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Table 2 SNPs and corresponding candidate genes associated with plant height (PH), stalk diameter (SD), rind thickness (RT), and vascular bundle density (BD)

From: Genome-wide association analysis of stalk biomass and anatomical traits in maize

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)
  1. 1Values after “rs” and “_” represent SNP chromosome number and physical position (bp), respectively
  2. 2SNPs upstream and downstream of candidate genes are specified with “–” and “+”, respectively. “0” indicates that SNPs are located within corresponding candidate gens
  3. 3Significance according to the Bonferroni genomic threshold (−log(p) = 7.55)
  4. 4Values not specified with “*” were above the –log(p) = 4 threshold but did not reach the Bonferroni genomic threshold