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QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map

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Using a fixed RIL population derived from a widely used foxtail millet backbone breeding line and an elite cultivar, we constructed a high-density bin map and identified six novel multi-environment effect QTLs and seven candidate genes for dwarf phenotype.

Abstract

Plant height is an important trait that determines tradeoffs between competition and resource allocation, which is crucial for yield potential. To improve the C4 model plant foxtail millet (Setaria italica) productivity, it is necessary to isolate plant height-related genes that contribute to ideal plant architecture in breeding. In the present study, we generated a foxtail millet population of 333 recombinant inbred lines (RILs) derived from a cross between a backbone line Ai 88 and an elite cultivar Liaogu 1. We evaluated plant height in 13 environmental conditions across 4 years, the mean plant height of the RIL population ranged from 89.5 to 149.9 cm. Using deep re-sequencing data, we constructed a high-density bin map with 3744 marker bins. Quantitative trait locus (QTL) mapping identified 26 QTLs significantly associated with plant height. Of these, 13 QTLs were repeatedly detected under multiple environments, including six novel QTLs that have not been reported before. Seita.1G242300, a gene encodes gibberellin 2-oxidase-8, which was detected in nine environments in a 1.54-Mb interval of qPH1.3, was considered as an important candidate gene. Moreover, other six genes involved in GA biosynthesis or signaling pathways, and fifteen genes encode F-box domain proteins which might function as E3 ligases, were also considered as candidate genes in different QTLs. These QTLs and candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height, and the linked markers will be useful for marker-assistant selection of varieties with ideal plant architecture and high yield potential.

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Acknowledgement

We thank Dr. Kun Xie helped in data analysis. This research was supported by the National Key R&D Program of China (2018YFD1000706, 2018YFD1000700), the National Natural Science Foundation of China (31871630, 31771807), China agricultural research system (CARS-06-13.5) and the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences.

Funding

This research was supported by the National Key R&D Program of China (2018YFD1000706, 2018YFD1000700), the National Natural Science Foundation of China (31871630, 31771807), China Agricultural Research System (CARS-06–13.5) and the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences.

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  1. Qiang He and Hui Zhi have contributed equally to this work.

Authors and Affiliations

  1. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, Haidian, 100081, China

    Qiang He, Hui Zhi, Sha Tang, Junjun Yang, Huifang Liu, Wei Zhang, Yanchao Jia, Guanqing Jia, Jun Liu & Xianmin Diao

  2. Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China

    Lu Xing, Suying Wang & Jinrong Liu

  3. Institute of Crop Germplasm, Shanxi Academy of Agricultural Sciences, Taiyuan, 030000, China

    Haigang Wang & Zhijun Qiao

  4. Institute of Millet Crops, Shanxi Academy of Agricultural Sciences, Changzhi, 046000, Shanxi, China

    Aiying Zhang, Yuhui Li & Erhu Guo

  5. Institute of Crop Sciences, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, 136100, China

    Ming Gao & Shujie Li

  6. Institute of Dry-Land Agriculture and Forestry, Liaoning Academy of Agricultural Sciences, Chaoyang, 122000, Liaoning, China

    Haijin Zhang & Guoqiu Chen

  7. Institute of Crop Sciences, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, Henan, China

    Shutao Dai & Junxia Li

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  1. Qiang He
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  2. Hui Zhi
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  3. Sha Tang
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Contributions

QH and HZ did data analysis and drafted the manuscript. Xd and HZ designed the experiment, developed the RIL population, and revised the manuscript. Jun Liu helped in the data analysis and discussion. ST, LX, SW, HW, AZ, YL, MG, HZ, GC, SD, JL, JY, HL, WZ, YJ, SL, JL, ZQ, EG, and GJ collected the phenotype. All authors have read and approved the final manuscript.

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Correspondence to Xianmin Diao.

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He, Q., Zhi, H., Tang, S. et al. QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map. Theor Appl Genet 134, 557–572 (2021). https://doi.org/10.1007/s00122-020-03714-w

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