Genetic Basis of Resistance against Fusarium and Verticillium Wilts in Multiple Populations of Lettuce

Lettuce (Lactuca sativa) is a member of the Compositae family with an estimated genome size of 2.7 Gb. We have sequenced and assembled the genome of L. sativa cv. Salinas. The assembled genome has a total length of 2.38 Gb covering 88% of the 2.7 Gb genome. The assembly has been validated genetically and organized in nine pseudomolecules corresponding to the nine chromosomes of lettuce. We have used this assembly as the reference genomic sequence for Genotyping By Sequencing (GBS) analysis of multiple mapping populations, including populations segregating for resistance to Fusarium oxysporum and Verticillium dahliae responsible of wilts of lettuce. After testing several endonucleases, we reduced the complexity of our samples by restriction digestion with AvaII followed by adapter ligation and PCR amplification. Samples were then pooled and sequenced. We used the TASSEL-GBS pipeline to identify polymorphic SNPs between parental lines and haplotype them on the segregating populations. Custom scripts were used for further data filtering and analysis. Genetic maps were constructed for all segregating populations. Phenotyping for resistance was conducted in infected field and greenhouse trials over multiple years. QTL analysis of the resistance identified multiple genomic regions associated with resistance to these two pathogens. In most cases different QTLs were identified between populations indicating multiple sources of resistance and providing the opportunity for gene pyramiding.