AFLP and CAPS linkage maps of Cryptomeria japonica

We have used two DNA marker systems, AFLP and CAPS, in a two-way pseudo-testcross strategy applied to an F₁ population to construct genetic linkage maps of two local sugi cultivars. The AFLP markers detected about eight polymorphisms per parent per primer combination. Using 38 primer combinations, 612 AFLPs were detected in 'Haara 4' and 'Kumotooshi', of which 305 segregated in a 1:1 ratio (P>0.05). A total of 91 markers (83 AFLP and 8 CAPS) in 'Haara 4' and 132 (123 AFLP and 9 CAPS) in 'Kumotooshi' were distributed among 19 and 23 linkage groups, respectively, each of which included 2-17 markers. Maps of 'Haara 4' and 'Kumotooshi' spanned 1266.1 cM and 1992.3 cM, and covered approximately 50% and 80% of the sugi genome, respectively. Sequences derived from cDNA, which were previously used to construct a sugi linkage map, were also placed on our linkage maps as CAPS markers. Where a 'two-way pseudo-testcross' is used, more than half of the sugi CAPS developed can be used to construct linkage maps for each parental family. The saturation of mapped markers, and the integration of several linkage maps derived from different mapping populations, is anticipated in the near future.