Table 1. Overview of intra-chromosomal LD in the whole genome and in the three genomes in the entire population.

	Marker pairs total	No. and ratea of significant (p<0.05) marker pairs (%)	Mean r2 of all marker pairs	critical r2	No and rateb of linked marker pairs (%)	No of marker pairs in perfect LD
A genome	106,384	29,405 (27.6%)	0.062	0.342	3,604 (12.2%)	971
B genome	209,186	78,450 (37.5%)	0.102	0.389	14,476 (18.5%)	3,785
D genome	21,010	10,543 (50.2%)	0.221	0.335	5,295 (50,2%)	855
Population	336,580	118,398 (35.2%)	0.097	0.372	23,084 (19.5%)	5,611

linked pairs: r²>critical r², perfect LD: r² = 1 and D’ = 1

^a the percentage of total marker pairs which were significant (p<0.05)

^b the percentage of significant marker pairs which had greater r² than the critical r²