RNA-seq–based mapping and candidate identification of mutations from forward genetic screens

Increasing the number of embryos in an RNA-seq–based mapping experiment decreases the linkage size of the mapped region. (A) Detail of chromosome 12 containing the linked interval for each hoxb1b¹²¹⁹ mapping experiment. Each row is labeled with the number of embryos used in the experiment. The average frequency of mutant markers (green discs) is plotted against chromosomal position. A red box marks each region of linkage, and a red line marks the position of the hoxb1b gene; linkage was defined as the region between the “leftmost” and “rightmost” positions within 1% of homozygosity. Each y-axis is the same as in the first row. (B) Comparison of linked regions to the number of embryos used in each RNA-seq–based mapping experiment. The hoxb1b¹²¹⁹ experiments are labeled in red; nhsl1b^fh131, in green; vangl^m209, in magenta; and egr2b^fh227, in blue; and unknown mutations mapped using this method, in cyan. Increasing the number of embryos decreases the linked region with diminishing returns.