Table 3.

Summary of genome-wide linkage disequilibrium analysis

Market class	No. marker pairsa	r2 estimatesb				Linkage disequilibrium decay (cM)e
		Median	St. Dev.	95th percentilec	P <0.01d	LOESSf		Moving meansg
						95th percentile method	Fixed r2 (0.1) method	95th percentile method	Fixed r2 (0.1) method
Combinedh	5248	0.011	0.102	0.160	8.1%	6.6	8.0	6	6
Processing	3294	0.037	0.131	0.248	5.5%	6.9	14.2	6	9
Fresh market	2622	0.031	0.187	0.464	2.0%	3.0	16.1	2	10

^aThe number of marker pairs includes only markers polymorphic within each market class.

^bLinkage disequilibrium was estimated as r² values for all possible marker pairs using TASSEL (Bradbury et al., 2007) and GGT (van Berloo, 2008) software.

^cThe 95th percentile of the distribution of r² values for the unlinked markers. This value is the baseline r² to estimate LD decay.

^dPercentage of r² estimates with P value <0.01. P values of r² estimates were calculated from 1000 permutations using TASSEL software (Bradbury et al., 2007).

^eLinkage disequilibrium decay was estimated over genetic distance by the relationship of a baseline r² estimate to linked marker pairs using two methods, LOESS and 1 cM moving means. The baseline r² value was either fixed at 0.1 or estimated using the 95th percentile of the unlinked markers. Values for r² that exceed the baseline are considered to be in linkage disequilibrium.

^fFor the LOESS estimation of LD decay, genetic distance was estimated as the point where the LOESS curve first crosses the baseline r² value.

^gFor the means estimation of LD decay, the r² values of linked markers were grouped into bins of 1 cM based on the distance between markers. LD decay was estimated as the first bin where the baseline r² value was lower than the bin mean.

^hThe combined analysis includes processing, fresh market, and vintage cultivars.