Skip to main content

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