Genome-wide association study on metabolite accumulation in a wild barley NAM population reveals natural variation in sugar metabolism

Abstract

Metabolites play a key role in plants as they are routing plant developmental processes and are involved in biotic and abiotic stress responses. Their analysis can offer important information on the underlying processes. Regarding plant breeding, metabolite concentrations can be used as biomarkers instead of or in addition to genetic markers to predict important phenotypic traits (metabolic prediction). In this study, we applied a genome-wide association study (GWAS) in a wild barley nested association mapping (NAM) population to identify metabolic quantitative trait loci (mQTL). A set of approximately 130 metabolites, measured at early and late sampling dates, was analysed. For four metabolites from the early and six metabolites from the late sampling date significant mQTL (grouped as 19 mQTL for the early and 25 mQTL for the late sampling date) were found. Interestingly, all of those metabolites could be classified as sugars. Sugars are known to be involved in signalling, plant growth and plant development. Sugar-related genes, encoding mainly sugar transporters, have been identified as candidate genes for most of the mQTL. Moreover, several of them co-localized with known flowering time genes like Ppd-H1, HvELF3, Vrn-H1, Vrn-H2 and Vrn-H3, hinting on the known role of sugars in flowering. Furthermore, numerous disease resistance-related genes were detected, pointing to the signalling function of sugars in plant resistance. An mQTL on chromosome 1H in the region of 13 Mbp to 20 Mbp stood out, that alone explained up to 65% of the phenotypic variation of a single metabolite. Analysis of family-specific effects within the diverse NAM population showed the available natural genetic variation regarding sugar metabolites due to different wild alleles. The study represents a step towards a better understanding of the genetic components of metabolite accumulation, especially sugars, thereby linking them to biological functions in barley.

The Application of Metabolomics in Recent Colorectal Cancer Studies: A State-of-the-Art Review

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Approach strategies and application of metabolomics to biotechnology in plants

“…The sample size needed for the analysis varies depending on the concentration of the target metabolites, pretreatment techniques, and analytical techniques, but it commonly falls between 10 and 100 mg fresh weight. Controls for consistent sampling in a short period of time are necessary for large-scale sampling, such as that required for mGWAS investigations, because the metabolome is sensitive to environmental influences ( Gemmer et al., 2021 ; Yao et al., 2021 ). To prevent chemical changes caused by enzymatic and chemical reactions, a quenching method such liquid nitrogen freezing and extraction with organic solvents should be carried out right away.…”

Barley with improved drought tolerance: Challenges and perspectives

“…In a barley RIL population, the mQTL study detected 98 different stress-responsive metabolites and observed that their abundance modulates through coordinated expression of several genes to function under drought conditions (Piasecka et al, 2017). A mQTL study, was applied in the large barley nested association mapping (NAM) population (Gemmer et al, 2021). Approximately 130 sugars and sugar-like metabolites were detected on ealry and late sampling dates.…”