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Home > Archive>Volume 22, Issue 3, 2021 >815-833. DOI:10.13430/j.cnki.jpgr.20201028003 Online First
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Development and Application of Soybean InDel Markers Based on Whole-genome Resequencing Datasets
DOI:
10.13430/j.cnki.jpgr.20201028003
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  • CHEN Zheng-jie

    CHEN Zheng-jie

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • WAN Yong-lu

    WAN Yong-lu

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • ZHONG Wen-juan

    ZHONG Wen-juan

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • CHEN Si-wei

    CHEN Si-wei

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • ZHOU Yong-hang

    ZHOU Yong-hang

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • SHI Sheng-jia

    SHI Sheng-jia

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • JANG Li

    JANG Li

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • JI Pei-cheng

    JI Pei-cheng

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • YANG Ze-hu

    YANG Ze-hu

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • MAO Zheng-xuan

    MAO Zheng-xuan

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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  • Mou Fang-sheng

    Mou Fang-sheng

    Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences
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Affiliation:

Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300

Clc Number:

Fund Project:

The 13th Five-Year Plan of Sichuan financial innovation and improvement project (2016ZYPZ-009),Sichuan Regional Innovation Cooperation Project (2020YFQ0044)

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    Abstract:

    Soybean (Glycine max (L.) Merr.) is one of the important grain and oil crops in China, and vegetable soybean is a nutrition-rich vegetable crop. However, few InDel markers are known for convenient use in soybean. In this study, 18 soybeans were tested for resequencing analysis, with InDel loci mined on the basis of the resequencing datasets, and the effectivity and application value of the InDel markers validated. After strict screening, 17,977 highly polymorphic InDel loci with Insert/Delete of 13-50 bp suitable for agarose gel electrophoresis detection were obtained. There were from 505 to 1355 InDel markers on each chromosome, and the average distribution density was 12.60-35.76 InDel/Mb across the chromosomes. Among the 73 InDel markers randomly selected for effectivity validation in 18 soybeans, 43 (56.16%) of the InDel markers showed polymorphism. Of those 73 InDel markers, 25 polymorphic InDel markers were used for genetic diversity analysis in 192 soybeans (including 64 vegetable soybeans, 65 spring soybeans, 36 summer soybeans, 19 landraces and 8 wild soybeans). The polymorphic information content (PIC) for each InDel marker was between 0.17 and 0.46 with an average of 0.35, and the 192 soybeans were classified into 24 groups with the different types in different groups. Among them, the vegetable soybeans were mainly classified into the 3# group with the genetic similarity coefficient of 0.66 and a few vegetable soybeans were classified into the 1# group with the genetic similarity coefficient of 0.71, which suggested that the genetic background of vegetable soybeans in China are relatively narrow, and we should select soybean lines with small genetic similarity coefficient as parents for breeding in future to enrich the genetic background. The 25 polymorphic InDel markers were also used to verify the F1 from 13 hybrid combinations, which agreed with the phenotypic identification, indicating the usefulness of the InDel markers developed for F1 identification. Taken together, the polymorphic InDel markers developed in this study will be widely used in genetic diversity analysis, hybrid identification, genetic linkage map construction, gene mapping and molecular marker assisted selection breeding in soybean.

    Key words:soybean; genome resequencing; InDel marker; genetic diversity analysis; F1 identification
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History
  • Received:October 28,2020
  • Revised:December 10,2020
  • Adopted:February 17,2021
  • Online: May 07,2021
  • Published:
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