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Key message <p>A novel QTL on chromosome 11 with 7 candidate genes regulating nematode resistance was identified by RNA-seq-based transcriptome and BSA-seq combination analyses, revealing the possible interactions between nematodes and plants.</p> Abstract <p>The resistant rice germplasms against <i>Meloidogyne graminicola</i>, which is a plant-parasitic nematode posing a significant threat to rice production, are very limited. Here, we identified HuaHang31 (HH31), an <i>indica</i> rice variety, as a novel source of high resistance against to <i>M. graminicola</i> through large-scale screening of 297 rice accessions using PF-127 assays. Histopathological and histochemical analyses revealed that HH31 significantly reduced nematode penetration, delayed juvenile development, and triggered reactive oxygen species accumulation and hypersensitive response in root tip cells post-infection. RNA-seq-based transcriptome profiling of HH31 and susceptible IR64 roots at 3-, 7-, and 12-days post-inoculation (dpi) highlighted the up-regulation of phenylpropanoid, flavonoid, lignin biosynthesis, and phytohormone signaling pathways (jasmonic acid, salicylic acid, ethylene) in HH31, suggesting their pivotal roles in nematode resistance. Additionally, bulk segregant analysis of two F₂ populations derived from HH31 crosses with susceptible varieties mapped a novel quantitative trait locus (QTL) on chromosome 11 (4.7–8.2&#xa0;Mb). Within this region, seven nonsynonymous nucleotide-binding site–leucine-rich repeat genes exhibited root-specific expression and responsiveness to nematode infection, implicating their roles in resistance. Importantly, this QTL represents a distinct genomic region compared to previously reported resistance loci, highlighting its novelty. This study provides a new understanding of the genetic basis of nematode resistance and a valuable source for the development of nematode-resistant rice varieties, offering a sustainable strategy to mitigate yield losses caused by this pervasive pathogen.</p>

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Integrated transcriptome and BSA-seq analysis identifies a novel QTL for Meloidogyne graminicola resistance in rice HuaHang31

  • 期刊论文

  • 发表日期：

    2025年8月11日

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  • Zhuhong Yang,
  • Qingyan Xiao,
  • Yao Wang,
  • Yingjun Zhang,
  • Shan Ye,
  • Pingyong Sun,
  • Wuhan Zhang,
  • Huafeng Deng,
  • Shiming Liu,
  • Zhong Ding

摘要

Key message

A novel QTL on chromosome 11 with 7 candidate genes regulating nematode resistance was identified by RNA-seq-based transcriptome and BSA-seq combination analyses, revealing the possible interactions between nematodes and plants.

Abstract

The resistant rice germplasms against Meloidogyne graminicola, which is a plant-parasitic nematode posing a significant threat to rice production, are very limited. Here, we identified HuaHang31 (HH31), an indica rice variety, as a novel source of high resistance against to M. graminicola through large-scale screening of 297 rice accessions using PF-127 assays. Histopathological and histochemical analyses revealed that HH31 significantly reduced nematode penetration, delayed juvenile development, and triggered reactive oxygen species accumulation and hypersensitive response in root tip cells post-infection. RNA-seq-based transcriptome profiling of HH31 and susceptible IR64 roots at 3-, 7-, and 12-days post-inoculation (dpi) highlighted the up-regulation of phenylpropanoid, flavonoid, lignin biosynthesis, and phytohormone signaling pathways (jasmonic acid, salicylic acid, ethylene) in HH31, suggesting their pivotal roles in nematode resistance. Additionally, bulk segregant analysis of two F₂ populations derived from HH31 crosses with susceptible varieties mapped a novel quantitative trait locus (QTL) on chromosome 11 (4.7–8.2 Mb). Within this region, seven nonsynonymous nucleotide-binding site–leucine-rich repeat genes exhibited root-specific expression and responsiveness to nematode infection, implicating their roles in resistance. Importantly, this QTL represents a distinct genomic region compared to previously reported resistance loci, highlighting its novelty. This study provides a new understanding of the genetic basis of nematode resistance and a valuable source for the development of nematode-resistant rice varieties, offering a sustainable strategy to mitigate yield losses caused by this pervasive pathogen.