C-41

Uncovering the genetic basis of quantitative resistance to cucumber mosaic virus in *Capsicum annuum* using
genome-wide association coupled with high-throughput image analysis

Judith Hirsch<fnref n="1" /> (judith.hirsch@inrae.fr), Lucie Tamisier<fnref n="2" />, Marion Szadkowski<fnref n="1" />, Sylvain Piry<fnref n="1" />, <fnref n="3" />, Louis McLeod<fnref n="2" />, <fnref n="4" />,
Anne Massire<fnref n="2" />, Christophe Gros<fnref n="2" />, Benoît Moury<fnref n="1" />, Véronique Lefebvre<fnref n="2" />

Using cultivars with genetic resistance to viruses is a key strategy for controlling viral epidemics in crops. Quantitative
resistance is likely to be more durable than qualitative resistance and can further enhance the durability of
major-effect resistance genes when combined in a pyramiding strategy. Thus, understanding the genetic basis of
quantitative resistance to viruses holds significant promise for improving resistance durability in breeding programs.
We addressed this question in the case of *Capsicum annuum* resistance to cucumber mosaic virus (CMV), an
economically important virus in pepper crops worldwide. We focused on the early stages of CMV infection to identify
resistance mechanisms that occur rapidly during the infection process. A panel of 336 *C. annuum* accessions from
the G2P-SOL H2020 core-collection (McLeod et al., 2023) was inoculated with the N strain of CMV, which induces
local lesions. Symptom severity, assessed by the extent of necrotic lesions on inoculated leaves (ten leaves per
accession), was analyzed through a deep learning pipeline. Phenotypic and genotypic data were then combined in
a genome-wide association study (GWAS) using mixed linear and multi-locus mixed models.

The deep learning pipeline achieved over 98% accuracy in detecting and classifying necrotic lesions, demonstrating its effectiveness as a high-throughput phenotyping tool. GWAS identified SNPs significantly linked to resistance, including a major SNP on chromosome 6 consistently detected using both models. Additional significant loci were found on chromosomes 1, 8, and 12. Notably, the region on chromosome 6 has previously been associated with resistance to potato virus Y, a phylogenetically unrelated virus.

This study illustrates the power of combining GWAS with deep learning phenotyping to accelerate resistance
breeding. Future research will explore candidate genes underlying the identified Quantitative Trait Loci (QTL),
particularly those associated with the QTL on chromosome 6, which may provide insights into early broad-spectrum
virus resistance mechanisms.

Mots clés : Capsicum annuum - Cucumber mosaic virus - Quantitative resistance - Durability - GWAS.

Références :

1. McLeod et al. 2023, Plant J. 116, 1508–1528.

<footnote n="1">¹ Pathologie végétale, INRAE, Montfavet, France</footnote>

<footnote n="2">² GAFL, INRAE, Montfavet, France</footnote>

<footnote n="3">³ CBGP, INRAE, Montpellier, France</footnote>

<footnote n="4">⁴ A2M, INRAE, Montfavet, France</footnote>