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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #371078

Research Project: Genetics and Breeding of Lettuce, Spinach, Melon, and Related Species to Improve Production and Consumer-related Traits

Location: Crop Improvement and Protection Research

Title: Genetic diversity, linkage disequilibrium and genome-wide association studies in lettuce

item Sthapit Kandel, Jinita
item Mou, Beiquan
item Simko, Ivan
item Hayes, Ryan

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/6/2020
Publication Date: 1/15/2020
Citation: Sthapit Kandel, J., Mou, B., Simko, I., Hayes, R.J. 2020. Genetic diversity, linkage disequilibrium and genome-wide association studies in lettuce. Plant and Animal Genome Conference, January 11-15, 2020, San Diego, California.

Interpretive Summary:

Technical Abstract: Lettuce (Lactuca sativa L.) is widely used as the main ingredient of packaged leafy vegetable salads. Diverse germplasm can be used as a resource for genetics studies and development of novel breeding lines with improved traits. A diversity panel of 493 genetically diverse lettuce accessions including cultivars, breeding lines, recombinant inbred lines, and primitive accessions from worldwide collections were selected for genome-wide association studies (GWAS) on quality, development, and morphological traits. Four thousand six hundred fifteen high-quality single-nucleotide polymorphism markers were used for assessing genetic diversity and linkage disequilibrium (LD) in the diversity panel. Population structure and principal component analyses, and neighbor-joining phylogenetic tree identified genetic relationships among accessions that were closely associated with lettuce type, color, and geographic distribution. Overall, 40.6% of the pairwise LD comparisons in the genome were significant (P < 0.01). In individual chromosomes, proportion of significant pairwise LD comparisons ranged from 36.0% (chromosome 4) to 46.3% (chromosome 9). GWAS was performed on data for shelf life, developmental rate, and seed color. Major quantitative trait loci were detected for shelf life on chromosome 4 (P = 3.44E-17, R2 = 24%), developmental rate on chromosome 7 (P = 2.43E-16, R2 = 16%), and seed color on chromosome 7 (P = 1.91E-25, R2 = 26%). The study identified accessions with extended shelf life and desirable developmental rate. Informative molecular markers closely linked to traits can be applied for selection of preferable genotypes and for identification of associated genes.