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Research Article

volume 43 issue 4 (august 2020) : 501-506,   Doi: 10.18805/LR-500

Genetic Mapping of a Soybean Glabrous Gene Using Specific-Locus Amplified Fragment Sequencing Method

X
Xiaomin Yu
H
Hangxia Jin
Q
Qinghua Yang
X
Xujun Fu
F
Fengjie Yuan
1Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou-310021, China.

  • Submitted20-05-2019|

  • Accepted28-10-2019|

  • First Online 03-12-2019|

  • doi 10.18805/LR-500

Cite article:- Yu Xiaomin, Jin Hangxia, Yang Qinghua, Fu Xujun, Yuan Fengjie (2019). Genetic Mapping of a Soybean Glabrous Gene Using Specific-Locus Amplified Fragment Sequencing Method. Legume Research. 43(4): 501-506. doi: 10.18805/LR-500.

ABSTRACT

Trichome is a natural trait related with plant defense and seed yield, however, the genetic control of this trait has not been extensively studied in soybean. In this study, a cross was made between a soybean landrace “Aijiaomaodou” with normal pubescence and a glabrous soybean line “39002”. The segregation ratio of the F2 population was fit to the expected value and the glabrous phenotype was controlled by a single dominant gene. Association analysis was conducted to identify candidate genes for the glabrous trait using a high-throughput sequencing technology, specific-locus amplified fragment sequencing. A total of 6,961 polymorphic specific-locus amplified fragments were analyzed and a region of 2.76 Mb at nucleotides 47,315,610-50,072,564 on chromosome 9 containing 551 candidate genes was identified. Four specific genes (Glyma09G280500, Glyma09G282600, Glyma09G259400 and Glyma09G283400) in the region appeared to be most important candidate genes that are highly related to the glabrous trait. Further studies of these genes may lead to isolation and cloning of the glabrous gene and facilitate the selection procedures in soybean breeding.

REFERENCES

  1. Abe, A., Kosugi, S., Yoshida, K., Natsume, S., Takagi, H., Kanzaki, H., Matsumura, H., et al. (2012). Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnology. 30:174-178.
  2. An, L., Zhou, Z., Yan, A. and Gan, Y. (2011). Progress on trichome development regulated by phytohormone signaling. Plant Signaling & Behavior. 6:1959-1962.
  3. Bernard, R.L. and Singh, B.B. (1969). Inheritance of pubescence type in soybeans: glabrous, curly, dense, sparse and puberulent. Crop Science. 9:192-197.
  4. Esch, J.J., Chen, M., Sanders, M., Hillestad, M., Ndkium, S., Idelkope, B., et al. (2003). A contradictory GLABRA3 allele helps define gene interactions controlling trichome development in Arabidopsis. Development. 130:5885-5894.
  5. Gao, Y., Gong, X., Cao, W., Zhao, J., Fu, L., Wang, X., Schumaker, K.S. and Guo, Y. (2008). SAD2 in Arabidopsis functions in trichome initiation through mediating GL3 function and regulating GL1, TTG1 and GL2 expression. Journal of Integrative Plant Biology. 50:906-917.
  6. Gao, Y., Guo, J.Q. and Zhao, J.F. (2011). Molecular mechanisms of Arabidopsis trichome development. Chinese Bulletin of Botany. 46:119-127. (In Chinese with English abstract)
  7. Geng, X., Jiang, C., Yang, J., Wang, L., Wu, X. and Wei, W. (2016). Rapid identification of candidate genes for seed weight using the SLAF-seq method in Brassica napus. PLoS ONE. 11:e0147580.
  8. Hunt, M., Kaur, N., Stromvik, M. and Vodkin, L. (2011). Transcript profiling reveals expression differences in wild-type and glabrous soybean lines. BMC Plant Biology. 11:145.
  9. Ishida, T., Kurata, T., Okada, K. and Wada, T. (2008). A genetic regulatory network in the development of trichomes and root hairs. Annual Review of Plant Biology. 59:365-386.
  10. Jain, R.K., Joshi, A., Chaudhary, H.R., Dashora, A. and Khatik, C.L. (2018). Study on genetic variability, heritability and genetic advance in Soybean [Glycine max (L.) Merrill]. Legume Research. 41:532-536.
  11. Jia, Q., Tan, C., Wang, J., Zhang, X., Zhu, J., Luo, H., Yang, J., Westcott, S., Broughton, S., Moody, D. and Li, C. (2016). Marker development using SLAF-seq and whole-genome shotgun strategy to finemap the semi-dwarf gene ari-e in barley. BMC Genomics. 17: 911.
  12. Jin, H., Dong, D., Yang, Q. and Zhu D. (2016). Salt-responsive transcriptome profiling of Suaeda glauca via RNA sequencing. PLoS ONE. 11: e0150504.
  13. Lam, W.K.F. and Pedigo, L.P. (2001). Effect of trichome density on soybean pod feeding by adult bean leaf beetles (Coleoptera: Chrysomelidae). Journal of Economic Entomology. 94:1459-1463.
  14. Murray, M.G. and Thompson, W.F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research. 8: 4321-    4325.
  15. Pu, L., Suo, J.F. and Xue, Y.B. (2003). Molecular control of plant trichome development. Acta Genetica Sinica. 30: 1078-1084. (In Chinese with English abstract)
  16. Rehal, J., Beniwal, V. and Gill, B.S. (2019). Physico-chemical, engineering and functional properties of two soybean cultivars. Legume Research. 42: 39-44.
  17. Ren, X.W., Yu, D.W., Yang, S.P., Gai, J.Y. and Zhu, Y.L. (2018). Effects of StP5CS gene overexpression on nodulation and nitrogen fixation of vegetable soybean under salt stress conditions. Legume Research. 41: 675-680.
  18. Singh, T. and Sharma, A. (2016). Early generation selection for yield and its related traits in soybean [Glycine max (L.) Merrill.]. Legume Research. 39: 343-348.
  19. Sun, J. (2007). Heredity analysis and molecular marker study on glabrous character of soybean. M.Sc. Thesis, Jilin Agricultural University. (In Chinese with English abstract)
  20. Sun, X., Liu, D., Zhang, X., Li, W., Liu, H., Hong, W., Jiang, C., Guan, N., Ma, C., Zeng, H., et al. (2013). SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE. 8: e58700.
  21. Xia, C., Chen, L., Rong, T., Li, R., Xiang, Y., Wang, P., Liu, C., Dong, X., Liu, B., et al. (2015). Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method. Euphytica. 202: 35-44.
  22. Yang, C. and Ye, Z. (2013). Trichomes as models for studying plant cell differentiation. Cellular and Molecular Life Sciences. 70: 1937-1948.
  23. Yuan, F., Yu, X., Dong, D., Yang, Q., Fu, X., Zhu, S. and Zhu, D. (2017). Whole genome-wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants. BMC Plant Biology. 17: 16. 
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    Research Article

    volume 43 issue 4 (august 2020) : 501-506,   Doi: 10.18805/LR-500

    Genetic Mapping of a Soybean Glabrous Gene Using Specific-Locus Amplified Fragment Sequencing Method

    X
    Xiaomin Yu
    H
    Hangxia Jin
    Q
    Qinghua Yang
    X
    Xujun Fu
    F
    Fengjie Yuan
    1Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou-310021, China.

    • Submitted20-05-2019|

    • Accepted28-10-2019|

    • First Online 03-12-2019|

    • doi 10.18805/LR-500

    Cite article:- Yu Xiaomin, Jin Hangxia, Yang Qinghua, Fu Xujun, Yuan Fengjie (2019). Genetic Mapping of a Soybean Glabrous Gene Using Specific-Locus Amplified Fragment Sequencing Method. Legume Research. 43(4): 501-506. doi: 10.18805/LR-500.

    ABSTRACT

    Trichome is a natural trait related with plant defense and seed yield, however, the genetic control of this trait has not been extensively studied in soybean. In this study, a cross was made between a soybean landrace “Aijiaomaodou” with normal pubescence and a glabrous soybean line “39002”. The segregation ratio of the F2 population was fit to the expected value and the glabrous phenotype was controlled by a single dominant gene. Association analysis was conducted to identify candidate genes for the glabrous trait using a high-throughput sequencing technology, specific-locus amplified fragment sequencing. A total of 6,961 polymorphic specific-locus amplified fragments were analyzed and a region of 2.76 Mb at nucleotides 47,315,610-50,072,564 on chromosome 9 containing 551 candidate genes was identified. Four specific genes (Glyma09G280500, Glyma09G282600, Glyma09G259400 and Glyma09G283400) in the region appeared to be most important candidate genes that are highly related to the glabrous trait. Further studies of these genes may lead to isolation and cloning of the glabrous gene and facilitate the selection procedures in soybean breeding.

    REFERENCES

    1. Abe, A., Kosugi, S., Yoshida, K., Natsume, S., Takagi, H., Kanzaki, H., Matsumura, H., et al. (2012). Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnology. 30:174-178.
    2. An, L., Zhou, Z., Yan, A. and Gan, Y. (2011). Progress on trichome development regulated by phytohormone signaling. Plant Signaling & Behavior. 6:1959-1962.
    3. Bernard, R.L. and Singh, B.B. (1969). Inheritance of pubescence type in soybeans: glabrous, curly, dense, sparse and puberulent. Crop Science. 9:192-197.
    4. Esch, J.J., Chen, M., Sanders, M., Hillestad, M., Ndkium, S., Idelkope, B., et al. (2003). A contradictory GLABRA3 allele helps define gene interactions controlling trichome development in Arabidopsis. Development. 130:5885-5894.
    5. Gao, Y., Gong, X., Cao, W., Zhao, J., Fu, L., Wang, X., Schumaker, K.S. and Guo, Y. (2008). SAD2 in Arabidopsis functions in trichome initiation through mediating GL3 function and regulating GL1, TTG1 and GL2 expression. Journal of Integrative Plant Biology. 50:906-917.
    6. Gao, Y., Guo, J.Q. and Zhao, J.F. (2011). Molecular mechanisms of Arabidopsis trichome development. Chinese Bulletin of Botany. 46:119-127. (In Chinese with English abstract)
    7. Geng, X., Jiang, C., Yang, J., Wang, L., Wu, X. and Wei, W. (2016). Rapid identification of candidate genes for seed weight using the SLAF-seq method in Brassica napus. PLoS ONE. 11:e0147580.
    8. Hunt, M., Kaur, N., Stromvik, M. and Vodkin, L. (2011). Transcript profiling reveals expression differences in wild-type and glabrous soybean lines. BMC Plant Biology. 11:145.
    9. Ishida, T., Kurata, T., Okada, K. and Wada, T. (2008). A genetic regulatory network in the development of trichomes and root hairs. Annual Review of Plant Biology. 59:365-386.
    10. Jain, R.K., Joshi, A., Chaudhary, H.R., Dashora, A. and Khatik, C.L. (2018). Study on genetic variability, heritability and genetic advance in Soybean [Glycine max (L.) Merrill]. Legume Research. 41:532-536.
    11. Jia, Q., Tan, C., Wang, J., Zhang, X., Zhu, J., Luo, H., Yang, J., Westcott, S., Broughton, S., Moody, D. and Li, C. (2016). Marker development using SLAF-seq and whole-genome shotgun strategy to finemap the semi-dwarf gene ari-e in barley. BMC Genomics. 17: 911.
    12. Jin, H., Dong, D., Yang, Q. and Zhu D. (2016). Salt-responsive transcriptome profiling of Suaeda glauca via RNA sequencing. PLoS ONE. 11: e0150504.
    13. Lam, W.K.F. and Pedigo, L.P. (2001). Effect of trichome density on soybean pod feeding by adult bean leaf beetles (Coleoptera: Chrysomelidae). Journal of Economic Entomology. 94:1459-1463.
    14. Murray, M.G. and Thompson, W.F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research. 8: 4321-    4325.
    15. Pu, L., Suo, J.F. and Xue, Y.B. (2003). Molecular control of plant trichome development. Acta Genetica Sinica. 30: 1078-1084. (In Chinese with English abstract)
    16. Rehal, J., Beniwal, V. and Gill, B.S. (2019). Physico-chemical, engineering and functional properties of two soybean cultivars. Legume Research. 42: 39-44.
    17. Ren, X.W., Yu, D.W., Yang, S.P., Gai, J.Y. and Zhu, Y.L. (2018). Effects of StP5CS gene overexpression on nodulation and nitrogen fixation of vegetable soybean under salt stress conditions. Legume Research. 41: 675-680.
    18. Singh, T. and Sharma, A. (2016). Early generation selection for yield and its related traits in soybean [Glycine max (L.) Merrill.]. Legume Research. 39: 343-348.
    19. Sun, J. (2007). Heredity analysis and molecular marker study on glabrous character of soybean. M.Sc. Thesis, Jilin Agricultural University. (In Chinese with English abstract)
    20. Sun, X., Liu, D., Zhang, X., Li, W., Liu, H., Hong, W., Jiang, C., Guan, N., Ma, C., Zeng, H., et al. (2013). SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE. 8: e58700.
    21. Xia, C., Chen, L., Rong, T., Li, R., Xiang, Y., Wang, P., Liu, C., Dong, X., Liu, B., et al. (2015). Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method. Euphytica. 202: 35-44.
    22. Yang, C. and Ye, Z. (2013). Trichomes as models for studying plant cell differentiation. Cellular and Molecular Life Sciences. 70: 1937-1948.
    23. Yuan, F., Yu, X., Dong, D., Yang, Q., Fu, X., Zhu, S. and Zhu, D. (2017). Whole genome-wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants. BMC Plant Biology. 17: 16. 
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