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Construction of introgression lines of Oryza rufipogon and evaluation of important agronomic traits

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Abstract

Cultivated rice (Oryza sativa) originated from common wild rice (Oryza rufipogon) and inherited its advantages. However, during the rice domestication process, some valuable features of wild rice, such as tolerance to biotic and abiotic stress, were lost. To fully utilize wild rice germplasm resources, we constructed a set of introgression lines (ILs) using a common wild rice material from Lingshui, China. A set of high-resolution InDel molecular markers with an average interval of 2.39 Mb were designed to carry out marker-assisted selection and identification of segment characteristics. The ILs contained 77 lines including 1.286 introgressed fragments with an average length of 6.511 Mb, covering 93.59% of the donor parent’s chromosomes. The agricultural traits of 77 lines were investigated. Many old quantitative trait loci (QTLs) involved in plant height, awn length, seed traits and other characteristics reappeared in our ILs, proving that our system was reliable. Further, many new QTLs were identified. A QTL related to drought tolerance located on chromosome 4 was thoroughly elaborated. This set of ILs provides a new resource for utilizing the excellent features of wild rice.

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Acknowledgements

Funding was provided by CAAS Innovation Project (Grant No. CAAS-XTCX2016002) and Fundamental Research Funds for central Non-profit scientific Institution (Grant No. 1610392018004)

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Author notes

  1. Guannan Qin, Hung Manh Nguyen and Sinh Ngoc Luu contributed equally to this work.

Authors and Affiliations

  1. Biotechnology Research Institute/National Key Facility for Genetic Resources and Gene Improvement, The Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Guannan Qin, Hung Manh Nguyen, Sinh Ngoc Luu, Yanwei Wang & Zhiguo Zhang

  2. Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China

    Guannan Qin

  3. University of Chinese Academy of Sciences, Beijing, 100049, China

    Guannan Qin

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  1. Guannan Qin
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  2. Hung Manh Nguyen
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  4. Yanwei Wang
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  5. Zhiguo Zhang
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Corresponding author

Correspondence to Zhiguo Zhang.

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Communicated by Takuji Sasaki.

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Figure S1

The plant stature comparison between LSWR and 9311 (TIFF 3830 kb)

Figure S2

The workflow of IL construction. The workflow of constructing an ideal population of ILs. In the first step, LSWR selected from Lingshui City, China, was treated as “female” and 9311 was treated as “male.” After 7 generations of backcrossing or selfing, the chromosomes from LSWR were introgressed into the 9311 background (TIFF 448 kb)

Figure S3

The physical map based on InDel markers. The markers were named after chromosome No. and physical location. The number before the dash indicates the chromosome No., and the number after the dash multiplied by 100,000 indicates the approximate physical distance (bp). (TIFF 68306 kb)

Figure S4

The Q-PCR analysis for the NAL1 gene expression level. A. Comparison of the NAL1 gene expression level among 9311, No. 28 and No. 63. B. Comparison of the NAL1 gene expression level between Nipponbare (Nip) and Ov1 (TIFF 3002 kb)

Table S1

InDel primers used in this study (XLSX 25 kb)

Table S2

The agricultural trait data of 77 ILs (XLSX 19 kb)

Table S3

The primers related to the Nal1 gene (XLS 19 kb)

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Qin, G., Nguyen, H.M., Luu, S.N. et al. Construction of introgression lines of Oryza rufipogon and evaluation of important agronomic traits. Theor Appl Genet 132, 543–553 (2019). https://doi.org/10.1007/s00122-018-3241-0

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