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Genome-Wide Association Study Using a Multiparent Advanced Generation Intercross (MAGIC) Population Identified QTLs and Candidate Genes to Predict Shoot and Grain Zinc Contents in Rice

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  • Shilei Liu

    (Group of Crop Genetics and Breeding, School of Agriculture Science, Jiangxi Agricultural University, Nanchang 330045, China
    CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China
    These authors contributed equally to this work.)

  • Wenli Zou

    (Group of Crop Genetics and Breeding, School of Agriculture Science, Jiangxi Agricultural University, Nanchang 330045, China
    CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China
    These authors contributed equally to this work.)

  • Xiang Lu

    (CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China)

  • Jianmin Bian

    (Group of Crop Genetics and Breeding, School of Agriculture Science, Jiangxi Agricultural University, Nanchang 330045, China)

  • Haohua He

    (Group of Crop Genetics and Breeding, School of Agriculture Science, Jiangxi Agricultural University, Nanchang 330045, China)

  • Jingguang Chen

    (CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China
    School of Agriculture, Sun Yat-sen University, Guangzhou 510275, China)

  • Guoyou Ye

    (CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518116, China
    Rice Breeding Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines)

Abstract

Zinc (Zn) is an essential trace element for the growth and development of both humans and plants. Increasing the accumulation of Zn in rice grains is important for the world’s nutrition and health. In this study, we used a multiparent advanced generation intercross (MAGIC) population constructed using four parental lines and genotyped using a 55 K rice SNP array to identify QTLs related to Zn 2+ concentrations in shoots at the seedling stage and grains at the mature stage. Five QTLs were detected as being associated with shoot Zn 2+ concentration at the seedling stage, which explained 3.7–5.7% of the phenotypic variation. Six QTLs were detected as associated with grain Zn 2+ concentration at the mature stage, which explained 5.5–8.9% of the phenotypic variation. Among the QTLs, qSZn2-1/qGZn2 and qSZn3/qGZn3 were identified as being associated with both the shoot and grain contents. Based on gene annotation and literature information, 16 candidate genes were chosen in the regions of qSZn1 , qSZn2-1/qGZn2 , qSZn3/qGZn3 , qGZn7 , and qGZn8 . Analysis of candidate genes through qRT-PCR, complementation assay using the yeast Zn-uptake-deficient double-mutant ZHY3, and sequencing of the four parental lines suggested that LOC_Os02g06010 may play an important role in Zn 2+ accumulation in indica rice.

Suggested Citation

  • Shilei Liu & Wenli Zou & Xiang Lu & Jianmin Bian & Haohua He & Jingguang Chen & Guoyou Ye, 2021. "Genome-Wide Association Study Using a Multiparent Advanced Generation Intercross (MAGIC) Population Identified QTLs and Candidate Genes to Predict Shoot and Grain Zinc Contents in Rice," Agriculture, MDPI, vol. 11(1), pages 1-14, January.
    • Handle: RePEc:gam:jagris:v:11:y:2021:i:1:p:70-:d:481644
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    References listed on IDEAS

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    1. Huili Yan & Wenxiu Xu & Jianyin Xie & Yiwei Gao & Lulu Wu & Liang Sun & Lu Feng & Xu Chen & Tian Zhang & Changhua Dai & Ting Li & Xiuni Lin & Zhanying Zhang & Xueqiang Wang & Fengmei Li & Xiaoyang Zhu, 2019. "Variation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    2. Zhenyu Gao & Yufeng Wang & Guang Chen & Anpeng Zhang & Shenglong Yang & Lianguang Shang & Danying Wang & Banpu Ruan & Chaolei Liu & Hongzhen Jiang & Guojun Dong & Li Zhu & Jiang Hu & Guangheng Zhang &, 2019. "The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
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    Cited by:

    1. Muhammad Junaid Zaghum & Kashir Ali & Sheng Teng, 2022. "Integrated Genetic and Omics Approaches for the Regulation of Nutritional Activities in Rice ( Oryza sativa L.)," Agriculture, MDPI, vol. 12(11), pages 1-17, October.

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