QTL-Seq and pyramiding of yield-related loci from wild rice (Oryza rufipogon Griff.) introgression lines under nutrient-deficient conditions.

IF 3 3区农林科学 Q1 AGRONOMY

Molecular Breeding Pub Date : 2026-04-20 eCollection Date: 2026-05-01 DOI:10.1007/s11032-026-01651-y

Bright G Adu, Aizelle Y S Argete, Fakhrul I Monshi, Yoshihiro Ohmori, Akifumi Shimizu, Hiroaki Hayashi, Toru Fujiwara

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引用次数: 0

Abstract

Developing rice cultivars adapted to low-nutrient conditions is essential for sustainable production, and wild rice offers valuable genetic resources for improving stress resilience in cultivated varieties. In this study, we demonstrate that pyramiding yield-related quantitative trait loci (QTLs) derived from wild rice enhances panicle yield under nutrient-limited conditions. Two wild rice introgression lines, KRIL8 and KRIL37, each carrying a small Oryza rufipogon genomic segment in the O. sativa L. cv. Koshihikari background, exhibited significantly higher panicle weight than the recurrent parent (KH) under limiting nitrogen and/or NPK (nitrogen, phosphorus, potassium) conditions. Using next-generation sequencing-based QTL-seq analysis, QTLs associated with panicle weight were identified in KRIL8 (qPW1) and KRIL37 (qPW6). Selected F₃ pyramiding lines (PyL) developed through marker-assisted selection showed a 16-40% increase in panicle weight under no nitrogen (-N) conditions. Under nutrient-deficient (-NPK) conditions, the selected pyramiding line PyL14 showed a tendency towards higher brown rice yield (approximately 12%) compared with the best introgression line parent (KRIL8). Although the difference was not statistically significant, the trend shows a positive interaction between the pyramided QTLs. Candidate genes harboring nonsynonymous SNPs with high SNP indices were identified, and cultivar-specific expression patterns were observed for these genes under low ammonium conditions, including genes associated with yield-related traits and nutrient transport. These results identify PyL14 as a promising genetic resource with the potential to improve rice yield under nutrient-deficient conditions.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-026-01651-y.

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营养缺乏条件下野生稻（Oryza rufipogon Griff.）渗入系产量相关位点的QTL-Seq和金字塔构建。

培育适应低营养条件的水稻品种对可持续生产至关重要，而野生水稻为提高栽培品种的抗逆性提供了宝贵的遗传资源。在本研究中，我们证明了在营养限制的条件下，野生稻的产量相关数量性状位点（qtl）的金字塔化提高了穗产量。两个野生水稻渗入系，KRIL8和KRIL37，各自携带一个小的Oryza rufipogon基因组片段。在限制氮素和/或氮磷钾（NPK）条件下，Koshihikari背景的穗重显著高于循环亲本（KH）。利用基于新一代测序技术的QTL-seq分析，鉴定出KRIL8 （qPW1）和KRIL37 （qPW6）中与穗重相关的qtl。通过标记辅助选择培育的F₃金字塔系（PyL）在无氮（-N）条件下，穗重增加了16-40%。在营养缺乏（-NPK）条件下，选择的金字塔系PyL14比最佳渗入系亲本KRIL8有更高的糙米产量（约12%）的趋势。虽然差异不具有统计学意义，但趋势表明金字塔qtl之间存在正交互作用。鉴定了具有高SNP指数的非同义SNP候选基因，并观察了这些基因在低铵条件下的品种特异性表达模式，包括与产量相关性状和营养转运相关的基因。这些结果表明，PyL14是一种有潜力的遗传资源，在营养缺乏条件下具有提高水稻产量的潜力。补充资料：在线版本包含补充资料，下载地址：10.1007/s11032-026-01651-y。

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来源期刊

Molecular Breeding 农林科学-农艺学

CiteScore

5.60

自引率

6.50%

发文量

审稿时长

1.5 months

期刊介绍： Molecular Breeding is an international journal publishing papers on applications of plant molecular biology, i.e., research most likely leading to practical applications. The practical applications might relate to the Developing as well as the industrialised World and have demonstrable benefits for the seed industry, farmers, processing industry, the environment and the consumer. All papers published should contribute to the understanding and progress of modern plant breeding, encompassing the scientific disciplines of molecular biology, biochemistry, genetics, physiology, pathology, plant breeding, and ecology among others. Molecular Breeding welcomes the following categories of papers: full papers, short communications, papers describing novel methods and review papers. All submission will be subject to peer review ensuring the highest possible scientific quality standards. Molecular Breeding core areas: Molecular Breeding will consider manuscripts describing contemporary methods of molecular genetics and genomic analysis, structural and functional genomics in crops, proteomics and metabolic profiling, abiotic stress and field evaluation of transgenic crops containing particular traits. Manuscripts on marker assisted breeding are also of major interest, in particular novel approaches and new results of marker assisted breeding, QTL cloning, integration of conventional and marker assisted breeding, and QTL studies in crop plants.