Biology subjects

Pozniak, C. J.

Publications and source records attributed to Pozniak, C. J..

6 recordsLinked to original sources

bioRxiv2026

WheatPanRef: a unified linear pan-reference genome for wheat genomics

Linear reference genomes provide coordinates for read mapping, variant discovery and multi-omics data integration, yet assembly-specific coordinate systems limit data reuse, particularly in the large, repetitive and polyploid wheat genome. Here, we present WheatPanRef, a scalable linear pan-reference and coordinate framework that integrates wheat sequence diversity within a stable coordinate system. We reconciled independent Chinese Spring assemblies by resolving structural and sequences discrepancies to constructed a 14.50-Gb consensus sequences CS-NP. Using CS-NP as backbone, we incorporated 4.37 Gb of non-redundant non-CS sequences from 37 diverse wheat accessions, generating WheatPanRef (18.87 Gb). WheatPanRef improves read-alignment performance and captures putative wild-relative introgressions and sequences absent or unanchored in conventional references. Bidirectional coordinate-translation system enables accurate projection between WheatPanRef and individual assemblies without remapping, facilitating genomic resource integration and reuse. WheatPanRef provides a common sequence and coordinate foundation for population-scale wheat genomics, with potential utility for genomic resource integration in other complex crops.

genomics↗

bioRxiv2026

Evolutionary dynamics of Aegilops revealed through comparative genome assembly of all 25 species

Aegilops species are the closest wild relatives of wheat and an important reservoir of genetic diversity for its improvement. Despite their potential, many Aegilops genomes remain poorly characterized. Here we present high-quality assemblies of 18 diploid, tetraploid, and hexaploid Aegilops genomes, which, along with the previously published genomes, complete the production of reference assemblies for all 25 genomes in this genus. Assembly sizes ranged from 5.24 Gb in diploids to 12.65 Gb in hexaploids, with scaffold N50 values up to 749.2 Mb. Gene annotation identified 53,035-156,779 protein-coding genes, of which 21,865-60,490 were classified as high-confidence. Orthogroup-based pangenome analysis across the 25 Aegilops genomes identified 80,521 orthogroups, including 15,809 core, 61,735 dispensable, and 2,977 species-specific orthogroups, highlighting substantial gene content variation among genomes. Phylogenetic analysis of 63 Triticum and Aegilops genomes/subgenomes based on near single-copy orthologs defines the phylogenetic relationships within the Triticum/Aegilops complex and confirms diploid progenitors of polyploid lineages. Ae. mutica (T) and Ae. speltoides (S) belong to the B lineage while the remaining Sitopsis grouped within the D lineage. Structural variation analyses using diploid progenitors as references revealed extensive large-scale rearrangements following polyploidization, emphasizing the dynamics of their evolution. Transposable element (TE) annotation further highlighted subgenome-specific TE expansions and contractions, providing insights into the mechanisms shaping genome structure after polyploidization. Collectively, these genomic resources provide a comprehensive framework for exploring Aegilops diversity, understanding polyploid evolution, and accelerating wheat improvement.

genomics↗

bioRxiv2024

Coordinated function of paired NLRs confers Yr84 -mediated stripe rust resistance in wheat

Cloning of resistance genes expands our understanding of their function and facilitates their deployment in breeding. Here, we report the cloning of two genes from wild emmer wheat (Triticum turgidum ssp. dicoccoides) underlying Yr84-mediated stripe rust resistance using a combination of fine mapping, long read-sequencing and mutation-induced functional validation. In contrast to all previously cloned stripe rust genes, the incompletely dominant Yr84 phenotype is conferred through the coordinated function of paired nucleotide-binding leucine-rich repeats (NLR) genes CNL and NL. We hypothesize that based on their genomic organization, annotation, expression profiles and predicted protein structure, CNL functions as a sensor NLR (sNLR) responsible for effector recognition, and NL acts as a helper NLR (hNLR) initiating downstream resistance cascades. The CNL and NL lack an integrated domain(s) previously implicated in effector recognition by paired NLRs, therefore these findings contribute new insights into plant paired NLRs structure and molecular mechanisms of function.

genetics↗

bioRxiv2022

Long-read genome sequencing accelerated the cloning of Pm69 by resolving the complexity of a rapidly evolving resistance gene cluster in wheat

Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks in the cloning of the powdery mildew (Pm) resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat (WEW). A conventional positional cloning approach encountered suppressed recombination due to structural variations, while chromosome sorting yielded an insufficient purity level. A Pm69 physical map, constructed by assembling ONT long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster. A single candidate NLR was identified within this cluster by anchoring RNASeq reads of susceptible mutants to ONT contigs and was validated by the virus-induced gene silencing (VIGS) approach. Pm69, comprising Rx_N with RanGAP interaction sites, NB-ARC, and LRR domains, is probably a newly evolved NLR discovered only in one location across the WEW distribution range in the Fertile Crescent. Pm69 was successfully introgressed into durum and bread wheat, and a diagnostic molecular marker could be used to accelerate its deployment and pyramiding with other resistance genes.

genetics↗

bioRxiv2022

An autoactive NB-LRR gene causes Rht13 dwarfism in wheat

Semidwarfing genes have greatly increased wheat yields globally, yet the widely used gibberellin (GA) insensitive genes Rht-B1b and Rht-D1b have disadvantages for seedling emergence. Use of the GA sensitive semidwarfing gene Rht13 avoids this pleiotropic effect. Here we show that Rht13 encodes a nucleotide-binding site/leucine-rich repeat (NB-LRR) gene. A point mutation in the semidwarf Rht-B13b allele autoactivates the NB-LRR gene and causes a height reduction comparable to Rht-B1b and Rht-D1b in diverse genetic backgrounds. The autoactive Rht-B13b allele leads to transcriptional upregulation of pathogenesis-related genes including class III peroxidases associated with cell wall remodelling. Rht13 represents a new class of reduced height (Rht) gene, unlike other Rht genes which encode components of the GA signalling or metabolic pathways. This discovery opens new avenues to use autoactive NB-LRR genes as semidwarfing genes in a range of crop species, and to apply Rht13 in wheat breeding programmes using a perfect genetic marker.

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↗