Table 2. SNPs identified in the MED genes associated with grain size traits in rice.
| OsMEDgenes | MSU locusIDs | Chromosomes | AssociatedSNPs | Physicalpositions(bp) | Minor allelefrequency(MAF %) | Functionalsignificanceof SNPs | Encoded aminoacid | P-value | PVE(R2%) | Associated grainsize traits |
|---|---|---|---|---|---|---|---|---|---|---|
| OsMED9_1 | LOC_Os01g31629 | Oschr01 | (C/G) | 17320769 | 17 | Intron | – | 1.7 × 10−5 | 21 | GWg |
| OsMED11_1 | LOC_Os02g09600 | Oschr02 | (G/A) | 4940189 | 15 | Non-Synonymous coding | Threonine (ACG)/Methionine (ATG) | 1.7 × 10−6 | 25 | GL and GWg |
| OsMED37_3 | LOC_Os03g16860 | Oschr03 | (A/G) | 9369204 | 16 | URR | – | 1.1 × 10−5 | 18 | GWi and GWg |
| OsMED15_1 | LOC_Os04g03860 | Oschr04 | (G/A) | 1754571 | 18 | Non-Synonymous coding | Glycine(GGG)/Arginine (AGG) | 0.8 × 10−5 | 17 | GL and GWg |
| OsMED5_3 | LOC_Os07g48350 | Oschr07 | (G/A) | 28899486 | 20 | Non-Synonymous coding | Alanine (GCG)/Threonine (ACG) | 1.5 × 10−5 | 20 | GWg and GWi |
| OsMED14_1 | LOC_Os08g24400 | Oschr08 | (G/T) | 14736149 | 18 | URR | – | 2.1 × 10−5 | 15 | GL and GWg |
| OsMED25_1 | LOC_Os09g13610 | Oschr09 | (T/A) | 7912591 | 26 | URR | – | 1.3 × 10−6 | 28 | GL and GWg |
| OsMED20_1 | LOC_Os09g27140 | Oschr09 | (A/G) | 16507513 | 21 | Non-Synonymous coding | Phenylalanine (TTC)/Leucine (CTC) | 0.9 × 10−7 | 26 | GL, GWi and GWg |
| OsMED12_2 | LOC_Os10g40260 | Oschr 10 | (G/C) | 21503285 | 22 | Non-Synonymous coding | Valine (GTT)/Leucine (CTT) | 1.1 × 10−5 | 24 | GL and GWg |
| OsMED4_2 | LOC_Os11g05150 | Oschr11 | (C/T) | 2260577 | 24 | Non-Synonymous coding | Glutamic acid (GAG)/Lysine(AAG) | 0.3 × 10−8 | 33 | GL, GWi and GWg |
GL: Grain Length, GWi: Grain Width and GWg: 1000-Grain Weight, PVE: Phenotypic Variation Explained and URR: Upstream Regulatory Region.