Extended Data Fig. 9: Recombination rate distribution in G. hirsutum and inheritance of haplotype blocks in two breeding populations.
a, Recombination rate distribution between A and D subgenomes. The recombination bins are based on overlapping 5-Mb windows. The dashed grey lines indicate 50% of individuals recombined in the window. The pale blue polygons link syntenic regions. The x axis is scaled independently for each homoeologous chromosome. b, Linkage disequilibrium heatmap of chromosome A08 of the G. hirsutumXG. mustelinum BC2F1 population. Genotypes of 18 lines each representative of one family, two parents, and F1 are shown using the CottonSNP63K array (top panel). Red, yellow, and blue colors show the genotypes homozygous for G. hirsutum, homozygous for G. mustelinum, and heterozygous for both species, respectively. Heatmap (bottom panel) consists of equidistant tiles that indicate linkage disequilibrium as determined by a normalized coefficient of linkage disequilibrium (D’) between pairs of markers. Markers corresponding to SNP positions above the heatmap are congruent to the introgressed genotypes (x axis). c, Linkage disequilibrium heatmap of chromosome A08 of the G. hirsutumXG. tomentosum BC3F1 population. Genotypes of 33 lines each representative of one family, two parents, and F1 are shown using the CottonSNP63K array (top panel). Red, yellow, and blue colors show the genotypes homozygous for G. hirsutum, homozygous for G. tomentosum, and heterozygous for both species, respectively. Heatmap (bottom panel) consists of equidistant tiles that indicate linkage disequilibrium as determined by a normalized coefficient of linkage disequilibrium (D’) between pairs of markers. Markers corresponding to SNP positions above the heatmap are congruent to the introgressed genotypes (x axis).
