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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Research Project #439349

Research Project: Improving Lettuce Cultivars against Bacterial Leaf Spot (BLS) through Breeding, Genetics, and Study of the BLS-Lettuce Interaction

Location: Crop Improvement and Protection Research

Project Number: 2038-21530-003-002-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Oct 1, 2020
End Date: Mar 31, 2024

Objective 1. To identify newer sources of resistances against Xcv to strains from Florida, California and Canada. Objective 2. To introgress novel resistance genes from Lactuca sativa to L. sativa and from L. serriola to L. sativa for Florida and California production. Objective 3. To identify genes conferring race status to strains of Xcv and to study the role of these genes in race specificity. Objective 4. To establish Genome Wide Association mapping of race specific and non-specific race resistance. Indicator Number of genotyped and phenotyped accessions. Objective 5. To use identified race specific genes or sequences to develop PCR protocols that can be used to develop a method for Xcv seed detection, quantification, and race identification. Objective 6. To put in place extension material related to Bacterial leaf spot management to be used by stakeholders in a bilingual publication (English and Spanish).

Genetic approaches have been successful for identifying a major resistance locus on LG2. We have already worked to transfer the resistance conferred by that locus into adapted breeding lines, but novel major and minor resistance loci should be sought after. The availability of an ultra-high density linkage map and the recently completed lettuce genome assembly allows genome-wide association studies (GWAS) on the diverse lettuce germplasm. Approximately 500 homozygous lettuce cultivars, plant introductions, and advanced breeding lines (combined called ‘accessions’ in this text) will be analyzed for their reaction to several Xcv strains. Testing for resistance will be performed in a greenhouse with spray-on inoculation. Using our existing pipeline, we can perform twelve, large-scale experiments per year. Multiple experiments will allow us to determine locations of major R-genes, QTLs, and stability of QTL-based resistance. All tests will include controls with known high susceptibility (cv. Vista Verde, PI 251246). Identical accessions will be used for GBS analysis. Single nucleotide polymorphism (SNP) markers detected by GBS approach will be aligned to the reference genome. Based on our previous results, we will likely be able to detect at this set of accessions about 140,000 SNPs. After filtering off SNPs with low reproducibility and/or high heterozygosity, we expect to retain approximately 40,000 –60,000 high-quality SNPs. Analyses of lettuce population structure and GWAS will be performed with programs Structure, TASSEL, and JMP Genomics. GBS markers closely linked to the R-genes and/or major QTLs for resistance will be used for development of marker assays. The genomic region around SNP markers will be sequenced and analyzed on the set of 20 accessions with high and low levels of resistance (10 accessions in each group). If no SNP marker matches perfectly with decay phenotypes, haplotypes will be constructed from closely spaced SNPs and used instead. The marker predictive accuracy will be evaluated on unrelated accessions with. variable levels of resistance. Genotyping will be performed with markers using high-resolution DNA melting (HRM) approach.