Table 1 Summary of genetic markers screened and mapped in the Senecio aethnensis × S. chrysanthemifolius F₂ genetic mapping family

Marker type	No. of screened	No. of developed	No. of genotyped	No. of mapped	Unlinked	Problematic
Codominant markers
EST indel	45	15	10	8		EC77, EC1687
EST SSR	216	48	33	31	ES91	ES19
Indel	7	4	3	3
SSR	72	9	8	8
Total	340	76	54	50	1	3
Dominant markers
E1M3, CAAC/ACAG	—	—	19	15	179, 219
E1M5, CAAC/ACTA	—	—	15	10	168, 213	88, 160, 204
E1M7, CAAC/ACTG	—	—	13	12	275
E4M7, CACT/ACTG	—	—	9	8	113
E5M3, CACC/ACAG	—	—	8	7	302
E5M6, CACC/ACTC	—	—	9	9
E8M5, CAGG/ACTA	—	—	11	9	114	196
E8M7, CAGG/ACTG	—	—	7	7
Total	—	—	91	77	8	6

Abbreviations: EST, expressed sequence tag; SSR, simple sequence repeat.
Marker types are divided into codominant or dominant markers. Codominant markers are further divided into markers derived from ESTs, SSRs or insertion-deletions (indel). Dominant markers are amplified fragment length polymorphisms (AFLPs). Each AFLP primer combination is shown as the primer names used in this study followed by the three selective bases for the EcoRI and MseI primers, respectively (Supplementary Methods). No. of screened is number of codominant marker primer pairs tested. No. of developed is number of codominant markers that could be scored in Senecio. No. of genotyped is number of markers showing polymorphism in the F2AC mapping family. No. of mapped is number of markers that were included in the final genetic map. Unlinked names markers that were unlinked at a >4 logarithm of odds score or>20 cM linkage threshold limits for mapping. Problematic refers to markers that caused problems with linkage group marker order or were present in multiple linkage groups. Dominant marker names are approximate fragment base-pair lengths used to label AFLP loci.

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