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

文献类型： 外文期刊

作者： Luo, Jie 1 ; Li, Guojing 1 ; Xu, Pei 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Inst Vegetables, Hangzhou, Zhejiang, Peoples R China

关键词： Asparagus bean;Bioinformatic system;Genomic studies.

期刊名称：LEGUME RESEARCH （ 影响因子：0.589； 五年影响因子：0.648 ）

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收录情况： SCI

摘要： 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.

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[1]Mapping Genes Governing Flower and Seedcoat Color in Asparagus Bean (Vigna unguiculata ssp sesquipedalis) Based on Single Nucleotide Polymorphism and Simple Sequence Repeat Markers. Xu, Pei,Hu, Tingting,Yang, Yuejian,Wu, Xiaohua,Wang, Baogen,Liu, Yonghua,Qin, Dehui,Lu, Zhongfu,Li, Guojing,Ehlers, Jeffrey,Close, Timothy. 2011

[2]QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits. Xu, Pei,Wu, Xiaohua,Wang, Baogen,Hu, Tingting,Lu, Zhongfu,Liu, Yonghua,Qin, Dehui,Wang, Sha,Li, Guojing. 2013

[3]Development and polymorphism of Vigna unguiculata ssp unguiculata microsatellite markers used for phylogenetic analysis in asparagus bean (Vigna unguiculata ssp sesquipedialis (L.) Verdc.). Xu, Pei,Wu, Xiaohua,Wang, Baogen,Liu, Yonghua,Hu, Tingting,Lu, Zhongfu,Li, Guojing,Qin, Dehui,Ehlers, Jeffery D.,Close, Timothy J.. 2010

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[5]Genotypic differences in pod wall and seed growth relate to invertase activities and assimilate transport pathways in asparagus bean. Liu, Yong-Hua,Li, Guo-Jing,Wu, Xiao-Hua,Wang, Bao-Gen,Xu, Pei,Hu, Ting-Ting,Lu, Zhong-Fu,Liu, Yong-Hua,Cao, Jia-Shu,Patrick, John W.,Ruan, Yong-Ling.

[6]Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: Implications for domestication history and genome wide association studies. Xu, P.,Wu, X.,Wang, B.,Liu, Y.,Lu, Z.,Wang, S.,Li, G.,Luo, J.,Ehlers, J. D.,Close, T. J.,Roberts, P. A..

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