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Association mapping and genetic dissection of nitrogen use efficiency-related traits in rice (Oryza sativa L.)

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Abstract

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.

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Abbreviations

ANOVA:

Analysis of variance

BIC:

Bayesian information criterion

EST:

Expressed sequence tag

GBS:

Genotyping by sequencing

GLR:

Grain length ratio of low N/normal N

LD:

Linkage disequilibrium

MAS:

Marker-assisted selection

NUE:

Nitrogen use efficiency

PHR:

Plant height ratio of low N/normal N

PVE:

Phenotypic variation explained

QTL:

Quantitative trait loci

TNR:

Tiller number ratio of low N/normal N

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Acknowledgments

This work was supported by a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD, 010809001), the Fundamental Research Funds for the Central Universities (KYRC201208, KYZ201202-6), and “Shuangchuang” projects, Jiangsu Province, China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Authors’ contributions

CW conceived the experiments, performed the experiments, and wrote the manuscript. JW and HZ supervised this project and revised the manuscript. CZ conceived the experiments, carried out the statistical analysis, and wrote the manuscript. ZL performed the experiments and analyzed the data. YJ, YT, JY, HA, WT, YL, JS, JT, and GC participated in the experiments. All authors read and approved the final manuscript.

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    Authors and Affiliations

    1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China

      Zhiyi Liu, Yue Jiang, Yunlu Tian, Jun Yu, Hongzhou An, Weijie Tang, Juan Sun, Jianpeng Tang, Gaoming Chen, Chunming Wang & Jianmin Wan

    2. Division of Plant Science, University of Missouri, Columbia, MO, 65211, USA

      Chengsong Zhu

    3. National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

      Huqu Zhai & Jianmin Wan

    4. Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China

      Chunming Wang

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    1. Zhiyi Liu
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    Correspondence to Chunming Wang or Jianmin Wan.

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    Zhiyi Liu and Chengsong Zhu contributed equally to this work.

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    Liu, Z., Zhu, C., Jiang, Y. et al. Association mapping and genetic dissection of nitrogen use efficiency-related traits in rice (Oryza sativa L.). Funct Integr Genomics 16, 323–333 (2016). https://doi.org/10.1007/s10142-016-0486-z

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