水稻协优9308重组自交系群体白叶枯病抗性的全基因组关联分析

赵海涵, 练旺民, 占小登, 徐海明, 张迎信, 程式华, 楼向阳, 曹立勇, 洪永波

Genetic dissection of the bacterial blight disease resistance in super hybrid rice RILs using genome-wide association study

ZHAO Hai-Han, LIAN Wang-Min, ZHAN Xiao-Deng, XU Hai-Ming, ZHANG Ying-Xin, CHENG Shi-Hua, LOU Xiang-Yang, CAO Li-Yong, HONG Yong-Bo

表2 全基因组关联分析检测的显著SNP位点和抗性相关候选基因的注释信息

Table 2 Genome-wide significant association signals of bacterial blight resistance using three Xoo stains (P ≤ 1×10-4)

菌株 Xoo SNP标记 SNP 染色体 Chr. 物理位置 Position P值 P-value 基因名称(MSU) Gene ID (MSU) 基因注释 Gene annotation CR4 11_26502942_C_A 11 26502942 1.71260×10-5 LOC_Os11g43890 WD domain, G-beta repeat domain containing protein, expressed CR4 9_1843902_G_A 9 1843902 1.83954×10-5 LOC_Os09g03660 Retrotransposon protein, putative, unclassified, expressed CR4 7_23436266_C_T 7 23436266 1.88459×10-5 LOC_Os07g39114 Expressed protein CR4 7_23436267_C_G 7 23436267 1.88459×10-5 CR4 7_23436291_C_T 7 23436291 1.88459×10-5 CR4 5_1383235_C_A 5 1383235 1.92989×10-5 LOC_Os05g03360 Retrotransposon protein, putative, unclassified, expressed CR4 7_23436858_C_T 7 23436858 2.13921×10-5 LOC_Os07g39114 Expressed protein CR4 7_23436871_A_T 7 23436871 2.13921×10-5 CR4 8_26662359_G_A 8 26662359 2.44334×10-5 LOC_Os08g42210 Expressed protein CR4 11_27792921_A_G 11 27792921 2.70257×10-5 LOC_Os11g45930 NBS-LRR type disease resistance protein, putative, expressed CR4 11_26056269_A_G 11 26056269 2.90443×10-5 LOC_Os11g43200 Tropinone reductase 2, putative, expressed CR4 2_11969901_C_T 2 11969901 3.20777×10-5 LOC_Os02g20330 Expressed protein CR4 11_23030967_G_A 11 23030967 3.55194×10-5 LOC_Os11g38760 Retrotransposon protein, putative, LINE subclass, expressed CR4 12_10252946_G_T 12 10252946 4.65692×10-5 LOC_Os12g17880 Armadillo/beta-catenin repeat protein-related, putative, expressed CR4 11_26220673_C_T 11 26220673 5.00378×10-5 LOC_Os11g43420 LZ-NBS-LRR class RGA, putative, expressed CR4 6_23077582_G_A 6 23077582 6.20380×10-5 LOC_Os06g38890 Transposon protein, putative, unclassified, expressed CR4 11_26410429_C_A 11 26410429 6.81889×10-5 LOC_Os11g43740 OsMADS68 - MADS-box family gene with MIKC* type-box CR4 11_25840166_C_A 11 25840166 7.97330×10-5 LOC_Os11g42900 Expressed protein CR4 11_25849255_T_C 11 25849255 8.02272×10-5 CR4 6_23441121_G_C 6 23441121 8.04677×10-5 LOC_Os06g39470 Transferase family protein, putative, expressed CR4 2_1831384_A_G 2 1831384 8.31200×10-5 LOC_Os02g04180 Transposon protein putative CACTA En/Spm sub-class expressed CR4 4_3331408_G_A 4 3331408 8.31200×10-5 LOC_Os04g06374 Retrotransposon protein putative Ty3-gypsy subclass expressed CR4 7_9599243_T_C 7 9599243 8.31200×10-5 LOC_Os07g16400 Retrotransposon protein putative Ty3-gypsy subclass expressed CR4 8_20838490_G_A 8 20838490 9.02380×10-5 LOC_Os08g33410 Hypothetical protein CR4 8_20838500_T_C 8 20838500 9.02380×10-5 LOC_Os02g21320 Retrotransposon protein putative unclassified expressed PXO96 6_25611297_T_C 6 25611297 8.66084×10-7 LOC_Os10g05510 PXO96 5_14854774_G_A 5 14854774 3.83500×10-6 LOC_Os06g42010 PXO96 2_12653706_C_A 2 12653706 4.27352×10-6 LOC_Os03g35500 Expressed protein PXO96 10_2723114_A_G 10 2723114 6.44760×10-6 LOC_Os10g20020 Expressed protein PXO96 6_25220112_T_G 6 25220112 1.45559×10-5 LOC_Os06g37790 Transposon protein putative unclassified expressed PXO96 3_19680871_T_C 3 19680871 2.49545×10-5 LOC_Os10g01510 Retrotransposon protein putative Ty3-gypsy subclass PXO96 10_10043595_C_T 10 10043595 2.53663×10-5 LOC_Os03g28010 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO96 6_22366894_G_A 6 22366894 2.89696×10-5 LOC_Os06g42010 Expressed protein PXO96 10_330955_C_T 10 330955 2.98270×10-5 LOC_Os06g42250 Transposon protein putative CACTA En/Spm sub-class expressed PXO96 3_16101988_G_T 3 16101988 3.07716×10-5 LOC_Os06g42370 Retrotransposon protein putative unclassified expressed PXO96 6_25219787_G_A 6 25219787 3.14674×10-5 LOC_Os06g33630 Transposon protein putative unclassified expressed PXO96 6_25373580_A_G 6 25373580 3.85706×10-5 LOC_Os02g32680 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO96 6_25462404_C_T 6 25462404 4.00401×10-5 LOC_Os06g49185 Retrotransposon protein putative unclassified expressed PXO96 6_19579269_C_T 6 19579269 4.66700×10-5 LOC_Os06g45410 Retrotransposon protein putative Ty3-gypsy subclass PXO96 2_19389629_A_G 2 19389629 4.76090×10-5 LOC_Os06g42310 Lectin receptor-type protein kinase putative expressed PXO96 6_29801791_T_C 6 29801791 4.82490×10-5 LOC_Os06g42010 Expressed protein PXO96 6_27455797_A_T 6 27455797 5.46665×10-5 LOC_Os06g42370 MYB family transcription factor putative expressedMYB PXO96 6_25409464_C_T 6 25409464 6.23488×10-5 LOC_Os07g33300 Beta-galactosidase precursor putative expressed PXO96 6_25226687_G_C 6 25226687 6.81127×10-5 LOC_Os05g40940 Transposon protein putative unclassified expressed PXO96 6_25465479_C_T 6 25465479 6.91484×10-5 LOC_Os06g41120 Retrotransposon protein putative unclassified expressed PXO96 7_19906050_T_A 7 19906050 7.23635×10-5 LOC_Os02g32520 Expressed protein PXO96 5_24009603_G_A 5 24009603 7.38552×10-5 LOC_Os06g42350 Retrotransposon protein putative unclassified expressed PXO96 6_24594013_A_C 6 24594013 7.54406×10-5 LOC_Os06g42560 Expressed protein PXO96 2_19249914_C_T 2 19249914 7.84868×10-5 LOC_Os06g42020 ERD1 protein chloroplast precursor putative expressed PXO96 6_25451288_C_G 6 25451288 9.02863×10-5 LOC_Os06g42350 Transposon protein putative CACTA En/Spm sub-class expressed PXO96 6_25592476_C_T 6 25592476 9.10497×10-5 LOC_Os06g42560 Tryptophan synthase beta chain 2 putative expressed PXO96 6_25233994_G_A 6 25233994 9.17863×10-5 LOC_Os06g42020 CSLA9 - cellulose synthase-like family A expressed PXO96 6_25446478_G_A 6 25446478 9.81605×10-5 LOC_Os06g42350 Transposon protein putative CACTA En/Spm sub-class expressed PXO96 6_25226517_G_A 6 25226517 9.81690×10-5 LOC_Os06g42010 Transposon protein putative unclassified expressed PXO96 6_25226850_C_T 6 25226850 9.81690×10-5 PXO96 6_28762618_T_C 6 28762618 9.93356×10-5 LOC_Os06g47500 Retrotransposon protein putative Ty3-gypsy subclass PXO96 6_27492113_G_A 6 27492113 9.99334×10-5 LOC_Os06g45470 Expressed protein PXO99 1_19343496_G_A 1 19343496 2.88795×10-7 LOC_Os01g34960 Retrotransposon putative centromere-specific PXO99 1_29753419_G_A 1 29753419 2.88795×10-7 LOC_Os01g51740 Expressed protein PXO99 1_33782923_T_C 1 33782923 2.88795×10-7 LOC_Os01g58444 Expressed protein PXO99 2_5398259_G_A 2 5398259 2.88795×10-7 LOC_Os02g10280 Transposon protein putative unclassified expressed PXO99 3_13482702_G_A 3 13482702 2.88795×10-7 LOC_Os03g23790 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 4_1315077_T_C 4 1315077 2.88795×10-7 LOC_Os04g03150 Retrotransposon protein putative unclassified expressed PXO99 4_25911404_C_T 4 25911404 2.88795×10-7 LOC_Os04g43770 Expressed protein PXO99 4_35500148_C_A 4 35500148 2.88795×10-7 LOC_Os04g59630 Prenylcysteine oxidase 1 precursor putative expressed PXO99 7_26936907_G_A 7 26936907 2.88795×10-7 LOC_Os07g45120 Expressed protein PXO99 8_10707525_C_A 8 10707525 2.88795×10-7 LOC_Os08g17480 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 9_13062864_A_G 9 13062864 2.88795×10-7 LOC_Os09g21580 OsFBX324 - F-box domain containing protein expressed PXO99 10_770633_A_C 10 770633 2.88795×10-7 LOC_Os10g02220 Peptide transporter PTR2 putative expressed PXO99 10_4768566_T_C 10 4768566 1.88802×10-6 LOC_Os10g08820 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 5_25082791_T_C 5 25082791 3.02499×10-6 LOC_Os05g43190 Expressed protein PXO99 9_682155_C_T 9 682155 3.65396×10-6 LOC_Os09g01980 Retrotransposon protein putative unclassified expressed PXO99 1_35729850_C_T 1 35729850 3.96584×10-6 LOC_Os01g61780 Vacuolar ATP synthase 98 kDa subunit putative expressed PXO99 3_20089598_G_A 3 20089598 4.86058×10-6 LOC_Os03g36220 Retrotransposon protein putative unclassified expressed PXO99 4_23009161_T_C 4 23009161 5.65336×10-6 LOC_Os04g38730 Hypothetical protein PXO99 10_10280800_G_A 10 10280800 8.21681×10-6 LOC_Os10g20430 Transposon protein putative CACTA En/Spm sub-class expressed PXO99 4_22488159_C_T 4 22488159 8.54439×10-6 LOC_Os04g37830 Retrotransposon protein putative unclassified expressed PXO99 1_6763731_G_A 1 6763731 1.45237×10-5 LOC_Os01g12381 GDSL-like lipase/acylhydrolase putative expressed PXO99 10_10622194_C_T 10 10622194 2.05682×10-5 LOC_Os10g20980 Transposon protein putative CACTA En/Spm sub-class expressed PXO99 11_19490121_G_C 11 19490121 2.45252×10-5 LOC_Os11g32980 Transposon protein putative unclassified expressed PXO99 6_15683763_C_T 6 15683763 2.50426×10-5 LOC_Os06g27700 Retrotransposon protein putative unclassified expressed PXO99 2_11530742_G_A 2 115307424 2.50426×10-5 LOC_Os02g19710 Retrotransposon protein putative unclassified expressed PXO99 8_14551707_C_T 8 14551707 2.58147×10-5 LOC_Os08g24080 Retrotransposon protein putative unclassified PXO99 1_37300757_C_T 1 37300757 2.64067×10-5 LOC_Os01g64230 Long cell-linked locus protein putative expressed PXO99 4_29550982_A_G 4 29550982 2.67698×10-5 LOC_Os04g49550 RING-H2 finger protein ATL2A putative expressed PXO99 4_29550988_A_T 4 29550988 2.67698×10-5 PXO99 4_29550990_T_C 4 29550990 2.67698×10-5 PXO99 8_20326896_C_T 8 20326896 2.96673×10-5 LOC_Os08g32790 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 7_9714575_A_T 7 9714575 3.05773×10-5 LOC_Os07g16560 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 12_23369262_A_G 12 23369262 3.32972×10-5 LOC_Os12g38030 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 6_9880157_A_G 6 9880157 3.68628×10-5 LOC_Os06g17040 Retrotransposon protein putative unclassified expressed PXO99 6_27238355_G_T 6 27238355 3.79721×10-5 LOC_Os06g45030 Transposon protein putative unclassified expressed PXO99 10_2015605_G_A 10 2015605 3.98789×10-5 LOC_Os10g04290 Transposon protein putative CACTA En/Spm sub-class expressed PXO99 10_2015606_T_C 10 2015606 3.98789×10-5 PXO99 10_2015616_T_C 10 2015616 3.98789×10-5 PXO99 7_9797928_A_T 7 9797928 4.00610×10-5 LOC_Os07g16710 Retrotransposon protein putative Ty3-gypsy subclass PXO99 12_23610190_C_T 12 23610190 4.37810×10-5 LOC_Os12g38460 RNA recognition motif family protein expressed PXO99 11_3704859_G_A 11 3704859 4.37973×10-5 LOC_Os11g07350 Expressed protein PXO99 6_27238423_T_C 6 27238423 4.48254×10-5 LOC_Os06g45030 Transposon protein putative unclassified expressed PXO99 6_27238426_A_G 6 27238426 4.48254×10-5 LOC_Os06g45030 Transposon protein putative unclassified expressed PXO99 11_16720749_G_A 11 16720749 5.24152×10-5 LOC_Os11g28890 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 3_28507186_C_T 3 28507186 5.35983×10-5 LOC_Os03g49980 Retrotransposon protein putative unclassified expressed PXO99 9_8088480_G_C 9 8088480 5.59333×10-5 LOC_Os09g13800 Retrotransposon protein putative Ty1-copia subclass expressed PXO99 8_15034247_T_G 8 15034247 6.82446×10-5 LOC_Os08g24850 Retrotransposon putative centromere-specific expressed PXO99 1_40956241_G_A 1 40956241 7.49332×10-5 LOC_Os01g70760 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 1_40956243_C_T 1 40956243 7.49332×10-5 PXO99 1_40956268_A_G 1 40956268 7.49332×10-5 PXO99 8_10707195_C_A 8 10707195 9.39077×10-5 LOC_Os08g17480 Retrotransposon protein putative Ty3-gypsy subclass expressed PXO99 12_23610183_G_A 12 23610183 9.70588×10-5 LOC_Os12g38460 RNA recognition motif family protein expressed