Table 2.
SNPs and corresponding candidate genes associated with plant height (PH), stalk diameter (SD), rind thickness (RT), and vascular bundle density (BD)
| Trait | SNP ID | MAF | -log(p) | Effect size (%) | Gene containing the SNP | Candidate gene | SNP position relative to the candidate gene2 | Candidate gene annotation |
|---|---|---|---|---|---|---|---|---|
| PH | rs9_1192487651 | 0.14 | 17.15*3 | 4.31 | Zm00001d047117 | Zm00001d047121 | −24.05 kb | NAD-dependent protein deacetylase Srt2 (Regulatory gene) |
| PH SD | rs3_160558889 | 0.23 0.24 | 14.34* 4.104 | 3.19 2.13 | Zm00001d042314 | Zm00001d042315 (Zmm22) | −32.60 kb | MADS box transcription factor 69 (Regulatory gene) |
| PH | rs9_141541062 | 0.37 | 10.83* | 2.23 | Zm00001d047779 | Zm00001d047780 | −26.53 kb | ABC transporter (Auxin transporter) |
| PH | rs8_145826594 | 0.49 | 8.06* | 1.67 | Zm00001d011285 (Lhcb1) | Zm00001d011285 (Lhcb1) | 0 | Light harvesting chlorophyll protein 1 (Photosynthesis related) |
| SD BD | rs8_1453700352 | 0.25 0.23 | 12.67*3 6.32 | 3.83 2.60 | Zm00001d011272 | Zm00001d011272 | 0 | CASC3/Barentsz eIF4AIII binding (Regulatory gene) |
| SD | rs5_189094902 | 0.20 | 11.83* | 4.25 | Zm00001d017213 | Zm00001d017213 | 0 | DUF 4378 |
| SD | rs9_15314439 | 0.19 | 9.25* | 3.40 | Zm00001d045179 | Zm00001d045180 | −8.26 kb | Cdk-activating kinase assembly factor MAT1 (Cell division regulator) |
| SD PH | rs7_145418275 rs7_145449766 | 0.29 0.50 | 8.64* 5.24 | 2.98 1.29 | Zm00001d021188 (Fpa ortholog) Zm00001d021192 | Zm00001d021188 (Fpa ortholog) | 0 + 31.23 kb |
Flowering time control protein (Regulatory gene) |
| SD | rs2_204222535 | 0.11 | 8.07* | 4.25 | Zm00001d006308 | Zm00001d006308 | 0 | Protein kinase (Regulatory gene) |
| SD | rs7_178139632 | 0.05 | 8.05* | 5.53 | Zm00001d022460 | Zm00001d022460 | 0 | Pectinesterase (Cell wall biosynthesis) |
| SD | rs1_191586515 | 0.40 | 7.95* | 2.55 | Zm00001d031485 | Zm00001d031485 | 0 | Cdc2 cell division control protein (Cell division regulator) |
| SD | rs1_192993003 | 0.10 | 7.69* | 3.83 | Zm00001d031531 | Zm00001d031531 | 0 | DUF1666 |
| RT PH | rs5_148922178 rs5_148941136 | 0.06 0.19 | 7.55* 4.58 | 6.25 1.62 | Zm00001d016181 Zm00001d016182 | Zm00001d016181 | 0 + 16.22 kb |
Glucuronosyltransferase (Cell wall biosynthesis) |
| BD | rs5_7499864 | 0.20 | 11.10* | 4.05 | Zm00001d013267 (Tlk2) | Zm00001d013267 (Tlk2) | 0 | TOUSLED- like kinase 2 (Cell division regulator) |
| BD | rs1_61042634 | 0.08 | 10.43* | 5.69 | Zm00001d029177 (Nsn1 ortholog) | Zm00001d029177 (Nsn1 ortholog) | 0 | Nucleolar GTP-binding protein 2 (Regulatory gene) |
| BD | rs9_2777619 | 0.22 | 8.05* | 3.30 | Zm00001d044802 (Rop5) | Zm00001d044802 (Rop5) | 0 | Rop family GTPase (Regulatory gene) |
1Values after “rs” and “_” represent SNP chromosome number and physical position (bp), respectively
2SNPs upstream and downstream of candidate genes are specified with “–” and “+”, respectively. “0” indicates that SNPs are located within corresponding candidate gens
3Significance according to the Bonferroni genomic threshold (−log(p) = 7.55)
4Values not specified with “*” were above the –log(p) = 4 threshold but did not reach the Bonferroni genomic threshold