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QTL Mapping by Whole Genome Re-sequencing and Analysis of Candidate Genes for Nitrogen Use Efficiency in Rice

文献类型： 外文期刊

作者： Yang, Xinghai 1 ; Xia, Xiuzhong 1 ; Zhang, Zongqiong 1 ; Nong, Baoxuan 1 ; Zeng, Yu 1 ; Xiong, Faqian 2 ; Wu, Yanyan 3 ;

作者机构： 1.Guangxi Acad Agr Sci, Rice Res Inst, Nanning, Peoples R China

2.Guangxi Acad Agr Sci, Cash Crops Res Inst, Nanning, Peoples R China

3.Guangxi Acad Agr Sci, Biotechnol Res Inst, Nanning, Peoples R China

4.Guangxi Acad Agr Sci, Guangxi Crop Genet Improvement & Biotechnol Lab, Nanning, Peoples R China

关键词： rice;nitrogen use efficiency;whole genome re-sequencing;QTL;candidate genes

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2017 年 8 卷

页码：

收录情况： SCI

摘要： Nitrogen is a major nutritional element in rice production. However, excessive application of nitrogen fertilizer has caused severe environmental pollution. Therefore, development of rice varieties with improved nitrogen use efficiency (NUE) is urgent for sustainable agriculture. In this study, bulked segregant analysis (BSA) combined with whole genome re-sequencing (WGS) technology was applied to finely map quantitative trait loci (QTL) for NUE. A key QTL, designated as qNUE6 was identified on chromosome 6 and further validated by Insertion/Deletion (InDel) marker-based substitutional mapping in recombinants from F-2 population (NIL-13B4 x GH998). Forty-four genes were identified in this 266.5-kb region. According to detection and annotation analysis of variation sites, 39 genes with large-effect single-nucleotide polymorphisms (SNPs) and large-effect InDels were selected as candidates and their expression levels were analyzed by qRT-PCR. Significant differences in the expression levels of LOC_Os06g15370 (peptide transporter PTR2) and LOC_Os06g15420 (asparagine synthetase) were observed between two parents (Y11 and GH998). Phylogenetic analysis in Arabidopsis thaliana identified two closely related homologs, AT1G68570 (AtNPF3.1) and AT5G65010 (ASN2), which share 72.3 and 87.5% amino acid similarity with LOC_Os06g15370 and LOC_Os06g15420, respectively. Taken together, our results suggested that qNUE6 is a possible candidate gene for NUE in rice. The fine mapping and candidate gene analysis of qNUE6 provide the basis of molecular breeding for genetic improvement of rice varieties with high NUE, and lay the foundation for further cloning and functional analysis.

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