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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