Molecular organization of the APA genomic region associated with resistance to seed bruchids in wild Phaseolus vulgaris L. genotypes

In common bean (Phaseolus vulgaris L.), lectin (phytohemagglutinin, PHA) and the lectin-related storage proteins arcelin (ARC) and ?-amylase inhibitor (?-AI) have evolved in a single complex genetic locus, called APA locus. Although these proteins are considered true storage proteins, several experimental data suggest a role in protection of the seed from two bruchid beetles, the bean weevil (Acanthoscelides obtectus Say) and the Mexican bean weevil (Zabrotes subfasciatus Bohemian). So far, seven ARC variants have been identified, all in wild accessions, however, only those containing ARC-4 or ARC-8 proteins were reported to be resistant to both species [1]. Molecular evolutionary analysis on this multigene family indicated that gene duplication with subsequent diversification has played a very important role in the evolution of this locus [2, 3]. We present biochemical and immunological data showing the variability of APA components in a collection of wild accessions, many of which identified as ARC variants. To shed light on the molecular structure and evolution of the APA locus, 23 BAC clones covering the whole APA locus of the wild accession G12946, which contains the most complex APA locus (Arc/PHA/?-AI) were submitted for paired-end read sequencing on an Illumina MiSeq platform (San Diego, CA, USA). This locus is over 500 Kbp, i.e. ten times larger than that found in published bean genomes (Andean G19833 and Mesoamerican Bat93). Sequencing data show that, beside genes coding for known APA proteins, many repetitive DNA sequences, microsatellites and retrotrasposons, together with several interrupted lectin and arcelin related sequences were also found at this locus, suggesting that it arised through a "birth and death" model of evolution, which is particularly true for the arcelin type sequences. Although many efforts have been made, a successful breeding of the bruchid resistance trait into cultivated genotypes has hardly been achieved. The availability of the sequence of this APA locus will provide a useful tool to develop new markers to help in breeding for such purpose.