Applying network and genetic analysis to the potato metabolome

Abstract

Compositional traits in potato [Solanum tuberosum L.] are economically important but genetically complex, often controlled by many loci of small effect; new methods need to be developed to accelerate analysis and improvement of such traits, like chip quality. In this study, we used network analysis to organize hundreds of metabolic features detected by mass spectrometry into groups, as a precursor to genetic analysis. 981 features were condensed into 44 modules; module eigenvalues were used for genetic mapping and correlation analysis with phenotype data collected by the Solanaceae Coordinated Agricultural Project. Half of the modules were associated with at least one SNP according to GWAS; 11 of those modules were also significantly correlated with chip color. Within those modules features associated with chipping provide potential targets for selection in addition to selection for reduced glucose. Loci associated with module eigenvalues were not evenly distributed throughout the genome but were instead clustered on chromosomes 3, 7, and 8. Comparison of GWAS on single features and modules of clustered features often identified the same SNPs. However, features with related chemistries (for example, glycoalkaloids with precursor/product relationships) were not found to be near neighbors in the network analysis and did not share common SNPs from GWAS. Instead, the features within modules were often structurally disparate, suggesting that linkage disequilibrium complicates network analyses in potato. This result is consistent with recent genomic studies of potato showing that chromosomal rearrangements that create barriers to recombination are common in cultivated germplasm.

The Use of Chlorophyll Fluorescence as an Indicator of Predicting Potato Yield, Its Dry Matter and Starch in the Conditions of Using Microbiological Preparations

“…The genes regulating these metabolic pathways may affect the availability of nutrients and the efficiency of their use by plants [63,64]. Genes responsible for regulating the development of roots, stems, leaves, and other plant organs can influence the plant's capacity to absorb water, nutrients, and the efficiency of photosynthesis [65]. These genes can interact with each other and with the plant environment, leading to changes in gene expression and metabolic function.…”

“…These genes can interact with each other and with the plant environment, leading to changes in gene expression and metabolic function. These interactions may affect physiological indices and yield characteristics depending on the environmental conditions [62][63][64][65]. Analysis of the genetic variability of potato traits could help identify cultivars more resistant to environmental stresses such as drought or cold.…”