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. 2016 Jun 10;6(8):2543–2552. doi: 10.1534/g3.116.029728

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Copyright © 2016 Pyle et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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F. verticillioides Sk is located within a 102 kb region of chromosome V. (A) A diagram of the 4.25 Mb sequence of chromosome V from Fv149-Sk^S is shown. The annotated chromosome V sequence was downloaded from NCBI (CM000582.1). The positions of the first (FVEG_03430 ) and last (FVEG_16592 ) genes on the chromosome are indicated in the diagram. The approximate location of RFLP marker 11p18 is also shown. Marker 11p18 overlaps most of gene FVEG_02851. (B) A total of 60 progeny were isolated from a cross between Fv999-Sk^K and Fv149-Sk^S. These progeny were genotyped with nine different CAPS markers. Markers CAPS-1 through CAPS-6 are located on chromosome V. Markers CAPS-9, CAPS-10, and CAPS-11 are found on chromosomes XI, VII, and I, respectively. Each bar represents the percentage of Fv999-Sk^K genotypes recovered for each marker. An asterisk is placed above all markers whose recovery deviated significantly from a Mendelian ratio of 1:1 according to a χ² test with P < 0.01. The biased transmission of Fv999-Sk^K sequences was detected for all markers on chromosome V, except for CAPS-5. (C) The marker patterns for progeny JP98.75-Sk^K, JP98.111-Sk^K, and JP98.118-Sk^K suggest that cross-over events occurred between CAPS-3 and CAPS-4 (for JP98.75-Sk^K), CAPS-4 and CAPS-5 (for JP98.111-Sk^K), and CAPS-2 and CAPS-3 (for JP98.118-Sk^K) (Table S3). These cross-overs did not identify an Fv999-Sk^K-derived region of chromosome V common to all three progeny. The predicted Fv999-Sk^K- and Fv149-Sk^S-inherited regions are shown in black and white, respectively. Irregular borders are used to indicate that exact cross-over positions could not be determined from the CAPS marker data. (D) SNP analysis was used to more accurately define cross-over positions for progeny JP98.75-Sk^K, JP98.111-Sk^K, and JP98.118-Sk^K. In addition to refining the location of the cross-overs identified by CAPS analysis, two additional cross-overs were identified between CAPS-3 and CAPS-4 on chromosome V of JP98.111-Sk^K. These findings helped delineate a single contiguous interval between position 665.7 kb and 767.4 kb on chromosome V as the only Fv999-Sk^K-derived chromosome V sequence common to all three progeny (red dotted lines). Therefore, this interval is referred to as the Sk region.