avoidance of a conflict cue imbued with both learned positive and negative outcomes, whereas inactivation of the ventral CA3 resulted in the opposite pattern of behavior, with significant preference for the conflict cue. In contrast, dorsal CA1- and CA3-inactivated rats showed no change in conflict behavior. Our findings provide important insight into the functions and circuitry of the ventral hippocampus by demonstrating that the ventral CA1 and CA3 subserve distinct and opposing roles in approach-avoidance conflict processing.

neuroscience↗