Table 3.
Gene-set analysis using GWAS of candidates identified within the hotspot genomic regions on chromosomes 5 associated with percent grain chalkiness.
| Gene ID† | SNP start | SNP end | No. of SNPs | Z-Score | P-value‡ | Corrected | Annotations |
|---|---|---|---|---|---|---|---|
| Zhenshan 97 reference | |||||||
| ZS05g0093700 | 4132269 | 4132855 | 10 | 2.49 | 0.0063 | 0.2852 | Unclassified |
| ZS05g0093800 | 4137048 | 4139938 | 24 | 2.39 | 0.0085 | 0.3821 | Reverse transcriptase |
| ZS05g0094700 | 4211463 | 4222967 | 3 | 3.28 | 0.0005 | 0.0236 | Phosphoinositide 3-kinase |
| Newly predicted gene (Chalk 5.1) | 4599233 | 4600542 | 8 | 4.87 | 5.68E−7 | 2.56E−5 | Unclassified |
| ZS05g0110100 | 4624872 | 4627897 | 1 | 2.68 | 0.0036 | 0.1639 | Aspartic peptidase |
| ZS05g0110200 | 4629326 | 4630336 | 1 | 3.84 | 0.0001 | 0.0028 | Unclassified |
| ZS05g0110300 | 4632404 | 4636282 | 1 | 2.92 | 0.0017 | 0.0785 | Der1-like protein |
| ZS05g0110700 | 4657254 | 4678577 | 40 | 2.16 | 0.0155 | 0.6953 | Armadillo-type fold |
| ZS05g0110900 | 4682839 | 4685046 | 2 | 2.45 | 0.0072 | 0.3244 | Ubiquinone biosynthesis protein |
| ZS05g0111000 | 4688129 | 4693152 | 11 | 3.05 | 0.0012 | 0.0521 | Acid phosphatase |
| ZS05g0111100 | 4698217 | 4699046 | 4 | 2.92 | 0.0017 | 0.0781 | Acid phosphatase |
| ZS05g0111200 | 4705604 | 4707744 | 5 | 2.12 | 0.0172 | 0.7729 | Acid phosphatase |
| ZS05g0112300 | 4793937 | 4795814 | 8 | 2.65 | 0.0040 | 0.1814 | Acid phosphatase |
| ZS05g0112500 | 4847621 | 4848943 | 2 | 1.71 | 0.0439 | 1.0000 | FAR1-DNA binding domain |
| ZS05g0112900 | 4878450 | 4879311 | 1 | 2.17 | 0.0150 | 0.6739 | Ulp1-protease-like protein |
| ZS05g0115100 | 5039853 | 5040292 | 1 | 1.82 | 0.0344 | 1.0000 | Unclassified |
| ZS05g0115200 | 5057235 | 5058552 | 2 | 3.01 | 0.0013 | 0.0593 | SANT/Myb domain |
| Minghui 63 reference | |||||||
| MH05g0089300 | 5011370 | 5012335 | 1 | 4.67 | 1.53E−6 | 6.14E−6 | Unclassified |
| MH05g0091000 | 5069302 | 5070093 | 2 | 1.91 | 0.0280 | 0.1120 | DUF protein |
| Nipponbare reference | |||||||
| LOC_Os05g09200 | 5140748 | 5143285 | 1 | 3.97 | 3.57E−5 | 0.0008 | Unclassified |
| LOC_Os05g09220 | 5152077 | 5154824 | 2 | 2.53 | 0.0057 | 0.1262 | Unclassified |
| LOC_Os05g09230 | 5157489 | 5160847 | 4 | 2.19 | 0.0142 | 0.3129 | Unclassified |
| Newly predicted gene (Chalk 5.1) | 5361454 | 5362761 | 8 | 6.41 | 7.23E−11 | 1.59E−9 | Unclassified |
| LOC_Os05g09530 | 5388454 | 5390458 | 4 | 3.80 | 7.38E−5 | 0.0016 | Protein degradation aspartate protease |
| LOC_Os05g09540 | 5391521 | 5392195 | 5 | 4.37 | 6.10E−6 | 0.0001 | Unclassified |
| LOC_Os05g09550 | 5394336 | 5398141 | 8 | 3.55 | 0.0002 | 0.0042 | Protein degradation |
| LOC_Os05g09590 | 5417150 | 5417753 | 15 | 3.72 | 0.0001 | 0.0022 | Unclassified |
| LOC_Os05g09600 | 5419267 | 5420744 | 1 | 4.15 | 1.67E−5 | 0.0004 | Unclassified |
| LOC_Os05g09620 | 5424306 | 5433090 | 26 | 3.51 | 0.0002 | 0.0049 | Unclassified |
†Genes showing the significance of P≤0.05 were included.
‡ P-values are corrected as per Bonferroni corrections.