Table 2. Genetic diversity within the low copy regions surrounding Y1.
| Region | Test set | n | S | π (×10−3) | Θw (×10−3) | D |
|---|---|---|---|---|---|---|
| STK* | All | 73 | 9 | 4.0 (0.45) | 3.2 (1.3) | 0.66 |
| Yellow/orange | 40 | 9 | 3.7 (0.55) | 3.5 (1.5) | 0.17NS | |
| White | 33 | 8 | 4.1 (0.73) | 3.3 (1.5) | 0.74NS | |
| PCO131338 | All | 75 | 8 | 8.0 (0.72) | 6.6 (2.8) | 0.55NS |
| Yellow/orange | 41 | 4 | 6.3 (0.27) | 3.7 (2.1) | 1.7NS | |
| White | 34 | 8 | 7.5 (1.3) | 6.8 (3.0) | 0.31NS | |
| LCBE1† | All | 75 | 4 | 1.4 (0.31) | 3.3 (1.8) | −1.2NS |
| Yellow/orange | 41 | 2 | 0.91 (0.34) | 1.9 (1.4) | −0.96NS | |
| White | 33 | 3 | 1.6 (0.37) | 2.6 (1.6) | −0.85NS | |
| YI* | All | 73 | 89 | 8.4 (0.70) | 6.2 (1.7) | 1.0NS |
| Yellow/orange | 40 | 28 | 0.54 (0.27) | 1.7 (0.58) | −2.4** | |
| White | 33 | 84 | 10.2 (0.56) | 7.0 (2.2) | 1.6NS | |
| MLO‡ | All | 72 | 9 | 7.8 (0.71) | 5.2 (2.1) | 1.3NS |
| Yellow/orange | 40 | 9 | 3.9 (1.1) | 4.7 (2.0) | −0.49NS | |
| White | 32 | 9 | 8.6 (0.72) | 6.3 (2.7) | 1.1NS | |
| LCBE2§ | All | 72 | 9 | 8.7 (1.6) | 7.7 (0.01) | 0.35NS |
| Yellow/orange | 40 | 1 | 1.8 (0.22) | 0.95 (0.0009) | 1.3NS | |
| White | 32 | 9 | 14.6 (0.0032) | 9.3 (0.017) | 1.8NS | |
| LC1 | All | 75 | 7 | 3.4 (0.95) | 5.5 (2.4) | −0.91NS |
| Yellow/orange | 41 | 0 | NA | NA | NA | |
| White | 34 | 7 | 6.5 (1.3) | 6.4 (3.0) | 0.06NS | |
| LCBE3 | All | 75 | 48 | 21.1 (4.8) | 24.9 (7.2) | −0.61NS |
| Yellow/orange | 41 | 1 | 1.3 (0.04) | 0.59 (0.59) | 1.7NS | |
| White | 34 | 47 | 37.4 (5.8) | 29.2 (9.6) | 0.83NS | |
| sbe 1¶ | All | 73 | 5 | 2.9 (0.36) | 3.2 (1.6) | −0.16NS |
| Yellow/orange | 40 | 2 | 2.3 (0.43) | 1.4 (1.1) | 1.1NS | |
| White | 33 | 5 | 3.6 (0.55) | 3.7 (1.9) | 0.051NS | |
| cyc3 | All | 73 | 8 | 4.2 (0.29) | 3.8 (1.6) | 0.29NS |
| Yellow/orange | 40 | 5 | 4.0 (0.22) | 2.6 (1.3) | 1.4NS | |
| White | 33 | 7 | 2.7 (0.49) | 3.7 (1.7) | −0.76NS |
n, number of sequences analyzed; S, number of segregating sites; π, nucleotide diversity per site; Θw, Watterson's estimator; and Tajima's D values are listed for all germplasm analyzed as well as separately for white and yellow germplasm. SD are shown in parentheses. Estimates are based on all nucleotide sites. NA, not applicable. NS, not significant; *, P > 0.10; **, P < 0.001; Θw was calculated by using no recombination assumption (more conservative).
One orange/yellow endosperm line, Ames24575, and one white endosperm line, PI595547, were excluded due to missing data.
One white endosperm line, Ames 22026, was excluded from analysis because it had a 201-bp deletion in the analyzed area.
PI59559, PI595547, and W45 were excluded due to heterozygous polymorphic loci.
Stock6, PI595547, and PI595559 were excluded due to heterozygous polymorphic loci.
PI595547 and PI595559 were excluded due to heterozygous polymorphic loci.