ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2025
Integrated transcriptome and BSA-seq analysis identifies a novel QTL for Meloidogyne graminicola resistance in rice HuaHang31.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Identification of QTLs and new candidate genes affecting ear shank length via BSA-seq and transcriptomic analysis in maize.Frontiers in plant science · 2026Article
- Identification of candidate gene controlling TSSL via BSA-seq and fine mapping and germplasm innovation in rice.BMC genomics · 2025Article
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10 authors.
Funding
Abstract
key messageA 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. 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.
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