Biology subjects

Gill, U.

Publications and source records attributed to Gill, U..

6 recordsLinked to original sources

bioRxiv2024

Genomic Architecture of the Resistance to Phytophthora Cactorum 2 (RPc2) Locus in Strawberry (Fragaria x ananassa)

Phytophthora crown rot (PhCR), caused by Phytophthora cactorum, is a soilborne disease with broad impacts to cultivated strawberries in the United States and worldwide. While a resistance locus, RPc2, has been identified in octoploid strawberries, the underlying genomic architecture and mechanism remain unclear. Here, we fine-mapped the RPc2 region to 546 kb, containing 92 genes, and constructed a chromosome-scale haplotype-phased genome of resistant breeding selection FL 16.33-8. Comparative genome analyses with high-quality octoploid reference genomes, Florida Brilliance (FaFB1) and Royal Royce (FaRR1), identified two candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1). Gene functions were validated using an Agrobacterium-mediated transient expression assay. Furthermore, by leveraging the population structure of the RPc2 locus among genetically diverse breeding populations, we unveiled the complexity of genetic architecture and recent selective sweeps associated with RPc2. Notably, the predominant resistant haplotype (RPc2-H3) is prevalent in most commercial strawberry varieties in the US. The findings from this study are facilitating the advancement of genome-assisted breeding strategies for resistance to PhCR in strawberries. SummaryO_LIPhytophthora crown rot (PhCR), caused by the soilborne pathogen Phytophthora cactorum, is a disease with broad impacts to cultivated strawberries worldwide. The Resistance to Phytophthora Cactorum 2 (RPc2) locus is widespread in important cultivars and is a target of selection in breeding programs. Despite its importance, the genomic architecture and mechanisms of RPc2 remain poorly characterized. C_LIO_LIWe performed fine-mapping and delimited the genomic region to a 546 kb segment containing 92 genes. We developed a chromosome-scale haplotype-phased genome from an elite resistant line, FL16.33-8, and made comparisons to reference genomes of Florida Brilliance (FaFB1) and Royal Royce (FaRR1) to uncover gene sequence and structural variants in resistant accessions. C_LIO_LIThrough comparative genomics and transcriptome profiling, we identified three candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1) and CNGC2. The functions of these genes were validated using a simplified Agrobacterium-mediated transformation method for transient gene expression in strawberry crowns and roots. C_LIO_LIAn examination of the population structure of the RPc2 locus among genetically diverse accessions (N=1029) revealed that the predominant H3 resistant haplotype is widespread in breeding accessions in the US, supporting the findings of a previous study on recent selective sweeps associated with RPc2. Results from this study are advancing genome-assisted breeding strategies for enhancing resistance to PhCR in strawberry. C_LI

plant biology↗

bioRxiv2024

Dispensable genome and segmental duplications drive the genome plasticity in Fusarium solani

Fusarium solani is a species complex encompassing a large phylogenetic clade with diverse members occupying varied habitats. We recently reported a unique opportunistic F. solani associated with unusual dark galls in sugarbeet. We assembled the chromosome-level genome of the F. solani sugarbeet isolate strain SB1 using Oxford Nanopore and Hi-C sequencing. SB1 has a large genome (59.38 Mb) organized into 15 chromosomes. The genome expansion is due to the high repeats and massive segmental duplications within its three potentially accessory chromosomes. These chromosomes are absent in the closest reference genome with chromosome-level assembly, F. vanettenii 77-13-4. The extensive segmental duplications between the two SB1 chromosomes suggest that this isolate may have doubled its accessory genes. Further comparison of the F. solani strain SB1 genome demonstrates inversions and syntenic regions to an accessory chromosome of F. vanettenii 77-13-4. The pan-genome of 12 publicly available F. solani isolates nearly reached gene saturation, with few new genes discovered after the addition of the last genome. Based on orthogroups and average nucleotide identity, F. solani is not grouped by lifestyle or origin. The pan-genome analysis further revealed the enrichment of several enzymes-coding genes within the dispensable (accessory + unique genes) genome, such as hydrolases, transferases, oxidoreductases, lyases, ligases, isomerase, and dehydrogenase. The evidence presented here suggests that genome plasticity, genetic diversity, and adaptive traits in Fusarium solani are driven by the dispensable genome with significant contributions from segmental duplications.

genomics↗

bioRxiv2024

Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust

Tetraploid durum wheat Triticum turgidum subsp. durum cv Kronos has extensive genetic variation resources, including a sequenced and cataloged ethyl methanesulfonate (EMS) mutagenized population. To utilize this allelic diversity, we screened over 2,000 mutant lines and identified over 30 enhanced disease resistance (EDR) mutants in a forward genetic field screen against stripe rust. Sixteen of the EDR lines have persistent resistance to stripe rust after four years, and several mutants showed differential disease responses against other fungal pathogens, indicating that the lines possess diverse alleles that affect multiple routes of pathogen suppression. Five of these 16 lines showed spontaneous lesion formation in the absence of pathogens. Only one showed a reduction in kernel weight under pathogen pressure, a testimony to the high mutational density that wheat can tolerate. Phenotypic selection for resistance at the adult stage identified useful EMS alleles for stripe rust resistance. The mutations in the 16 EDR lines were newly mapped to a recently released long-read Kronos genome to enhance their utility in molecular breeding for fungal resistance and for fundamental studies of plant-pathogen interactions.

plant biology↗

bioRxiv2024

Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement

Aegilops spp. serve as an important reservoir for novel sources of resistance or tolerance to biotic and abiotic stresses. To harness this reservoir, we have generated a high-quality chromosome-level genome assembly of an Ae. umbellulata accession PI 554389 using a combination of PacBio HiFi, Oxford nanopore, and chromosome conformation capture (Hi-C) sequencing technologies and resequenced 20 Ae. umbellulata genomes using Illumina sequencing. We assembled a 4.20 Gb genome spanned over seven chromosomes, rich in repetitive elements ([~]84%), achieving a QV of 59.54 with 98.14% completeness. The phylogenetic analysis places the U-genome with D-lineage, but major and distinct rearrangements were revealed in the U-genome. Unique transposon landscape of diploid U-genome and complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes uncovered a distinct evolutionary trajectory of Ae. umbellulata. Additionally, the resequencing of geographically and morphologically diverse Ae. umbellulata accessions revealed three distinctive evolutionary sub-populations. Resequencing also identified six new haplotypes for Lr9, the first leaf rust resistance gene introgressed and cloned from Ae. umbellulata. These genomics resources along with high levels of resistance in the resequenced accessions against five devastating wheat diseases affirmed the genetic potential of Ae. umbellulata for wheat improvement.

plant biology↗

bioRxiv2022

Identification of leaf rust resistance loci in a geographically diverse panel of wheat using genome-wide association analysis

Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.

plant biology↗

bioRxiv2022

IBRAP: Integrated Benchmarking Single-cell RNA-sequencing Analytical Pipeline

Single-cell RNA-sequencing (scRNA-seq) is a powerful tool to study cellular heterogeneity. The high dimensional data generated from this technology are complex and require specialised expertise for analysis and interpretation. The core of scRNA-seq data analysis contains several key analytical steps, which include pre-processing, QC, normalisation, dimensionality reduction, integration, and clustering. Each step often has many algorithms developed with varied underlying assumptions and implications. With such a diverse choice of tools available, benchmarking analyses have compared their performances and demonstrated that tools differentially operate according to the data types and complexity. Here, we present Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP) - a tool, which contains a range of analytical components that can be interchanged throughout the pipeline alongside multiple benchmarking metrics that enables users to compare results and determine the optimal pipeline combinations for their data. We apply IBRAP to single and multi-sample integration analysis using pancreas, cell line and simulated data accompanied with ground truth cell labels, demonstrating the interchangeable and benchmarking functionality of IBRAP. Our results confirm that the optimal pipelines are dependant of individual samples and studies, further supporting the rationale and necessity of our tool. We then compare reference-based cell annotation with unsupervised analysis, both included in IBRAP, and demonstrate the superiority of the reference-based method in identifying robust major and minor cell types. Thus, IBRAP presents a valuable tool to integrate multiple samples and studies to create reference maps of normal and diseased tissues, facilitating novel biological discovery using the vast volume of scRNA-seq data available.

bioinformatics↗