Unlocking genetic diversity in tomato : shedding light on resistance to Tomato yellow leaf curl disease

Abstract

Tomato yellow leaf curl disease (TYLCD) caused by Tomato yellow leaf curl virus (TYLCV) and a group of related species is a worldwide constraint of tomato (Solanum lycopersicum L.) production. Many countries have established quarantine measures to control this disease. Despite quarantine restrictions, TYLCD epidemic is still spreading due to the influence of climate change on insect vector population, rapid evolution of virus variants and global exchange of plant materials. Breeding for host plant resistance is considered as one of the most promising and sustainable methods in TYLCD control. Resistance to TYLCD was found in several wild relatives of tomato from which six TYLCV resistance genes (Ty-1 to Ty-6) have been identified. Breeding for TYLCV resistance has been focused on the introgression of the Ty-1 gene derived from S. chilense and the Ty-2 gene derived from S. habrochaites. Here it is shown that Ty-1 confers generic resistance against geminiviruses via enhancement of the transcriptional gene silencing (TGS) response. On the other hand, acquisition of beta-satellites by TYLCV can suppress the Ty-1-mediated TGS during co-infection. Ty-2 was not cloned yet at the start of this thesis research, thus we aimed to clone the Ty-2 gene. We fine-mapped Ty-2 to a small region of 32 kb using ‘intraspecific’ crosses between a Ty-2 introgression line and susceptible S. habrochaites accessions. In this region four genes were predicted, one of which was a full-length nucleotide binding leucine-rich repeat (NB-LRR) type gene. This gene proved to be the Ty-2 gene which confers species-specific resistance. A highly specific DNA marker tightly linked to the Ty-2 gene was developed permitting marker-assisted selection in tomato breeding. The other line of the thesis focuses on to diversify the current resistance profile by screening for novel resistance sources and mapping new tomato genes for TYLCV resistance. A large scale screening on 708 accessions from 13 wild tomato species representing a broad range of genetic diversity of tomato was performed for their phenotypic responses upon TYLCV infection. One hundred and thirty-eight accessions exhibited no TYLCV symptoms. Majority of the screened S. chilense accessions were symptomless. Besides, many identified symptomless accessions are from S. arcanum, S. corneliomulleri, and S. peruvianum. Importantly, a great effort has been made on the screening of 408 S. pimpinellifolium accessions for sources of resistance since they are closely-related to the domesticated tomato species making introgression breeding much easier than with other wild resistant species. However, all the tested S. pimpinellifolium accessions were symptomatic although symptom severity varied among accessions. The majority of the symptomless accessions identified from the present study have never been reported before in publications. This work constitutes a treasure of knowledge for the breeder interested in extending the very limited germplasm used to date as resistance generator in commercial varieties. Among these symptomless accessions, mapping populations (pseudo-F2) derived from a resistant S. arcanum accession were available and QTL mapping was performed. A major QTL, qRTych3 on chromosome 3 with a LOD score of 12.5 and explaining 40% of the phenotypic variation was identified. Subsequently, a bulked segregant analysis (BSA) in combination with whole genome sequencing (WGS) was performed on two DNA bulks each consisting of pseudo-F2 individuals which showed resistance (symptomless) or susceptibility (symptomatic) to TYLCV. Comparison of single nucleotide polymorphism (SNP) profiles on chromosome 3 between the two bulks allowed the identification of resistant bulk-specific SNPs for fine-mapping of the QTL. Due to the presence of multiple alleles per locus in the pseudo-F2 population, fine-mapping had to be performed using backcross families obtained through immature seed culture. Finally, qRTych3 was mapped to an interval of 2.93 Mb. Allele-specific markers in the QTL region have been developed, which are very useful for marker-assisted selection in breeding programs to introgress RTych3 for TYLCV resistance. All these information together provide plant breeders with tools and knowledge for developing TYLCV resistant varieties.