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United States Department of Agriculture

Agricultural Research Service

Research Project: Evaluation, Enhancement, Genetics and Breeding of Lettuce, Spinach, and Melon Title: Computing Integrated Ratings from Heterogeneous Phenotypic Assessments: A Case Study of Lettuce Postharvest Quality and Downy Mildew Resistance

Authors
item Simko, Ivan
item Hayes, Ryan
item Kramer, Matthew

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 11, 2012
Publication Date: August 3, 2012
Citation: Simko, I., Hayes, R.J., Kramer, M.H. 2012. Computing integrated ratings from heterogeneous phenotypic assessments: A case study of lettuce postharvest quality and downy mildew resistance. Crop Science. 52:2131-2142.

Interpretive Summary: Comparing performance of a large number of accessions simultaneously is not always possible. Typically, only subsets of all accessions are tested in separate trials with only some (or none) of the accessions overlapping between subsets. Here we compare two approaches that can compute an overall linear rating for the performance of all accessions across a set of trials, even for accessions that were never tested together and were rated on dissimilar scales. We use data from lettuce (Lactuca sativa L.) post-harvest quality evaluated on 178 accessions in 18 trials, and assessment of lettuce resistance to downy mildew (Bremia lactucae Regel) performed on 583 accessions in 53 trials. We found high correlation between ratings produced by the two approaches for the post-harvest quality, and the resistance to downy mildew. Combining data from multiple experiments identified lettuce accessions with high a level of resistance to the disease and a slow rate of deterioration when processed for salad. However, for some horticultural types of lettuces, no cultivars had both desirable traits. Though the present analyses focused on combining data from sparsely populated accession trial matrices, both statistical approaches can be used to combine data from different laboratories or databases (accession, database or accession, laboratory matrix), thus improving the major bottleneck in obtaining phenotypic data for large-scale studies (e.g. association mapping).

Technical Abstract: Comparing performance of a large number of accessions simultaneously is not always possible. Typically, only subsets of all accessions are tested in separate trials with only some (or none) of the accessions overlapping between subsets. Using standard statistical approaches to combine data from such sparsely populated accession x trial matrix is precluded if different rating scales are used to evaluate accessions in those trials. Here we compare two approaches that can compute an overall linear rating for the performance of all accessions across a set of trials, even for accessions that were never tested together and were rated on dissimilar scales. We use data from lettuce (Lactuca sativa L.) post-harvest quality evaluated on 178 accessions in 18 trials, and assessment of lettuce resistance to downy mildew (Bremia lactucae Regel) performed on 583 accessions in 53 trials. The projected values (PV) approach uses a combination of principal component analysis and resampling to merge trial results and calculates an overall rating from real values. In contrast, the rank-aggregation (RA) approach uses an extension of the Rasch model to combine rank-ordered data from individual trials. We found high correlation between ratings produced by the two approaches for the post-harvest quality (r = 0.802), and the resistance to downy mildew (r = 0.748). Combining data from multiple experiments identified lettuce accessions with high a level of resistance to the disease and a slow rate of deterioration when processed for salad. However, for some horticultural types of lettuces, no cultivars had both desirable traits. Though the present analyses focused on combining data from sparsely populated accession trial matrices, both statistical approaches can be used to combine data from different laboratories or databases (accession database or accession laboratory matrix).

Last Modified: 10/31/2014