Baldwin, T. T. | Search bioRxiv

bioRxiv2025

A subset of world barley collection was used in the identification of sources of resistance and marker-trait association for resistance for bacterial leaf streak

The bacterial leaf streak (BLS) disease of barley, caused by Xanthomonas translucens pv. translucens (Xtt), has become increasingly important worldwide in recent years. Inefficacy of chemical control methods leaves deployment of host resistance to be the only option to manage this disease. However, current commercial varieties are mainly susceptible to BLS. Therefore, our goal was to identify sources of resistance from diverse barley germplasms and map associated genetic factors. To do so, we evaluated a subset of the World Barley Core Collection (BCC), consisting of 198 accessions, on their reaction to BLS from 2013 to 2016 under natural or artificially inoculated disease pressures. Ten accessions exhibited consistently low disease severities over four years of evaluations. Using genotype data from the T3/Barley database, genome-wide association studies were conducted to identify marker-trait associations (MTAs) in this barley mini-core panel for BLS resistance. Utilizing four mixed-model analyses (MLM, MLMM, FarmCPU, BLINK), five significant MTAs were consistently identified from at least two mixed model analyses including two in chromosome 2H, and one each in chromosomes 5H, and 7H. Associations in chromosomes 2H and 5H appear to be in the same region with loci identified in a previous association study, reinforcing their potential relevance. The identified resistant barley accessions and associated markers will be valuable inbreeding BLS-resistant barley varieties. Core ideas- A subset of world barley collection was used in the identification of sources of resistance and marker-trait association for resistance for bacterial leaf streak. - Ten accessions consistently showed low disease severity across different years, highlighting their value in BLS resistance breeding. - Five MTAs were consistently identified using different models, with two aligning with previously identified resistance QTLs.

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↗