A multi-omics framework reveals strawberry flavor genes and their regulatory elements

背景回顾：Flavor is essential to consumer preference of foods and is an increasing focus of plant breeding programs. In fruit crops, identifying genes underlying volatile organic compounds has great promise to accelerate flavor improvement, but polyploidy and heterozygosity in many species have slowed progress. 

主要研究：Here we use octoploid cultivated strawberry to demonstrate how genomic heterozygosity, transcriptomic intricacy and fruit metabolomic diversity can be treated as strengths and leveraged to uncover fruit flavor genes and their regulatory elements. 

结果1-多组学数据：Multi-omics datasets were generated including an expression quantitative trait loci map with 196 diverse breeding lines, haplotype-phased genomes of a highly-flavored breeding selection, a genome-wide structural variant map using five haplotypes, and volatile genome-wide association study (GWAS) with > 300 individuals. 

结果2-鉴定结果：Overlaying regulatory elements, structural variants and GWAS-linked allele-specific expression of numerous genes to variation in volatile compounds important to flavor. 

结果3-实例：In one example, the functional role of anthranilate synthase alpha subunit 1 in methyl anthranilate biosynthesis was supported via fruit transient gene expression assays. 

结论：These results demonstrate a framework for flavor gene discovery in fruit crops and a pathway to molecular breeding of cultivars with complex and desirable flavor. 

Genes putatively required for or regulating methyl anthranilate biosynthesis.

 摘 要 

果实风味对于消费者的食物偏好至关重要，也是植物育种项目日益关注的焦点。在水果作物中，鉴定挥发性有机化合物的关键基因有望加快水果作物的风味改良，但很多水果作物是多倍体且杂合度较高，因此减缓了这一育种进程。本文中，作者以八倍体的栽培种草莓为材料，来表明如何利用基因组杂合性、转录组复杂性以及水果代谢组多样性，来揭示控制水果作物果实风味的关键基因及其调控元件。作者在本文的研究中综合分析了多组学数据，包括一份含有196个不同育种系的表达数量性状位点图谱、一个风味很强的育种选择系的单倍型基因组、基于五种单倍型的全基因组结构变异图，以及一个基于超过 300个体的风味全基因组关联分析数据。作者鉴定到了很多与风味化合物相关基因的重叠调节元件、结构变异以及和GWAS关联的等位基因特异性表达变异，这些对于果实风味的形成十分重要。举例来说，作者通过果实的瞬时转化实验证明了邻氨基苯甲酸甲酯生物合成通路中邻氨基苯甲酸合酶α亚基1的功能。本文的研究结果揭示了一个鉴定水果作物风味基因的分子框架，并为具有复杂和理想风味作物品种的分子育种提供了途径。

 Vance M. Whitaker