Supplementary Table S1. Annotation data of the putative genes in the qBR9.1 region in Nipponbare genome database from Gramene.

Gene Locus / Physical Location(bp) / Predicted gene function
LOC_Os09g15770 / 9,633,450-9,637,120 / eukaryotic translation initiation factor 5, putative, expressed ( CRG 1)
LOC_Os09g15775 / 9,635,408-9,636,760 / expressed protein
LOC_Os09g15780 / 9,637,865-9,641,416 / expressed protein
LOC_Os09g15790 / 9,642,528-9,645,171 / ras-related protein Rab11B, putative, expressed
LOC_Os09g15800 / 9,646,716-9,649,346 / pentatricopeptide repeat protein PPR868-14, putative
LOC_Os09g15810 / 9,651,177-9,653,971 / folD bifunctional protein, putative, expressed (CRG 2)
LOC_Os09g15820 / 9,654,423-9,658,126 / apospory-associated protein C, putative, expressed
LOC_Os09g15830 / 9,660,772-9,661,911 / hypothetical protein
LOC_Os09g15835 / 9,662,455-9,664,793 / OBP32pep, putative, expressed
LOC_Os09g15840 / 9,672,999-9,673,694 / NBS-LRR disease resistance protein, putative, expressed
LOC_Os09g15850 / 9,680,879-9,688,737 / Leucine Rich Repeat family protein, expressed (CRG 3)
LOC_Os09g15860 / 9,692,656-9,694,069 / expressed protein
LOC_Os09g15870 / 9,697,514-9,697,813 / hypothetical protein
LOC_Os09g15880 / 9,704,395-9,705,944 / retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os09g15890 / 9,709,204-9,711,070 / retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os09g15900 / 9,712,598-9,715,502 / retrotransposon protein, putative, unclassified
LOC_Os09g15910 / 9,717,101-9,717,337 / hypothetical protein
LOC_Os09g15920 / 9,719,008-9,721,699 / retrotransposon protein, putative, unclassified
LOC_Os09g15930 / 9,724,415-9,724,741 / hypothetical protein
LOC_Os09g15940 / 9,739,076-9,741,224 / retrotransposon protein, putative, Ty1-copia subclass
LOC_Os09g15950 / 9,741,900-9,745,357 / conserved hypothetical protein
LOC_Os09g15960 / 9,752,018-9,754,524 / retrotransposon protein, putative, unclassified
LOC_Os09g15970 / 9,759,791-9,760,995 / hypothetical protein
LOC_Os09g15980 / 9,767,948-9,774,758 / expressed protein
LOC_Os09g16000 / 9,776,526-9,779,697 / NBS-LRR disease resistance protein, putative (CRG 4)
LOC_Os09g16010 / 9,780,579-9,782,841 / polygalacturonase-1 non-catalytic beta subunit precursor, putative, expressed
LOC_Os09g16020 / 9,784,871-9,785,143 / hypothetical protein
LOC_Os09g16030 / 9,789,430-9,791,206 / cytokinin-O-glucosyltransferase 1, putative, expressed
LOC_Os09g16040 / 9,795,728-9,797,952 / retrotransposon protein, putative, unclassified
LOC_Os09g16050 / 9,801,156-9,803,312 / ACD6, putative (CRG 5)
LOC_Os09g16060 / 9,806,843-9,808,072 / hypothetical protein
LOC_Os09g16070 / 9,809,122-9,809,503 / expressed protein
LOC_Os09g16080 / 9,811,121-9,816,623 / retrotransposon protein, putative, unclassified
LOC_Os09g16090 / 9,824,479-9,825,835 / cytokinin-O-glucosyltransferase 1, putative, expressed
LOC_Os09g16100 / 9,826,313-9,830,619 / retrotransposon protein, putative, unclassified
LOC_Os09g16110 / 9,830,968-9,831,266 / expressed protein
LOC_Os09g16120 / 9,833,418-9,834,694 / hypothetical protein
LOC_Os09g16130 / 9,838,411-9,838,923 / expressed protein
LOC_Os09g16140 / 9,842,456-9,842,881 / retrotransposon protein, putative, unclassified
LOC_Os09g16150 / 9,848,245-9,849,101 / conserved hypothetical protein
LOC_Os09g16160 / 9,856,201-9,859,809. / conserved hypothetical protein
LOC_Os09g16170 / 9,860,268-9,861,866 / conserved hypothetical protein
LOC_Os09g16180 / 9,863,112-9,864,236 / hypothetical protein
LOC_Os09g16190 / 9,874,701-9,875,672 / hypothetical protein
LOC_Os09g16200 / 9,880,133-9,887,172 / conserved hypothetical protein
LOC_Os09g16210 / 9,896,097-9,897,478 / hypothetical protein
LOC_Os09g16220 / 9,899,753-9,903,720 / hypothetical protein
LOC_Os09g16230 / 9,908,175-9,908,868 / hypothetical protein
LOC_Os09g16240 / 9,909,745-9,916,710 / expressed protein

Note: 11 genes within the qBR9.1 region flanking by CRG1 and RM24031 were highlighted by gray color.

ATGGCGGGGAAAGCGACCGCCTTCGACGTGCTACGCGGCCTCAAGCGACGCGTCGACCGCTGCCGCCGCCAGTACGCGCCGTGGCTGCCGTGGAAGCTCGACGAGGCCTTGAGCGTGGGCGTCAACCCGACCCTCTCCCTGCTGCTGGACATGCTGCTGCTGCCGCCGCCGGCGCCGGTGCCGGGCGACGAGCTGGGCACCATCAAGGGGGCGCTCTACGAGCTGGAGGATCTGCTCGACGACCTCGACGAACACGCCGGCGTCAGGCGCCGGCCGGGTCGCCCCACCTGGAAGGTGAGTTTGGATTAATTGGACAAGTTTTCTCCCCTCCTCTCCACATCACACAATTCGATACTCCATCTGTTTCAGGTCATAAGATGTTTTGACTCTAGTAATTTAACTAATTTTATAGAAAAAAGTACTAATATTTTTAACCCAAGACAAAATTTATTTAATTATAGATTTAATTAAAACTATGCTGGTGTTATAAATGTCACTACTTTTTTTAATACATAATTAATCAAACTTAGAGTAATTTGACTTTGACCAAAGTCAAAACGTTTTATAATTTGAAACGGAAGGAGTAATTTTCAGTATCTCACTATCAAATTTTGTTCATCATTTGGTACTGTGATATGATATTGTCGATTGACACGCTTCGTAATGTCTTTGTCTCGGATATTGAATTGAAGTATTGCCTCGCAAAGGAAATAAGGTACTATTTATGTAAAGATATTGAGCCTACAGAGTTTCATGTTATTATGTCAGATAGCAATTTGTTGGTTGGGGGTAGAGTGGACATGAACATTTTTCCTGTTCAAAGCTATGGCTCAGTGCCTCACATATATCAGTTGATACATCGATCCGTTGAGATAAATGTGATTTCTTAAGCCTTGCATTAGCAGAAGTAGTTTTATGCTAGTACTTTTTCTACTGTCTGTTTTAGATTGAAGAATTAAAAGAAAAAAAAACACATTGTTGTGTTGTATTGCTGCTTGGCATTTCTTGGCTAGCTAATTGTCTACTGCCACAGTTTCACTAATTTTTTGCATACATAAATCAGTTCTTTTTTTAGCCTAGCAATTTGTTGTTCTGTAACTTGACTAAAAATTATCCAACCCACACTTCATATTTACCGTGCACCTCTTCCACAGCACTGTTGGTTGTACAATACTACAGACTATACAGTAATGCTTGCAATTGAGTAACTCATGAAAATCTGTAACTTGTGCGGACAACTGCAATACCATTTGCTACCATACTAATCATGTTGACTTGAGTTGCTAGATGTTCATTAGAGTTTAACTATATATGCCAATATAATTTTGTACTATATTGGCATAGTCTTTTGGGAACCCAAAGTATTTCAACTAATGGGAGCAATTTTTGCAGGAGACATTATTCTGGTTATCGAGTCCAGCACTCTTGCATTCAACTGTGGCCCATAGATTGAATATAGTCAGTACAAAATTGAATTTTGTGGCTGGAAGTTTTTCCTTATTTCTGAAGCGGAATAATGATGCGCAACTTCAAATTACATCATCAGCACACTAATCCAAAACACGAGAAATACAAGGAGATGGCAGGATTTGATGAACCCACAATCATTGGAAGGGATACTGAGAAAGAAGATTTAAAAGATTTGCTCTCGCAAAGTAATCCTGATGACATATCAATCCTTCCTATTGTTGGCCTTCTAGGTTTGGGTAAAACAAGTCTTGCCAGGTTAGTTTTTGAGGATAATGAAGAAGGTTGGGACTTTGATCTTAGGATATGGATTCATGTCGACGACAATTTTGACCTTGAGAAATTTGCAGTGTCCATTATCTCGGAAGCTAACAAATTGATGAAAGGAAAATTTTCCCACATTCTCAATAGATCAGATTGTCCAAGCTACTTAAAGTTCAAGGATTGTATTGAAGAGATTCTTTCTAGTAGTAGCTGTTTAATTGTTCTAGATGGTCTATTATATGCAAACGAACACTGGTTGCCTGATCTGAAGTATGTGCTGGGGAAGACTAAACATAAATGTACAAGATTTATAGTGACGACTTCTAGTGAAGAAGTTGCAGAAGTGATGCAGACTATTCCATCTTACAAGTTAGGCGGTTTATCTGAAGATGATTGCTGGACTTTATTTTCTGAGAAAGCATTTGGAAGTAGGGATGCAACAATTCATTCATGGCAGACAAAAATTGGCAAGGAGATTGTAAAGCAGTGCATGGGCATGCCTATATTAGCTCAATCTCTTGGTCTGATGGTGCACAATCAAGACATGGAAACTTGGCTTGCTGCAGGAAACGATGAACTGTGGGAACTAGTGGAAAGACATTCCCTTGAAAGGGAAGTGTTCTCATCATTCAAGCAGATATATTACGACATGTCCTTGATGTTAAAATCATGTTTCTTATACCTGTCAGTCTTTCCGAGAGGATCCGATATAGATAAGGATGAACTGATTCGTCAATGGATTGCATTAGACTTGATTAACTCAAACAGACATGGGACCTTACCTGCAGTTCTACACGGGGAGATGTTCATTGAAGCACTTGTATCAATATCATTTCTTCAAATTGTCAACACATCCTTAGTAAGTTGTTAAATATTTTTTCAGTTATATTTTTTTCCTGTTTTTTCATGAACAATAAGCTTGGTTAGCTTGTTACTGTTGCAATATTGGTGGTTGCATACTGTGCTTACACTAACAAGAAAACATTTTTTTTGCAAGTAATGTATATTCTTTTATTTTTCACATCTTCTGGGTTTTTGGTCAGGCTTATTACATGTTTAAGTGTTCAGTTTGGATTGTTATTATAATATTTTCCCTAATAGTTCTGATAAACTGATGATCTTCTTTTTTAGGTTACCAAGAAGAAATGCAAGAATCCTCCTCCTACCATTCTTAAAGTGCACAGCTTGGTTTATGATTTTTTGAGATATATTGCCGCGGCTGATATCTTTACTTTGGATTATGCGAAATCACCAAATATTTCTGTAAGAAATCAACCTNTCCGGTATGCAGTATTAACTAATTACAGTTGGCAAGCTACAATGCACGAAGATTTGATAGCCAAGGCCAAGGCGGCAAAAGCAGCAATTTTCAGAAACTGTGAGGCAACAATGCCTATTGCGGATATATTCCCAATACTAAGATACTCACGTCTCTTGGATCTCAGTGGATGTCTCTTTCAAGAATTACCTGCTTCTATCGGTGAATTGAAGCATTTGAGATTTCTCAATGTTTCGTGCTTCAGGATAACAGAACTGCCCAACGAAATGTGCTGCTTGCGAAGCCTTGAGTATTTTGATCTCTCAAAAACTTGCATCGAAGTTCTGCCCTTGTTTGTCGGAGCTTTTGATAAGCTGAAATACTTCAATCTGCATGGATGTGGCAAACTCAAGAACTTGCCCCGAAACATTGGTGATCTCAAGAGGCTAGAACACCTCAACCTGTCATGCTGTCCTGAAATCCGTGAGTTACCTTCATCTATCTCCGGTCTTGATGAACTTAAGTTGCTCAACCTATCAAGTTGCACCAAGCTTGAGCTACTGCCTCATCAGTTCGGTAACTTATCTCGTTTAGAAATTCTTGAATTGGAAAGATGCTGCAATCTTCAGCGATTACCAGAATCGTTTGGTGGCCTCTCTAAGCTCTGTTCTTTAAGCTTAGCGAGTTGCTCTGGGCTTCAACGGTTGCCAGATTGTATTGGTGAGTTGTGTAGTTTGGAGCACTTGAACATTTCACATGCTCACCTTGAGCTACCGGATTCACTGACCAAGCTCCAGAGCCTCCACATAGTGAACTCATAG

Supplementary Fig. S1. The genomic sequence of Pi56(t) in SHZ-2 is 3810 bp in length. The exon was highlighted by gray color. The sequence highlighted by red color is the 335bp insertion compared with the allele sequence in the Nipponbare.

Supplementary Fig. S2. The genomic sequence of the allele of Pi56(t) in TXZ-13 is 3045bp in length. The exon was highlighted by gray color. The 106bp insertion in the first intron was highlighted by red color. The hyphens indicated the 233 deletion in the exon region compared with the sequence in the Nipponbare.

SHZ-2 ATGGCGGGGAAAGCGACCGCCTTCGACGTGCTACGCGGCCTCAAGCGACGCGTCGACCGC

TXZ-13 ATGGCGGGGAAAGCGACCGCCTTCGACGTGCTACGCGGCCTCAAGCGACGCGTCGACCGC

************************************************************

SHZ-2 TGCCGCCGCCAGTACGCGCCGTGGCTGCCGTGGAAGCTCGACGAGGCCTTGAGCGTGGGC

TXZ-13 TGCCGCCGCCAGTACGCGCCGTGGCTGCCGTGGAAGCTCGACGAGGCCTTGAGCGTGGGC

************************************************************

SHZ-2 GTCAACCCGACCCTCTCCCTGCTGCTGGACATGCTGCTGCTGCCGCCGCCGGCGCCGGTG

TXZ-13 GTCAACCCGACCCTCTCCCTGCTGCTGGACATGCTGCTGCTGCCGCCGCCGGCGCCGGTG

************************************************************

SHZ-2 CCGGGCGACGAGCTGGGCACCATCAAGGGGGCGCTCTACGAGCTGGAGGATCTGCTCGAC

TXZ-13 CCGGGCGACGAGCTGGGCACCATCAAGGGGGCGCTCTACGAGCTGGAGGATCTGCTCGAC

************************************************************

SHZ-2 GACCTCGACGAACACGCCGGCGTCAGGCGCCGGCCGG---GTCGCCCCACCTGGAAGGTG

TXZ-13 GACCTCGACGAGCATGCCGGCGTCAGGCGCCGACCCGGCGGCCGCCCCACCTGGAAGGTG

***********.** *****************.** * * ******************

SHZ-2 AG----TTTGGATTAATTGGACAAGTTTTCT-CCCCTCCTCTCCACATCACACAATTCGA

TXZ-13 AGTTAATTCGGATTAATTCGACAAGCTTTCTCCCCCTCCTCTCCACATCACACAATTTG-

** ** ********* ****** ***** ************************* *

SHZ-2 TACTCCATCTGTTTCAGGTCATAAGATGTTTTGACTCTAGTAATTTAACTAATTTTATAG

TXZ-13 ------

SHZ-2 AAAAAAGTACTAATATTTTTAACCCAAGACAAAATTTATTTAATTATAGATTTAATTAAA

TXZ-13 ------

SHZ-2 ACTATGCTGGTGTTATAAATGTCACTACTTTTTTTAATACATAATTAATCAAACTTAGAG

TXZ-13 ------

SHZ-2 TAATTTGACTTTGACCAAAGTCAAAACGTTTTATAATTTGAAACGGAAGGAGTAATTTTC

TXZ-13 ------ATAATTTTT

.*******

SHZ-2 AGTATCTCACTATCAAATTTTGTTCATCATTTGGTACTGTGATATGATATTGTCGATTGA

TXZ-13 AATATCTCGCTATCAAATTTTGTTCATCATTTGGTACTGCGATATGATATTGTCGATTGG

*.******.****************************** *******************.

SHZ-2 CACGCTTCGTAATGTCTTTGTCTCGGATATTGAATTGAAGTATTGCCTCGCAAAGGAAAT

TXZ-13 CCG------CCCCACGTGGAAGGT

*. ** *.*.:.*.*..*

SHZ-2 AAGGTACTATTTATGTAAAGATATTGAGCCTACAGAGTTTCATGTTATTATGTCAGATAG

TXZ-13 TAGTTGGATTTAAGAATTTGCTAGAAAACCTTCG----CACGTTTTTTTACCCCCTAAAA

:** *. ::**:* .::::*.** :.*.***:*. :*.* **:*** *. *:*.

SHZ-2 CAATTTGTTGGTTGGGGGTAGAGTGGACATGAACATTTTTCCTGTTCAAAGCTATGGCTC

TXZ-13 CTTTTAGATTTGTGACTATTAGATCGTCTCAAGATTTTTTCATGAAGAGAAAAAAG----

*::**:*:* **. .*:...* *:*: .*..:******.**:: *.*..:*:*

SHZ-2 AGTGCCTCACATATATCAGTTGATACATCGATCCGTTGAGATAAATGTGATTTCTTAAGC

TXZ-13 ------TTGCTAGAAAAAAAAA-TTTACAAGTGT

* *...*:***:.: :**:*::.:*

SHZ-2 CTTGCATTAGCAGAAGTAGTTTTATGCTAGTACTTTTTCTACTGTCTGTTTTAGATTGAA

TXZ-13 CATGCTTAAG------

*:***:*:**

SHZ-2 GAATTAAAAGAAAAAAAAACACATTGTTGTGTTGTATTGCTGCTTGGCATTTCTTGGCTA

TXZ-13 ------ATCCCAGTGCTAAGTTTTAAT------

*:*.** ** *.:*** **:*

SHZ-2 GCTAATTGTCTACTGCCACAGTTTCACTAATTTTTTGCATACATAAATCAGTTCTTTTTT

TXZ-13 --AAGTTTATTGTAGTTGCAGTTACAGTAATTCT------ACTTCAATCATGTTATAGTT

:*.** : *. :* .*****:** ***** * **:*.***** * :*: **

SHZ-2 TAGCCTAGCAATTTGTTGTTCTGTAACTTGACTAAAAATTATCCAACCCACACTTCATAT

TXZ-13 ACATCTGAAAATTTTTGACCAAAAAACTTGTG------ACGTTTTTTAA

:.. **...***** * . .:.:******: **. ** :**:

SHZ-2 TTACCGTGCACCTCTTCCACAGCACTGTTGGTTGTACAATACTACAGACTATACAGTAAT

TXZ-13 GCCCCTTTCTCCTCT-CCACTTCACA------TGACAAAAAAAATTG

.** * *:***** ****: ***: :***:*:*.*.:::

SHZ-2 GCTTGCAATTGAGTAACTCATGAAAATCTGTAACTTGTGCGGACAACTGCAATACCATTT

TXZ-13 GCGTACTTTTTAG------CATTTC

** *.*::** ** *.:**

SHZ-2 GCTACCATACTAATCATGTTGACTTGAGTTGCTAGATGTTCATTAGAGTTTAACTATATA

TXZ-13 ACTATCAAATTACATAT------

.*** **:* **.: **

SHZ-2 TGCCAATATAATTTTGTACTATATTGGCATAGTCTTTTGGGAACCCAAAGTATTTCAACT

TXZ-13 ------TGGGAACTCAAAGTATTTCAACT

******* ***************

SHZ-2 AATGGGAGCAATTTTTGCAGGAGACATTATTCTGGTTATCGAGTCCAGCACTCTTGCATT

TXZ-13 GATAGGAGCAATTTTTGCAGGAGACATTATTCTGGTTATCAAGTCCACTACTCTTGCATT

.**.************************************.****** ***********

SHZ-2 CAACTGTGGCCCATAGATTGAATATAGTCAGTACAAAATTGAATTTTGTGGCTGGAAGTT

TXZ-13 CAACTGTAGCCCATAGATTGAATATAGTCAGTACAAAATTGAATTTTGTGGCTGGAAGTT

*******.****************************************************

SHZ-2 TTTCCTTATTTCTGAAGCGGAATAATGATGCGCAACTTCAAATTACATCATCAGCACACT

TXZ-13 TTTCCTTGTTTTTGAAGCGAAATAATGATGC-TGAATTCAAATTACATCATCAACACGCT

*******.*** *******.*********** .*.*****************.***.**

SHZ-2 AATCCAAAACACGAGAAATACAAGGAGATGGCAGGATTTGATGAACCCACAATCATTGGA

TXZ-13 AATCCACAACACGAGAAATACAAGGAGATGGTAGGAGTTAATGGAGTCACAATCATTGGA

******.************************ **** **.***.* *************

SHZ-2 AGGGATACTGAGAAAGAAGATTTAAAAGATTTGCTCTCGCAAAGTAATCCTGATGACATA

TXZ-13 AGGGATACTGAGAAACAATATTTAAAAGATTTGCTCTCGCAAAGTAATCCTGATGACCTA

*************** ** **************************************.**

SHZ-2 TCAATCCTTCCTATTGTTGGCCTTCTAGGTTTGGGTAAAACAAGTCTTGCCAGGTTAGTT

TXZ-13 TCAATCCTTCCTATTGTTGGCCTTCCAGGTTTGGGTAAAACAAGTCTTGCCAGGTTAGTT

************************* **********************************

SHZ-2 TTTGAGGATAATGAAGAAGGTTGGGACTTTGATCTTAGGATATGGATTCATGTCGACGAC

TXZ-13 TTTGAGGATAAGGAAGAAGGTTGGGACTTTGATCTTAGGATATGGATTCATGTCGACGAC

*********** ************************************************

SHZ-2 AATTTTGACCTTGAGAAATTTGCAGTGTCCATTATCTCGGAAGCTAACAAATTGATGAAA

TXZ-13 AATTTTGACCTTGAGAAATTTGCAGTGTGCATTATCTCGGAAGCTAACAAATTGATGAAA

**************************** *******************************

SHZ-2 GGAAAATTTTCCCACATTCTCAATAGATCAGATTGTCCAAGCTACTTAAAGTTCAAGGAT

TXZ-13 GGAAAATTTTCTCACATTCTCAATAGATCAGATTGTCCAAGCTACTTAAAGTTTAAGGAT

*********** ***************************************** ******

SHZ-2 TGTATTGAAGAGATTCTTTCTAGTAGTAGCTGTTTAATTGTTCTAGATGGTCTATTATAT

TXZ-13 TGTATTGAAGAGATTCTTTCTAGTAGTAGCTGTTTAATTGTTCTAGATGGTCTATTATAT

************************************************************

SHZ-2 GCAAACGAACACTGGTTGCCTGATCTGAAGTATGTGCTGGGGAAGACTAAACATAAATGT

TXZ-13 GCAAACGAACACTGGTTGCCTGATCTGAAGTATGTGCTGGGGGAGACTAAACATAAATGT

******************************************.*****************

SHZ-2 ACAAGATTTATAGTGACGACTTCTAGTGAAGAAGTTGCAGAAGTGATGCAGACTATTCCA

TXZ-13 ACAAGATTTATAGTGACGACTTCTAGTGAAGAAGTTGCACAAGTGATGCACACTGTTCCA

*************************************** ********** ***.*****

SHZ-2 TCTTACAAGTTAGGCGGTTTATCTGAAGATGATTGCTGGACTTTATTTTCTGAGAAAGCA

TXZ-13 TCCTACAAGTTAGGCGGTTTATCTGAAGATGATTGCTGGACTTTATTTTCTGAGAAAGCA

** *********************************************************

SHZ-2 TTTGGAAGTAGGGATGCAACAATTCATTCATGGCAGACAAAAATTGGCAAGGAGATTGTA

TXZ-13 TTTGGAAGTAGGGATGCAACAATTCATTCATGGCAGACAAAGATTGGCAAGGCGATTGTA

*****************************************.**********.*******

SHZ-2 AAGCAGTGCATGGGCATGCCTATATTAGCTCAATCTCTTGGTCTGATGGTGCACAATCAA

TXZ-13 AAGCGGTGCATGGGCATGCCTATATTAGCTCAATCTCTTGGTCTGATGGTGCAGAATCAA

****.************************************************ ******

SHZ-2 GACATGGAAACTTGGCTTGCTGCAGGAAACGATGAACTGTGGGAACTAGTGGAAAGACAT

TXZ-13 GACATGGAAACTTGGCTTGCTGCAGGGAATGATGAATTGTGGGAACTAGTGGAAAGACAT

**************************.** ****** ***********************

SHZ-2 TCCCTTGAAAGGGAAGTGTTCTCATCATTCAAGCAGATATATTACGACATGTCCTTGATG

TXZ-13 TCCCTTGAAAGGGAAGTGTTCTCATCATTCAAGCAGATATATTACGACATGTCCTTGATG

************************************************************

SHZ-2 TTAAAATCATGTTTCTTATACCTGTCAGTCTTTCCGAGAGGATCCGATATAGATAAGGAT

TXZ-13 TTAAAATCATGTTTCTTATACCTGTCAGTCTTTCCGAGAGGATCCGACATAGATAAGGAT

*********************************************** ************

SHZ-2 GAACTGATTCGTCAATGGATTGCATTAGACTTGATTAACTCAAACAGACATGGGACCTTA

TXZ-13 GAACTCATTCGTCAATGGATTGCATTAGACTTGATTAACTCTAGCAGACATGGGACCTTA

***** ***********************************:*.****************

SHZ-2 CCTGCAGTTCTACACGGGGAGATGTTCATTGAAGCACTTGTATCAATATCATTTCTTCAA

TXZ-13 CCTGCATTTCTACACGGGGAGATGTTCATTGAAGCACTTGTATCAAGATCATTTCTTCAA

****** *************************************** *************

SHZ-2 ATTGTCAACACATCCTTAGTAAGTTGTTAAATATTTTTTCAGTTATATTTTTTTCCTGTT

TXZ-13 ATTGTCAACACATCCTCAGTAAGTTGTTAAATATTTTTTCGGTTATAATATTTTCCTGTT

**************** ***********************.******:*:**********

SHZ-2 TTTTCATGAACAATAAGCTTGGTTAGCTTGTTACTGTTGCAATATTGGTGGTTGCATACT

TXZ-13 TTTTCATGACCAATAAGCTTGGTTAGCTTGTTACTGTTGCAATATTGGTGGTTGCATGTT

*********.***********************************************. *

SHZ-2 GTGCTTACACTAACAAGAAAACATTTTTTTTGCAAGTAATGTATATTCTTTTATTTTTCA

TXZ-13 GTGCTTACACTAACAAGAAAACATATTTTTTGCAAGTAATGTATATTCTTTTATTTTTCA

************************:***********************************

SHZ-2 CATCTTCTGGGTTTTTGGTCAGGCTTATTACATGTTTAAGTGTTCAGTTTGGATTGTTAT

TXZ-13 CATCTTCTGAGTTTTTGGTCAGGCTTATTACATGTTTAAGTGTTCAGTTTGGATTGTTAT

*********.**************************************************

SHZ-2 TATAATATTTT------CCCTAATAGTTCTGATAA

TXZ-13 TATGATAAATTGTTGGCCAACATCTAATATGAATTCCATACTGACAGATAGTTCTGATAA

***.***::** .*:.*************

SHZ-2 ACTGATGATCTTCTTTTTTAGGTTACCAAGAAGAAATGCAAGAATCCTCCTCCTACCATT

TXZ-13 ACTGACAGTCTTCTTTTTTAGGTTACCGAGAAGAAATGCAAGAACCCTCCTCCTACCATT

***** ..*******************.**************** ***************

SHZ-2 CTTAAAGTGCACAGCTTGGTTTATGATTTTTTGAGATATATTGCCGCGGCTGATATCTTT

TXZ-13 CTTAAAGTGCACAGCTTGGTTTACGATTTTTTGAGATATATTGCAGCGGATGATATATTT

*********************** ********************.****.******.***

SHZ-2 ACTTTGGATTATGCGAAATCACCAAATATTTCTGTAAGAAATCAACCTNTCCGGTATGCA

TXZ-13 ACTTTGGATTATGCGAAATCACCAAATATTTCTGTAAGAAATCAACCTTTCCGGTATGCA

************************************************.***********

SHZ-2 GTATTAACTAATTACAGTTGGCAAGCTACAATGCACGAAGATTTGATAGCCAAGGCCAAG

TXZ-13 GTATTAACTAATTACAGTTGGCAAGCTAAAATGCACGAAGATTTCATAGCCAAGGCCAAG

****************************.*************** ***************

SHZ-2 GCGGCAAAAGCAGCAATTTTCAGAAACTGTGAGGCAACAATGCCTATTGCGGATATATTC

TXZ-13 GCGGCAAAAGCAGCAATTTTCAGAAATTGTGAGGCAACAATGCCTACTGCGGATATATTC

************************** ******************* *************

SHZ-2 CCAATACTAAGATACTCACGTCTCTTGGATCTCAGTGGATGTCTCTTTCAAGAATTACCT

TXZ-13 CCAATACTAAGATACTCAAG------

******************.*

SHZ-2 GCTTCTATCGGTGAATTGAAGCATTTGAGATTTCTCAATGTTTCGTGCTTCAGGATAACA

TXZ-13 ------

SHZ-2 GAACTGCCCAACGAAATGTGCTGCTTGCGAAGCCTTGAGTATTTTGATCTCTCAAAAACT

TXZ-13 ------

SHZ-2 TGCATCGAAGTTCTGCCCTTGTTTGTCGGAGCTTTTGATAAGCTGAAATACTTCAATCTG

TXZ-13 ------

SHZ-2 CATGGATGTGGCAAACTCAAGAACTTGCCCCGAAACATTGGTGATCTCAAGAGGCTAGAA

TXZ-13 ------AACTCAAGAACTTGCCCCAAAACATTGGTGATCTCAAGAGGCTAGAA

******************.****************************

SHZ-2 CACCTCAACCTGTCATGCTGTCCTGAAATCCGTGAGTTACCTTCATCTATCTCCGGTCTT

TXZ-13 CACCTCAACCTGTCATGCTGTCCTGAAATCCGTGAGTTACCTTCATCTATCTCCGGTCTT

************************************************************

SHZ-2 GATGAACTTAAGTTGCTCAACCTATCAAGTTGCACCAAGCTTGAGCTACTGCCTCATCAG

TXZ-13 GATGAACTTAAGTTGCTCAACCTATCAAGTTGCACCAAGCTTGAGCTACTGCCTCATCAG

************************************************************

SHZ-2 TTCGGTAACTTATCTCGTTTAGAAATTCTTGAATTGGAAAGATGCTGCAATCTTCAGCGA

TXZ-13 TTCGGTAACTTATCCTGTTTAGAGAGTCTTGAGATGGCAGGATGCTGTAGTCTTCAGAGA

************** *******.* ******.:***.*.******* *.*******.**

SHZ-2 TTACCAGAATCGTTTGGTGGCCTCTCTAAGCTCTGTTCTTTAAGCTTAGCGAGTTGCTCT

TXZ-13 TTACCAGAATCGTTTGGTGGCCTCTCTAAGCTCTGTTCTTTAAGCTTAGCAAGTTGTTCT

**************************************************.***** ***

SHZ-2 GGGCTTCAACGGTTGCCAGATTGTATTGGTGAGTTGTGTAGTTTGGAGCACTTGAACATT

TXZ-13 AGCCTTCAACGATTGCCAGATTATATTGGTGAGTGGTGTAGTTTAGAGTACTTGAACATT

.* ********.**********.*********** *********.*** ***********

SHZ-2 TCACATGCTCACCTTGAGCTACCGGATTCACTGACCAAGCTCCAGAGCCTCCACATAGTG

TXZ-13 TCACATGCTCACCGTGAGCTACCGGATTCACTGACCAAGCTCCAGAGCCTCCACATAGTG

************* **********************************************

SHZ-2 AACTCATAG

TXZ-13 AACTCATAG

*********

Supplementary Fig. S3. The comparison of genomic sequence of Pi56(t) in SHZ-2 variety with the allele sequence of Pi56(t) in TXZ-13 variety by CLUSTAL 2.1. Hyphens indicate sequence gaps

Supplementary Fig. S4. The use of the candidate gene specific markers in eight rice varieties to identify rice varieties displaying blast resistance to PO6-6, (a) using CRG4-1 primer, (b) using CRG4-3 primer. M: 1kb plus DNA ladder; R: resistance to PO6-6; S: susceptible to PO6-6; PR: partial resistance to PO6-6.

Supplementary Fig. S5. The polymorphism of Pi56(t)-specific markers relative to 13 selected varieties with good agricultural traits using a simple PCR method. The first row was the PCR products of mega varieties using primer pair of CRG4-1; the second row was the PCR products of mega varieties using primer pair of CRG4-2; the third row was the PCR products of mega varieties using primer pair of CRG4-3.

M: 1kb plus marker; 1: SHZ-2; 2: TXZ-13; 3: BC-10; 4: IR64-Sub1; 5 Swarma-Sub1; 6: HYB30;

7: BR11-Sub1; 8: TDK-Sub1; 9: Ciherang-Sub1; 10: Samba Mahsuri-Sub1; 11: FARO44;

12: NERICA-L-19; 13: NERICA-L-49; 14: WITA-4

Supplementary Fig. S6. Multiple protein sequences alignment of Pi56(t), Pi5-1 and Pi5-2 using ClustalW2 software. The accession numbers are as follows: Pi5-1 (EU869185), Pi5-2 (EU869186) (Lee et al. 2009).