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Background <p>Host genetics is known to determine the composition of the plant microbiome, which plays an essential role in plant growth and nutrient use efficiency. Although an increasing number of candidate genetic loci controlling microbial selection have been identified through the population-level association studies in plants, only a few have been shown to shape microbiome assembly, and the genetic factors driving microbiome assembly remain largely elusive.</p> Results <p>In this study, we use a segregating F2 population of LYP9, the widely cultivated super hybrid rice, to map root microbiome-associated loci by simultaneous whole genome resequencing and 16S rDNA amplicon sequencing. We identify 60 quantitative trait loci (QTLs) that correlate with the abundance of 43 ASVs of the root microbiome and reveal several microbiome-associated hotspot genomic regions. One such region is associated with different microbial taxa and contains 7 cytochrome P450 genes potentially involved in the brassinosteroid (BR) biosynthesis pathway. We further show that the miR444-overexpressing rice plants with increased BR biosynthesis alter the composition of the root microbiome and that the BR receptor OsBRI1 confers the distinction between nitrate- and ammonium-grown rice root microbiomes.</p> Conclusions <p>Using QTL analysis, our study identifies a set of genetic loci that link the root microbiome composition of the hybrid rice LYP9 and reveals that OsBRI1 regulates the assembly of the nitrogen-dependent rice root microbiome.</p>

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Identification of microbiome-associated loci in super hybrid rice reveals the regulation of OsBRI1 on nitrogen-dependent root microbiome assembly

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月25日

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  • Mengting Zhang,
  • Yinyue Wang,
  • Qiongqiong Zhang,
  • Huacai Wang,
  • Yongsheng Yan

摘要

Background

Host genetics is known to determine the composition of the plant microbiome, which plays an essential role in plant growth and nutrient use efficiency. Although an increasing number of candidate genetic loci controlling microbial selection have been identified through the population-level association studies in plants, only a few have been shown to shape microbiome assembly, and the genetic factors driving microbiome assembly remain largely elusive.

Results

In this study, we use a segregating F2 population of LYP9, the widely cultivated super hybrid rice, to map root microbiome-associated loci by simultaneous whole genome resequencing and 16S rDNA amplicon sequencing. We identify 60 quantitative trait loci (QTLs) that correlate with the abundance of 43 ASVs of the root microbiome and reveal several microbiome-associated hotspot genomic regions. One such region is associated with different microbial taxa and contains 7 cytochrome P450 genes potentially involved in the brassinosteroid (BR) biosynthesis pathway. We further show that the miR444-overexpressing rice plants with increased BR biosynthesis alter the composition of the root microbiome and that the BR receptor OsBRI1 confers the distinction between nitrate- and ammonium-grown rice root microbiomes.

Conclusions

Using QTL analysis, our study identifies a set of genetic loci that link the root microbiome composition of the hybrid rice LYP9 and reveals that OsBRI1 regulates the assembly of the nitrogen-dependent rice root microbiome.