Limitations and advantages of using metabolite-based genome-wide association studies: Focus on fruit quality traits

José G. Vallarino, Jun Hong, Shouchuang Wang, Xia Wang, Nir Sade, Isabel Orf, Dabing Zhang, Jianxin Shi, Shuangqian Shen, Álvaro Cuadros-Inostroza, Qiang Xu, Jie Luo, Alisdair R. Fernie, Yariv Brotman

Research output: Contribution to journalReview articlepeer-review

3 Scopus citations


In the last decades, linkage mapping has help in the location of metabolite quantitative trait loci (QTL) in many species; however, this approach shows some limitations. Recently, thanks to the most recent advanced in high-throughput genotyping technologies like next-generation sequencing, metabolite genome-wide association study (mGWAS) has been proposed a powerful tool to identify the genetic variants in polygenic agrinomic traits. Fruit flavor is a complex interaction of aroma volatiles and taste being sugar and acid ratio key parameter for flavor acceptance. Here, we review recent progress of mGWAS in pinpoint gene polymorphisms related to flavor-related metabolites in fruits. Despite clear successes in discovering novel genes or regions associated with metabolite accumulation affecting sensory attributes in fruits, GWAS incurs in several limitations summarized in this review. In addition, in our own work, we performed mGWAS on 194 Citrus grandis accessions to investigate the genetic control of individual primary and lipid metabolites in ripe fruit. We have identified a total of 667 associations for 14 primary metabolites including amino acids, sugars, and organic acids, and 768 associations corresponding to 47 lipids. Furthermore, candidate genes related to important metabolites related to fruit quality such as sugars, organic acids and lipids were discovered.

Original languageEnglish
Article number111748
JournalPlant Science
StatePublished - 1 Aug 2023

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science


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