Genome-wide association mapping reveals loci for shelf life and developmental rate of lettuce
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ORIGINAL ARTICLE
Genome‑wide association mapping reveals loci for shelf life and developmental rate of lettuce Jinita Sthapit Kandel1 · Hui Peng2 · Ryan J. Hayes3 · Beiquan Mou1 · Ivan Simko1 Received: 1 November 2019 / Accepted: 18 February 2020 © This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2020
Abstract Key message Two major QTL, one for shelf life that corresponds to qSL4 and one, qDEV7, for developmental rate, were identified. Associated markers will be useful in breeding for improved fresh-cut lettuce. Abstract Fresh-cut lettuce in packaged salad can have short shelf life, and visible deterioration may start within a week after processing. Yield and developmental rate are an important aspect of lettuce production. Genetic diversity and genome-wide association studies (GWAS) were performed on 493 accessions with the genotypic data of 4615 high-quality single nucleotide polymorphism markers. Population structure (Q), principal component (PC), and phylogenetic analyses displayed genetic relationships associated with lettuce types and geographic distribution. Data for shelf life, yield, developmental rate, and their stability indices were used for statistical analysis, and GWAS was performed by general and mixed linear models. The genetic relationship among the individuals was incorporated into the models using kinship matrix, PC, and Q. Broad-sense heritability (H2) across environments was 0.43 for shelf life, 0.36 for yield, and 0.60 for developmental rate. There was a negative correlation between yield and developmental rate. Significant marker–trait association (SMTA) was detected for shelf life on chromosome 4. The most significant quantitative trait locus (QTL, qSL4, P = 2.23E−17) explained 24% of the total phenotypic variation (R2). The major QTL for developmental rate was detected on chromosome 7 (qDEV7, P = 2.43E−16, R2 = 17%), while additional QTLs with smaller effect were found in all chromosomes. No SMTA was detected for yield. The study identified lettuce accessions with extended and stable shelf life, stable yield, and desirable developmental rate. Molecular markers closely linked to traits can be applied for selection of preferable genotypes and for identification of genes associated with these traits.
Introduction Communicated by Albrecht E. Melchinger. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03568-2) contains supplementary material, which is available to authorized users. * Jinita Sthapit Kandel [email protected] * Ivan Simko [email protected] 1
Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Agricultural Research Service, 1636 E. Alisal Street, Salinas, CA 93905, USA
2
The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
3
Forage Seed and Cereal Research Unit, U.S. Department of Agriculture, Agricultural
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