Table 2.

Detailed information regarding the different marker sets that have been used for population structure analysis in our germplasm

Marker set	Number of markers	Marker system	Marker data type	Type of analysis	Software package
Complete set	3,364	AFLP	Normalised log-transformed band intensities	Hierarchical clustering	DARWIN 5.0.155
			Normalised log-transformed band intensities	Principal coordinate analysis	DARWIN 5.0.155
Qualitative set	1,772	AFLP	Presence/absence	Hierarchical clustering	DARWIN 5.0.155
Total mapped set	315	AFLP	Presence/absence	Bayesian	STRUCTURE 2.1
			Presence/absence	Hierarchical clustering	DARWIN 5.0.155
Subset total mapped set	229	AFLP	Presence/absence	Principal component analysis	EIGENSOFT 2.0
Equidistant set	103	AFLP	Presence/absence	Bayesian	STRUCTURE 2.1
			Presence/absence	Hierarchical clustering	DARWIN 5.0.155
			Normalised log-transformed band intensities	Hierarchical clustering	DARWIN 5.0.155
			Presence/absence	Principal coordinate analysis	DARWIN 5.0.155
Centromeric set	37	AFLP	Presence/absence	Bayesian	STRUCTURE 2.1
Telomeric set	48	AFLP	Presence/absence	Bayesian	STRUCTURE 2.1
Microsatellite set	53	SSR	Co-dominant	Bayesian	STRUCTURE 2.1
				Hierarchical clustering	DARWIN 5.0.155