Zhang Zhiyuan, Zhai Laiyuan, Liu Yuzhuo, Tian Lin, Zhu Shuangbing, Shen Congcong, Jia Juqing, Chen Kai, Xu Jianlong
College of Agriculture, Shanxi Agricultural University, Taigu 030801, China.
Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Int J Mol Sci. 2025 Jun 16;26(12):5749. doi: 10.3390/ijms26125749.
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. 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 . Nine () 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 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.
氮是影响水稻产量及其构成因素的关键元素。低氮水平对产量构成的影响是一个由多个基因控制的复杂数量性状，其遗传基础有待进一步探索。本研究利用562个多亲本高级世代互交系群体和284份种质品种进行全基因组关联分析（GWAS）和单倍型分析，旨在检测与低氮耐受性相关的数量性状位点（QTL）和候选基因。本研究测定了低氮与正常氮条件下的单株有效穗数（REPN）、每穗粒数（RTGN）、结实率（RSSR）、千粒重（RTGW）、生物量（RBM）、收获指数（RHI）和单株籽粒产量（RGY）的比值。RBM和RHI与RGY直接密切相关，而RSSR通过RHI间接正向影响RGY，REPN和RTGN主要通过RBM间接正向影响RGY。位于第6号染色体上2.898 Mb至3.046 Mb（148 kb）区域内的 是水稻中最有可能影响低氮耐受性相关性状的基因，单倍型AA在多亲本高级世代互交系群体和种质品种中的平均RGY分别显著更大，为0.95和1.53，是 的优良等位基因。选择9个携带 优良单倍型（AA）且RGY较高的品种（IRIS_313-11624、IRIS_313-10932、CX382、B067、B249、IRIS_313-8215、IRIS_313-10544、B052和B233）进行水稻低氮耐受性的分子标记辅助选择。这些结果将增进我们对低氮耐受性遗传基础的了解，并为提高水稻育种计划中的低氮耐受性提供有价值的信息。
