J Integr Plant Biol. ›› 2006, Vol. 48 ›› Issue (4): -.DOI: 10.1111/j.1744-7909.2006.00249.x

• Research Articles •    

Diversity Suppression-Subtractive Hybridization Array for Profiling Genomic DNA Polymorphisms

Tong-Xiang Li, Jin-Ke Wang, Yun-Fei Bai and Zu-Hong Lu   

Abstract: Genomic DNA polymorphisms are very useful for tracing genetic traits and studying biological diversity among species. Here, we present a method we call the “diversity suppression-subtractive hybridization array” for effectively profiling genomic DNA polymorphisms. The method first obtains the subtracted gDNA fragments between any two species by suppression subtraction hybridization (SSH) to establish a subtracted gDNA library, from which diversity SSH arrays are created with the selected subtracted clones. The diversity SSH array hybridizes with the DIG-labeled genomic DNA of the organism to be assayed. Six closely related Dendrobium species were studied as model samples. Four Dendrobium species as testers were used to perform SSH. A total of 617 subtracted positive clones were obtained from four Dendrobium species, and the average ratio of positive clones was 80.3%. We demonstrated that the average percentage of polymorphic fragments of pairwise comparisons of four Dendrobium species was up to 42.4%. A dendrogram of the relatedness of six Dendrobium species was produced according to their polymorphic profiles. The results revealed that the diversity SSH array is a highly effective platform for profiling genomic DNA polymorphisms and dendrograms.(Author for correspondenceTel: 025 8361 9983;Fax: 025 8361 9983;E-mail: zhlu@seu.edu.cn.)

Key words: dendrogram, diversity suppression-subtractive hybridization array, genomic DNA polymorphisms.

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