Table 4 Significant SNPs identified for six traits using GEMMA and the modified LASSO method

From: Prediction and association mapping of agronomic traits in maize using multiple omic data

Trait

Method

Chr

Position (kb)

Allele

Candidate gene

Annotation

P-value

R2(%)

CW

GEMMA

2

185 583

A/G

GRMZM2G414252

Putative HLH DNA-binding domain superfamily protein

6.23E−06

7.15

 

GEMMA

7

123 850

T/C

GRMZM2G305406

Unknown

9.60E−06

7.50

 

LASSO

2

59 011

C/T

GRMZM2G412524

Protein kinase G11A-like

0.045

0.59

EW

GEMMA

5

213 292

G/A

GRMZM2G018573

Unknown

6.15E−06

6.35

 

LASSO

8

14 542

G/T

GRMZM2G052869

Metallothionein-like protein 2A

0.046

0.51

RN

GEMMA

1

294 137

C/T

GRMZM2G055834

Unknown

7.12E−06

9.69

 

LASSO

1

1877

C/G

GRMZM2G060265

Scarecrow-like protein 6

0.024

0.76

 

LASSO

1

293 269

G/A

GRMZM2G060702

Actin depolymerizing factor

0.042

0.4

  1. Abbreviations: Chr, chromosome; CW, cob weight; EW, ear weight; GEMMA, genome-wide efficient mixed model association; LASSO, least absolute shrinkage and selection operator; RN, ear row number; SNP, single-nucleotide polymorphism.
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