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Table 1 Significantly associated loci for sheath blight resistance in rice based on a genome-wide association study

From: Genome-Wide Association Analysis of the Genetic Basis for Sheath Blight Resistance in Rice

SAL ID Chr. LD block interval (bp) LD block size (kb) No. of suggestive SNPs in LD block Panel Lead SNP position (bp) Lead SNP P value MSU ID of genes harboring lead SNP QTL/Marker/Gene previously reported
L1 1 23,999,888–23,999,975 0.1 1 Whole 23,999,975 1.3E-08 LOC_Os01g42294-LOC_Os01g42310  
L2 1 25,337,514–25,449,724 112.2 1 Whole 25,350,468 6.8E-08 LOC_Os01g44200-LOC_Os01g44210  
L3 2 17,849,943–17,960,809 110.9 1 Whole 17,889,517 4.8E-14 LOC_Os02g30114  
L4 2 35,718,082–35,816,634 98.6 17 Aus 35,752,298 8.9E-07 LOC_Os02g58470 QDs2b and QRh2b (Li et al. 2009)
L5 3 16,203,266–16,251,439 48.2 1 Xian 16,214,232 9.5E-07 LOC_Os03g28170  
L6 3 21,967,065–22,099,455 132.4 1 Whole 22,062,214 4.2E-09 LOC_Os03g39660-LOC_Os03g39670  
L7 3 33,180,575–33,294,172 113.6 1 Geng 33,211,402 9.3E-07 LOC_Os03g58290-LOC_Os03g58300 qSBR-3 (Kunihiro et al. 2002); qSBPL-3-2 (Wen et al. 2015); qHNLH3 (Zeng et al. 2015); OsWRKY4 (Wang et al. 2015)
L8 4 9,578,771–9,768,308 189.5 1 Geng 9,676,399 4.5E-06 LOC_Os04g17660-LOC_Os04g17669  
L9 4 17,248,318–17,355,392 107.1   Whole 17,255,541 5.8E-07 LOC_Os04g29080-LOC_Os04g29090  
L10 5 28,879,416–28,948,601 69.2 1 Aus 28,939,653 4.4E-06 LOC_Os05g50480 RM5784 and RM3286 (Taguchi-Shiobara et al. 2013)
L11 6 1,826,635–1,964,451 137.8 1 Geng 1,913,825 1.3E-06 LOC_Os06g04460  
L12 6 22,541,170–22,604,225 63.1 1 Whole 22,546,226 2.0E-06 LOC_Os06g38100-LOC_Os06g38110  
L13 6 28,352,324–28,363,626 11.3 1 Whole 28,362,652 2.1E-06 LOC_Os06g46680-LOC_Os06g46690 QRlh6 (Xie et al. 2008); qshb6.1 (Yadav et al. 2015); OsCHI11 (Karmakar et al. 2017)
L14 7 8,485,551–8,669,352 183.8 1 Aus 8,569,372 4.2E-06 LOC_Os07g14940-LOC_Os07g14950  
L15 7 15,236,665–15,247,698 11.0 1 Whole 15,244,300 4.4E-10 LOC_Os07g26490-LOC_Os07g26500 qSBR7–1 (Channamallikarjuna et al. 2010)
L16 9 6,313,772–6,328,962 15.2 1 Whole 6,317,362 2.3E-07 LOC_Os09g11360-LOC_Os09g11370 qHZaDR9 (Zeng et al. 2015)
L17 9 10,897,450–10,929,683 32.2 1 Whole 10,915,359 8.2E-07 LOC_Os09g17830-LOC_Os09g17840  
L18 9 18,082,609–18,092,891 10.3 1 Geng 18,092,604 3.9E-06 LOC_Os09g29760-LOC_Os09g29780 qSB-9 (Han et al. 2002); qSBR9–1 (Channamallikarjuna et al. 2010); qshb9.1 (Yadav et al. 2015); RM6251 and RM3533 (Taguchi-Shiobara et al. 2013); bc15/OsCTL1 (Wu et al. 2012)
L19 10 3,996,721–4,021,580 24.9 1 Whole 4,011,130 2.5E-09 LOC_Os10g07520-LOC_Os10g07530 QRlh10b (Xie et al. 2008)
L20 10 9,226,748–9,327,350 100.6 1 Geng 9,326,435 8.1E-07 LOC_Os10g18360  
L21 10 11,281,341–11,387,999 106.7 1 Whole 11,381,173 1.2E-08 LOC_Os10g22030  
L22 10 11,610,905–11,623,071 12.2 1 Whole 11,620,213 2.1E-08 LOC_Os10g22440-LOC_Os10g22450  
L23 10 14,423,809–14,585,826 162.0 1 Geng 14,523,517 5.3E-12 LOC_Os10g28009-LOC_Os10g28020 qDs10 (Li et al. 2009)
L24 10 16,612,339–16,716,107 103.8 1 Whole 16,616,152 6.1E-08 LOC_Os10g31680-LOC_Os10g31700  
L25 11 5,702,715–5,767,077 64.4 1 Geng 5,708,512 1.8E-07 LOC_Os11g10460-LOC_Os11g10470 qSB-11LE (Zuo et al. 2013); qSBPL-11-2 (Wen et al. 2015)
L26 11 25,530,571–25,595,331 64.8 33 Aus 25,580,510 6.9E-07 LOC_Os11g42450-LOC_Os11g42470 QDs11b and QRh11 (Li et al. 2009); qSBR11–1 (Channamallikarjuna et al. 2010)
L27 12 21,483,436–21,483,932 0.5 1 Whole 21,483,904 8.4E-08 LOC_Os12g35340-LOC_Os12g35350 qSBPL-12 (Wen et al. 2015)