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. 2010 Jan;17(1):43-9.
doi: 10.1016/j.sjbs.2009.12.007.

Phylogenetic analyses of peanut resistance gene candidates and screening of different genotypes for polymorphic markers

Osman E Radwan  1 , Talaat A Ahmed, Steven J Knapp
Affiliations

Phylogenetic analyses of peanut resistance gene candidates and screening of different genotypes for polymorphic markers

Osman E Radwan et al. Saudi J Biol Sci. 2010 Jan.

Abstract

The nucleotide-binding-site-leucine-rich-repeat (NBS-LRR)-encoding gene family has attracted much research interest because approximately 75% of the plant disease resistance genes that have been cloned to date are from this gene family. Here, we describe a collection of peanut NBS-LRR resistance gene candidates (RGCs) isolated from peanut (Arachis) species by mining Gene Bank data base. NBS-LRR sequences assembled into TIR-NBS-LRR (75.4%) and non-TIR-NBS-LRR (24.6%) subfamilies. Total of 20 distinct clades were identified and showed a high level of sequence divergence within TIR-NBS and non-TIR-NBS subfamilies. Thirty-four primer pairs were designed from these RGC sequences and used for screening different genotypes belonging to wild and cultivated peanuts. Therefore, peanut RGC identified in this study will provide useful tools for developing DNA markers and cloning the genes for resistance to different pathogens in peanut.

Keywords: Arachis hypogaea L.; NBS–LRR; Peanut diseases; Phylogentic and DNA markers; Resistance gene.

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Figures

Figure 1
Figure 1
Partial alignment of deduced amino acid sequences of non-TIR-NBS–LRR (CC), TIR-NBS–LRR (TIR) and of two R-genes, A. thalianaRPP8 (Accession No. AAC78631) and A. thalianaRPP5 (Accession No. NP_849398). The computer program Clustal_X was used in alignment analysis. Alignments were shaded using the Genedoc software. The P-loop, Kin-2, Kin-3a (RNBS-B) and GLPL are underlined. The RNBS-A of non-TIR-NBS–LRR (FDL × AWVCVSQ × F) and RNBS-A of TIR-NBS–LRR.
Figure 2
Figure 2
A neighbor-Joining tree of peanut RGCs with 7 cloned R-genes encoding NBS–LRR. The tree constructed by Neighbor-Joining method after multiple alignments of polypeptide sequences with CLUSTAL_X (Thompson et al., 1997). Sequences which share more than 90% identity are not included. The confidence levels of nodes were tested by the bootstrapping of 1000 replications, and bootstrap values >70% are indicated on the branches. The sunflower NBS–LRR RGCs are grouped into 20 subfamilies, each being indicated by bold-faced letter N1–N10 for non-TIR-NBS subfamily and by bold-faced letter T1–T10 for TIR-NBS subfamily. The plant R-genes representing the NBS–LRR class selected from GenBank are italicized and bold-faced.
Figure 3
Figure 3
Polymorphic RGC markers detected by SSCP (A, B and C) and INDEL agarose (D) using different wild and cultivated peanut genotypes as DNA templates. A = RGC 18, B = RGC5, C = RGC33 and D = RGC16. M = DNA marker.
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