A LOW-DENSITY GENETIC-MAP OF ONION REVEALS A ROLE FOR TANDEM DUPLICATION IN THE EVOLUTION OF AN EXTREMELY LARGE DIPLOID GENOME

The bulb onion, allium cepa L., is a diploid (2n = 2x = 16) plant with a huge nuclear genome. Previous genetic and cytogenetic analyses have not supported a polyploid origin for onion, We developed a low-densit y genetic map of morphological markers, randomly amplified polymorphic DNAs (RAPD), and restriction fragment length polymorphisms (RFLP) as a tool for onion improvement and to study the genome organization of o nion. A mapping population of 58 F-3 families was produced from a sing le F-1 plant from the cross of two partially inbred lines (Brigham Yel low Globe 15-23 and Alisa Craig 43). Segregations were established for restoration of male fertility in sterile cytoplasm, complementary lig ht-red bulb color, 14 RAPDs. 110 RFLPs revealed by 90 anonymous cDNA c lones. and 2 RFLPs revealed by a cDNA clone of alliinase, the enzyme r esponsible for the characteristic Allium flavors. Duplicated RFLP loci were detected by 21% of the clones, of which 53% were unlinked (> 30 cM). 5% loosely linked (10-30 cM), and 42% tightly linked (< 10 cM). T his duplication frequency is less than that reported for paleopolyploi ds but higher than for diploid species. We observed 40% dominant RFLPs , the highest pet reported among plants. Among duplicated RFLP loci, 1 9% segregated as two loci each with two codominant alleles, 52% segreg ated as one locus with codominant alleles and one locus with only a do minant fragment, and 29% segregated as two loci with only dominant fra gments. We sequenced cDNAs detecting duplicated RFLPs: 63% showed homo logy to known gene families (e.g., chlorophyll binding proteins, ubiqu itin, or RuBISCO). and 37% were unique clones showing significant homo logy to known genes of low-copy number or no homology to database sequ ences. Duplicated RFLPs showing linkage could be due to retroviral-lik e sequences in adjacent coding regions or intrachromosomal, as opposed to whole genome, duplications. Previous cytological analyses and this genetic map support intrachromosomal duplication as a mechanism contr ibuting to the huge onion genome.