Table S1. the list and the origin of the twenty-one world-wide rice cultivars and 14 wild rice accessions

Accession name / Species / Subspecies / Country of origin / Remark
Lemont / Oryza sativa / Japonica / USA
Calrose / Oryza sativa / Japonica / USA
Nipponbare / Oryza sativa / Japonica / Japan
Dadaotou / Oryza sativa / Japonica / Jiangsu, East China / Native variety
Yunjing1 / Oryza sativa / Japonica / Yunnan, South-west China / Native variety
C416 / Oryza sativa / Japonica / Liaoning, North-east China / Newly bred
Beiguang / Oryza sativa / Japonica / Japan
Hokuriku / Oryza sativa / Japonica / Japan
Dular / Oryza sativa / Indica / India
IR24 / Oryza sativa / Indica / IRRI, Philippines
Tadukan / Oryza sativa / Indica / Philippines
93-11 / Oryza sativa / Indica / Jiangsu, East China / Newly bred
Milyang / Oryza sativa / Indica / Korea
NJ11 / Oryza sativa / Indica / Jiangsu, East China / Newly bred
PA64 / Oryza sativa / Indica / Hunan, Central China / Newly bred
Minghui 63 / Oryza sativa / Indica / Fujian, South-east China / Newly bred
Tianxiang 313 / Oryza sativa / Indica / Hubei, Central China / Native variety
S4542A3-49B-2-12 / Oryza sativa / ND. / Arkansas, USA
Grassy / Oryza sativa / ND. / Haiti
Vintula / Oryza sativa / ND. / Guyana
WC 2634 / Oryza sativa / ND. / Tanzania
W0106 / Oryza rufipogon / Wild rice / Orissa, India
S03005 / Oryza rufipogon / Wild rice / Fujian, South-east China
S01169 / Oryza rufipogon / Wild rice / Jiangxi, Central China
S1010 / Oryza rufipogon / Wild rice / Guangdong, South China
S6222 / Oryza rufipogon / Wild rice / Hainan, South China
A100912-R / Oryza rufipogon / Wild rice / Arkansas, USA
W0120 / Oryza rufipogon / Wild rice / Cuttack, Orissa, India
W2003 / Oryza rufipogon / Wild rice / Pajani to Bombay, India
W0630 / Oryza rufipogon / Wild rice / Magwe, Burma
W0593 / Oryza rufipogon / Wild rice / Binjai Rendah, Malaya
W1852 / Oryza rufipogon / Wild rice / Chiang Saen, Thailand
W1551 / Oryza rufipogon / Wild rice / Saraburi, Thailand
RE 551 / Oryza glaberrima / Wild rice / Zaire
NSGC 5935 / Oryza nivara / Wild rice / India

ND,
Table S2 PCR primers for the sampled R-genes

R-gene loci / Gene family / Forward primer (5′-3′) / Reverse primer (5′-3′)
AC134922 / Multi- / GTTGCCGAAGGCTTTGTAGA / TTGGTGATTGCACTTGCTCC3
AP005828 / Multi- / AGCAATAGTGAACATCGGCAG / TACTGGCGATTTATCCTTGACTACT
CTACAATGATCTGCCCTAC / AACAACTCCAGAAAGGGCTTCCAA
TTGGGCTCTGAACTTGAAAC / GCCGCTCCTTGACCACTATA
Pib / Multi- / AGCAACTGGAAGGGAGATAAG / AACATCGTGCTCCAATAGCCT
Os01g72390 / Single- / AGGGCATCAACCAAAACAAC / TTGGAGCATCTTCGGTATCTT
Os01g23380 / Single- / GAGGCGATGGATTGCTGAAG / CGTTCCTCACAGAAGCGATT
Os12g28250 / Single- / GGCACCTACGCTCCTTGAT / TGGCTGTCACTTCAACCTCT
Os07g29820 / Single- / ACAGATRGGTAGAGCCGAGAA / ACAAGTGGGCAGCAACAAA
Os02g25900 / Single- / AAAGCAGCAGATGAGCCTAAG / AGTGGCCGATGATGATGAAG
AL006613 / Single- / AATCACAGACATCCCAGAAGAA / GTGCCATCATCCCCATAGAA
Os06g48520 / Single- / GCCAATATCGAACAAGTTCC / TTGATAGGGCCTTTAGCATT
Os08g09430 / Single- / GCCCAGCACAGTGACCAA / CTGGGCGCTACAGTGATGGA
Os04g02110 / Single- / TCAACTTGCGGCACCTTAAC / ACCTTGGCGAAGACAATCTG
Os02g18510 / Single- / ATGGCTTCCGTATCAATCGTCC / GGTGCTGTGCATCATCTTCTGG
Os01g16390 / Single- / TCCTTGAGCATTGGGAGCTTATC / TAGCTTTGCGAAACTGATTACC
Os01g16400 / Single- / CTGCGGCAATTGACCATG / ACCCAGTCGCAATGTATC
AAAA02018013 / P/A / GACAATTCAGGGAGGTTACGG / CCACTGCTTCTGCTCGCTC
AAAA02032842 / P/A / AAGGTGAAAGTGTGGAGGAGAT / CTACGAATCCCCAACCTCTG
AAAA02036172 / P/A / CATGCGACGAAGGTTGACTA / TGACACCAAAGCACTCCCTC
AAAA02015568 / P/A / GAACAAGAAGGGGCGGTGAA / TTCACCATTGCGACACCTGC
AAAA02032841 / P/A / TTACGAGATTCCAAGAGACCAA / CTTGATGGAAACTCTGGTGGA
AAAA02032153 / P/A / GTTTTGCGAGTATTGGATGTTG / TCAATAATCCCAACAATCCAAT
AAAA02024519 / P/A / ACAACAAGAGCCCCCATAGC / CTATGCCGATGTTGGAGACG
AAAA02021826A / P/A / GGATGCTTGGGGTCAGATTT / ACAATGACGAAATGAGCACTG
AAAA02035731 / P/A / AGGGAGGAGCCATCTTCTATT / GACATTAGGTGAAGGCGGAA
Os11g45330 / P/A / GTTGATTTGTGCCGAAGAGA / TCTAATAAACCTCCGTGGCAT
Os12g09730 / P/A / ACGAGCAGCGACGAATCAAG / TTCTGTGTGCCCTCCTCGC
Os10g04670 / P/A / GTGAGTTGGCGATTGACCTG / ACTGCGGGACTTGCCTAATC
Os11g11550 / P/A / TTGTTTCCTCGCCTGATGGT / TAAGATGCTGCTCTGGCGTTT

Supplemental Table 3. Distribution of R-genes at AC134922 among three rice genomes

Rice Cultivars / Length of locus (kb) / All gene number / R-gene Number / No. of R-gene in gene groups
A / B / C / D
Nipponbare* / 130 / 24 / 10 / 3 / 4 / 2 / 1
93-11* / 420 / 53 / 12 / 6 / 5 / 1 / 0
Guangluai 4* / 95 / 17 / 6 / 5 / 0 / 0 / 1

*The R-gene name from TIGR in Nipponbare: Os11g44960, Os11g44970, Os11g44990, Os11g45050, Os11g45060, Os11g45090, Os11g45130, Os11g45160, Os11g45180, Os11g45190; The R-gene name from BGI in 93-11: OsIFCC036006, OsIFCC036010, OsIFCC036026, OsIFCC045759, OsIFCC045760, OsIFCC045761, OsIFCC036035, OsIFCC036043, OsIFCC036062, OsIFCC036047, OsIFCC036048, OsIFCC036049; The R-gene were predicted by GENESCAN (Burge and Karlin, 1997) and FGENESH ( in Guangluai 4 (GLA4): G2, G4, G5, G9, G14 and G17.

Supplemental Figure 1. Phylogenetic tree of 105 P/A R-genes in Nipponbare and 93-11