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Table 4 Summary of association analyses between FGP of F 2:3 seeds and SSR genotypes on chromosome 5

From: Agronomic and genetic analysis of Suweon 542, a rice floury mutant line suitable for dry milling

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
  1. 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.
  2. 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.
  3. 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.
  4. dMean floury grains percentage (FGP) for each genotype category revealed by the SSR markers.
  5. 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.
  6. 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.