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Table 1 Digestibility QTL regions, the significant SNPs, and selected candidate genes in the QTL regions in 2014; the significant SNPs are selected by false discovery rate (FDR) < 0.05

From: Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw

Chromosome (CH)

QTL regions (Mbp)

No of significant SNPs in QTL regions

Most significant p value of SNP in QTL regions

MAFa

R2 (%)b

Candidate genes

1

CH1_29.5 ± 0.2

9

4.92E−08

0.179

22.6

LOC_Os01g51260 (OsMYB26 TF) [79]

LOC_Os01g50720 Homologous to BdMYB48 [80, 81]

2

CH2_2.9 ± 0.2

2

8.04E−05

0.18

13.8

 

CH2_19.2 ± 0.2

2

8.94E−06

0.2

17.3

 

CH2_24.4 ± 0.2

1

5.30E−05

0.13

13.1

 

CH2_28.5 ± 0.2

14

4.06E−08

0.191

25.9

LOC_Os02g46970 (4CL2) [82]; LOC_Os02g46780 (OsMYB58/63 L) [46]

6

CH6_6.2 ± 0.2

1

3.61E−09

0.23

30.0

 

CH6_23.4 ± 0.2

2

1.37E−05

0.23

15.7

LOC_Os06g39470 (BADH)

LOC_Os06g39390 (OsAT10) [16, 43]; LOC_Os06g39970 (CESA11) [83]

7

CH7_26.2 ± 0.2

9

2.78E−09

0.18

27.5

 

CH7_27.5 ± 0.2

12

3.34E−11

0.14

39.1

 

CH7_29.4 ± 0.2

8

2.17E−11

0.14

36.0

Os07g49370 (OsIRX9) [44]:

8

CH8_2.1 ± 0.2

5

8.34E−11

0.18

30.1

 

CH8_26.8 ± 0.2

5

1.30E−08

0.09

26.8

 

CH8_27.3 ± 0.2

3

6.38E−09

0.2

28.3

LOC_Os08g43040 and LOC_Os08g43020(Orthologous to AT5G48930, HCT)

CH8_28.0 ± 0.2

5

4.15E−08

0.17

22.5

 

11

CH11_2.3 ± 0.2

6

2.05E−08

0.16

24.1

 

CH11_4.1 ± 0.2

8

7.51E−06

0.2

15.5

LOC_Os11g07960 (Orthologous to AT5G48930, HCT)

CH11_5.1 ± 0.2

1

3.00E−06

0.18

18.1

 

CH11_6.3 ± 0.2

9

5.56E−07

0.17

19.01

 
  1. aMinimum allele frequency
  2. bPhenotypic variance explained (PVE) by significant SNP