Mapping quantitative trait loci for lettuce resistance to Verticillium dahliae race 3, plant development, and leaf color using an ultra-high-density bin map constructed from F2 progeny

Authors: Simko, Ivan; PURI, KRISHNA - University Of California; DHAR, NIKHILESH - University Of California; PENG, HUI - University Of California; SUBBARAO, KRISHNA - University Of California

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/6/2022
Publication Date: 9/22/2022
Citation: Simko, I., Puri, K.D., Dhar, N., Peng, H., Subbarao, K.V. 2022. Mapping quantitative trait loci for lettuce resistance to Verticillium dahliae race 3, plant development, and leaf color using an ultra-high-density bin map constructed from F2 progeny. Phytofrontiers. 2(3):257-267. https://doi.org/10.1094/PHYTOFR-11-21-0078-R.
DOI: https://doi.org/10.1094/PHYTOFR-11-21-0078-R

Interpretive Summary: Verticillium wilt, caused by fungus Verticillium dahliae, is one of the most devastating soilborne diseases in lettuce and the use of host resistance is the most optimal choice for its management. Though there were previously only two races of this pathogen that affected lettuce, more recently an additional race 3, originally identified in Japan, has become a concern for the lettuce industry. This study focused on identifying and mapping the genetic loci for resistance against race 3 of V. dahliae in a mapping population of plant families developed from a cross between moderately resistant red-leaf lettuce 'Sentry' and susceptible green leaf lettuce 'La Brillante'. Cultivar Sentry contains loci for resistance to V. dahliae race 3 and thus can be used to develop lettuce breeding lines with partial resistance against this pathogen. Markers linked to the resistance loci described in this study can aid in the introgression of Verticillium resistance genes into desirable genotypes using marker-assisted selection. Additional genetic and functional studies are needed, however, to identify the genes that confer phenotypes with partial resistance to V. dahliae race 3.

Technical Abstract: Verticillium wilt is one of the most devastating soilborne diseases in lettuce and the use of host resistance is the most optimal choice for its management. This study focused on identifying and mapping the genetic loci for resistance against race 3 in a mapping population of 200 F2:3 families developed from a cross between moderately resistant red-leaf lettuce 'Sentry' and susceptible green leaf lettuce 'La Brillante'. The population was genotyped using the tunable Genotyping by Sequencing (tGBS) approach. An ultra-high-density genetic linkage map containing 34,838 single nucleotide polymorphism (SNP) markers grouped into 1,734 bins was constructed using F2 progeny and a sliding window approach. Three quantitative trait loci (QTLs) for resistance to V. dahliae race 3 were located on linkage groups (LGs) LG 2 (qVR3-2.1), and LG 4 (qVR3-4.1 and qVR3-4.2). Each of these QTLs explained up to ~10% of the total phenotypic variation for the trait. At each locus, the resistance alleles originated from cultivar Sentry that is partially resistant to the pathogen. Additional resistance loci to the disease are expected in this population, and transgressive segregation indicates that some of those loci could originate from the susceptible cultivar La Brillante. In addition, two QTLs for plant development were identified on LG 2 (qIPD-2.1) and LG 7 (qIPD-7.1). No relationship was detected between resistance in genotypes and the rate of plant development. A major effect QTL for red leaf color was detected on LG 9 (qRLC-9.1). Candidate genes linked to some of the QTLs for resistance, plant development, and leaf color were identified. The QTLs for resistance identified in Sentry may diversify the resistance gene pool and provide an alternative tool to manage a newly emerged V. dahliae race 3.