Liu Zhiyi, Zhu Chengsong, Jiang Yue, Tian Yunlu, Yu Jun, An Hongzhou, Tang Weijie, Sun Juan, Tang Jianpeng, Chen Gaoming, Zhai Huqu, Wang Chunming, Wan Jianmin
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
Division of Plant Science, University of Missouri, Columbia, MO, 65211, USA.
Funct Integr Genomics. 2016 May;16(3):323-33. doi: 10.1007/s10142-016-0486-z. Epub 2016 Feb 27.
The increases in the usage of nitrogen fertilizer result in deleterious impacts on the environment; thus, there is an urgent need to improve nitrogen use efficiency (NUE) in crops including rice (Oryza sativa L.). Attentions have focused on quantitative trait loci (QTL) mapping of NUE-related traits using single experimental population, but to date, very few studies have taken advantage of association mapping to examine hundreds of lines for identifying potentially novel QTLs in rice. Here, we conducted association analysis on NUE-related traits using a population containing 184 varieties, which were genotyped with 157 genome-wide simple sequence repeat (SSR) markers. We detected eight statistically significant marker loci associating with NUE-related traits, of which two QTLs at RM5639 and RM3628 harbored known NUE-related genes GS1;2 and AspAt3, respectively. At a novel NUE-related locus RM5748, we developed Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers and searched for putative NUE-related genes which are close to the associated SNP marker. Based on a transcriptional map of N stress responses constructed by our lab, we evaluated expressions of the NUE-related genes in this region and validated their effect on NUE. Meanwhile, we analyzed NUE-related alleles of the eight loci that could be utilized in marker-assisted selection. Moreover, we estimated breeding values of all the varieties through genomic prediction approach that could be beneficial for rice NUE enhancement.
氮肥使用量的增加对环境产生了有害影响；因此，迫切需要提高包括水稻（Oryza sativa L.）在内的作物的氮素利用效率（NUE）。人们已将注意力集中在利用单一实验群体对与氮素利用效率相关性状进行数量性状基因座（QTL）定位上，但迄今为止，很少有研究利用关联分析来检测数百个品系，以鉴定水稻中潜在的新QTL。在此，我们使用一个包含184个品种的群体对与氮素利用效率相关的性状进行了关联分析，这些品种用157个全基因组简单序列重复（SSR）标记进行了基因分型。我们检测到8个与氮素利用效率相关性状关联的具有统计学意义的标记位点，其中位于RM5639和RM3628的两个QTL分别含有已知的与氮素利用效率相关的基因GS1;2和AspAt3。在一个新的与氮素利用效率相关的位点RM5748，我们开发了竞争性等位基因特异性PCR（KASP）单核苷酸多态性（SNP）标记，并搜索了靠近相关SNP标记的假定的与氮素利用效率相关的基因。基于我们实验室构建的氮胁迫响应转录图谱，我们评估了该区域内与氮素利用效率相关基因的表达，并验证了它们对氮素利用效率的影响。同时，我们分析了这8个位点的与氮素利用效率相关的等位基因，这些等位基因可用于标记辅助选择。此外，我们通过基因组预测方法估计了所有品种的育种值，这可能有助于提高水稻的氮素利用效率。
