Table 4.
Summary of association analyses between FGP of F 2:3 seeds and SSR genotypes on chromosome 5
| Locusa | Mirror-map informationb | Segregation testc | Genotype meand | ANOVAe | Genetic effectf | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Marker | Ap | Size (bp) | Mbp | BAC/PAC | cM | A | H | B | χ2 | A | H | B | F | R 2 | Add | Dom | DeD |
| RM5693 | 1 | 200 | 0.46 | OSJNBa0068N01 | 4.6 | 18 | 59 | 17 | 5.4 | 44.4 | 34.2 | 23.6 | 1.6 | ||||
| RM3322 | 1 | 121 | 4.26 | P0685E10 | 32.0 | 31 | 44 | 17 | 3.8 | 52.0 | 30.5 | 13.7 | 8.7 | 0.164 | -19.2 | -2.3 | 0.12 |
| RM3193 | 2 | 126 | 4.97 | P0453H11 | 36.4 | 29 | 48 | 17 | 2.6 | 56.3 | 29.3 | 10.4 | 13.6 | 0.231 | -23.0 | -4.1 | 0.18 |
| RM5844 | 1 | 195 | 9.15 | OSJNBa0032D15 | 53.5 ~ 54.3 | 30 | 40 | 24 | 2.4 | 66.3 | 25.7 | 8.1 | 39.3 | 0.463 | -29.1 | -11.5 | 0.39 |
| RM3838 | 2 | 198 | 16.55 | OSJNBa0077J17 | 60.7 | 28 | 39 | 26 | 2.0 | 63.0 | 26.3 | 15.4 | 21.5 | 0.323 | -23.8 | -12.9 | 0.54 |
| RM6024 | 2 | 178 | 17.81 | OJ1118_F06 | 67.5 | 25 | 41 | 27 | 1.1 | 75.6 | 26.0 | 7.1 | 70.8 | 0.612 | -34.3 | -15.3 | 0.45 |
| RM18614 | 2 | 164 | 19.22 | OSJNBa0014C03 | 73.9 ~ 75.0 | 22 | 51 | 21 | 0.5 | 81.9 | 27.0 | 1.8 | 101.7 | 0.691 | -40.1 | -14.9 | 0.37 |
| RM164 | 2 | 265 | 19.26 | OSJNBa0014C03 | 73.9 ~ 75.0 | 20 | 54 | 20 | 1.7 | 91.6 | 25.5 | 0.4 | 272.0 | 0.857 | -45.6 | -20.5 | 0.45 |
| RM18620 | 3 | 245 | 19.28 | OSJNBb0092G21 | 73.9 ~ 75.0 | 20 | 54 | 20 | 1.7 | 91.6 | 25.5 | 0.4 | 272.0 | 0.857 | -45.6 | -20.5 | 0.45 |
| RM18624 | 3 | 304 | 19.33 | OSJNBb0092G21 | 73.9 ~ 75.0 | 20 | 54 | 20 | 1.7 | 91.6 | 25.5 | 0.4 | 272.0 | 0.857 | -45.6 | -20.5 | 0.45 |
| RM18639 | 3 | 317 | 19.73 | OJ1174_H11 | 75.0 ~ 77.4 | 19 | 53 | 22 | 1.4 | 95.5 | 26.3 | 0.4 | 538.7 | 0.922 | -47.6 | -21.6 | 0.45 |
| RM18648 | 3 | 296 | 19.86 | P0040B10 | 75.0 ~ 77.4 | 18 | 53 | 23 | 1.7 | 95.2 | 27.6 | 1.7 | 290.8 | 0.865 | -46.8 | -20.9 | 0.45 |
| RM1386 | 3 | 197 | 20.06 | P0668F02 | 75.0 ~ 77.4 | 18 | 53 | 23 | 1.7 | 95.2 | 27.6 | 1.7 | 290.8 | 0.865 | -46.8 | -20.9 | 0.45 |
| RM3351 | 1 | 134 | 20.76 | OJ1212_B02 | 80.7 | 20 | 44 | 30 | 2.1 | 77.8 | 31.1 | 9.8 | 49.2 | 0.520 | -34.0 | -12.7 | 0.37 |
| RM5558 | 2 | 173 | 21.25 | OJ1301_G07 | 86.0 | 23 | 40 | 31 | 3.0 | 71.3 | 30.6 | 11.2 | 37.0 | 0.448 | -30.1 | -10.7 | 0.35 |
| RM5642 | 2 | 129 | 22.25 | OJ1126_D01 | 92.0 | 22 | 38 | 33 | 5.1 | 62.4 | 31.9 | 18.4 | 14.2 | 0.240 | -22.0 | -8.5 | 0.38 |
| RM3870 | 2 | 193 | 22.96 | OJ1387_F08 | 95.3 | 23 | 38 | 33 | 5.0 | 65.5 | 29.7 | 17.6 | 19.5 | 0.300 | -24.0 | -11.9 | 0.50 |
| RM3476 | 1 | 132 | 23.91 | OJ1004_E02 | 101.0 | 18 | 46 | 30 | 2.6 | 62.8 | 35.6 | 15.0 | 14.3 | 0.239 | -23.9 | -3.3 | 0.14 |
| RM7653 | 2 | 121 | 27.42 | OSJNBa0079H23 | 111.6 | 18 | 43 | 33 | 4.8 | 52.1 | 31.7 | 27.7 | 3.4 | 0.069 | -12.2 | -8.1 | 0.67 |
| RM1054 | 1 | 150 | 29.23 | OJ1007_H05 | 122.0 | 23 | 41 | 30 | 2.2 | 49.8 | 28.1 | 30.6 | 3.4 | 0.069 | -9.6 | -12.1 | 1.26 |
aDNA markers were tested in 94 F2 progenies derived from Suweon 542/Milyang 23. After conducting a first round of association analyses over well-defined 6 anchor markers (application: Ap = 1), an additional 9 SSR markers (Ap = 2) were applied to narrow down the putative location responsible for the floury endosperm characteristics on chromosome 5. Five SSR markers (Ap = 3) were further applied to localize the flo7(t) nearby a BAC lone OJ1174_H11 (BenBank Acc. = AC104708.2), tagged by a SSR marker, RM18639.
bThe expected PCR product size inferred by e-Landings on a reference rice genome, ‘Os-Nipponbare-Reference-IRGSP-1.0’ (http://rapdb.dna.affrc.go.jp/download/%irgsp1.html). The cM position was directly adopted from the IRGSP Build5 Pseudomolecules (http://rgp.dna.affrc.go.jp/E/%IRGSP/Build5/build5.html) according to the locations of BAC/PAC clones harboring priming sites for each SSR marker.
cA and B are homozygous for Suweon 542 and Milyang 23 allele types, respectively, and H indicates heterozygous progenies at the tested locus. All χ2 values for the segregation distortion test were not significant at P < 0.05.
dMean floury grains percentage (FGP) for each genotype category revealed by the SSR markers.
eSingle-locus ANOVA to test associations between SSR marker genotypes and FGP. For the F-test, markers having less than 0.05 for significance were declared as significant empirically (*P < 0.05 and ***P < 0.001). The explainable variation portion of FGP at the tested locus (R2) is also shown.
fAdditive effect (Add), dominance effect (Dom), and degree of dominance (DeD) were estimated for the significant loci: Add = (B mean – A mean) / 2, Dom = H mean – (B mean + A mean) / 2, and DeD = Dom / Add, where A and B are homozygous F2 individuals for Suweon 542 and Milyang 23 while H is heterozygous individuals at the tested locus.