(19) United States
`(12) Patent Application Publication (10) Pub. No.: US 2013/0023416 A1
`Hinga et al.
`(43) Pub. Date:
`Jan. 24, 2013
`
`US 2013 0023416A1
`
`(54)
`
`(75)
`
`METHODS AND COMPOSITIONS TO
`PRODUCERCERESISTANT TO ACCASE
`INHIBITORS
`
`Inventors: Melissa Hinga, League City, TX (US);
`Steven Griffin, Alvin, TX (US); Melissa
`Shannon Moon, Pearland, TX (US);
`Russell D. Rasmussen, League City, TX
`(US); Federico Cuevas, League City, TX
`(US)
`
`(73)
`
`Assignee: RICETEC
`AKTIENGESELLSCHAFT, Vaduz
`(LI)
`
`(21)
`
`Appl. No.: 13/554,675
`
`(22)
`
`Filed:
`
`Jul. 20, 2012
`
`(60)
`
`Related U.S. Application Data
`Provisional application No. 61/510,585, filed on Jul.
`22, 2011, provisional application No. 61/541,832,
`filed on Sep. 30, 2011.
`
`Publication Classification
`
`(51) Int. Cl.
`(2006.01)
`AOIH 5/00
`(2006.01)
`CI2N 5/82
`(2006.01)
`AOIPI3/00
`(2006.01)
`CI2N 5/54
`(2006.01)
`CI2N 9/10
`(2006.01)
`AOIN 43/60
`(2006.01)
`CI2N5/10
`(2006.01)
`AOIH I/02
`(52) U.S. Cl. ........ 504/235: 800/300; 435/418; 800/278:
`800/260,536/23.2:435/193
`ABSTRACT
`(57)
`Mutant rice resistant/tolerant to ACCase inhibiting herbi
`cides, in particular FOP herbicides, are listed in Table 1. The
`ACCase inhibiting herbicides used for selection include
`quizalofop. An exemplary mutant rice tolerant to an ACCase
`herbicide is disclosed, with a rice genome having G20.96S or
`the equivalent, in the carboxyl transferase domain of the
`ACCase coding gene, using the Black-Grass numbering sys
`tem. This mutation shows differential response to FOPs vs.
`DIMs herbicides, and a greater differential with comparable
`non-resistant rice lines. Methods to control weeds and meth
`ods to produce herbicide resistant rice including transgenic
`rice, are disclosed.
`
`Ex. 1004
`RiceTec, Inc.
`Page 001
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 1 of 10
`
`US 2013/0023416 A1
`
`
`
`F.G. 1
`
`FG, 2.
`
`Ex. 1004
`RiceTec, Inc.
`Page 002
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 2 of 10
`
`US 2013/0023416 A1
`
`
`
`FIG 3
`
`Ex. 1004
`RiceTec, Inc.
`Page 003
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 3 of 10
`
`US 2013/0023416 A1
`
`NPPCNBARETXE CCGCGCAGGAAAAAGAACTACARACTGCAEGACCACEGGGAG (GAC
`R 46 XT
`CCTGECGCTAGGAATAAAGAACTACATACGCTAGATECCACGGEGAGTGAC
`C 972399 x
`CCEGCGCAGGAAAAAGAACTACACAC GCEAGAT CCACEGGGAGEGAC
`
`NEPECNBAERE IX: {{{TCCCEAACA A} {{AREACCA; AGCAAA (AEAEGEECAGREGECAA AA
`RC 3.46. TX
`GCCCCATA CAAGCATACCATAGCAAACAATCGTCAE GTG CAAAA
`O9 PM 72399. TX
`GCTCCCTATATCAATGCATTACCATAGCAAATTCATATTCGTCAGTTGE CAAAA
`
`NPPCNEARETX, AAGCCGAGAAAACAAAACTTAGGCATTGAAACGCAGGAGGAAGTCATG
`RO 46, TX
`AAGCCGATGAAAATCAAAACGAGGCATTGAAACEGCAGTGAGGAAGCATGG
`(G
`O 9 MT 2399. TX
`AAGCCGAGAAAACAAAACTAGGCATEGAAACEGCAGGAGGAAGTCA
`
`NPCN3ARE. TXE CAGACCECGGGCCEAAAGGGGAAAAGCCCAAGE AGAAAGCEACAG
`RCA 6'X.
`CAGACCTCGGGCECTAAAGGGTTGAAAAGCCCAATGTAGAAAGCTACAG
`O 9M 2399 RXT CTAGACCTCGGGCECTAAAGGGGAAAAEGCCCAAGTAGAAAGCEACAG
`
`NPCNEARETXT AGTTGGTATTGCGGACAAACAGGGECAGGGGCACTCCTAG CAAAGGACCGGC
`RO .46, TXT
`AGGGAEGCGGACAAACAGGGECATGGGGCACECCTEAGTCAAATGGACCGGC
`O 9 PM 72399. TXT AGGGTATTGCGCACAAACAGGGCATGGGCACCCTTTAGTE CAAAEGGACCGGC
`
`NPCNBA REX CGCGGGCCAAGACAGGE AGAGCEGGACCGAAGAGCCACECCGAA
`RO 46, TXT
`CTGCGGGCT CAATGACAEGGAEGGAGCEGGACCTGAAGAGCCACCCGAA
`O3-M, 2.399. TX
`CEGCGGGCCAAGACAEG TAGGAGCTGGACCTTGAACAGCCA TCCCAA
`
`NECNBARE IX
`R 46. TXT
`O9 M723.99 X
`
`CCEAGGGTAGGGAGAEAGGGCAAATGARATTACGTCAGAGCTGGAECA
`TTCCAGTGGAGGGAGATTAGETG: GCAAATGARATACGT CAGAGCTGACAT
`TCCAGGGAGGGAGATAGGGCAAATGAEAT AGECAGAGCGGACA
`
`NIPCNARE X:
`RO 46 XT
`O9 M72339 EX
`
`(GGCCCAAGGGA, AGAGCAEREA AGCEGEEACA ACCAGCC:GEGA GAAGAAAC
`GGCCCAAG (GAAGAGCATTGAACCGEACCAACCAGCCGGAGAAGAAAC
`GGCCCAAGGGAAGA:GCAREEGAAGCGEACCA ACCAGCCEGGAGAAGAAAC
`
`NPCNBA&E TX ECCCTATA TGGCACCAAATCGGGCCGAAGCCAAGCAGAEGAAGEGA
`RO 46. TX
`TCCCTATATTGGCAGCAAATCGGGCTCGAAEGGCAEAGCAGAGAAGTGA.
`O 9M 2399. TX
`CCCTATATGGCAG8 AAAECTGGGCTCGAATGGCAEAGCAGATGAACTGA
`
`NPCNBARE IX: AACEGC (CGGGGGSECGAAGGCAGCCCEGAA CGGGGECASEACA
`RO 48 TXT
`AACEGCTCCG (GGGGGECT CACAGGCAGCCCTGAACGGGCT CASACA
`(9 PM 723.99. TX; AACEGECCGGG (GGTGGCGAGAGCCACCCTGAACGGGTTCACACA
`
`NPCNEARETXT TEACTAAGCGAAGAAGACTAGCTCGTATTGGCACTCGTCAEAGCACARAAGAGC
`3C 46X
`EEEAA ACCGAAGAAGACEA CECGEAEEG{CACECGICAEAGCACARA A GACC
`O 9 PM 72399. TXT
`TACTAAGCGAAGAAGACAGCCGTAGGCACTCTGT CA; AGCACAEAAGATGC
`
`GGGGCAAGGAAGARGGAC
`NPPCNBAKE X: AGCAGACAGGGGAAAAGGGGGA
`RO 46, TXT
`AGCTAGACAGGGTGAAATAGGGGGTTATTGATTCTGTGTGGGCAAGGAAGAEGGAC
`O
`MR2.3 G. C. TX;
`AGCTA ACAGGGGAAAA. GGGGEAGATCGGGGAAGGAAGAAC
`
`
`
`FIG. 4
`
`Ex. 1004
`RiceTec, Inc.
`Page 004
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 4 of 10
`
`US 2013/0023416 A1
`
`NEONARE EXT
`RCA 6.x.
`O 9M2399 x
`
`TGGGGGAGAAAACACAAGGCGCTAGCCAGGCEATCACGCAEAA
`TTCC
`(ACAATA TACAFCC, AACCCTC CTAFCCCACCCT: ATTCTACC (CAFATA
`ICC
`CAAAAACA CAA (CCCEA CA (CACACCCAAA
`
`PONBARETX
`RO 46, TXE
`O923.99 EX
`
`
`AGGAGACAFACACTACATEGGACTGGAAGAACEG TGGAAEAGGAGCEACTG,
`AGGAGACARACACEACA
`GACGGAAGAACEG
`GGAAEAGGAGCEACG
`AGGAGACAEACACACAEGGAEGGAAGAACGGGAAAGGAGCACIG
`
`NEON BAR.E.X.
`RO 46. TX
`9PM 723.99. TX
`
`CCGACEGGCACCGGGCAEACAGCGCGACCAGCCAAEC
`CCGACEGGCACCGGGCAEACAGCGC GACCACCCAATC
`SCCGACEGGCATCCGGGCAEA CAGCGCGACCAGCCAATC
`
`ACAGGCA
`ACAGGCTATE
`ACAGGCEATE
`
`NONEARE
`ROA6. TXT
`39 P.2399-XT
`
`X
`
`CCCA CATCCAC, "CCG (GTC
`AACAAGC'C' (CCC(AACTGACAO:
`(GCAC:
`CEGCA
`EGAACAAGCECTGGGCGGGAAGTGTACAGC
`CCCACAGCAGTEGGGGGC
`CEGCACEGAACAAGCECTGGGCGGGAAGTGACAGC
`CCCACAEGCAGTEGGGGGTC
`
`EPONEARE EXT
`RC 46. TXT
`9:2399 x
`
`GGCAACEAAGGTGT, GCCACT; ACTGTAGATGACTGAAGGCG
`GGCAACEAAGGTGTGCCAECTACTGTCAGAEGACCTGAAGGCG
`3CAAAACA.
`(GGCAACAAGGGGCCACACEGECAGAGACCEEGAAGGCG
`
`NONEARE
`RO 48 . TX
`O 9M 72399 FX
`
`X
`
`CAA, TATA CACCCCCAC, ATCCCCCCFACAF CCGGACCACCCAC
`TriCAATAA FCACGTCCCAC, ATCTCCF CCCFACAF CCTCCACCACCCAC
`TECTAATAAG ACGTCCC; ACTAT (TECCTGCACAITC. "GCACCACT CAC
`
`NPPONBARE X
`RO 46, TX
`O972399. TX
`
`EAACAACACCG
`GGACCCACCGGACAGACCEGEEGCA
`ACACCGAGAACCGEGG
`
`EAACAACACCGTGGACCAC (GGACAGACCTGTE CA
`ACATTCCTGAGAACTCGGG
`
`
`EAACAACACCGGGACCCACGGA CAGACCGGCA ACATCCGAGAACTCGTG
`
`NPONBARE
`ROA 6. TX
`(9 PM 723.99. TX
`
`X
`
`
`
`AECCCGAGCGGCACCG GGGGAGACAGCCAAG G{GAAAG GITAGGGGAG:
`
`
`A CCTCGAGCGGCACCG GGGGAGACAGCCAAG GGAAAEGGTTAGGGGTAG:
`
`
`ACCCAGCGGCACCG GGGGAEGACAGCCAAG GGAAAEGGAGGGGATG:
`
`NEPRONRAREXE
`RO 46. TXT
`39 P.2399 XT
`
`
`TTGAAAAGACAGCTTGGGAAACATGAAGGTTGGG CAAGACAGGGTACGGCA
`
`TTGAAAAGACAGCEGTGGAAACA EGAAGGGGG CTA AGACAGTGGETACTGGCA
`
`EEGAAAAGACAGCEGTGGAAACAEGAAGGTGGG CAAGACAGTGGEEACGGCA
`
`NEON3ARE X
`RC 46. TXT
`O9
`23.93 EX
`
`3AGCAAAGCTGGTGGAA
`
`CCAGGGGGGAAGCG TGGAGACCAGACCAEGAGC
`
`
`GAGCAAAGCEGGTGGAATCCAG. 'GGGTGTGATAGCTG TGGAGACECAGACCAGAGC
`3AGAAAGCGGGGAA
`
`CCAGGGGGGAAGCG (GGAGASCAGAC3A (AGC
`
`
`
`EXT
`
`NONEARE
`RO 46
`x
`O9 PAT 2.399, TX
`
`
`CCGCT CACCCCGT CAGCFTCAT
`ACCCGCTGACCCGGTCAGCTTGAT
`
`AAACACCCCCCACCCCCCAGCCACCCC, FC ACCAA CGCCFCCCCC
`CCCC, CCTC.
`CCCGGCTG
`
`NPOBARE EXT
`RO 46, TX
`O9E72399. X
`
`GC
`GTGGEECCAGATTCGCACCAA
`AGGCAEEGCGGATTC
`
`
`TCCAGA TCEGCAACCAAG ACTGCSC AGGCAEEGCGS ACTEC
`--,
`AGGCAEGCGGACTEC
`GGGECCAGATTCGCA ACCAAGACEGCGC
`
`F.G. 4 (cont.)
`
`Ex. 1004
`RiceTec, Inc.
`Page 005
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 5 of 10
`
`US 2013/0023416 A1
`
`NEPON3ARE X
`R.C.
`46 X
`O9.
`wi2399. X
`
`GAAGGATTACCTCTGTECACCCGC AACTGGAGAGGCTTCTCGGGGACAAAGAG
`GGAAGGATEACCCTGTECAC CTCGCTAACGGAGAGGCTTCCTGGGGACAA AGAG
`GTGAAGGATTACCTCGTTCACCCGCEAACGGAGAGGCETCCGGGGACAAAGAG
`
`N.
`PONBARE X
`46. TXT
`RC.
`
`O 39 A, 23.99 XT
`
`ACE AAC(AACECAGGCGGCTCGACTAGGAGAACCEAGGACATACA
`ACE GAAGGAATTCECAGGGGCCGACATEGGAGAACC TAGGAAACA
`ACE: GAAGGAAECCA ((CEGCCTCC ACTA'''G''CAOAACCACCACA ACA
`
`NE
`RC
`
`PON3ARE X
`46 XT
`s. 2399. X
`
`ACACCC:{{C}
`A CACCCCCC
`ACAGCCEGCC
`
`:
`
`CTACACCCAEGGCGCAGAGCEACGAGGAGGGGCETGGGTT
`CTACACCCAGGCGCAGAGCACGAGGAGGGGCTGGGTTG
`CTACACCCAGGCGAGAGCACGAGGAGGGGCCS GREG
`
`NEPONARE X
`RO 46X
`O 9 p.472.399. XI
`
`GGTTGA: AGCAAGATAAACCCAGACCGCATEGAGFGCTATGC:GAGAGGACTGCAAAA&
`TGGTTGAAGCAAGAAAACCCA GACCGCAGAGEGCTACE GAGAGGACGCAAAA
`GGTTCA: ACCAAGATAAACCCAGACCGCAT GAGFGCTATGC: GAGAGGACTGCAAAA
`
`NPPONBARE, EX
`R 46 X
`O 92,239. X
`
`(CAATGE (GGAACCiCAAGGGAA.G.A.GATCAAGECACGTCAGA (AACTCCAGG
`GCAT
`ICCAA CCAA (CCAA CA (ACAA, ACT AG (GAACTCCACG
`GCAAEGEECTGGAACCGCAAGGGEAAEGAGACAAGCAC GCAGAGGAACECCAGG
`
`PONARE X
`No
`Ri:
`46 XT
`w? 239 XT
`C 9.
`
`CCAFCAC, CCCCCACCCAACAA
`GCAGAGCGGCEGACCCA.ACAEA
`AGCAEGA (CGGCGACCAACAAATGA
`
`{AAAGAAAACCCAAGAGCAA
`GAAAGCAAAACCGAAGEAGCAA
`GAAAGCAAAA (CCGAAGAGCAA
`
`NP ONEARE,
`
`R.
`A 6x
`A 2399. XT
`O 39
`
`:GGAAGIGCEGACACAAAAECGCERCAAGAAAAYAAGAAGCECGAACAAAAC
`AAAAAAGGAAGCCGACACAAAACGCCAAAAAAATAAA CTCCAAAAAAC
`ATAAAAAGGAAGTGCGACACAAAACGCTCAAGAAAAAAGAAGCCGAACAAAAC
`
`Nip
`PONEARE, EX
`RO
`46 XT
`9.
`AF2339. XT
`
`ACCACCCCAAA CACACC(AACC, CCAA, CCACA ACA TCCC
`AGGAGCCCEAAEACCAGAEGCGAACGGGCGAAGCAGA ACACCC
`AGTGAGCCCAAASCAGAGCGAACGGGCTGAATGAGA ACACCC
`
`PONEARE EX
`NP
`R
`A 6.X.
`O 9
`V2399 x
`
`AGAATGGCTGCGAAAGGGTGATTAAGAAAGE
`A.
`GGAAAGAAAGE
`AGAAEGGCEGCGAAAGGGGATAAGAAAGT G
`
`
`
`ECACGATC
`CACCAC
`TCACGAICT
`
`PONARE EX
`No
`RO
`A 6.XT
`923.89 x
`
`TCECAEAAGAGATTACGGAGGAGGACTCGAGGAEGEECT, GCAAAAGAAAAGAG
`CTCAEAAGAGATEACSGAGGAGGATCECGAGGAEGCGCAAAAGAAAEAGAG
`CCAAAGAGATTACGGAGGAGGAECTCEGAGGAEGEECTEGCAAAAGAAAT AGAG
`
`NPONBARE, EX
`RO a 6
`x
`O 9M 2399 x
`
`CGAGCAGGGAGCAGTCCCACCAACCAGCAA CGAGCTGACAAGAAAEGGTATT
`CGAGSAGGGAGEAGTTCCCACCAA.C.AGCAAECGAGCTGACAAGAAAG GTA
`CTGAGCAGGTGAGCAGTTTCCCACCAACCAGCAATCGAGCTGACAAGAAATGGTATT
`
`NPONBARE, EXT
`RO A 6.X.
`O923.89 x
`
`CAGCCACAGCAGCEGAAGGGAEGAGA CGAGCTGGCEGGAEGGAEAACC
`CAGCCACAEGCAGCCAAGGGAEGAGACGATGCTGTEGCEGGAEGGAEAACC
`CAGCTTACAEGCAGCGAATGGGAGAGACGATGCTTGTEGCGGAEGGAEAACC
`
`FIG. 4 (cont.)
`
`Ex. 1004
`RiceTec, Inc.
`Page 006
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 6 of 10
`
`US 2013/0023416 A1
`
`NPON3ARE EX (CTGAAAACTTACAAGGAAATTCAAATCAAGGC CAAAGAGATCCCAATCCCCT
`RO 46. X:
`CGAAAACACAAGGATAA (AAEACEAAGGCECAAA GAG ACCCAAC CCC
`O9 PM 723.99, TX;
`CGAAAASEACAAG{AAACAATACAAG3CCAAAGAGACCCAAECCCC
`
`NPONBARE, EXT CAAGCECAGACCAGCCAGAGCAAGCCCGC:CACAGGGCT(CCAGAC
`RC 46. Ex:
`CAAGCECAGACCAGCCAAGCAAGCCCCCCACAGGGCTCCATAC
`OCM 2399 x
`CAAGECT CAGATTCCAG8 CAGATTGCAAGCCCGCCACAGGGTCTCCAGTAC
`
`NPONBARE. TX
`RC 46. TX;
`(9M 723.99. TX:
`
`CATTACAATGGCG G
`AGAAAGAAAGCTACTGAGCTTAAAAAC
`AGAAAGGTAAAGCACESA (CTAATAAA CRTET (AACAATGGCG
`EAGAAAGGAA; AGCTACGATGCTATATAAATCECATTACAAGGCTGG
`
`NONEARE XT AGAACTACA ACAAAAACAATAACCAAC CTTAGCCAAATC
`RO 46. TX;
`AGAACTACTAACAAAAAGAAAATCCAATCGCTATGCCATTAGAC
`O3 MF 2399 X:
`AGAACTACEAACAAATAAGATTAAAECCAA CGCTTAGCCAAGAC
`
`
`
`NPONARE EXT
`RO 346. TX:
`Q9M 723.99. TX:
`
`CGAAA CCCTTGACACACAGAT (GATCCCCTAGAAGAGCCAAC
`CTGAAAICCCEGGACACTATCAGATGGAE.CCCCEAGAAGAGCCA ACT
`CGAAAECCCTTGGACACACAGAEGGAECCCCTAGAAGAGCCAAC
`
`NPPON BARE EXT GIGAAGAAATCAGGAAGGCCGGGAATCAATGAG
`ROA6. X:
`GTGAAGAAATCAGGAAGGECCTTGGTTGAACAATGATG
`O9 N72399 X:
`GEGAAGAAATCAGGAAGGCCTTGGGAACAATGAG
`
`FIG. 4 (cont.)
`
`Ex. 1004
`RiceTec, Inc.
`Page 007
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 7 of 10
`
`US 2013/0023416 Al
`
`NIPP-PRO.TXT
`ROL46-PRO.TXT
`OOPM723
`$9-PRO.
`
`TX
`
`EAVTNLAC
`GLNDIGMVAWTLKAMSTPEPPSGRETIVVANDITFE RAGSFGPREDArE
`BDREA
`RPAGLNDE IT GMVAWTLEMSTPRFPSGE
`IVVANDITFRAGSFGP REDAPE EAVTNLAC
`
`RPAGLAD LOMVAWT
`
`LAMSTPRFE PSG
`TVVANDTTRRAGSFGPREDAPF BAVTINLAC
`
`NIPP~PRO. TAT
`ROL46-PRO.TXT
`O09PM72399-PRQ.
`
`
` LTy
`
`
`
`LAANSGART GIADEVKSCFRVGWSDDGSPERGFOYIYLSHEEDYARIGTSVIA
`AANSGARTGIADEVKSCF RVGWSDDGSPERGFOYIYLSHEDYARIGTSVIA
`LAANSGART GIADEVKSCFRVGWSDDGSPERGFOYIYLSEEDYARIGTSVIA
`
`NIPP-PRO. TAT
`ROL46-PRO. TXT
`09PM72399-PRO
`
`TX
`
`
`fOLDSGEIRWVIDSVVGRECDGLGVENT HGSAATASAYSRAYKETFTLTPVIGRIVGIG
` LOLD SG!
`
`BIRWVIDSVVGKEDG*LGVENTHGSAATASAY SRAYKETETL VIGRIVGIG
`SAYSRA
`YKETFTLTEVIGRIVGIG
`fOLDSGEI RWVIDSVVGRECDGLGVENT HGSAATA
`
`
`
`NIPP-PRO.TXT
`ROL46-PRO.TXT
`O9PM72399-PRO.
`
`TX
`
`AYLARLGT.
`AYLARLGI
`AYLARLGI
`
`RCTORLDOPTILTGYSALNELUGREVY SSHMOLGGPER IT MATNGVV.
`GPKIMATNGVV.
`RCTORLDOPITLTGYSALNKLLGREVYSS
`HMOLG
`RC TORLDOPTILTGYSALNKALLGREVY SSHMOLGGPRIMATNGVV.
`
`LTVSDD
`HLTVSDD
`LTVSDD
`
`LEGVSNIL
`RWLSYVPAY IGGPLPVITPLDPPDRPVAY IPENSCDPRAATRGVDDS
`QGKWL
`LEGVSNILR
`WLSYVPAYIGGPLPVITPLDOPPDRPVAY IPENSCDPRAATIRGVD
`DSOGKWL
`{ LEGVS
`RWLSYVPAY IGGPLPVITPLDPPDRPVA
`YIPENSC
`DPRAATRGVDDSOGKWL
`
`
`
`GGME'DEDS
`EVETPEGWARKTVVTGRAKLG
`GIPVGVIAVETOTMMOTIPADPGOLDSR
` iBDISDSEaQ NS
`
`PV!GVIAVE TOTM
`VETBPEGWAKTVYTGRAKLI
`
`GCMGh
`MF DEDS
`PVETFPEGWARTVVTGRAKLGGIPVGVIAVETOTMMOTI PADPGOL
`
`BOSv
`EQS.
`MOT IPADPGOLDSRnoRnosy
`
`
`
`
`
`PRAGOVWE
`FOSATKTAGALLDENREGLPLF ILANWRGFSGGO
`PRAGOVWFFDSATKTAQGALLDFNREGLPLF [LANWRGFSGGO
`PRAGOVWF PDSATKTAGQALLDFNREGLPLF ILANWRGFSGGO
`
`NIPP-PRO.TXAT
`RO1L46—PRO.TXT
`09PM7/2399~-PRO.
`
`TX
`
`RIYNOPAFVY IPMAABRLRGGAWVVVDSKINP
`RTYNOPAPFVY IPMASBLRGGAWVVVDSRINP
`REYNOPAFVY IPMAAELRGGAWVVVDSKINP
`
`DRIECYAERTA
`DRIECYAERTA
`DRIECYARRTA
`
`NIPP-PRO.TAT
`ROL46—PRO.TXT
`09PM72399-PRO.
`
`TX
`
`ELODCMSRLDPTLIDL
`ELODCMSRLDPTLIDL
`ELODCMSRLDPTLIDL
`
`KAKLEVANKNGSADT
`<AKLEVANKNGSADT
`KAKLEVANKNGSADT
`
`RS LOENIEART
`<SLOENTEART
`<S LQENTEART
`
`ROLMPLYTOQIATRFAELH
`COLMPLYTOTATREAERLH
`KOLMPLYTOTAIRFAELH
`
`jDWE
`ESRSFFYKRLRRE.
`DISLRMAAKGVIKR\
`
`DI'SLRMAAKGVIKKVV.
`DWEESRSFFYKRLRR
`DI'SLRMAAKGVIKRKVV
`DWEESRSFFYKRLRR
`
`
`
`RISEDVLARETL
`RI SEDVLARET
`RI SEDVLARETL
`
`KWYSAS HAAEWDDDDA
`KWYSAS HAAEWDDDDAI
`KWYSASBRAARWDDDDAL
`
`PVAWMDNPENYKDY LOY LKAGRVSOSLSSLSD
`EPVAWMCDNPENY®?
`DYIQYLKAQRVSQSLSSLS
`LSSLSDS
`EP VAWMDNPENY ADY LOY LKAGRVSOS
`
`NIPP-PRO.TAT
`ROL46—PRO.TXT
`09PM72399~-PRO.
`
`TX
`
`SMLLDEVISLLMLI
`SMLLDRVISLLMLT
`SMLLDEVISLLMLI
`
`FIG. 5
`
`PGR2021-00114 Ex. 1004
`RiceTec,Inc.
`Page 008
`
`NIPP-PRO, TXT
`RO1L46-PRO.TXT
`O9PM72399-PRQ.
`
`NIPP-PRO. TAT
`ROL46-PRO. TXT
`OSPM723
`99-PRO.
`
`TX
`
`NIPP-PRO. UXT
`RO1L46-PRO.TXT
`O09PM72399~-PRO.
`
`TX
`
`NIPP-FRO.TAT
`ROL46—PRO.TXT
`09FM72399-PRO.
`
`TX
`
`NIPP-FRO. TXT
`RO1L46~PRO.TXT
`09PM72399-PRO_T
`
`
`
`
`
`RDLFEGTLOAGSTIVENE
`RDLPECGILOAGSTIVENL
`RDLFEGILOAGSTIVENL
`
`ENVLEPOGLIEIKPRSE
`
`
`INVLEPOGLIEIKFRSE
`(ENVLEPQGL IEIKFRSE
`
`
`RAVAGEOF SHOPATELIKN
`RAVAGEOF SHOPATELIK
`RAVAGEOF SHOPATELIK
`
`
`
`eeePOGL
`POQOGL
`
`
`
`
`
`Ex. 1004
`RiceTec, Inc.
`Page 008
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 8 of 10
`
`US 2013/0023416 A1
`
`88.83.323S-8:
`
`s S. w $ &
`
`s
`
`s
`s
`as
`
`3.
`s
`
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`
`..
`
`&
`
`Ex. 1004
`RiceTec, Inc.
`Page 009
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 9 of 10
`
`US 2013/0023416 A1
`
`TTTTCCACTG,
`ACTGCTATGA
`CCTCTCTCC
`TAGGAAAA
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`CAAATTCATA
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`CTAGTAC CTC
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`
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`GGGGCACTCC
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`
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`
`
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`
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`CTGGGAAGAA
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`TCACGATCTT
`CTGTAGCAGG
`
`AGGAGGACT CTGAGGATG
`CAAATTAGAG
`TCTCCAAAA
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`TCCCACCAAC
`CAGCAATCGA
`GCTGATCAAG
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`
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`TGTTGCTTGG
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`TTAAG GCTCA
`AAGAGTATCC
`CAATCCCTC.
`
`CAAGCTTTC AGATTCCAGC
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`TAGATAAG GT
`AATTAGCTTA
`TTCATAC ATATGGCTGG
`CTGATGCTTA
`AGAACTATCT
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`TCCAATCOTTI
`CTTTTTATCC
`CATTAGATC
`CT CAAATT
`GACACTTATT
`CAGATGGATC
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`
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`
`F.G. 8
`
`Ex. 1004
`RiceTec, Inc.
`Page 010
`
`PGR2021-00114
`
`

`

`Patent Application Publication
`
`Jan. 24, 2013 Sheet 10 of 10
`
`US 2013/0023416 A1
`
`
`
`G20.96S mutant
`
`Adapted from
`WO 201 /O28833
`
`Clodinafop-propargyl
`(112 gai?ha)
`
`diclofop-methyl
`2285 gai/ha)
`8 Mutant : Original line
`(
`FIce
`(b)
`
`Clodinafop-propargyl
`(56 gai?ha)
`
`diclofop-methyl
`(340 gai?ha)
`
`Ex. 1004
`RiceTec, Inc.
`Page 011
`
`PGR2021-00114
`
`

`

`US 2013/0023416 A1
`
`Jan. 24, 2013
`
`METHODS AND COMPOSITIONS TO
`PRODUCERCERESISTANT TO ACCASE
`INHIBITORS
`
`BACKGROUND
`0001. This application claims priority from U.S. Provi
`sional Application No. 61/510,585 filed Jul. 22, 2011 and
`U.S. Provisional Application No. 61/541,832 filed Sep. 30,
`2011, both incorporated by reference. Novel rice plants are
`described and disclosed that are characterized by tolerance/
`resistance to herbicides that are ACCase inhibitors and
`exhibit other characteristics beneficial to rice crops. Methods
`to control weeds by use of herbicide resistant rice in fields,
`and methods to produce herbicide resistant rice using e.g.
`transgenes encoding for a mutant ACCase enzyme, are also
`disclosed.
`
`SEQUENCE LISTING
`0002 The instant application contains a Sequence Listing
`which has been submitted in ASCII format via EFS-Web and
`is hereby incorporated by reference in its entirety. Said ASCII
`copy, created on Jul. 20, 2012, is named 119566 SEQ ST25.
`txt and is 32,768 bytes in size.
`
`Value of Rice Crops
`0003 Rice is an ancient agricultural crop and is today one
`of the principal food crops of the world. There are two culti
`vated species of rice: Oryza sativa L., the Asian rice, and
`Oryza glaberrima Steud., the African rice. The Asian species
`constitutes virtually all of the world’s cultivated rice and is the
`species grown in the United States. Three major rice produc
`ing regions exist in the United States: the Mississippi Delta
`(Arkansas, Mississippi, northeast Louisiana, Southeast Mis
`souri), the Gulf Coast (Southwest Louisiana, Southeast
`Texas), and the Central Valleys of California.
`0004 Rice is one of the few crops that can be grown in a
`shallow flood as it has a unique structure allowing gas
`exchange through the stems between the roots and the atmo
`sphere. Growth in a shallow flood results in the best yields and
`is the reason that rice is usually gown in heavy clay soils or
`soils with an impermeable hard pan layer just below the soil
`surface. These soil types are usually either not suitable for
`other crops or at the best the crops yield poorly.
`0005. The constant improvement of rice is imperative to
`provide necessary nutrition for a growing world population.
`A large portion of the world population consumes rice as their
`primary source of nutrition. Rice improvement is carried out
`through conventional breeding practices and by recombinant
`genetic techniques. Though appearing straight forward to
`those outside this discipline, crop improvement requires keen
`Scientific and artistic skill.
`0006 Although specific breeding objectives vary some
`what in the different rice producing regions, increasing yield
`is a primary objective in all programs.
`0007 Plant breeding begins with the analysis and defini
`tion of strengths and weaknesses of the current cultivars,
`followed by the establishment of program goals, to address
`the latter including the definition of specific breeding objec
`tives. The goal is to combine in a single cultivar an improved
`combination of desirable traits from the parental sources.
`These important traits may include higher yield, resistance to
`
`environmental stress, diseases and insects, better stems and
`roots, tolerance to low temperatures, better agronomic char
`acteristics, and grain quality.
`0008. The breederinitially selects and crosses two or more
`parental lines, followed by selection among the many new
`genetic combinations. The breeder can theoretically generate
`billions of new and different genetic combinations via cross
`ing. The breeder has no direct control at the cellular level;
`therefore, two breeders will never develop the same line, or
`even very similar lines, having the same rice traits.
`0009 Pedigree breeding is used commonly for the
`improvement of self-pollinating crops such as rice. Two par
`ents which possess favorable, complementary traits are
`crossed to produce an F generation. One or both parents may
`themselves represent an F from a previous cross. Subse
`quently a segregating population is produced, growing the
`seeds resulting from selfing one or several FS if the two
`parents are pure lines, or by directly growing the seed result
`ing from the initial cross if at least one of the parents is an F.
`Selection of the best individuals may begin in the first segre
`gating population or F, then, beginning in the F, the best
`individuals in the best families are selected. “Best” is defined
`according to the goals of a particular breeding program e.g.,
`to increase yield, resist diseases. Overall a multifactorial
`approach is used to define “best because of genetic interac
`tions. A desirable gene in one genetic background may differ
`in a different background. In addition, introduction of the
`gene may disrupt other favorable genetic characteristics.
`Replicated testing of families can begin in the F generation to
`improve the effectiveness of selection for traits with low
`heritability. At an advanced stage of inbreeding (i.e., F and
`F7), the best lines or mixtures of phenotypically similar lines
`are tested for potential release as new parental lines.
`0010 Backcross breeding has been used to transfer genes
`for a highly heritable trait into a desirable homozygous cul
`tivar or inbred line which is the recurrent parent. The source
`of the trait to be transferred is called the donor parent. The
`resulting plant is expected to have the attributes of the recur
`rent parent (e.g., cultivar) and the desirable trait transferred
`from the donor parent. After the initial cross, individuals
`possessing the phenotype of the donor parent are selected and
`repeatedly crossed (backcrossed) to the recurrent parent. The
`process is used to recover all of the beneficial characteristics
`of the recurrent parent with the addition of the new trait
`provided by the donor parent.
`0011
`Promising advanced breeding lines are thoroughly
`tested and compared to appropriate standards in environ
`ments representative of the commercial target area(s) for at
`least three or more years. The best lines are candidates for
`new commercial varieties or parents of hybrids; those still
`deficient in a few traits may be used as parents to produce new
`populations for further selection.
`0012. These processes, which lead to the final step of
`marketing and distribution, usually take from 8 to 12 years
`from the time the first cross is made and may rely on the
`development of improved breeding lines as precursors.
`Therefore, development of new cultivars is a time-consuming
`process that requires precise forward planning, efficient use
`of resources, and a minimum of changes in direction.
`0013 The improvement of rice through breeding is
`restricted to the natural genetic variation in rice and hybrid
`izing species, such as wild rice. The introduction of new
`variation in a breeding program is usually through the cross
`ing program as described. Such as pedigree or backcross
`
`Ex. 1004
`RiceTec, Inc.
`Page 012
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`PGR2021-00114
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`

`

`US 2013/0023416 A1
`
`Jan. 24, 2013
`
`breeding. However, occasionally natural mutations are found
`that result in the introduction of new traits such as disease
`resistance or height changes. Breeders have also developed
`new traits by inducing mutations (Small changes in the DNA
`sequence) into a rice genome. Commonly, EMS or sodium
`azide plus MNU are used as mutagenic agents. These chemi
`cals randomly induce single base changes in DNA, usually of
`G and C changed to A and T. Most of these changes have no
`effect on the crop as they fall either outside the gene coding
`regions or don't change the amino acid sequence of the gene
`product.
`0014. The breeder has no direct control of mutation sites in
`the DNA sequence.
`0015 The identification of useful changes is due to the
`random possibility that an effective mutation will be induced
`and that the breeder will be able to select that mutation. Seeds
`are treated with the mutagenic chemical and immediately
`planted to grow and produce M2 seed. The M2 seed will carry
`numerous new variations; therefore, no two experiments will
`produce the same combinations. Among these variations new
`traits previously not existing in rice and unavailable for selec
`tion by a plant breeder may be found and used for rice
`improvement.
`0016 To find new traits the breeder must use efficient and
`strategic selection strategies as the process is completely ran
`dom and has an extremely low frequency of useful new com
`binations. Among thousands of induced new genetic variants
`there may be only one with a desirable new trait. An optimal
`selection system will screen through thousands of new vari
`ants and allow detection of a few or even a single plant that
`might carry a new trait. After identifying or finding a possible
`new trait the breeder must develop a new cultivar by pedigree
`or backcross breeding and extensive testing to Verify the new
`trait and cultivar exhibits stable and heritable value to rice
`producers.
`0.017. Using recombinant genetic techniques, nucleic acid
`molecules with mutations, that encode improved characteris
`tics in rice, may be introduced into rice with commercially
`Suitable genomes. After a mutation is identified, it may be
`transferred into rice by recombinant techniques.
`
`Applications of Herbicide Resistance Patents in Rice
`0018 Weeds in crops compete for resources and greatly
`reduce the yield and quality of the crop. Weeds have been
`controlled in crops through the application of selective her
`bicides that kill the weeds but do not harm the crop. Usually
`selectivity of the herbicides is based on biochemical varia
`tions or differences between the crop and the weeds. Some
`herbicides are non-selective, meaning they kill all or almost
`all plants. Non-selective or broad spectrum herbicides can be
`used in crops if new genes are inserted that express specific
`proteins that convey tolerance or resistance to the herbicide.
`Resistance to herbicides has also been achieved in crops
`through genetic mutations that alterproteins and biochemical
`processes. These mutations may arise in nature, but mostly
`they have been induced in crops or in vitro in tissue cultures.
`Unfortunately in Some instances, especially with repeated use
`of a particular herbicide, weeds have developed resistance
`through the unintended selection of natural mutations that
`provide resistance. When weeds become resistant to a par
`ticular herbicide, that herbicide is no longer useful for weed
`control. The development of resistance in weeds is best
`
`delayed through alternating the use of different modes of
`action to control weeds, interrupting development of resistant
`weeds.
`0019 Rice production is plagued by a particularly hard to
`control weed called red rice. The difficulty arises because red
`rice is so genetically similar to cultivated rice (they occasion
`ally cross pollinate) that there are no selective herbicides
`available that target red rice, yet do not harm the cultivated
`rice. Control is currently provided in commercial rice pro
`duction through the development of mutations found in rice
`that render rice resistant to broad spectrum herbicides e.g.
`imidazolinone and sulfonylurea herbicides.
`0020 Finding new mutations in rice that makes it resistant
`to herbicides, and to combinations of herbicides with alter
`native modes of action would greatly benefit rice production.
`Obtaining and incorporating genes for herbicide resistance
`into rice genomes with additional favorable characteristics
`and alternative resistances is challenging, unpredictable, time
`consuming and expensive, but necessary to meet the world’s
`increasing food needs.
`
`SUMMARY
`Described herein are distinctive rice lines with
`0021
`unique resistances to herbicides with alternative modes of
`action. These rice lines should extend the useful life of several
`herbicides due to being able to rotate the kinds of herbicides
`applied in grower's fields thus slowing the development of
`weed resistance. Several methods are possible to deploy these
`resistances into hybrids or varieties for weed control, as well
`as options for hybrid seed production. The rice lines
`described herein represent new methods for weed control in
`rice and can be deployed in any of many possible strategies to
`control weeds and provide for long-term use of this and other
`weed control methods. In particular, mutant rice tolerant to
`ACCase inhibiting herbicides is disclosed. These are plants
`with defined amino acid sequences.
`(0022. For example, rice with the ACCase mutant G20.96S
`is already agronomically adapted and through breeding or
`backcrossing as described herein, will provide herbicide
`resistance in commercially suitable biological material.
`0023. A mutant rice tolerant to an ACCase inhibitor her
`bicide is disclosed that has a mutation G2096S in the carboxyl
`transferase coding region of the ACCase gene, using the
`Black Grass (Alopecurus myosuroides) numbering system.
`The mutation makes the acetyl-coenzyme A carboxylase
`enzyme tolerant/resistant to ACCase inhibitors used as her
`bicides.
`0024 Cells derived from herbicide resistant seeds, plants
`grown from Such seeds and cells derived from Such plants,
`progeny of plants grown from Such seed and cells derived
`from Such progeny are within the scope of this disclosure. The
`growth of plants produced from deposited seed, and progeny
`of such plants will typically be resistant/tolerant to acetyl
`Coenzyme A carboxylase-inhibiting herbicides at levels of
`herbicide that would normally inhibit the growth of a corre
`sponding wild-type plant.
`0025. A method for controlling growth of weeds in vicin
`ity to rice plants is also within the scope of the disclosure. One
`example of Such methods is applying one or more herbicides
`to the weeds and to the rice plants at levels of herbicide that
`would normally inhibit the growth of a rice plant. For
`example, at least one herbicide inhibits acetyl-Coenzyme A
`carboxylase activity. Such methods may be practiced with
`any herbicide that inhibits acetyl-Coenzyme A carboxylase
`
`Ex. 1004
`RiceTec, Inc.
`Page 013
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`

`

`US 2013/0023416 A1
`
`Jan. 24, 2013
`
`activity and any resistant rice mutation, e.g., the three
`embodiments disclosed herein.
`0026. A method for growing herbicide-tolerant rice plants
`include (a) planting resistant rice seeds; (b) allowing the rice
`seeds to sprout; (c) applying one or more herbicides to the rice
`sprouts at levels of herbicide that would normally inhibit the
`growth of a rice plant. For example, at least one of the herbi
`cides inhibits acetyl-Coenzyme A carboxylase. Such meth
`ods may be practiced with any herbicide that inhibits acetyl
`Coenzyme A carboxylase activity.
`0027 Methods of producing herbi