Dataset on the single nucleotide variation in diversity panel of 500 lettuce accessions genotyped with tunable genotyping-by-sequencing (tGBS) method

Authors: Simko, Ivan

Submitted to: Data in Brief
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2023
Publication Date: 7/20/2023
Citation: Simko, I. 2023. Dataset on the single nucleotide variation in diversity panel of 500 lettuce accessions genotyped with tunable genotyping-by-sequencing (tGBS) method. Data in Brief. 49. Article 109419. https://doi.org/10.1016/j.dib.2023.109419.
DOI: https://doi.org/10.1016/j.dib.2023.109419

Interpretive Summary: Lettuce is an important leafy vegetable cultivated in moderate climates around the world. Based on phenotypic characteristics, such as formation and size of ‘heads’ (leaves arranged in a dense rosette), size, and texture of leaves, length of stems, and size and composition of seeds, lettuce cultivars can be classified into several distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine, and stem). L. serriola, a wild progenitor of cultivated lettuce, is frequently utilized in breeding programs to introgress desirable genes and alleles (e.g., resistance to diseases) into lettuce gene pool. A diversity panel of ~500 lettuce accessions was genotyped with tunable genotyping-by-sequencing method to identify genetic variations. The described diversity panel together with the set of identified DNA markers can be used for mapping genes for economically important traits and to develop marker assays for marker assisted selection. Descibed DNA markers can also be used to identify F1 hybrids, genotype gene bank collections, and in other areas of lettuce genetics and breeding.

Technical Abstract: Lettuce (Lactuca sativa L.) is an important leafy vegetable cultivated in moderate climates around the world. Based on phenotypic characteristics, such as formation and size of ‘heads’ (leaves arranged in a dense rosette), size, and texture of leaves, length of stems, and size and composition of seeds, lettuce cultivars can be classified into several distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine, and stem). L. serriola, a wild progenitor of cultivated lettuce, is frequently utilized in breeding programs to introgress desirable genes and alleles (e.g., resistance to diseases) into lettuce gene pool. A diversity panel of ~500 lettuce accessions was genotyped with tunable genotyping-by-sequencing (tGBS) method to identify single nucleotide polymorphism (SNP) sites. SNPs were positioned on lettuce genome using the reference genome of cultivar Salinas. Sequences flanking each of 115,261 SNPs (200 bp upstream and 200 bp downstream) are also provided. The described diversity panel together with the set of SNP markers can be used for mapping quantitative trait loci (QTL) and to develop marker assays for marker assisted selection (MAS). Identified SNP sites can also be used to identify F1 hybrids, genotype gene bank collections, and in other areas of lettuce genetics and breeding.