Table 2 SNPs significantly associated with stover saccharification efficiency (SACC) and stover yield, including the QTL interval, p-value for the association between the SNP and the phenotype, additive effect for the SNP (across years, 2016, 2017), parental lines alleles, minor and major frequency alleles and favourable allele.

From: Association mapping for maize stover yield and saccharification efficiency using a multiparent advanced generation intercross (MAGIC) population

Trait a

SNPb

Binc

QTL interval

P-valued

R2

Add effect e

Add effect 2016 f.

Add effect 2017 g

A509

EP125

EP17

EP43

EP53

EP86

F473

PB130

Minor

Major

Effect ( +)

Stover Yield

S1_24739947

1.02

 ± 500 kbp

1.14E−09

0.001

0.16**

0.03

0.31*

C

T

N

C

C

C

C

C

40

180

Minor (T)

Stover Yield

S1_5087216

1.01

 ± 100 kbp

6.64E−07

0.04

0.46***

0.46**

0.41**

G

G

G

G

G

G

C

G

29

224

Minor (C)

Stover Yield

S2_23558946

2.03

 ± 700 kbp

2.54E−06

0.03

0.46**

0.36

0.64**

G

G

N

N

G

N

N

G

13

198

Minor (T)

Stover Yield

S2_42097780

2.04

 ± 1.2 Mbp

1.96E−08

0.02

0.34**

0.31*

0.10

T

C

T

C

C

C

C

N

15

204

Minor (T)

Stover Yield

S3_40940154

304

 ± 2Mbp

1.07E−06

0.03

0.49**

0.47*

0.39

A

G

N

A

A

A

A

A

20

184

Major (A)

Stover Yield

S3_143233104

3.05

 ± 1.5 Mbp

1.50E−07

0.07

0.53***

0.47***

0.48***

C

N

N

C

C

G

C

G

62

248

Minor (G)

Stover Yield

S3_175552327

3.06

 ± 300 kbp

1.05E−06

0.04

0.46**

0.48*

0.29

G

A

G

N

G

A

A

G

14

162

Minor (A)

Stover Yield

S4_150637846

4.05

 ± 600 kbp

4.29E−08

0.04

0.56**

0.61**

0.29

G

G

N

N

G

N

N

G

16

177

Minor (A)

Stover Yield

S5_67669376

5.03

 ± 700 kbp

3.90E−07

0.04

0.38**

0.49***

0.23

C

C

A

C

C

N

C

C

47

168

Minor (A)

Stover Yield

S5_194837018

5.05

 ± 700 kbp

1.84E−08

0.05

0.37***

0.35**

0.33**

T

T

T

G

G

G

G

T

85

129

Minor (T)

Stover Yield

S7_100264894

7.02

 ± 800 kbp

7.32E−09

0.02

0.25**

0.28**

0.20

G

G

C

C

C

C

C

G

105

153

Major (C)

Stover Yield

S8_152321302

8.06

 ± 900 kbp

8.00E−08

0.06

0.40***

0.41***

0.33**

C

C

C

A

A

A

A

C

72

167

Minor (A)

Stover Yield

S10_141557921

10.06

 ± 100 Kbp

6.32E−07

0.07

0.42***

0.25*

0.41***

N

G

N

G

G

G

N

G

78

99

Major (G)

SACC

S6_163628712

6.07

 ± 100 Kbp

6.04E−06

0.09

3.11***

1.50*

4.14***

A

T

N

N

A

T

N

T

102

105

Minor (T)

SACC

S6_163830244

6.07

 ± 100 Kbp

3.97E − 06

0.08

2.90***

2.22***

2.90*

C

C

C

C

N

C

C

T

116

119

Major (T)

  1. *p < 0.05.
  2. **p < 0.01.
  3. ***p < 0.001.
  4. aSACC Saccharification efficiency.
  5. bThe number before the underscore indicates the chromosome number and the number after the underscore indicates the physical position in bp within the chromosome.
  6. cA bin is the interval that includes all loci from the leftmost or top Core Marker to the next Core Marker. The genetic maps are divided into 100 segments of approximately 20 centiMorgans designated with the chromosome number followed by a two-digit decimal.
  7. dp-value obtained in FarmCPU.
  8. e,f,gThe Additive ffect Add effect)—combined (e), 2016 (f) and 2017 (g), ): was calculated in TASSEL as half the difference between the mean of the homozygous for the allele with the largest value and the mean of the homozygous for the allele with the smallest value.
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