Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance

Authors: BOTKIN, JACOB - University Of Minnesota; FARMER, ANDREW - National Center For Genome Resources; YOUNG, NEVIN - University Of Minnesota; Curtin, Shaun

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/10/2024
Publication Date: 2/23/2024
Citation: Botkin, J., Farmer, A.D., Young, N.D., Curtin, S.J. 2024. Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance. BMC Genomics. 25. Article 204. https://doi.org/10.1186/s12864-024-10112-9.
DOI: https://doi.org/10.1186/s12864-024-10112-9

Interpretive Summary: Fungi are some of the most devastating plant pathogens, causing the majority of plant diseases, and resulting in $200 billion in crop losses annually. Spring black stem and leaf spot (SBS), caused by the fungus Ascochyta medicaginicola, is a devasting disease of alfalfa affecting stand survival, yield, and quality of the forage used for livestock feed. Disease resistant cultivars are needed for reducing damage, but little resistance is found in alfalfa. The fungus also causes disease on barrel medic, an alfalfa relative, with disease resistance identified in the accession HM078. To increase understanding of disease resistance in barrel medic, we assembled the DNA sequence for the HM078 genome and identified several possible genes for SBS disease resistance. Overall, the HM078 genome sequence is a valuable resource for investigating SBS disease resistance genes in crop plants and enhancing resistance to agronomically important diseases.

Technical Abstract: Medicago truncatula, a model legume species, is a valuable a resource for functional genetics and translational genomics studies for legume crop improvement. Spring black stem and leaf spot (SBS), caused by the necrotrophic fungus Ascochyta medicaginicola, is a devasting foliar disease of alfalfa affecting stand survival, yield, and forage quality. Host resistance is poorly understood, and control methods rely on cultural practices. The M. truncatula accession HM078 is resistant to SBS, with two recessively inherited quantitative-trait loci (QTL), rnpm1 and rnpm2, previously reported. To shed light on host resistance, we carried out a de novo genome assembly and annotation of HM078. The genome, referred to as MtHM078 v1.0, is comprised of 23 contigs totaling 481.19 Mbp. Notably, this assembly contains a substantial amount of novel centromeric-related repeat sequences. Genome annotation resulted in 98.4% of BUSCO proteins being complete. The assembly enabled sequence level analysis of rnpm1 and rnpm2 for variation in gene content, synteny, and structural variation. Fourteen candidate genes were identified, and several have previously been implicated in resistance to necrotrophic fungi. In rnpm1, these include a disease resistance gene with a premature stop codon and a retrotransposon-like meditated insertion disrupting a ubiquitin conjugating E2. Loss-of-function events provide candidate genes for the inverse gene-for-gene model, where resistance is recessively inherited. In rnpm2, a missense and frameshift mutation altering an F-box family protein was identified. This study generated a high-quality genome of HM078 and has identified promising resistance genes that, once validated, could be extended to alfalfa to generate robust genetic resistance.