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InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice ( Oryza sativa L.)

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  • Huanran Yuan

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
    These authors contributed equally to this work.)

  • Weilong Yang

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
    These authors contributed equally to this work.)

  • Jianing Zou

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China)

  • Mingxing Cheng

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China)

  • Fengfeng Fan

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China)

  • Ting Liang

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China)

  • Yajie Yu

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China)

  • Ronghua Qiu

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China)

  • Shaoqing Li

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China)

  • Jun Hu

    (State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China)

Abstract

A molecular marker is a valuable tool in genetic research. Insertions–deletions (InDels) are commonly used polymorphisms in gene mapping, analysing genetic diversity, marker-assisted breeding, and phylogenetics. The 3000 Rice Genome Project, a re-sequencing project, discovered millions of genome-wide InDels. We found that the proportion of >50-bp long InDels (699,475) of the total (1,248,503) is 56.02%. The number of InDels on each chromosome was consistent with the corresponding chromosome length. The maximum InDels were on chromosome 1 (78,935), and the minimum InDels were on chromosome 9 (41,752), with an average density of 1.87 InDels/kb (range: 1.50–2.36 InDels/kb). Furthermore, 96 InDels of about 3.98 Mb/InDel were selected to detect the polymorphism. The results exhibited ideal performance in 2% agarose gel electrophoresis. Phylogenetic analysis exhibited that InDel markers had excellent polymorphisms between rice varieties of japonica and indica, and varieties could be classified based on the statistical results of their polymorphisms. The InDel markers could be applied to identify the recombinant inbred lines in a population. These results reveal that the high-density long InDel markers could help us examine the functional diversity, species variation, and map-based cloning.

Suggested Citation

  • Huanran Yuan & Weilong Yang & Jianing Zou & Mingxing Cheng & Fengfeng Fan & Ting Liang & Yajie Yu & Ronghua Qiu & Shaoqing Li & Jun Hu, 2021. "InDel Markers Based on 3K Whole-Genome Re-Sequencing Data Characterise the Subspecies of Rice ( Oryza sativa L.)," Agriculture, MDPI, vol. 11(7), pages 1-15, July.
    • Handle: RePEc:gam:jagris:v:11:y:2021:i:7:p:655-:d:592342
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    References listed on IDEAS

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    1. Marie-Christine Carpentier & Ernandes Manfroi & Fu-Jin Wei & Hshin-Ping Wu & Eric Lasserre & Christel Llauro & Emilie Debladis & Roland Akakpo & Yue-Ie Hsing & Olivier Panaud, 2019. "Retrotranspositional landscape of Asian rice revealed by 3000 genomes," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
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    Cited by:

    1. Hui Yang & Jiawei Song & Chengbin Qiao & Kairong Duan & Peiyuan Feng & Weiru Kong & Tianliang Bai & Chunyan Zhu & Shuaiguo Ma & Yinxia Zhang & Peifu Li & Lei Tian, 2023. "Genome-Wide Association Studies of Salt-Tolerance-Related Traits in Rice at the Seedling Stage Using InDel Markers Developed by the Genome Re-Sequencing of Japonica Rice Accessions," Agriculture, MDPI, vol. 13(8), pages 1-20, August.

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