Biology subjects

Maughan, P. J.

Publications and source records attributed to Maughan, P. J..

8 recordsLinked to original sources

bioRxiv2026

Mapping Pc94-Mediated Crown Rust Resistance in Oat Reveals a zfBED NLR and Introgression Variation

Host resistance is a critical component of oat crown rust disease management. Pc94 is a qualitative resistance locus derived from diploid Avena strigosa with several independent introgressions into A. sativa that have been used in cultivar deployment. Quantitative trait locus (QTL) analysis combining previously published data for a historic A. strigosa population segregating for Pc94 revealed a large effect QTL on the distal end of A. strigosa chromosome 7A. Genome assembly of the parents identified a cluster of five nucleotide binding site leucine-rich repeat receptor (NLR) candidate genes within the QTL region. A single candidate NLR with an integrated zinc finger BED domain, AstNLR94, was determined as necessary for Pc94 resistance based on map-based cloning and forward mutagenesis. A presence/absence allele specific PCR marker was designed in AstNLR94 and verified for accuracy and specificity in a diverse panel of A. strigosa and A. sativa. Pc94 introgressions in A. sativa ranged in size from 1.7-71 Mbp and two different introgression locations appear to have occurred. In A. sativa Leggett, a 6.3 Mbp Pc94 introgression is located at the end of chromosome 2A, and the same sized introgression was discovered in the OT3098 v2 genome. Finally, a QTL analysis identified an additional minor resistance locus on A. strigosa chromosome 4A, which has complicated previous efforts to characterize the Pc94 locus. This is the first report of an NLR gene underlying disease resistance in Avena spp. and delivers a Pc94 marker for marker assisted selection to produce disease resistant cultivars. Key messageWe mapped a zfBED-NLR encoding gene necessary for Pc94 resistance, developed a diagnostic marker, and revealed diverse introgression sizes, clarifying Pc94s history and utility for durable oat crown rust resistance.

plant biology↗

bioRxiv2025

Domestication shaped the chromatin landscape of grain amaranth

Plant domestication has had profound impacts on the morphology and genetic diversity of crops. Beyond sequence diversity, changes in chromatin structure can play an important role in plant adaptation. However, the interplay between the chromatin landscape and plant domestication remains unclear. We present a high-quality genome assembly and chromatin landscape map of the ancient pseudo-cereal, amaranth. Using ATAC-sequencing of multiple accessions of three grain amaranth species and two wild relatives, we show that the overall amount of accessible chromatin is highly conserved, but about 2.5% of all chromatin switched states, with a higher fraction of the genome repeatedly opening during domestication processes. These differentially accessible chromatin regions, between the crops and their wild ancestor, were species-specific and significantly associated with selective sweeps - reflecting the repeated independent domestication of amaranth. Our findings reveal the dynamic interplay between domestication and the chromatin landscape, highlighting an additional layer of diversity in crops.

genomics↗

bioRxiv2025

The Genome of Chenopodium ficifolium: Developing Genetic Resources and a Diploid Model System for Allotetraploid Quinoa

High-quality nuclear, chloroplast, and preliminary mitochondrial genomes have been assembled and annotated for the B-genome diploid (BB: 2n = 2x = 18) figleaf goosefoot (Chenopodium ficifolium). The primary objective was to advance a simplified model system for genetic characterization and improvement of allotetraploid (AABB: 2n = 4x = 36) quinoa (Chenopodium quinoa), a nutritionally valuable, halophytic orphan crop. In addition to its diploidy and favorably small genome size, the C. ficifolium model provides a shorter generational period and smaller overall plant size as compared to C. quinoa, while displaying relevant agronomic trait variations amenable to gene-trait association studies. The C. ficifolium Portsmouth nuclear genome was sequenced using PacBio HiFi Long Read technology and assembled using Hifiasm. After manual adjustments, the final ChenoFicP_1.0 assembly consisted of nine pseudochromosomes spanning 711.5 Mbp, while 22,617 genes were identified and annotated. BUSCO analyses indicated a nuclear genome completeness of 97.5%, and a proteome and transcriptome completeness of 98.4 percent. The chloroplast genome assembly detected two equally represented structural haplotypes differing in the orientation of the Short Single Copy region relative to the Long Single Copy region. Phylogenetic and parentage analyses pointed to an unspecified AA diploid species and away from C. ficifolium as the likely maternal chloroplast and mitochondrial genome donor(s) during the initial tetraploidization event in the C. quinoa lineage. Using the new ChenoFicP_1.0 reference genome, a GWAS was performed on a previously studied C. ficifolium F2 population to further define region(s) implicated in the control of three key agronomic traits: days to flowering, plant height, and branch number. This analysis localized control of all three traits to a 7 Mb interval on pseudochromosome Cf4. This region contains approximately 770 genes, including the FTL1 locus, thus confirming and extending our prior, single-marker analysis showing association of these three traits with an FTL1 amplicon length polymorphism. The use of these data to further develop C. ficifolium as a model species for genetics and breeding of quinoa serves to expand knowledge and germplasm resources for quinoa improvement.

genetics↗

bioRxiv2024

LEAF SHAPE OF QUINOA WILD ANCESTOR CHENOPODIUM HIRCINUM IN A GEOGRAPHIC CONTEXT

PremiseIntraspecific variation in plant traits, such as leaf morphology, offers insights into local adaptation and the ecological niche breadth of species. Chenopodium hircinum, the wild ancestor of quinoa, is widely distributed across various ecoregions in Argentina. A detailed comparative analysis of leaf morphology across 23 populations covering its entire distribution was conducted to understand patterns of intraspecific variation along geographic gradients. Materials and MethodsUsing 104 leaves from these populations, leaf shapes were described through shape, landmarks, and Fourier descriptors. Both univariate and multivariate analyses were employed to evaluate variations among and within populations and to link leaf shape patterns with climatic and geographical variables at the sites of origin. ResultsA significant variability in leaf shapes was found across all ecoregions, with marked integration among populations. While landmark-based and Fourier analyses differentiated populations, shape descriptors introduced complexity in identification. Leaf morphology varied widely, from rounded and toothed to sharply lobed, with prominent lobes located at the base or middle of the leaf. The key environmental factors influencing leaf shape, particularly lobulation and relative positioning, were mean annual temperature and altitude. ConclusionsThe findings suggest that in C. hircinum, leaf shape variability goes beyond the simple lobed vs. entire dichotomy and is shaped by environmental temperatures. Leaf morphology and margin traits are primarily governed by the relative position of the lobes, which are strongly correlated with the mean temperature at the populations origin. This convergence across different ecoregions highlights the need for further research to explore the functional significance of such variation.

plant biology↗

bioRxiv2024

Genome assembly of a diversity panel of Chenopodium quinoa

Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security. Deep characterization of quinoa diversity is needed to support the agronomic improvement and adaptation of quinoa as its worldwide cultivation expands. In this study, we report the construction of chromosome-scale genome assemblies of eight quinoa accessions covering the range of phenotypic and genetic diversity of both lowland and highland quinoas. The assemblies were produced from a combination of PacBio HiFi reads and Bionano Saphyr optical maps, with total assembly sizes averaging 1.28 Gb with a mean N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for the eight new quinoa genomes, and on average, 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies allowed the identification of structural rearrangements including inversions, translocations, and duplications. These eight novel quinoa genome assemblies provide a resource for association genetics, comparative genomics, and pan-genome analyses for the discovery of genetic components and variations underlying agriculturally important traits.

genomics↗

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↗

bioRxiv2023

The International Weed Genomics Consortium: Community Resources for Weed Genomics Research

The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Our goal is to use genomic information to develop sustainable and effective weed control methods and to provide insights about biotic and abiotic stress tolerance to assist crop breeding. Here, we outline resources under development by the consortium and highlight areas of research that will be impacted by these enabling resources.

genomics↗

bioRxiv2021

Genome size evolution in the diverse insect order Trichoptera

BackgroundGenome size is implicated in form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: Polyploidy (i.e., whole genome duplication: WGD) or smaller duplication events and bursts in the activity of repetitive elements (RE). Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. ResultsWe detect a ~14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element (RE) expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). ConclusionOur findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.

evolutionary biology↗