Bulk segregant analysis of RAD markers identifies two regions associated with the lateral plate phenotype. Sixteen RAD markers (small black bars) with large hybridization differences in the bulk experiments of the complete plate pool versus low plate pool were sequenced and placed on linkage group IV. (A) Six markers clustered in a 3-Mb region surrounding Eda, the previously identified lateral plate locus. Seven markers also cluster in a 2-Mb region near position 25 Mb, suggesting that this region is also associated with the lateral plate phenotype. A microsatellite marker near the center of this cluster, OrSSR256, confirmed this result. (B) Individual RAD marker data confirm the bulk mapping results. The RAD-tag sample from each of eight F2 individuals was run directly against the tags from BP (Bear Paw individual) in one hybridization experiment and RS (Rabbit Slough individual) in a separate experiment. These RAD-tag hybridization patterns can be used to determine individual genotypes (open box, homozygous BP; gray box, heterozygous; black box, homozygous RS) (see Supplemental Fig. 1 for raw data). Columns represent individuals; rows represent markers. One of the four complete plate individuals (04) is heterozygous at the RAD markers around Eda (presence of both complete plate and low plate tags), but is homozygous for the complete plate allele at the 25-Mb cluster and the two markers at 19 Mb, suggesting a recombination event between the Eda cluster and the markers at 19 Mb. Individual 03 lacked the complete plate allele at RS004K08 but had a complete plate allele at RS001J15 and the cluster around Eda, suggesting both a recombination event between RS001J15 and RS004K08 and another recombination event in the region between RS004K08 and the cluster around Eda. Microsatellite markers confirmed the recombination event between RS001J15 and RS004K08 and further localized the second recombination event between OrSSR252 and OrSSR251.
