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Table 4 Marker–trait associations with –LogP value ≥ 3.0, their equivalent false discovery rate (FDR), proportion of phenotypic variance explained (PVE), and the average allele effects (AAE) across five environments for GT (ASS), GC and AC traits

From: Favorable alleles mining for gelatinization temperature, gel consistency and amylose content in Oryza sativa by association mapping

Traits

No.

SSR marker

Chr.

position (bp)a

Environment

-LogP

FDR

PVE(%)

AAEb

GT

1

RM232

3

8409404-8410886

E4

3.48

0.0022

9.74

0.80

2

RM267

5

21881317-21881455

E3

3.48

0.0023

7.04

0.66

3

RM264

8

27926632-27926652

E1

3.60

0.0024

7.43

1.16

4

RM3600

9

17107752-17107843

E2

4.92

0.0029

10.12

1.38

GC

1

RM6712

3

35020004-35020027

E2

3.30

0.0042

7.46

16.60

2

RM5753

6

30452023-30452067

E4

3.20

0.0028

10.54

20.52

AC

1

RM6712

3

35020004-35020027

E1

4.27

0.0022

8.83

-3.57

E2

3.66

0.0022

7.89

-4.56

E3

3.22

0.0019

7.17

-4.87

E5

3.17

0.0020

7.17

-4.76

2

RM5753

6

30452023-30452067

E2

3.08

0.0065

10.48

-3.66

3

RM258

10

17570591-17570612

E1

3.04

0.0043

5.69

-5.28

4

RM6327

11

364257-364310

E2

3.09

0.0043

12.87

-2.66

E3

3.19

0.0038

11.39

-2.75

  1. Bold markers represent that they were associated with two traits
  2. aThe estimated physical position (bp) was inferred from the Gremene (http://www.gramene.org/markers) and NCBI (https://www.ncbi.nlm.nih.gov/Blast.cgi)
  3. bAverage positive allele effects of SSR loci associated significantly with GT and GC traits, average negative allele effects of SSR loci associated significantly with AC trait