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

Abstract

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.

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones

“…However, correlations between traits and selection criteria for each market group should be considered when defining the list of traits included in the index and their respective weights. Assigning traits with their weights are subjective and under the discretion of each breeder [ 30 ]. These should match to the priority of growers, market demands, industry standards, and consumer preferences [ 69 ].…”

“…Genomic-estimated breeding values (GEBV) were calculated using the StageWise package (version 0.26) [ 73 ] which is based on a two-stage approach in R [ 74 ] using ASReml-R v4 [ 75 ] for REML estimation of variance components. The standardized weighted multi-trait-selection index (WMIS) (for selection of parents/advance clones) within each market group was calculated on Z values of GEBVs on yield and defects traits following a similar approach to the one described by Pandey et al [ 30 ]. A simple WMIS for each market group was obtained by summing the product of Z values of GEBVs on the total yield and external and internal defects, keeping their associated trait weights equal.…”

“…Genomic selection has the potential to accelerate breeding for a variety of traits, including those with complex genetic inheritance. In potato breeding, genomic selection can be especially useful in early clonal generations to predict and select traits that are difficult or expensive to measure, or those with low heritability [ 30 ]. The availability of higher-density SNPs that span the entire genome of many plants now allows for the prediction of breeding values by regressing phenotypic values on all available markers [ 31 ].…”

“…In potato breeding programs, multiple traits are influenced by both major and minor effect loci but lack causal markers. However, the success of genomic selection depends on factors such as the size and similarity of the training and validation populations, as well as the genetic makeup of the traits being investigated [ 30 ].…”

Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content

“…In this study we utilized the standardized indexes for the chipping clones. Not all traits will have the same importance, and not all traits are measured using the same units or scales; thus, standardized scores and relative weight should be assigned to each trait to facilitate the selection of superior and inferior genotypes 97 . Market demands, industry needs, and several other considerations drive the relative importance of traits.…”