Assessment of Genetic Diversity in Zingiberaceae Through Nucleotide Binding Site-Based Motif-Directed Profiling

Abstract

Functional motif-directed profiling was performed with 15 nucleotide binding site (NBS) primer-enzyme combinations to identify and elucidate the phylogenetic relationships among 15 genotypes of the family Zingiberaceae. We retrieved 167 polymorphic bands (24.85 %), with an average of 11.13 bands per primer. Mean polymorphism rates were detected using MseI (26 %), RsaI (21 %), and AluI (28 %) as restriction enzymes. The polymorphism information content (PIC) for each NBS primer-enzyme combination ranged from 0.48 to 0.76 with a mean value of 0.65. The 38 NBS profiling markers had PIC values ranging from 0.3 to 0.6 and exhibited good power to discriminate between genotypes. Comparison of NBS profiling with microsatellite data for the same set of genotypes exhibited a correlation value of 0.78, P ≤ 0.001. Our study suggests that genetic variability assessment could be more efficient if it targeted genes that exhibit functionally relevant variation, rather than random markers.

Isolation, characterization and evolution of NBS-LRR encoding disease-resistance gene analogs in eggplant against bacterial wilt

“…Resistance gene markers target conserved motifs of R-genes and reduce the chance of homoplasy. This has been proved in Zingiberaceae where NBS markers scored over SSR markers due to a highly conserved NBS region (Joshi et al 2012;Peter et al 2013). According to Leister et al (1996) using R-like gene specific primers, developing PCR makers linked to resistance genes can be easy and fast (Leister et al 1996;Peter et al 2013).…”

Advances in plant gene-targeted and functional markers: a review

“…The targeting of more conserved regions of resistance-genes makes RGMs more appropriate for many applications, since the chance of homoplasy is reduced. It has been shown in the Zingiberaceae that NBS markers score over SSRs since they are highly conserved [165]. This may be due to several factors such as constraints on allele size range, high mutation rates, size homoplasy and low levels of conservation of SSRs among Zingiberaceae, which hampered the use of microsatellites in this study.…”

Isolation, characterization and genetic diversity of NBS-LRR class disease-resistant gene analogs in multiple virus resistant line of chilli (Capsicum annuum L.)

“…Identification of RGAs and their use in identification of markers for disease resistance for marker assisted selection is an ideal approach (Yang et al 2013;An and Yang 2014;Mutlu et al 2008). These studies indicate the potentiality of R-gene analogues in identification of markers linked to disease resistance, as R-gene markers target conserved motifs of resistant genes (Joshi et al 2012). To our knowledge, the isolated RGAs in this study are the first report of NBS-LRR class of RGAs isolated from multiple virus resistance chilli genotype and the phylogenetic results suggested wide genetic diversity of isolated Capsicum RGAs with previous studies (Fig.…”