Genetic analysis of potato tuber metabolite composition: Genome‐wide association studies applied to a nontargeted metabolome

Abstract

Plant improvement requires a response to selection, which can be complicated when the biochemical bases of a trait are poorly understood, difficult to measure, genetically complex, or some combination of these common obstacles. We applied nontargeted metabolomic profiling to generate a deep (but largely anonymous) dataset of potato (Solanum tuberosum L.) tubers to increase our understanding of the genetic bases for compositional traits. We examined water–methanol extracts of cooked potato tuber cores from 185 clones that had previously been single nucleotide polymorphism (SNP) genotyped by the Solanaceae Coordinated Agricultural Project (SolCAP) and detected 981 features that represent a mixture of primary metabolites, specialized metabolites, and hydrolyzed fragments of abundant proteins. Using GWASpoly, an R package that considers gene dosage through a series of genetic models, 472 features could be associated with at least one SNP marker, markedly increasing the number of marker–trait associations that have been made in potato to date. An additive genetic model detected the most associations, where 301 compositional features were associated with SNPs; in contrast, a duplex‐dominant model detected the least (160 features). Unexpectedly, SNPs associated with features were not uniformly distributed throughout the genome but were instead clustered on chromosomes 3, 7, and 8, with dozens of features associated with several small (∼2 Mbp) regions. Also interesting was that the most significant SNPs for several glycoalkaloids (α‐chaconine, β‐chaconine, and α‐solamarine)—detected on chromosomes 2, 7, and 8—are unlinked to any known glycoalkaloid biosynthetic genes.

Genome‐wide association analysis of agronomical and physiological traits linked to drought tolerance in a diverse potatoes (Solanum tuberosum) panel

“…The polymorphisms belonging to S. tuberosum spp andigena , wild species and interspecific hybrid genotypes in the potatoes panel could be the reason for the SNPs with no‐call genotypes. Nevertheless, currently, the use of Infinium SNP arrays is a wide and suitable approach to perform GWAS analysis in potatoes panels (Kaiser et al., 2020; Khlestkin et al., 2019; Levina et al., 2021; Selga et al., 2021). Moreover, the use of BLUPs values for phenotypic selection in potatoes breeding has proven to be an adequate strategy (Piepho et al., 2008).…”

Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae

“…105,176,177 In some cases, these genetic resources are being utilized to investigate metabolic diversity via targeted and untargeted metabolomics and renement of these efforts should facilitate linking genotype to phenotype. 178,179 An alternative, less frequently utilized, approach to harness genetic variation to interrogate metabolism is to combine untargeted metabolite proling with targeted disruption or over-expression of known enzymes or transcription factors. 180,181 This approach, while more targeted than a strategy incorporating genome-wide genetic variation, can be utilized in any species where genetic manipulation is feasible and has signicant potential to increase understanding of plant SM networks.…”

“…105,176,177 In some cases, these genetic resources are being utilized to investigate metabolic diversity via targeted and untargeted metabolomics and refinement of these efforts should facilitate linking genotype to phenotype. 178,179…”

Applying network and genetic analysis to the potato metabolome

“…The full methods for sample processing, analysis, and data pre-processing are cited in ( Levina et al., 2021 ); a brief summary is presented below. The potato clones selected for the study were a subset of a diversity panel assembled by the Solanaceae Coordinated Agricultural Project (SolCAP) ( Douches, 2008 ; Hirsch et al., 2013 ).…”