Caught red-handed Rc encodes a basic helix-loop-helix protei(4)

precise position of each break point.All plants in this class had red pericarp,and because they were all homozygous for cv Jefferson DNA downstream of RID15,we were able to eliminate that region as the location of rg7.1.Class3consisted of a single red-seeded recombinant plant that contained an intragenic break point between RM21197and RID12.It had cv Jefferson DNA upstream of RM21197,allowing us to eliminate the region between RID13and RM21197from further consideration.We thus defined an18.5-kb target region for rg7.1bracketed by RM21197and RID15(Figure1B,iii).

Physical/Genetic Distance

The evaluation of4000plants for recombination allowed us to identify recombinational hot and cold spots within the401-kb region.The most recombinagenic interval was a6-kb region that contained no annotated gene models,defined by markers RID16 and RID17(Figure2).Within this interval,the physical/genetic distance was4kb/cM,a recombination rate significantly higher than the average across the401-kb region(P<0.001).The4-kb interval just downstream(RID17to RID18)also lacked gene models but had no detectable recombination.The second most recombinagenic region(12.3kb/cM;P<0.001)was the14-kb interval between RID14and RID15that contained two TEs. Again,this region was juxtaposed with a2.3-kb region upstream in which there was no detectable recombination.The large interval between RM21177and RM21194(;300kb),with50 annotated gene models only3of which are TEs,had a recom-bination rate significantly lower than the average for the region (P<0.001),even after recombination rates from the two hot spots were excluded from the average(Figure2).

Positional and Functional Candidate Genes

One non-TE gene was detected within the18.5-kb target region. LOC_Os07g11020.1is a single-copy gene668amino acids in length and containing a predicted bHLH domain.This domain is common among transcription factors known to regulate

pigment

Figure2.Physical/Genetic Distance around the Rc Locus.

Graph showing recombination rates across the410-kb region examined in the BC2F6generation offine-mapping.The x axis is positioned along the psuedomolecule,and the y axis shows the number of recombination events per100plants.Physical/genetic distance is given in kb/cM above each interval.TIGR gene models are shown above the marker designations,with TEs in gray.Gene models are ordered as in Figure1.Intervals indicated by asterisks have recombination rates significantly different from the average at the5%level after Bonferroni correction;those indicated by double asterisks are significant at0.1%.

286The Plant Cell