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SLAF-Based Linkage Map Construction and QTL Mapping of Nitrogen Use Efficiency in Rice (Oryza sativa L.)

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Abstract

Rice production relies on large amounts of synthetic nitrogen fertilizer to meet crop nutritional demands. However, the current fertilizer use efficiency is poor, with an average of 30–50% of total applied nitrogen (N) recovered in grains. Consequently, optimizing N availability and N use efficiency (NUE) has become a major target for rice yield improvement, and looking for quantitative trait loci (QTL) associated with NUE can provide useful information for developing nitrogen efficient rice genotypes. The present study aims to identify QTLs associated with NUE and its two components, agronomic NUE (agNUE) and grain nitrogen increase rate (GIR). A recombinant inbred line population (RIL) derived from a cross between Nipponbare and OM052, consisting of 159 F3 individuals was developed and cultivated in low-N (8 kg N/0.67 ha, N8) and high-N (18 kg N/0.67 ha, N18) conditions. Specific length amplified fragment sequencing (SLAF) was used to genotype the RILs and construct a high-density linkage map spanning 1587.70 cM, consisting 2707 SLAF markers with an average interval of 0.59 cM between adjacent marker loci. QTL analysis confirmed four significant QTLs distributed among chromosome 1, 6, and 11, with the proportion of phenotypic variance explained by each QTL ranging from 2.96 to 11.11% and LOD scores from 1.67 to 3.75. Functional annotation of genes located within the QTL intervals revealed NUE putative candidate genes. Overall, the QTLs identified in this study contribute information that could be useful for NUE improvement in rice.

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Acknowledgements

This work was supported by the National Key Research and Development Program (2017YFD0301304), International cooperation project of Anhui province (1704e1002232), Shanghai Agriculture Applied Technology Development Program (Grant No. T20180201), SAAS Excellent Research Team (No. NKC2017A05), and International Cooperation Project of China and South Korea (PJ013647).

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Author notes

  1. Jianjiang Bai and Zhongze Piao these authors contributed equally to this work.

Authors and Affiliations

  1. Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Fengxian District, 1000 Jingqi Road, Shanghai, 201403, China

    Jianjiang Bai, Zhongze Piao, Changzhao Wan & Ruifang Yang

  2. National Academy of Agricultural Science (South Korea), Suwon City, 441-857, Korea

    Gangseob Lee

  3. Rice Research Institute, Anhui Academy of Agricultural Sciences, Anhui, China

    Xinmin Ruan, Zhixiang Luo, Fuzhi Shi & Xihan Cong

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  1. Jianjiang Bai
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  2. Zhongze Piao
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  3. Changzhao Wan
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  4. Gangseob Lee
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  5. Xinmin Ruan
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Contributions

All authors contributed to the study conception and design. Material preparation were performed by Jianjiang Bai, Zhongze Piao, Changzhao Wan, and Gangseob Lee. Data collection and analysis were performed by Jianjiang Bai, Xinmin Ruan, Zhixiang Luo, Fuzhi Shi, Xihan Cong, and Jun Fang. The first draft of the manuscript was written by Jianjiang Bai, Zhongze Piao, Gangseob Lee, and Ruifang Yang. All authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Gangseob Lee or Ruifang Yang.

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Key message

• Specific length amplified fragment sequencing (SLAF)-based technology was used to build a high-density genetic linkage map, develop high-throughput SNP-based markers and identify four QTLs associated with rice nitrogen use efficiency (NUE). Analysis of gene functions located within the QTL intervals revealed the potential candidate genes involved in rice NUE

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Bai, J., Piao, Z., Wan, C. et al. SLAF-Based Linkage Map Construction and QTL Mapping of Nitrogen Use Efficiency in Rice (Oryza sativa L.). Plant Mol Biol Rep 39, 727–738 (2021). https://doi.org/10.1007/s11105-021-01281-y

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