GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

Yayu Wang, Xiaolin Wang, Shuai Sun, Canzhi Jin, Jianmu Su, Jinpu Wei, Xinyue Luo, Jiawen Wen, Tong Wei, Sunil Kumar Sahu, Hongfeng Zou, Hongyun Chen, Zhixin Mu, Gengyun Zhang, Xin Liu, Xun Xu, Lone Gram, Huanming Yang, Ertao Wang () and Huan Liu ()
Additional contact information
Yayu Wang: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Xiaolin Wang: Chinese Academy of Sciences
Shuai Sun: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Canzhi Jin: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Jianmu Su: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Jinpu Wei: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Xinyue Luo: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Jiawen Wen: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Tong Wei: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Sunil Kumar Sahu: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Hongfeng Zou: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Hongyun Chen: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Zhixin Mu: Shanxi Agricultural University
Gengyun Zhang: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Xin Liu: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Xun Xu: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Lone Gram: Technical University of Denmark
Huanming Yang: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen
Ertao Wang: Chinese Academy of Sciences
Huan Liu: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract Genetic and environmental factors collectively determine plant growth and yield. In the past 20 years, genome-wide association studies (GWAS) have been conducted on crops to decipher genetic loci that contribute to growth and yield, however, plant genotype appears to be insufficient to explain the trait variations. Here, we unravel the associations between genotypic, phenotypic, and rhizoplane microbiota variables of 827 foxtail millet cultivars by an integrated GWAS, microbiome-wide association studies (MWAS) and microbiome genome-wide association studies (mGWAS) method. We identify 257 rhizoplane microbial biomarkers associated with six key agronomic traits and validated the microbial-mediated growth effects on foxtail millet using marker strains isolated from the field. The rhizoplane microbiota composition is mainly driven by variations in plant genes related to immunity, metabolites, hormone signaling and nutrient uptake. Among these, the host immune gene FLS2 and transcription factor bHLH35 are widely associated with the microbial taxa of the rhizoplane. We further uncover a plant genotype-microbiota interaction network that contributes to phenotype plasticity. The microbial-mediated growth effects on foxtail millet are dependent on the host genotype, suggesting that precision microbiome management could be used to engineer high-yielding cultivars in agriculture systems.

Date: 2022
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DOI: 10.1038/s41467-022-33238-4

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