Rare germinal unequal crossing-over leading to recombinant gene formation and gene duplication in Arabidopsis thaliana

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Abstract
Small, multigene families organized in a tandem array can facilitate the rapid evolution of the gene cluster by a process of meiotic unequal crossing-over. To study this process in a multicellular organism, we created a synthetic RBCSB gene cluster in Arabidopsis thaliana and used this to measure directly the frequency of meiotic, intergenic unequal crossing-over between sister chromatids. The synthetic RBCSB gene cluster was composed of a silent ΔRBCS1B∷LUC chimeric gene fusion, lacking all 5′ transcription and translation signals, followed by RBCS2B and RBC3B genomic DNA. Expression of luciferase activity (luc+) required a homologous recombination event between the ΔRBCS1B∷LUC and the RBCS3B genes, yielding a novel recombinant RBCS3B/ 1B∷LUC chimeric gene whose expression was driven by RBCS3B 5′ transcription and translation signals. Using sensitive, single-photon-imaging equipment, three luc+ seedlings were identified in more than 1 million F2 seedlings derived from self-fertilized F1 plants hemizygous for the synthetic RBCSB gene cluster. The F2 luc+ seedlings were isolated, and molecular and genetic analysis indicated that the luc+ trait was caused by the formation of a recombinant chimeric RBCS3B/1B∷LUC gene. A predicted duplication of the RBCS2B gene also was present. The recombination resolution break points mapped adjacent to a region of intron I at which a disjunction in sequence similarity between RBCS1B and RBCS3B occurs; this provided evidence supporting models of gene cluster evolution by exon-shuffling processes. In contrast to most measures of meiotic unequal crossing-over that require the deletion of a gene in a gene cluster, these results directly measured the frequency of meiotic unequal crossing-over (≈3 × 10−6), leading to the expansion of the gene cluster and the formation of a novel recombinant gene.