Genome-wide association mapping reveals loci for shelf life and developmental rate of lettuce

Authors: Sthapit Kandel, Jinita; PENG, HUI - University Of California; Hayes, Ryan; Mou, Beiquan; Simko, Ivan

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/21/2020
Publication Date: 5/22/2020
Citation: Sthapit Kandel, J., Peng, H., Hayes, R.J., Mou, B., Simko, I. 2020. Genome-wide association mapping reveals loci for shelf life and developmental rate of lettuce. Theoretical and Applied Genetics. 133:1947–1966. https://doi.org/10.1007/s00122-020-03568-2.
DOI: https://doi.org/10.1007/s00122-020-03568-2

Interpretive Summary: Lettuce is widely used in packaged leafy vegetable salads. Fresh-cut lettuce in packaged salad can have short shelf life and deterioration can occur within a week after processing. Deteriorated lettuce is not marketable, must be disposed, and results in the need for more lettuce to be grown, processed, and transported. Lettuce varieties with consistently long shelf life across different growing seasons and locations are desirable for the lettuce industry and can be selected for breeding purposes. Yield stability within and among seasons ensures a more consistent volume of raw product in order to enhance processing plant efficiency, including workforce employment and product for customers. Early bolting (stem elongation) of lettuce plants affects the quality of fresh-cut lettuce by making the leaves bitter and tough, and can make the crop unmarketable, so, late-bolting accessions are preferred by the salad industry. This research evaluated 493 lettuce accessions for shelf life in modified atmosphere packaging, yield, developmental rate of the plants, and stability of the three traits across different environments. Assessments were performed in five field experiments in three locations in Salinas Valley, CA during years 2016, 2017, and 2019. The accessions were genotyped, and 4,615 high-quality genetic markers were used for analyses. Genome-wide association studies were performed using phenotypic and genotypic data to determine the genetic region associated with the traits. We identified lettuce accessions with long and stable shelf life, stable yield, and stable slow-bolting. These accessions can be used in breeding programs to develop better lettuce cultivars for fresh-cut lettuce. Genetic regions associated with long shelf life, yield, and bolting were identified. Molecular markers from the identified genetic regions can be used to make selection in lettuce breeding.

Technical Abstract: Deterioration rate of fresh-cut lettuce in packaged salads varies greatly among lettuce cultivars but can be evident within a week of processing. Long shelf life of fresh-cut lettuce reduces loss through the marketing chain to end-users. Yield stability within and among seasons ensures a more consistent volume of raw product in order to enhance processing plant efficiency, including workforce employment and product for customers. Early bolting of lettuce plants affects the taste, leaf tissue quality and processable yield of fresh-cut lettuce and can make the crop unmarketable, thus, cultivars with slow or delayed reproductive development are preferred by the salad industry. Variation of shelf life, yield, reproductive development rate, and stability of all three traits of 493 lettuce accessions were subjected to genome-wide association study (GWAS) with 4,615 high-quality, single-nucleotide polymorphism (SNP) markers. The accessions were grown in five replicated field experiments in Salinas Valley, CA in 2016, 2017, and 2019. Lettuce heads were harvested, processed into salad and evaluated weekly for five weeks using a visual scale from 0 to 10, where each step of the scale corresponds to 10 % of the estimated percentage of deteriorated tissue. Yield (head fresh weight) was estimated in three of the experiments. Reproductive development at the time of harvest was assessed using 1 to 7 scale (1, rosette; 2, bolted; 3, visible flower buds; 4, expanded inflorescence; 5, anthesis; 6, majority buds at anthesis (>70%); 7, open involucres). Stability indices for shelf life, yield, and reproductive development rate for each accession were calculated for GWAS and to identify accessions with stable shelf life, stable yield, and stable developmental rate. Significant marker-trait associations (SMTA) for shelf life were detected on chromosome 4 in all four experiments; the most significant SMTA with P-value 3.44E-17 explained 24% of the total phenotypic variation (R2 = 0.24). The major QTL for developmental rate was detected on chromosome 7 (P-value 2.43E-16, R2 = 16%), while additional QTLs with smaller effect were found in all chromosomes. 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.