Assessment of cytochrome P450 sequences offers a useful tool for determining genetic diversity in higher plant species

Abstract

To investigate and develop new genetic tools for assessing genome-wide diversity in higher plant-species, polymorphisms of gene analogues of mammalian cytochrome P450 mono-oxygenases were studied. Data mining on Arabidopsis thaliana indicated that a small number of primer-sets derived from P450 genes could provide universal tools for the assessment of genome-wide genetic diversity in diverse plant species that do not have relevant genetic markers, or for which, there is no prior inheritance knowledge of inheritance traits. Results from PCR amplification of 51 plant species from 28 taxonomic families using P450 gene-primer sets suggested that there were at least several mammalian P450 gene mammalian-analogues in plants. Intra- and inter- specific variations were demonstrated following PCR amplifications of P450 analogue fragments, and this suggested that these would be effective genetic markers for the assessment of genetic diversity in plants. In addition, BLAST search analysis revealed that these amplified fragments possessed homologies to other genes and proteins in different plant varieties. We conclude that the sequence diversity of P450 gene-analogues in different plant species reflects the diversity of functional regions in the plant genome and is therefore an effective tool in functional genomic studies of plants.

Isolation and Characterization of Novel Microsatellite Markers in Chayote [<i>Sechium edule</i> (Jacq.) Sw.]

“…Genetic diversity values from the same set of Mexican chayote samples were evaluated using PBA markers [11] [15]. The PBA primer sets comprised of three forward primers (CYP1A1F, CYP2B6F, and CYP2C19F) and three reverse primers (CYP1A1R, CYP2B6R, and CYP2C19R).…”

Genomics Meets Biodiversity: Advances in Molecular Marker Development and Their Applications in Plant Genetic Diversity Assessment

“…Sequence diversity of P450 gene-analogues in different plant species has been studied and it has been reported that such analogues can be used as genetic markers for diversity studies in plants, at both functional and genome-wide scales (Somerville & Somerville, 1999). Based on these findings a technique called Cytochrome P450 Based Analog (PBA) markers was developed by Yamanaka et al (2003). Further, data mining of the genome of the model plant Arabidopsis thaliana (L.) Heynh.…”

Construction of Integrated Genetic Map between Various Existing DNA Markers and Newly Developed P450-related PBA Markers in Diploid Potato (Solanum tuberosum)

“…A total of 401 molecular markers, including 111 SSRs (Provan et al 1996, Ghislain et al 2003, Solanaceae Genomics Network (SGN) HP, http://www.sgn.cornell.edu/ index.html), 33 RFLPs (Tanksley et al 1992), 87 STSs (constructed in this study), 45 CAPS (Chen et al 2001), 94 RAPDs (Williams et al 1990), nine AFLPs (Vos et al 1995), 15 PBAs (P450-based analogues, Yamanaka et al 2003), three RGLs (resistant gene-like fragments, Leister et al 1996, Hämäläinen et al 1998 and four ISSRs (Prevost and Wilkinson 1999), were used for a parental polymorphism survey (Table 2). STS primer sets were designed from RFLP probe sequence information (SGN database, http://www.sgn.cornell.…”