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. 2022 Mar 14;12:787767. doi: 10.3389/fgene.2021.787767

TABLE 3.

QTL associated by GWA with straighthead disease response (qStHD) in the Rice Minicore Panel (RMC) arranged in chromosomal order. Overlaps with QTL for other traits within this study, and candidate genes are also noted. Panels for which QTL are listed include “all RMC” containing all RMC accessions, indica subspecies, japonica subspecies, IND subgroup, and AUS subgroup.

QTL Chr Start of QTL region (bp) a End of QTL region (bp) a QTL size (Mb) Peak SNP location (bp) a Panel the QTL peak details are from b -log10(p) Effect of most common allele c Most common allele Alternate allele Nu. acc. with common allele Nu. acc. with alternate allele % Panel having alt. All RMCele QTL overlaps among traits in this RMC study Co-location with QTL or genes for same/similar trait reported in literature Candidate gene RAP ID d Candidate gene symbol(s) or name(s) e
qStHD1-1 1 50,85,464 70,49,182 1.964 57,83,885 All RMC 5.18 1.48 T C 61 17 21.79 Si, PHT Agrama and Yan (2009) LOC_Os01g10530 NIP1;5
↓ LOC_Os01g10600 NIP1;2
↓ LOC_Os01g11946 ABCD1
qStHD1-2 1 93,23,012 1,02,02,956 0.880 97,59,244 All RMC 5.52 2.26 C T 60 15 20.00 none Agrama and Yan (2009) LOC_Os01g18670 ABCB1
qStHD1-3 1 2,26,92,755 2,46,17,484 1.272 2,33,95,696 All RMC 5.57 1.75 C G 67 11 14.10 As, Si, DHD — LOC_Os01g41250 thru _Os01g41530 8 Fbox genes, Fbox021 thru Fbox028
↓ LOC_Os01g42430 vacuolar H + -ATPase subunit C
↓ LOC_Os01g42830 ABCI13
↓ LOC_Os01g42900 ABCG2
qStHD1-4 1 3,15,81,270 3,53,78,105 3.797 3,26,58,417 All RMC 5.88 1.98 C T 60 12 16.67 As, Si, Cu, DHD, PHT — LOC_Os01g55210 thru _Os01g60920 11 Fbox genes, Fbox038 thru Fbox048
↓ LOC_Os01g56050 MATE, multidrug and toxic compound extrusion
↓ LOC_Os01g58290 Root development & fertility gene
qStHD2-1 2 37,23,340 48,46,184 1.123 37,73,340 All RMC 6.16 2.23 G A 104 6 5.45 S — — —
qStHD2-2 2 1,85,76,987 2,00,69,547 1.493 1,86,26,987 japonica 5.98 2.69 G A 33 6 10.81 Si, DHD — — —
↓ 1,94,06,191 indica 5.09 2.63 G C 30 6 11.76 — — —
qStHD2-3 2 2,87,47,996 2,94,74,023 0.726 2,92,36,156 indica 5.96 2.10 A C 46 7 13.21 Si, DHD, PHT — LOC_Os02g45380 MATE, multidrug and toxic compound extrusion
qStHD3 3 1,30,69,711 1,40,35,564 0.966 1,31,19,711 All RMC 5.39 1.71 C A 96 11 10.28 S Pan et al. (2012) — —
qStHD4 4 2,21,73,581 2,23,30,955 0.157 2,22,23,581 All RMC 5.95 1.86 G T 87 12 12.12 DHD, PHT — — —
qStHD5-1 5 69,56,741 95,87,466 2.631 93,11,338 All RMC 5.03 2.55 C T 85 5 5.56 Si, Ca — — —
qStHD5-2 5 1,58,46,555 1,87,68,896 2.922 1,79,96,989 All RMC 5.43 1.53 A T 83 15 15.31 PHT Talukdar et al. (2015) — —
qStHD5-3 5 2,72,13,787 2,92,55,905 2.042 2,92,05,905 All RMC 5.78 1.66 T A 52 42 44.68 Si — LOC_Os05g33910 MATE2, multidrug and toxic compound extrusion protein 2
qStHD6-1 6 2,12,68,226 2,27,22,667 1.454 2,13,32,716 All RMC 5.73 1.83 A T 96 10 9.43 Ca, PHT — LOC_Os06g35930 NIP1;4
↓ LOC_Os06g36330 MATE, multidrug and toxic compound extrusion
qStHD6-2 6 2,78,50,453 2,80,83,810 0.233 2,79,26,998 All RMC 5.02 1.94 A T 80 16 16.67 Si — — —
qStHD7 7 2,60,79,985 2,84,51,701 1.935 2,76,86,009 All RMC 7.8 1.43 A G 72 34 32.08 Si, DHD — — —
qStHD8-1 8 4,50,806 28,59,799 2.409 28,09,799 All RMC 6.63 2.16 G T 87 7 7.45 As, Si, S, DHD — LOC_Os08g03020 RLK1, membrane-anchored receptor-like kinase1
↓ LOC_Os08g03380 heat shock protein
↓ LOC_Os08g03470, 03480, 03490, 03500, 03510, 03530, 03650 7 BTB-domain containing genes: MB17, MB18, MBTB16 thruough MBTN19, BTBN17
↓ LOC_Os08g05580 NIP3;4
↓ LOC_Os08g05590 NIP3;2
↓ LOC_Os08g05600 NIP3;3
qStHD8-2 8 50,81,786 94,26,592 4.345 60,13,173 All RMC 6.59 1.49 C T 59 19 24.36 DHD, PHT Pan et al. (2012), Li et al. (2016), Murugaiyan et al. (2019) LOC_Os08g10480 ATX1; antioxidant protein1
↓ LOC_Os08g09860 GLO6;glycolate oxidase6
↓ LOC_Os08g15149 Oxidoreductase
↓ LOC_Os08g15204 thioredoxin domain-containing protein 9
↓ LOC_Os08g15230 heat shock protein
↓ LOC_Os08g15330 anthocyanidin 3-O-glucosyltransferase
qStHD9-1 9 15,20,138 51,86,402 3.666 29,93,757 All RMC 6.35 2.88 A G 41 34 45.33 As, P — LOC_Os09g03939 ABCG19
↓ LOC_Os09g06499 SULTR4;1, sulphate transporter4;1
↓ LOC_Os09g07450 flavonol synthase
↓ LOC_Os09g07670 ABC20
↓ LOC_Os08g08920 GLP8-1
↓ LOC_Os08g08970 GLP8-3
↓ LOC_Os08g08990 GLP8-5
↓ LOC_Os08g09000 GLP8-6
↓ LOC_Os09g09930 heavy metal transport/detoxification protein
qStHD9-2 9 1,01,82,415 1,23,66,105 2.184 1,22,98,325 All RMC 5.06 -2.38 A C 59 23 28.05 none Agrama and Yan (2009) LOC_Os09g18390 flavonol synthase
↓ 9 LOC_Os09g18450 flavonol synthase
↓ 9 LOC_Os09g18470 Oxidoreductase
↓ 9 LOC_Os09g18520 Oxidoreductase
↓ 9 LOC_Os09g19650 ABCA6
↓ 9 LOC_Os09g20000 heavy metal-associated domain containing protein
↓ 9 LOC_Os09g20220 GST5, glutathione S transferase5
qStHD10 10 4,19,002 12,79,577 0.861 11,41,117 All RMC 7.24 2.13 G A 75 8 9.64 Si, Ca, DHD, PHT LOC_Os10g02300 PCR1, plant cadmium resistance1
↓ LOC_Os10g02350 transmembrane 9 superfamily member
↓ LOC_Os10g02750 PAP3B;purple acid phosphatase3B
qStHD11-1 11 26,20,435 36,39,030 1.018 26,73,334 All RMC 5.57 2.64 A G 86 6 6.52 none — LOC_Os11g05700 ABCC16/MRP16, multidrug resistance-associated protein16
↓ LOC_Os11g05410 PAP20A;purple acid phosphatase20A
qStHD11-2 11 2,11,29,594 2,29,93,035 1.863 2,29,43,035 All RMC 5.5 2.04 G A 92 6 5.15 none Pan et al. (2012) LOC_Os11g36430 AIR2, arsenic induced ring protein2
qStHD12 12 1,09,38,230 1,31,11,966 2.174 1,21,15,679 indica 6.86 3.05 G A 15 10 40.00 PHT LOC_Os12g22110 ABCG29
↓ LOC_Os12g22284 ABCG30
a

O. sativa SNPs are identified by their physical location based on the Os-Nipponbare-Reference-IRGSP-1.0 assembly (Kawahara et al., 2013).

b

The panels are defined as the complete Rice Minicore Diversity Panel (RMC, n = 166). The O. sativa subpopulation groups were tropical japonica (TRJ), temperate japonica (TEJ), aus (AUS), and indica (IND). The two O. sativa subspecies are indica, composed of IND and AUS combined, and japonica comprised TEJ and TRJ. QTL were often identified in GWA-mapping of more than one population (e.g., in INDAUS and AUS). Because alternate alleles became very rare in the smaller subpopulations, the table presents the results based on the entire RMC panel when the QTL was significant there.

c

A negative allele effect reflects a reduction in the trait associated with the most common allele.

d

RAP ID is the Rice Annotation Project identification locus identified for the candidate gene.

e

Gene nomenclature followed the standardized nomenclature for rice genes used in Oryzabase (Yamazaki et al., 2010).