Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose pathway in tomato

Tomato (Solanum lycopersicum) is one of the highest-value vegetable crops worldwide. Understanding the genetic regulation of primary metabolite levels can inform efforts aimed toward improving the nutrition of commercial tomato cultivars, while maintaining key traits such as yield and stress toleran...

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Published in:	PLoS genetics 2019-05, Vol.15 (5), p.e1008149-e1008149
Main Authors:	Ye, Jie, Li, Wangfang, Ai, Guo, Li, Changxing, Liu, Genzhong, Chen, Weifang, Wang, Bing, Wang, Wenqian, Lu, Yongen, Zhang, Junhong, Li, Hanxia, Ouyang, Bo, Zhang, Hongyan, Fei, Zhangjun, Giovannoni, James J, Ye, Zhibiao, Zhang, Yuyang
Format:	Article
Language:	eng
Subjects:	Alleles Amino acids Ascorbic acid Ascorbic Acid - genetics Ascorbic Acid - metabolism Association analysis Basic Helix-Loop-Helix Transcription Factors - genetics Bioinformatics Biology and Life Sciences Biosynthesis Chromosome 9 Chromosome Mapping - methods Crop yields Cultivars Domestication Education Flavor Flowers & plants Fruit - genetics Fruits Funding Galactose Galactose - biosynthesis Galactose - metabolism Gene Expression Regulation, Plant - genetics Genes Genetic aspects Genetic diversity Genetic regulation Genetic Variation - genetics Genome, Plant - genetics Genome-wide association studies Genome-Wide Association Study Genomes Genomics Helix-loop-helix proteins Horticulture Laboratories Lycopersicon esculentum - genetics Lycopersicon esculentum - metabolism Mannose Mannose - biosynthesis Mannose - metabolism Metabolism Metabolites Novels Nutrition Phylogeny Physical sciences Physiological aspects Plant biology Promoter Regions, Genetic - genetics Quantitative trait loci Quantitative Trait Loci - genetics Software Solanum lycopersicum Supervision Tomatoes Transcription factors Vegetables Vitamin C
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Summary:	Tomato (Solanum lycopersicum) is one of the highest-value vegetable crops worldwide. Understanding the genetic regulation of primary metabolite levels can inform efforts aimed toward improving the nutrition of commercial tomato cultivars, while maintaining key traits such as yield and stress tolerance. We identified 388 suggestive association loci (including 126 significant loci) for 92 metabolic traits including nutrition and flavor-related loci by genome-wide association study from 302 accessions in two different environments. Among them, an ascorbate quantitative trait locus TFA9 (TOMATO FRUIT ASCORBATEON CHROMOSOME 9) co-localized with SlbHLH59, which promotes high ascorbate accumulation by directly binding to the promoter of structural genes involved in the D-mannose/L-galactose pathway. The causal mutation of TFA9 is an 8-bp InDel, named InDel_8, located in the promoter region of SlbHLH59 and spanned a 5'UTR Py-rich stretch motif affecting its expression. Phylogenetic analysis revealed that differentially expressed SlbHLH59 alleles were selected during tomato domestication. Our results provide a dramatic illustration of how ascorbate biosynthesis can be regulated and was selected during the domestication of tomato. Furthermore, the findings provide novel genetic insights into natural variation of metabolites in tomato fruit, and will promote efficient utilization of metabolite traits in tomato improvement.
ISSN:	1553-7404 1553-7390 1553-7404