LD in the entire panel, groups and subgroups at the whole genome level.

aGroups G1 and G2 were classified based on the results of STRUCTURE analysis of the 158 cotton lines.bThe G1 group were further partitioned into G1a, G1b and G1c subgroups, and the G2 group into G2a, G2b, G2c and G2d subgroups. But the G1b, G2a, G2c and G2d subgroups were not included in the analysis due to their small population size.cThe whole set of marker pairs, including linked and unlinked markers pairs.dPairs of markers from different chromosomes.ePairs of markers on the same chromosome.fSignificant threshold is set to P