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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects. / Li, Xukai; Gao, Jianhua; Song, Jingyi; Guo, Kai; Hou, Siyu; Wang, Xingchun; He, Qiang; Zhang, Yanyan; Zhang, Yakun; Yang, Yulu; Tang, Jiaoyan; Wang, Hailang; Persson, Staffan; Huang, Mingquan; Xu, Lishuai; Zhong, Linlin; Li, Dongqin; Liu, Yongming; Wu, Hua; Diao, Xianmin; Chen, Peng; Wang, Xiaowen; Han, Yuanhuai.

In: Molecular Plant, Vol. 15, No. 8, 2022, p. 1367-1383.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Li, X, Gao, J, Song, J, Guo, K, Hou, S, Wang, X, He, Q, Zhang, Y, Zhang, Y, Yang, Y, Tang, J, Wang, H, Persson, S, Huang, M, Xu, L, Zhong, L, Li, D, Liu, Y, Wu, H, Diao, X, Chen, P, Wang, X & Han, Y 2022, 'Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects', Molecular Plant, vol. 15, no. 8, pp. 1367-1383. https://doi.org/10.1016/j.molp.2022.07.003

APA

Li, X., Gao, J., Song, J., Guo, K., Hou, S., Wang, X., He, Q., Zhang, Y., Zhang, Y., Yang, Y., Tang, J., Wang, H., Persson, S., Huang, M., Xu, L., Zhong, L., Li, D., Liu, Y., Wu, H., ... Han, Y. (2022). Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects. Molecular Plant, 15(8), 1367-1383. https://doi.org/10.1016/j.molp.2022.07.003

Vancouver

Li X, Gao J, Song J, Guo K, Hou S, Wang X et al. Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects. Molecular Plant. 2022;15(8):1367-1383. https://doi.org/10.1016/j.molp.2022.07.003

Author

Li, Xukai ; Gao, Jianhua ; Song, Jingyi ; Guo, Kai ; Hou, Siyu ; Wang, Xingchun ; He, Qiang ; Zhang, Yanyan ; Zhang, Yakun ; Yang, Yulu ; Tang, Jiaoyan ; Wang, Hailang ; Persson, Staffan ; Huang, Mingquan ; Xu, Lishuai ; Zhong, Linlin ; Li, Dongqin ; Liu, Yongming ; Wu, Hua ; Diao, Xianmin ; Chen, Peng ; Wang, Xiaowen ; Han, Yuanhuai. / Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects. In: Molecular Plant. 2022 ; Vol. 15, No. 8. pp. 1367-1383.

Bibtex

@article{827296006fea4c68aa1b8279707f5240,
title = "Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects",
abstract = "Foxtail millet (Setaria italica), which was domesticated from the wild species green foxtail (Setaria viridis), is a rich source of phytonutrients for humans. To evaluate how breeding changed the metabolome of foxtail 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 we validated the function of PHYTOENE SYNTHASE 1 (PSY1) gene in affecting millet grain color and quality. Interestingly, our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects. Taken together, our multi-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.",
keywords = "anti-inflammatory effects, foxtail millet, genetic association, metabolome, multi-omics, transcriptome",
author = "Xukai Li and Jianhua Gao and Jingyi Song and Kai Guo and Siyu Hou and Xingchun Wang and Qiang He and Yanyan Zhang and Yakun Zhang and Yulu Yang and Jiaoyan Tang and Hailang Wang and Staffan Persson and Mingquan Huang and Lishuai Xu and Linlin Zhong and Dongqin Li and Yongming Liu and Hua Wu and Xianmin Diao and Peng Chen and Xiaowen Wang and Yuanhuai Han",
note = "Publisher Copyright: {\textcopyright} 2022 Elsevier Inc.",
year = "2022",
doi = "10.1016/j.molp.2022.07.003",
language = "English",
volume = "15",
pages = "1367--1383",
journal = "Molecular Plant",
issn = "1674-2052",
publisher = "Cell Press",
number = "8",

}

RIS

TY - JOUR

T1 - Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects

AU - Li, Xukai

AU - Gao, Jianhua

AU - Song, Jingyi

AU - Guo, Kai

AU - Hou, Siyu

AU - Wang, Xingchun

AU - He, Qiang

AU - Zhang, Yanyan

AU - Zhang, Yakun

AU - Yang, Yulu

AU - Tang, Jiaoyan

AU - Wang, Hailang

AU - Persson, Staffan

AU - Huang, Mingquan

AU - Xu, Lishuai

AU - Zhong, Linlin

AU - Li, Dongqin

AU - Liu, Yongming

AU - Wu, Hua

AU - Diao, Xianmin

AU - Chen, Peng

AU - Wang, Xiaowen

AU - Han, Yuanhuai

N1 - Publisher Copyright: © 2022 Elsevier Inc.

PY - 2022

Y1 - 2022

N2 - Foxtail millet (Setaria italica), which was domesticated from the wild species green foxtail (Setaria viridis), is a rich source of phytonutrients for humans. To evaluate how breeding changed the metabolome of foxtail 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 we validated the function of PHYTOENE SYNTHASE 1 (PSY1) gene in affecting millet grain color and quality. Interestingly, our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects. Taken together, our multi-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.

AB - Foxtail millet (Setaria italica), which was domesticated from the wild species green foxtail (Setaria viridis), is a rich source of phytonutrients for humans. To evaluate how breeding changed the metabolome of foxtail 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 we validated the function of PHYTOENE SYNTHASE 1 (PSY1) gene in affecting millet grain color and quality. Interestingly, our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects. Taken together, our multi-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.

KW - anti-inflammatory effects

KW - foxtail millet

KW - genetic association

KW - metabolome

KW - multi-omics

KW - transcriptome

U2 - 10.1016/j.molp.2022.07.003

DO - 10.1016/j.molp.2022.07.003

M3 - Journal article

C2 - 35808829

AN - SCOPUS:85135368185

VL - 15

SP - 1367

EP - 1383

JO - Molecular Plant

JF - Molecular Plant

SN - 1674-2052

IS - 8

ER -

ID: 318547861