Genome-wide association mapping reveals genomic regions frequently associated with lettuce field resistance to downy mildew

Authors: Simko, Ivan; PENG, HUI - University Of California; Sthapit Kandel, Jinita; Zhao, Rebecca

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2022
Publication Date: 6/17/2022
Citation: Simko, I., Peng, H., Sthapit Kandel, J., Zhao, R.B. 2022. Genome-wide association mapping reveals genomic regions frequently associated with lettuce field resistance to downy mildew. Theoretical and Applied Genetics. 135:2009–2024. https://doi.org/10.1007/s00122-022-04090-3.
DOI: https://doi.org/10.1007/s00122-022-04090-3

Interpretive Summary: Lettuce downy mildew is one of the most economically important disease of cultivated lettuce worldwide. We have applied the genome-wide association mapping (GWAS) approach to detect qDMR loci for field resistance to downy mildew in the panel of 493 accessions tested in 21 field experiments. The analysis identified 63 qDMR loci, at least 53 QTLs were novel. qDMR loci were randomly distributed across all nine lettuce chromosomes. The genomic regions frequently associated with lettuce field resistance to downy mildew are located on chromosomes 4 and 5 and could be used for detailed study of the mechanism of polygenic resistance. The most resistant accessions identified in the current study (cvs. Auburn, Grand Rapids, Romabella, PI 226514, and PI 249536) are being incorporated into our breeding program. Up to date this is the most comprehensive study of QTLs for field resistance to downy mildew and the first study that uses GWAS for mapping disease resistance loci in lettuce.

Technical Abstract: Lettuce downy mildew is one of the most economically important disease of cultivated lettuce worldwide. We have applied the genome-wide association mapping (GWAS) approach to detect QTLs for field resistance to downy mildew in the panel of 493 accessions tested in 21 field experiments. The analysis identified 131 significant marker – trait associations that could be grouped into 63 QTLs. At least 53 QTLs were novel, while remaining 10 QTLs overlapped with previously described QTLs for lettuce field resistance to downy mildew. Unlike race-specific, dominant Dm genes that mostly cluster on three out of nine lettuce chromosomes, QTLs (qDMR loci) for polygenic resistance are randomly distributed across all nine chromosomes. The genomic regions frequently associated with lettuce field resistance to downy mildew are located on chromosomes 4 and 5 and could be used for detailed study of the mechanism of polygenic resistance. The most resistant accessions identified in the current study (cvs. Auburn, Grand Rapids, Romabella, PI 226514, and PI 249536) are being incorporated into our breeding program. Markers closely linked to the resistance QTLs could be potentially used for marker-assisted selection, or in combination with other markers in the genome, for a combined genomic and marker-assisted selection. Up to date this is the most comprehensive study of QTLs for field resistance to downy mildew and the first study that uses GWAS for mapping disease resistance loci in lettuce.