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Background <p>Pre-harvest sprouting (PHS), which adversely impacts grain yield and quality, is controlled by seed dormancy genes. However, only a few dormancy-related genes have been characterized, and the effects of allelic variation in genes and the genetic basis of seed dormancy in rice remain largely unknown. Here, we performed a whole-genome meta-quantitative trait loci study to elucidate the genetic basis of seed dormancy in rice.</p> Result <p>One hundred and sixty-seven QTL were identified for PHS from which 134 were successfully projected onto the reference map yielding 20 consensus regions, meta-QTL (mQTL). The mean confidence interval of the mQTL was narrower (9.56-fold reduction) than that of the initial QTL. Six of the 20 identified mQTL were designated as breeders’ mQTL based on their small confidence intervals, large phenotypic variance explained, and the involvement of high number of QTL. Further, we retrieved 559 high-confidence genes from breeders’ mQTL regions conferring resistance to PHS. Comparative analysis of genes found in breeders’ mQTL loci and an RNA-seq-based transcriptomic dataset discovered 34 common genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed a significant enrichment of the common genes in amino sugar and nucleotide sugar metabolism, carbon metabolism, and carbon fixation in photosynthetic organs. Combined in silico expression profiling and qRT-PCR validation showed that <i>LOC_Os10g18364</i>, <i>LOC_Os10g21940</i>, <i>LOC_Os10g22590</i>, and <i>LOC_Os10g25140</i> exhibited high fold-change expression in PHS resistant cultivar (23xS-261) than PHS susceptible cultivar (23xS-262). Association analysis of these genes with germination rate index demonstrated that <i>LOC_Os10g18364</i><sup><i>Hap1</i></sup>, <i>LOC_Os10g21940</i><sup><i>Hap1</i></sup>, <i>LOC_Os10g22590</i><sup><i>Hap1</i></sup>, and <i>LOC_Os10g25140</i><sup><i>Hap1/Hap3</i></sup> exhibited low germination rate (GR) in cultivars carrying these haplotypes.</p> Conclusion <p>In summary, this study delineates the genetic basis of PHS and provides a new set of target genes for improving PHS resistance. The natural variants identified in these genes and markers associated with breeders’ mQTL serve as potential resources for incorporating PHS resistance in rice. </p>

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Whole-genome meta-analysis coupled with haplotype analysis reveal new genes and functional haplotypes conferring pre-harvest sprouting in rice

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年4月25日

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  • Kelvin Dodzi Aloryi,
  • Nnaemeka Emmanuel Okpala,
  • Mawuli Korsi Amenyogbe,
  • Daniel Bimpong,
  • Benjamin Karikari,
  • Hong Guo,
  • Semiu Folaniyi Bello,
  • Selorm Akaba,
  • Akwasi Yeboah,
  • Abdul Razak Ahmed,
  • Patrick Maada Ngegba,
  • Nabieu Kamara,
  • Juliet Nkiruku Anyanwu,
  • Danielle Ama Essandoh,
  • Xianjin Qiu,
  • Xiaohai Tian,
  • Guoli Wang,
  • Tianyue An

摘要

Background

Pre-harvest sprouting (PHS), which adversely impacts grain yield and quality, is controlled by seed dormancy genes. However, only a few dormancy-related genes have been characterized, and the effects of allelic variation in genes and the genetic basis of seed dormancy in rice remain largely unknown. Here, we performed a whole-genome meta-quantitative trait loci study to elucidate the genetic basis of seed dormancy in rice.

Result

One hundred and sixty-seven QTL were identified for PHS from which 134 were successfully projected onto the reference map yielding 20 consensus regions, meta-QTL (mQTL). The mean confidence interval of the mQTL was narrower (9.56-fold reduction) than that of the initial QTL. Six of the 20 identified mQTL were designated as breeders’ mQTL based on their small confidence intervals, large phenotypic variance explained, and the involvement of high number of QTL. Further, we retrieved 559 high-confidence genes from breeders’ mQTL regions conferring resistance to PHS. Comparative analysis of genes found in breeders’ mQTL loci and an RNA-seq-based transcriptomic dataset discovered 34 common genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed a significant enrichment of the common genes in amino sugar and nucleotide sugar metabolism, carbon metabolism, and carbon fixation in photosynthetic organs. Combined in silico expression profiling and qRT-PCR validation showed that LOC_Os10g18364, LOC_Os10g21940, LOC_Os10g22590, and LOC_Os10g25140 exhibited high fold-change expression in PHS resistant cultivar (23xS-261) than PHS susceptible cultivar (23xS-262). Association analysis of these genes with germination rate index demonstrated that LOC_Os10g18364Hap1, LOC_Os10g21940Hap1, LOC_Os10g22590Hap1, and LOC_Os10g25140Hap1/Hap3 exhibited low germination rate (GR) in cultivars carrying these haplotypes.

Conclusion

In summary, this study delineates the genetic basis of PHS and provides a new set of target genes for improving PHS resistance. The natural variants identified in these genes and markers associated with breeders’ mQTL serve as potential resources for incorporating PHS resistance in rice.