Evolutionary, genetic and physical analysis of resistance gene-like sequences in the peanut genome and exploratory work toward integration of peanut genetic and physical maps
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The scarcity of genetic diversity in the domesticated peanut, Arachis hypogaea, gene pool makes the future of peanut cultivation especially vulnerable. We constructed and characterized a peanut HindIII BAC library containing 182,784 clones with an average insert size of 104 kb with the hope of providing better means for analysis of peanut genome organization and evolution. Although no disease resistance genes have been cloned from peanut itself, the conserved motifs in cloned resistance genes from other plants provided a means to isolate and analyze similar genes from peanut. To survey the number, diversity, evolutionary history, and genomic organization of resistance gene-like sequences in Arachis hypogaea, we isolated 234 resistance gene analogs (RGA) from the peanut genome by using primers designed from conserved regions of different classes of resistance genes including NBS-LRR, and LRR-TM classes. Phylogenetic and sequence analyses of the RGA sequences were done to explore evolutionary relationships. Overgos designed from the RGA sequences on the basis of their phyletic association were applied to the peanut BAC library; 736 uniquely detected BAC clones were fingerprinted and contigs were formed in order to gain insights into the genomic organization of these genes. As a result, we identified 250 putative resistance gene loci. As a secondary part of this project, we investigated the practicality of physical mapping in A. hypogaea, by integrating 117 previously genetically mapped probes into the physical map. A total of 576 Arabidopsis derived overgos, which were designed from the most conserved regions of orthologous genes, were also applied to the library with about a 61.5% success rate. The study has shown that Arabidopsis genome sequence is a valuable stepping stone towards opening new avenues in the analysis of complex genomes like peanut.