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Diversity Suppression‐Subtractive Hybridization Array for Profiling Genomic DNA Polymorphisms
Author(s) -
Li TongXiang,
Wang JinKe,
Bai YunFei,
Lu ZuHong
Publication year - 2006
Publication title -
journal of integrative plant biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.734
H-Index - 83
eISSN - 1744-7909
pISSN - 1672-9072
DOI - 10.1111/j.1744-7909.2006.00249.x
Subject(s) - suppression subtractive hybridization , biology , dendrobium , genomic dna , dendrogram , genetics , genetic diversity , dna profiling , comparative genomic hybridization , dna , computational biology , genome , botany , gene , complementary dna , demography , cdna library , sociology , population
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. (Managing editor: Li‐Hui Zhao)