# Novel Molecular Markers and Immune-Related Candidate Genes for Blackleg Resistance in Rapeseed: A Genome-Wide Analysis

## TL;DR

This study identifies new genetic markers and immune-related genes in rapeseed that help resist blackleg disease, offering tools for breeding more resilient crops.

## Contribution

The study introduces novel molecular markers and candidate genes for blackleg resistance in rapeseed using GWAS and transcriptomic analysis.

## Key findings

- Over 104,000 markers were identified, with 61% being SilicoDArTs and 39% SNPs.
- 33 significant markers (p < 0.01) were associated with blackleg resistance, 76% of which were SilicoDArTs.
- Thirteen marker-linked genes were expressed during infection, with seven showing significant differential expression.

## Abstract

Rapeseed (Brassica napus L.) faces escalating threats from abiotic and biotic stresses, notably blackleg caused by Leptosphaeria maculans. Due to limited chemical control efficacy and stringent GMO regulations, marker-assisted selection (MAS) leveraging natural genetic variation has become an indispensable strategy for crop improvement. This study identified novel molecular markers for blackleg resistance by integrating genome-wide association study (GWAS) results with high-throughput genotyping by Diversity Arrays Technology sequencing. Phenotypic screening across the population demonstrated a wide spectrum of disease severity (scores 0–6), confirming the segregation of key resistance genes. The DArTseq platform identified nearly 104,000 markers, comprising 61% SilicoDArTs and 39% SNPs. Among the 33 most significant markers associated with resistance (p < 0.01), 76% were SilicoDArTs. Transcriptomic data further validated these findings, revealing 13 marker-linked genes expressed during infection, seven of which exhibited significant differential expression. Comprehensive functional annotation of Arabidopsis thaliana orthologs associated these genes with diverse cellular and plant-wide processes, particularly during stress responses. Collectively, these findings emphasize the complex polygenic nature of blackleg resistance and provide robust genomic tools for the accelerated breeding of resilient B. napus cultivars.