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Table 3 Results for SNP loci with root traits and consistent candidate genes jointly identified by association and RNA-Seq

From: Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

         

Candidate genes based on RNA-Seqc

 

Trait

SNP

Chr

Positiona

P

Alleles

R2 (%)

Geneb

Reference

Annotation

Fold change

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048998

Mu et al. 2017 [21]

Chlorophyll a-b binding protein CP26

−2.03939

Crossings

PZE-104092320

4

167,437,768

4.7 × 10−5

A/G

1.8

Zm00001d051804

Luo et al. 2015 [22]

Glutamine synthetase root isozyme 4

1.65671

Forks

PZE-104043052

4

61,411,237

6.5 × 10− 5

A/C

11

Zm00001d049995

Nitrate reductase [NADH]

−2.39002

Crossings

PZE-104092320

4

167,437,768

4.7 × 10−5

A/G

1.8

Zm00001d051666

Zanin et al. 2015 [23]

Neutral/alkaline invertase

1.83246

PRL

ZM005894–0463

4

31,060,531

5.6 × 10−5

A/C

9.9

Zm00001d049380

Putative aminotransferase superfamily protein

0.66934

CRN

PZE-104016717

4

16,500,659

5.2 × 10−5

A/G

11

Zm00001d049059

He et al. 2016 [24]

Alcohol dehydrogenase2

0.766936

Tips

PZE-104049074

4

75,505,829

5.2 × 10−5

A/G

8.7

Zm00001d050195

WRKY DNA-binding domain protein

−0.795948

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048866

(Z)-3-hexen-1-ol acetyltransferase

1.07489

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048736

S-alkyl-thiohydroximate lyase SUR1

−0.576864

CRN

PZE-105047147

5

36,470,371

6.1 × 10−5

A/G

13

Zm00001d014200

Expressed protein

0.402627

Forks

PUT-163a-91,875,212-4781

5

7,724,698

5.9 × 10−5

A/G

10

Zm00001d013263

Expressed protein

1.51149

Forks

PZE-104043052

4

61,411,237

6.5 × 10−5

A/C

11

Zm00001d050092

Zhang et al. 2015 [25]

Putative subtilase family protein

0.585778

Forks

PZE-104043052

4

61,411,237

6.5 × 10−5

A/C

11

Zm00001d049990

Putative ENTH/ANTH/VHS protein

1.38056

PRL

ZM005894–0463

4

31,060,531

5.6 × 10−5

A/C

9.9

Zm00001d049554

Putative glycerol-3-phosphate transporter 1

−0.807844

PRL

ZM005894–0463

4

31,060,531

5.6 × 10−5

A/C

9.9

Zm00001d049551

Putative cytochrome P450 protein

2.50626

PRL

ZM005894–0463

4

31,060,531

5.6 × 10−5

A/C

9.9

Zm00001d049502

maternal effect embryo arrest 60

0.542646

PRL

ZM005894–0463

4

31,060,531

5.6 × 10−5

A/C

9.9

Zm00001d049464

B-box type zinc finger family protein

0.980937

PRL

ZM005894–0463

4

31,060,531

5.6 × 10−5

A/C

9.9

Zm00001d049418

Germin-like protein subfamily 1 member 8

1.11388

PRL

ZM005894–0463

4

31,060,531

5.6 × 10−5

A/C

9.9

Zm00001d049407

Polyphenol oxidase chloroplastic

−0.61096

PRL

ZM005894–0463

4

31,060,531

5.6 × 10−5

A/C

9.9

Zm00001d049365

Methionine aminopeptidase

0.319478

CRN

PZE-104016717

4

16,500,659

5.2 × 10−5

A/G

11

Zm00001d049187

Phosphogluconate dehydrogenase3

−1.54203

CRN

PZE-104016717

4

16,500,659

5.2 × 10−5

A/G

11

Zm00001d049158

Transcription factor bHLH62

1.27949

CRN

PZE-104016717

4

16,500,659

5.2 × 10−5

A/G

11

Zm00001d049127

Putative serine/threonine protein

−0.848596

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048979

Putative sucrose-phosphate synthase protein

2.06952

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048925

Hydroquinone glucosyltransferase

1.25909

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048901

Transcription factor bHLH47

2.69849

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048843

Math-btb9

1.16984

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048795

SPR1

1.27812

Forks

PZE-104010552

4

7,929,588

5.0 × 10−5

A/G

8.9

Zm00001d048709

benzoxazinless1

−5.53653

Forks

PZE-110109365

10

148,503,798

4.7 × 10−5

A/G

7.5

Zm00001d026605

Endoglucanase 5

−5.62458

Forks

PZE-110108403

10

148,106,661

5.4 × 10−5

A/C

8.9

Zm00001d026603

Mg chelatase subunit H 1

0.836012

Forks

PZE-110108403

10

148,106,661

5.4 × 10−5

A/C

8.9

Zm00001d026573

Methylthioribose kinase

−1.75366

Forks

PZE-110108403

10

148,106,661

5.4 × 10−5

A/C

8.9

Zm00001d026542

Myb family transcription factor PHL5

−4.47132

CRN

PZE-105047221

5

36,532,569

5.6 × 10−5

A/G

11

Zm00001d014555

Tyrosine-sulfated glycopeptide receptor 1

−1.98805

Forks

PUT-163a-91,875,212-4781

5

7,724,698

5.9 × 10−5

A/G

10

Zm00001d013287

–

0.957732

Forks

PUT-163a-91,875,212-4781

5

7,724,698

5.9 × 10−5

A/G

10

Zm00001d013269

Beta-glucanase3

−0.88007

Crossings

PZE-104092320

4

167,437,768

4.7 × 10−5

A/G

1.8

Zm00001d051829

U-box domain-containing protein 44

0.605786

Crossings

PZE-104092320

4

167,437,768

4.7 × 10−5

A/G

1.8

Zm00001d051692

Aspartyl protease AED1

0.609318

Crossings

PZE-104092320

4

167,437,768

4.7 × 10−5

A/G

1.8

Zm00001d051664

2OG and Fe (II)-dependent superfamily protein

0.924731

Crossings

PZE-104092320

4

167,437,768

4.7 × 10−5

A/G

1.8

Zm00001d051598

Plant-specific domain TIGR01570 protein

1.82658

  1. a The physical position of significant SNPs were based on the Maize B73 RefGen_v3. b The Genes were screened near these significantly associated SNP markers. c The candidate genes were identified by combining with RNA-Seq and previous studies, the expression (Log2(fold change)) based on us RNA-Seq