Metabolic GWAS-based dissection of genetic basis underlying nutrient quality variation and domestication of cassava storage root
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Published:2023-12-14
Issue:1
Volume:24
Page:
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ISSN:1474-760X
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Container-title:Genome Biology
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language:en
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Short-container-title:Genome Biol
Author:
Ding Zehong, Fu Lili, Wang Bin, Ye Jianqiu, Ou Wenjun, Yan Yan, Li Meiying, Zeng Liwang, Dong Xuekui, Tie Weiwei, Ye Xiaoxue, Yang Jinghao, Xie Zhengnan, Wang Yu, Guo Jianchun, Chen Songbi, Xiao Xinhui, Wan Zhongqing, An Feifei, Zhang Jiaming, Peng Ming, Luo JieORCID, Li Kaimian, Hu Wei
Abstract
AbstractBackgroundMetabolites play critical roles in regulating nutritional qualities of plants, thereby influencing their consumption and human health. However, the genetic basis underlying the metabolite-based nutrient quality and domestication of root and tuber crops remain largely unknown.ResultsWe report a comprehensive study combining metabolic and phenotypic genome-wide association studies to dissect the genetic basis of metabolites in the storage root (SR) of cassava. We quantify 2,980 metabolic features in 299 cultivated cassava accessions. We detect 18,218 significant marker-metabolite associations via metabolic genome-wide association mapping and identify 12 candidate genes responsible for the levels of metabolites that are of potential nutritional importance.Me3GT,MeMYB4, andUGT85K4/UGT85K5, which are involved in flavone, anthocyanin, and cyanogenic glucoside metabolism, respectively, are functionally validated through in vitro enzyme assays and in vivo gene silencing analyses. We identify a cluster of cyanogenic glucoside biosynthesis genes, among whichCYP79D1,CYP71E7b, andUGT85K5are highly co-expressed and their allelic combination contributes to low linamarin content. We findMeMYB4is responsible for variations in cyanidin 3-O-glucoside and delphinidin 3-O-rutinoside contents, thus controlling SR endothelium color. We find human selection affects quercetin 3-O-glucoside content and SR weight per plant. The candidate geneMeFLS1is subject to selection during cassava domestication, leading to decreased quercetin 3-O-glucoside content and thus increased SR weight per plant.ConclusionsThese findings reveal the genetic basis of cassava SR metabolome variation, establish a linkage between metabolites and agronomic traits, and offer useful resources for genetically improving the nutrition of cassava and other root crops.
Funder
the National Key Research and Development Program of China the Central Public-Interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences the National Natural Science Foundation of China the earmarked fund for Modern Agro-industry Technology Research System the Key Research and Development Program of Hainan Province the Project of Sanya Yazhou Bay Science and Technology City the Major Science and Technology Plan of Hainan Province the Project of National Key Laboratory for Tropical Crop Breeding
Publisher
Springer Science and Business Media LLC
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