Biology subjects

Jellen, E. N.

Publications and source records attributed to Jellen, E. N..

3 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

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

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↗