Genome-wide association study of salt tolerance at the seed germination stage in lettuce

Authors: Das, Modan; Park, Sunchung - Sun; ADHIKARI, NEIL - California Department Of Public Health; Mou, Beiquan

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/26/2024
Publication Date: 10/18/2024
Citation: Das, M.K., Park, S., Adhikari, N.D., Mou, B. 2024. Genome-wide association study of salt tolerance at the seed germination stage in lettuce. PLoS ONE. 19(10). Article e0308818. https://doi.org/10.1371/journal.pone.0308818.
DOI: https://doi.org/10.1371/journal.pone.0308818

Interpretive Summary: Developing lettuce varieties having salt tolerance at the seed germination stage is important since lettuce seeds are planted half an inch deep in soil where salt levels are often highest in the salinity affected growing region. Greater knowledge of genetics and genomics of salt tolerance in lettuce will facilitate breeding improvement of lettuce with salt tolerance. Molecular markers are abundant in plants. In recent years, genomic analysis has emerged as a powerful tool for detecting molecular markers associated with traits of interest in plants. Accordingly, we conducted genomic analyses in lettuce for identifying molecular markers associated with two salt tolerance related traits: salinity susceptibility index and germination rate under salinity stress condition. The study involved 445 diverse lettuce accessions and 56,820 molecular markers. Six significant markers associated with these salt tolerance related traits were identified in the current study. Each of the six markers explained six to seven percent variations in the two traits for salt tolerance. The six significant salt tolerance related markers identified in the present study will be valuable resources for molecular marker development and marker assisted selection for breeding lettuce with improved salinity tolerance at the seed germination stage.

Technical Abstract: Developing lettuce varieties having salt tolerance at the seed germination stage is important since lettuce seeds are planted half an inch deep in soil where salt levels are often highest in the salinity affected growing region. Greater knowledge of genetics and genomics of salt tolerance in lettuce will facilitate improved breeding of lettuce with salt tolerance. Accordingly, we conducted a genome-wide association study (GWAS) in lettuce to identify marker-trait association for salt tolerance at the seed germination stage. The study involved 445 diverse lettuce accessions and 56,820 single nucleotide polymorphism (SNP) markers obtained through genotype-by-sequencing technology. Distributions of the SNP markers ranged from 4,189 on lettuce chromosome 6 to 10,112 on chromosome 4 with an average genome-wide SNP coverage of 24 SNPs/Mb. Principal component analysis revealed the presence of population structure among the lettuce accessions used. Linkage disequilibrium (LD) and LD decay study for the set of 445 accessions including wild type and for the set of 417 cultivated accessions showed average genome-wide LD of 0.188 and 0.202 respectively, and LD decayed to half of maximum LD at 199.5 Kb and 351.8 Kb, respectively for the two sets of accessions. GWAS using Mixed Linear Model (MLM) for a salinity susceptibility index based on germination rate under salinity stress and control conditions at day 5 (SSI_GR5d) and germination rate under salinity stress at day 5 (GR5d_S) revealed six significant SNPs on lettuce chromosome 7. Additive effects of each of the six SNPs was significant while dominance effect was non-significant. For each of the six SNPs, minor alleles were favorable for the phenotypic expression of SSI_GR5d and GR5d_S. Six to seven percent phenotypic variation for both SSI_GR5d and GR5d_S were explained by each of the six SNPs. The six significant salt tolerance related SNPs and their favorable allele effects identified in the current study will be a valuable resource for molecular marker development and marker assisted selection for breeding improvement of lettuce with salinity tolerance at the seed germination stage.