Genomic selection and genome‐wide association studies in tetraploid chipping potatoes

• Published in: The plant genome 2023-03, Vol.16 (1), p.e20297-n/a
• Main Authors: Pandey, Jeewan, Scheuring, Douglas C., Koym, Jeffrey W., Endelman, Jeffrey B., Vales, M. Isabel
• Format: Article
• Language: English
• Subjects: Agricultural production; Chromosome 5; Cloning; Crop yield; Cultivars; Density; Gene loci; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Gravity; Plant Breeding; Polyploidy; Potatoes; Quantitative trait loci; Reproducibility of Results; Skin; Solanum tuberosum - genetics; Sugar; Tetraploidy
• ISSN: 1940-3372; 1940-3372
• DOI: 10.1002/tpg2.20297

Potato is a major food crop in the United States and around the world. Most potatoes grown in the United States are destined for processing. Genomic selection can speed up breeding progress for important traits, including those with complex inheritance by guiding the identification of the best parents and guiding selection to advance clones in the breeding program. However, the application of genomic selection in polyploid species has been challenging. In this study, we obtained breeding values of 384 chipping clones evaluated in Texas between 2017 and 2020. The mean reliability of the genomic‐estimated breeding values obtained were 0.77, 0.41, 0.61, 0.71, and 0.24 for chip color, chip quality, specific gravity, vine maturity, and total yield, respectively. Potato clones with good chip quality, high yield, high specific gravity, and light‐color chips were identified using a multi‐trait selection index based on weighted standardized genomic‐estimated breeding values. Genome‐wide association studies identified quantitative trait loci on chromosome 5 for vine maturity and chromosomes 1, 3, and 7 for chip color. This research has laid the groundwork for implementing genomic selection in tetraploid potato breeding and understanding the genetic basis of chip processing traits in potatoes. Core Ideas Developing improved potato chip cultivars would be extremely beneficial for the chip processing industry. Genomic‐estimated breeding values (GEBVs) should guide parental selection and advancement of clones. Potato chipping clones with high standardized weighted multitrait index values were identified. Standardized weighted multitrait indexes should be more effective than nonstandardized unweighted GEBVs. Genome‐wide association studies identified quantitative trait loci for vine maturity and chip color.