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Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor

Yuhon Li, Changlong Wen, Yiqun Weng
Theoretical and applied genetics 2013 v.126 pp. 2187-2196
Cucumis sativus, DNA, chromosome walking, color, cucumbers, dominant genes, fruit quality, fruits, gene expression, genetic markers, inbred lines, inheritance (genetics), introns, loci, microsatellite repeats, pleiotropy, population size, sequence alignment, transcription factors
In cucumber, Cucumis sativus L., the spine and skin colors on fruits are two important fruit quality traits in cucumber for variety improvement. In this study, we investigated the inheritance of spine and mature fruit colors F2 and F3 populations derived from a cross between two inbred lines WI7200 (black spine and orange fruit skin colors) and WI7201 (white spine and creamy fruit skin colors). We confirmed that a single, dominant gene, B, controlled both black spine color and orange mature fruit color. Initial framework mapping with microsatellite markers located the B locus in the distal region of the short arm of cucumber chromosome 4. Fine mapping was conducted with draft genome scaffold-assisted chromosome walking and stepwise increase of mapping population sizes, which allowed for the assignment of the B locus to a 50 kb genomic DNA region with two flanking markers that were 0.06 and 0.09 cM, respectively, from the B locus in a mapping population of 2,001 F2 plants. Gene annotation of this 50 kb region identified six genes including one encoding for an R2R3-MYB transcription factor. Sequence alignment of the R2R3-MYB homologs between the two parent inbreds identified a 1 bp deletion in the third intron of this gene in WI 7201. A molecular marker based on this indel co-segregated with the spine and fruit colors. Quantitative RT-PCR revealed higher level of expression of this R2R3-MYB gene in WI7200 than in WI7201 in both immature and mature fruits. This R2R3-MYB gene is the best candidate gene for the B locus conditioning black spine and orange mature fruit colors of cultivated cucumber.