Figure 1.
Plots of the first three principal components derived from a principal component analysis (PCA) of 263 alfalfa genotypes using SNP markers generated on an Infinium array, with (a) PC1 vs. PC2 and (b) PC2 vs. PC3.
(C1: diploid subsp. falcata, C2: diploid subsp. caerulea, C3: miscellaneous tetraploid alfalfa, C4: dormant and semi-dormant tetraploid subsp. sativa, and C5: semi-dormant and non-dormant tetraploid subsp. sativa)
Table 1.
The number of individual plants evaluated of the standard fall dormancy and winter hardiness check cultivars and the number that were assigned to either cluster 4 (C4) or cluster 5 (C5).
Table 2.
The number of individual plants evaluated for each of five breeding populations developed from non-dormant germplasm and the number of each population that were assigned to a particular cluster.
Table 3.
Pairwise genetic distances among five clusters of alfalfa genotypes based on SNP markers generated by the Infinium array.
Figure 2.
Neighbor-joining tree among 21 alfalfa cultivars and breeding populations based on SNP markers generated from an Infinium array.
The fall dormancy (FD) classifications of the cultivars, which include standard check cultivars for fall dormancy and winter hardiness, are indicated on a scale of FD = 1 as very dormant to FD = 11 as very non-dormant.
Figure 3.
The number of polymorphic SNPs within and between four clusters developed based on a model-based clustering analysis.
Cluster 3, which included only six genotypes, was omitted from the analysis.
Figure 4.
Genome-wide linkage disequilibrium patterns within clusters and populations.
(C1: diploid subsp. falcata, C2: diploid subsp. caerulea, C4: dormant and semi-dormant tetraploid subsp. sativa, and C5: semi-dormant and non-dormant tetraploid subsp. sativa)
Figure 5.
Correlation of LD values between pairs of SNP markers grouped based on three different physical distances apart and plotted as a function of genetic distances between clusters and breeding populations being correlated.