Identification of Advantaged Genes for Low-Nitrogen-Tolerance-Related Traits in Rice Using a Genome-Wide Association Study

文献类型： 外文期刊

第一作者： Zhang, Zhiyuan

作者： Zhang, Zhiyuan;Jia, Juqing;Zhang, Zhiyuan;Zhai, Laiyuan;Zhu, Shuangbing;Shen, Congcong;Chen, Kai;Xu, Jianlong;Zhang, Zhiyuan;Xu, Jianlong;Liu, Yuzhuo;Tian, Lin

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关键词： rice; lower nitrogen; genome-wide association study (GWAS); haplotype analysis; candidate gene

期刊名称：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES （ 影响因子：4.9； 五年影响因子：5.7 ）

ISSN： 1661-6596

年卷期： 2025 年 26 卷 12 期

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收录情况： SCI

摘要： Nitrogen is a crucial element that impacts rice yield and its constituent factors. The effects of reduced nitrogen levels on yield constitute is a complex quantitative trait that is controlled by multiple genes, and its genetic basis requires further exploration. In this study, 562 MAGIC line population and 284 germplasm varieties were used for genome-wide association analysis (GWAS) and haplotype analysis, aiming to detect quantitative trait loci (QTL) and candidate genes associated with tolerance to low nitrogen levels. The ratio of effective panicle number per plant (REPN), total number of grains per panicle (RTGN), seed setting rate (RSSR), thousand grain weight (RTGW), biomass (RBM), harvest index (RHI), and grain yield per plant (RGY) of low to normal nitrogen conditions were measured in this study. The RBM and RHI were directly closely related to RGY, while the RSSR indirectly and positively affected RGY through RHI, and the REPN and RTGN mainly indirectly and positively affected RGY through RBM. LOC_Os06g06440 was the most likely gene affecting low-nitrogen-tolerance-related traits in rice within the region, ranging from 2.898 Mb to 3.046 Mb (148 kb) on chromosome 6, and the haplotype AA, with a significantly larger mean RGY of 0.95 and 1.53 in the MAGIC and germplasm varieties, respectively, was the advanced allele of LOC_Os06g06440. Nine xian (indica) varieties (IRIS_313-11624, IRIS_313-10932, CX382, B067, B249, IRIS_313-8215, IRIS_313-10544, B052, and B233) carrying the superior haplotype (AA) of LOC_Os06g06440 and having a higher RGY were selected for the molecular marker-assisted selection of low nitrogen tolerance in rice. These results will enhance our knowledge of the genetic basis of tolerance to low levels of nitrogen and provide valuable information for improving tolerance to low levels of nitrogen in rice-breeding programs.

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