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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #341106
Title: Genome-wide association study for lettuce cultivars with improved salad processing efficiency

Author
item STHAPIT KANDEL, JINITA - Oak Ridge Institute For Science And Education (ORISE)
item Mou, Beiquan
item Simko, Ivan
item Hayes, Ryan

Submitted to: American Society of Horticulture Science Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 4/27/2017
Publication Date: 9/21/2017
Citation: Sthapit, J.K., Mou, B., Simko, I., Hayes, R.J. 2017. Genome-wide association study for lettuce cultivars with improved salad processing efficiency. American Society for Horticultural Science Annual Meeting, September 19-22, 2017, Waikoloa, Hawaii.

Interpretive Summary:

Technical Abstract: Lettuce (Lactuca sativa L.) is widely used as the main ingredient of packaged leafy vegetable salads. Salad lettuce can have short shelf life, decaying as early as eight days after harvest and reducing the nutritional quality. Decayed lettuce is not marketable, produces extra waste, and results in the need for more lettuce to be grown, processed, and transported. Lettuce cultivars with extended shelf life will help reduce waste products and increase efficiency. Genetic diversity, population structure, and a genome-wide association study (GWAS) were performed on a set of 498 lettuce accessions of mostly romaine types. All but 12 accessions underwent single-seed increase before genotyping using the genotyping-by-sequencing technique. A total of 4,615 high-quality polymorphic SNP (single-nucleotide polymorphism) markers were used for analysis. For shelf life assessment, lettuce heads were harvested from a single replicated field, processed into three salad bags (340 g each) per accession, and stored at 4°C for evaluation. Salad bags were evaluated on weekly intervals using the scale of 0 through 10, where the rating corresponds to 1/10th of the estimated percentage of decayed tissue. Area under disease progress stairs (AUDPS) was calculated for each accession. GWAS of shelf-life data was performed by general linear model (GLM) and mixed linear model (MLM) analyses. Information about the genetic relationships among the individuals was incorporated in the analyses using principal component analysis (PCA) in GLM, and PCA and kinship in MLM. Significant marker-trait association (SMTA) was detected on Linkage Group 4 (LG4) in both methods. P-values were as low as 3.55E-14 in MLM, which explained 16% of the variation (R2 = 0.16). The lowest P-value in GLM was 1.11E-53, which explained 42% of the variation (R2 = 0.42). Significant markers can be used for marker-assisted breeding for improved salad processing efficiency. Major quantitative trait loci (QTL) for decay of fresh-cut lettuce have been reported previously in LG4 in a recombinant inbred line population of Salinas 88 x La Brillante. Thus, information on these SMTA and QTL can be used for further studies leading to the identification and functional studies of gene(s) responsible for extended shelf life of lettuce.