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Current IssueEditorial BoardOnline First ArticlesArchive
Current IssueEditorial BoardOnline First ArticlesArchive

volume 38 issue 3 (june 2015) : 321-323,   Doi: 10.5958/0976-0571.2015.00117.4

AMBAB: A Bioinformatic system for the assistance of molecular breeding in asparagus bean (V. unguiculata ssp. sesquipedialis) and other plant species

J
Jie Luo
G
Guojing Li
P
Pei Xu*
1Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, PR China.
Cite article:- Luo Jie, Li Guojing, Xu* Pei (2025). AMBAB: A Bioinformatic system for the assistance of molecular breeding in asparagus bean (V. unguiculata ssp. sesquipedialis) and other plant species. Legume Research. 38(3): 321-323. doi: 10.5958/0976-0571.2015.00117.4.

ABSTRACT

AMBAB (http://60.191.1.10:7777/cowpea/) is a user-friendly web server system for genomic research and breeding of asparagus bean (V. unguiculata ssp. sesquipedialis). This system integrates multiple analytical tools including Blast, Sim4, Primer3 and e-PCR to enable an easy and effective use of the current genomic resources to assist breeding by geneticists, breeders and trained farmers. Presently, the reference genome sequences of Oryza sativa, Arabidopsis thaliana and the in-house genome re-sequencing data of four asparagus bean accessions are available for blast search and e-PCR. Using this system, users can query an EST, unigene or genomic sequence of interest against the asparagus bean genome dataset, to retrieve the information of gene location, similarity, intron-exon junctions and more. PCR primers can subsequently be developed by using Primer3 based on the retrieved genomic sequences. If the development of a polymorphic primer is required, e-PCR will be very useful in predicting the amplicon patterns of various primers. In addition, the AMBAB system is also valuable for general bioinformatic analyses for other plant species.

REFERENCES

  1. Burland, T. G. (2000) DNASTAR’s Lasergene sequence analysis software. Methods in Molecular Biology 132:71-91
  2. Chen X., Laudeman T., Rushton P., Spraggins T. and Timko M. (2007) CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8:129
  3. Fang J. , Chao C. T., Roberts P. A., Ehlers J. D. (2007) Genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis. 54:1197-1209
  4. Florea L., Hartzell G., Zhang Z., Rubin G. M. and Miller W. (1998) A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence. Genome Research 8(9):967-974
  5. Mount D. W. (2007) Using the Basic Local Alignment Search Tool (BLAST). Cold Spring Harbor Protocols 2007(7):pdb.top17
  6. Muchero W., Diop N. N., Bhat P. R., Fenton R. D., Wanamakerb S., Pottorffb M., Hearnec S., Cissed N., Fatokunc C., Ehlersb J. D., Robertsa P. A., and Closeb T. J. (2009) A consensus genetic map of cowpea [Vigna unguiculataL. Walp] and synteny based on EST-derived SNPs. Proceedings of the National Academy of Sciences of the United States of America. 106(43):18159-18164
  7. Nelson W. and Soderlund C. (2009) Integrating sequence with FPC fingerprint maps. Nucleic Acids Research 37(5): e36
  8. Schuler G. D. (1997) Sequence Mapping by Electronic PCR. Genome Research 7(5):541-550
  9. Thomas A. H. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/ 98/NT. Nucleic acids symposium series 41:95-98
  10. Untergasser A., Cutcutache I., Koressaar T., Ye J., Faircloth B. C., Remm M. Ye J., Coulouris G., Zaretskaya I., Cutcutache I., Rozen S. and Madden T. (2012) Primer-BLAST: A tool to design targetspecific primers for polymerase chain reaction. BMC Bioinformatics 13:134
  11. Wu X.H., Wang B.G., Lu Z.F., Wu X.Y., Li G.J., and Xu P. (2014) Identification and mapping of a powdery mildew resistance gene Vu-Pm1 in the Chinese asparagus bean landrace ZN016. Legume Research 7: 32-36
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    volume 38 issue 3 (june 2015) : 321-323,   Doi: 10.5958/0976-0571.2015.00117.4

    AMBAB: A Bioinformatic system for the assistance of molecular breeding in asparagus bean (V. unguiculata ssp. sesquipedialis) and other plant species

    J
    Jie Luo
    G
    Guojing Li
    P
    Pei Xu*
    1Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, PR China.
    Cite article:- Luo Jie, Li Guojing, Xu* Pei (2025). AMBAB: A Bioinformatic system for the assistance of molecular breeding in asparagus bean (V. unguiculata ssp. sesquipedialis) and other plant species. Legume Research. 38(3): 321-323. doi: 10.5958/0976-0571.2015.00117.4.

    ABSTRACT

    AMBAB (http://60.191.1.10:7777/cowpea/) is a user-friendly web server system for genomic research and breeding of asparagus bean (V. unguiculata ssp. sesquipedialis). This system integrates multiple analytical tools including Blast, Sim4, Primer3 and e-PCR to enable an easy and effective use of the current genomic resources to assist breeding by geneticists, breeders and trained farmers. Presently, the reference genome sequences of Oryza sativa, Arabidopsis thaliana and the in-house genome re-sequencing data of four asparagus bean accessions are available for blast search and e-PCR. Using this system, users can query an EST, unigene or genomic sequence of interest against the asparagus bean genome dataset, to retrieve the information of gene location, similarity, intron-exon junctions and more. PCR primers can subsequently be developed by using Primer3 based on the retrieved genomic sequences. If the development of a polymorphic primer is required, e-PCR will be very useful in predicting the amplicon patterns of various primers. In addition, the AMBAB system is also valuable for general bioinformatic analyses for other plant species.

    REFERENCES

    1. Burland, T. G. (2000) DNASTAR’s Lasergene sequence analysis software. Methods in Molecular Biology 132:71-91
    2. Chen X., Laudeman T., Rushton P., Spraggins T. and Timko M. (2007) CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8:129
    3. Fang J. , Chao C. T., Roberts P. A., Ehlers J. D. (2007) Genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis. 54:1197-1209
    4. Florea L., Hartzell G., Zhang Z., Rubin G. M. and Miller W. (1998) A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence. Genome Research 8(9):967-974
    5. Mount D. W. (2007) Using the Basic Local Alignment Search Tool (BLAST). Cold Spring Harbor Protocols 2007(7):pdb.top17
    6. Muchero W., Diop N. N., Bhat P. R., Fenton R. D., Wanamakerb S., Pottorffb M., Hearnec S., Cissed N., Fatokunc C., Ehlersb J. D., Robertsa P. A., and Closeb T. J. (2009) A consensus genetic map of cowpea [Vigna unguiculataL. Walp] and synteny based on EST-derived SNPs. Proceedings of the National Academy of Sciences of the United States of America. 106(43):18159-18164
    7. Nelson W. and Soderlund C. (2009) Integrating sequence with FPC fingerprint maps. Nucleic Acids Research 37(5): e36
    8. Schuler G. D. (1997) Sequence Mapping by Electronic PCR. Genome Research 7(5):541-550
    9. Thomas A. H. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/ 98/NT. Nucleic acids symposium series 41:95-98
    10. Untergasser A., Cutcutache I., Koressaar T., Ye J., Faircloth B. C., Remm M. Ye J., Coulouris G., Zaretskaya I., Cutcutache I., Rozen S. and Madden T. (2012) Primer-BLAST: A tool to design targetspecific primers for polymerase chain reaction. BMC Bioinformatics 13:134
    11. Wu X.H., Wang B.G., Lu Z.F., Wu X.Y., Li G.J., and Xu P. (2014) Identification and mapping of a powdery mildew resistance gene Vu-Pm1 in the Chinese asparagus bean landrace ZN016. Legume Research 7: 32-36
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