Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication,metabolite traits,and antiinflammatory effects  

作　　者：Xukai Li Jianhua Gao Jingyi Song Kai Guo Siyu Hou Xingchun Wang Qiang He Yanyan Zhang Yakun Zhang Yulu Yang Jiaoyan Tang Hailang Wang Staffan Persson Mingquan Huang Lishuai Xu Linlin Zhong Dongqin Li Yongming Liu Hua Wu Xianmin Diao Peng Chen Xiaowen Wang Yuanhuai Han 

机构地区：[1]Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding,College of Life Sciences,Shanxi Agricultural University,Taigu,China [2]Key Laboratory of Brewing Molecular Engineering of China Light Industry,Beijing Technology and Business University,Beijing,China [3]Department of Neurology,University of Michigan,Ann Arbor,MI,USA [4]Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding,College of Agriculture,Shanxi Agricultural University,Taigu,China [5]Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing,China [6]Colllege of Plant Science and Technology,Huazhong Agricultural University,Wuhan,China [7]Copenhagen Plant Science Centre,Department of Plant&Environmental Sciences,University of Copenhagen,Frederiksberg C,Denmark [8]Joint International Research Laboratory of Metabolic and Developmental Sciences,School of Life Sciences and Biotechnology,Shanghai Jiao Tong University,Minhang,Shanghai 200240,China [9]College of Resources and Environment,Shanxi Agricultural University,Taigu,China [10]College of Horticulture and Forestry Sciences,Huazhong Agricultural University,Wuhan,China [11]National Key Laboratory of Crop Genetic Improvement,Huazhong Agricultural University,Wuhan,China [12]Grandomics Biosciences Company Limited,Beijing,China [13]College of Food Science and Engineering,Shanxi Agricultural University,Taigu,China

出　　处：《Molecular Plant》2022年第8期1367-1383,共17页分子植物（英文版）

基　　金：This workwas supportedby the National KeyR&DProgramof China(2019YFD1000700 and 2019YFD1000702);the JointFunds of theNational Natural Science Foundation of China(U21A20216);the Key R&D Program of Shanxi Province(201903D11006);theMajor Special Science and Technology Projects in Shanxi Province(202101140601027);the National Natural Science Foundation of China(32001608 and 31771810);the Scientific and Technological Innovation Programs of Shanxi Agricultural University(2017YJ27);Lundbeck Foundation(R346-2020-1546)grants.S.P.also acknowledges the financial aid of an ARC Discovery grant(DP19001941),Villum Investigator(25915),DNRF Chair(DNRF155),Novo Nordisk Laureate(NNF190C0056076),NovoNordisk Emerging Investigator(NNF20OC0060564).

摘　　要：Foxtail millet(Setaria italica),which was domesticatedfromthewild speciesgreenfoxtail(Setaria viridis),isa richsource of phytonutrientsfor humans.To evaluate how breeding changed themetabolome offoxtail millet grains,we generated and analyzed the datasets encompassing the genomes,transcriptomes,metabolomes,and anti-inflammatory indices from 398 foxtail millet accessions.We identified hundreds of common variants that influence numerous secondary metabolites.We observed tremendous differences in natural variations of the metabolites and their underlying genetic architectures between distinct sub-groups of foxtail millet.Furthermore,we found that the selection of the gene alleles associated with yellow grains led to altered profiles of metabolites such as carotenoids and endogenous phytohormones.Using CRiSPR-mediated genome editing wevalidated the function of PHYTOENE SYNTHASE1(PSY1)gene in affecting milletgrain colorand quality.Interestingly,our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects.Taken together,ourmulti-omics study illustrates how the breeding history of foxtail millet has shaped its metabolite profile.The datasets we generated in this study also provide important resources for further understanding how millet grain quality is affected by different metabolites,laying the foundations for future millet genetic research and metabolome-assisted improvement.

关 键 词：foxtail millet multi-omics genetic association METABOLOME transcriptome anti-inflammatory effects 

分 类 号：S515[农业科学—作物学]