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Sequence Diversity of Puroindoline-a, Puroindoline-b, and the Grain Softness Protein Genes in Aegilops tauschii Coss

^a Dep. of Crop & Soil Sciences, Washington State Univ., Pullman, WA 99164-6394
^b USDA-ARS Western Wheat Quality Lab., E-202 Food Sci. & Human Nutrition East, Washington State Univ., Pullman, WA 99164-6394
^c Dep. of Plant Pathology, Kansas State Univ., Manhattan, KS 66506-5502

View larger version (17K): [in a new window]   Fig. 1. Gene genealogy of Pinb-D1 (A), Pina-D1 (B), and Gsp-D1(C) for 50 Aegilops tauschii accessions using the statistical parsimony reconstruction method, as implemented by TCS version 1.13. All branches represent a single mutational change. Haplotypes are indicated by the alleles. The haplotypes with the highest outgroup probability are displayed as squares. The size of squares and ovals correspond to the haplotype frequency. Small, unlabeled ovals represent haplotypes inferred from mutational changes, but absent in this data set.

View larger version (36K): [in a new window]   Fig. 2. Comparative analysis of the deduced amino acid sequences of Puroindoline-a, -b and Grain Softness Protein-1 from Ae. tauschii and the wild-type ‘a’ alleles of T. aestivum. A dot (.) shows identity with the first sequence. Underlined amino acids indicate synonymous substitutions relative to the wild-type. Double underlined amino acids indicate synonymous and nonsynonymous substitutions.

View larger version (21K): [in a new window]   Fig. 3. Sliding window analysis of overall polymorphic sites across loci. Abscissa indicates nucleotide position. Ordinate indicates nucleotide diversity between Ae. tauschii alleles (Pi) and divergence between Ae. tauschii and T. urartu (K) as estimated by the Jukes and Cantor (1969) correction.

View larger version (98K): [in a new window]   Fig. 4. Linkage disequilibrium estimates for Pina-D1, Pinb-D1, and Gsp-D1 from Aegilops tauschii. Estimates consider only the 41 polymorphic sites that were present in at least 5% of the accessions examined (nucleotide site numbers are listed down the left-hand side and across the top, and are arranged according to the concatenated three-gene model). The lower left of the black-square diagonal indicates the significance level of each pair-wise comparison as determined by the Fisher's exact test (color code appears in the lower right as "Lower P value"). The upper right of the black-square diagonal indicates the correlation (r2) between the 41 pairs of polymorphic sites (color code appears in the upper right as "Upper R2"). At the bottom of the figure is a display of the polymorphic sites along the concatenated three genes.