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Sequencing of common bean
genotypes provides a
comprehensive resources for
genetic introgression studies
and molecular breeding
j.d.lobaton@cigar.org
b.raatz@cgiar.org
June 2016
Lima, Peru
Juan David Lobaton, Tamara
Miller Juanita Gil, Alvaro Soler,
Jorge Duitama, Paul Gepts and
Bodo Raatz
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
Population
structure
Variants detection
SNPs , small /large indels,
SNVs and
translocations
Population
genetics
SNPs
Phylogenetics
Genotyping
Chips
SNP
selection
Andean Ref G19833
P. coccineus G35346 P. acutifolious G40001
G5686
Mesoamerican MD_23-24
AFR_298 AND_665
VAX_1 G10474SEA_5
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
Reads, Overall SNPs and coding SNPs
P.coccineous
P.acutifolious
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
Phaseolus sp. WGS SNPs
neighbor join distance
dendogram
2. Rice O. sativa
Nipponbare
3. Bean P. vulgaris
G19833
4. Bean P. coccineous
G35346 – G 36106
4. Bean P. vulgaris
G19833
3. Rice O. sativa
Nipponbare
5. Bean P. acutifolious
G40001 – G40020
Phaseolus vulgaris WGS SNPs
neighbor join distance
dendogram
Mesoamerican Andean
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
SNPs Markers for
Angular Leaf spot
(ALS) resistance
ALS is caused by the fungus Phaeoisariopsis griseola, is
considered a serious disease of beans in many regions
Marker PF5 in red was the previous SCAR
marker for ALS resistance. With WGS we were
Able to saturate the ALS QTL Region with a total
Of 23 SNPs markers. In this set 5 SNPs had
been selected for the CIAT
breeding program (highlighted in blue).
G5686
Resistance allele
Susceptibility allele
Heterozygous
ALS_SNP_C08_58703505
SNP marker tagging ALS resistance on chromosome 8.
SNP selected from WGS and GBS data specific for G10474 and MD23-24 (WGS), MAB348 and MAB349 (GBS). All Andean and other Meso (WGS)
have the reference allele.
Indel markers for Mesoamerican
Andean differentiation
AFR_298
AND_696
G5686
G10474
SEA_5
VAX_1
Indel markers for Mesoamerican Andean
differentiation 5'-3' EXORIBONUCLEASE 2-RELATED
AFR_298
AND_696
G5686
G10474
SEA_5
VAX_1
AND_696
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
Chro11 10’159701 1500bp
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
G19833
AFR_298
G5686
G10474
SEA_5
VAX_1
(-c)
Chro1 Chro1 Chro1 Chro1
Chro3 Chro4 Chro4 Chro5
Chro8 Chro8 Chro8 Chro9
Chro9 Chro9 Chro10 Chro11
Genome deletions
AND_696
Chr09
1Kbpladde
H2O
VAX_1
SEA_5
G10474
MD23-24
G5686
G19833
AFR_298
Mesoamerican-Andean introgression blocks 50 SNPs window analysis
Chr01 Chr08Chr02 Chr03 Chr09 Chr10 Chr11Chr04 Chr05
179.140
Chr06 Chr07
180.401
22’423.90
2
2’016.825
Mesoamerican introgression regions in Andean G19833 line
= Mesoamerican introgression blocks
On G19833 line (bp)
171.674
293.050
1”429.941
502.790
152.288
120.527
490.960
456.284
28.106
258.426
1’288.778
676.174
837.932
139.819
INB 841: A unique introgression line
• Resulted from a cross among several introgression lines from a previous
project
• Selected originally under drought
• Expressed resistance to wilting under intense mid-season drought
• May have rapid pod elongation
• Has been an excellent parent…progeny express:
• Heat resistance
• Resistance to wilting
• Uniform and stable maturity
• We have RILs of INB 841 x RCB 293
• Tim has evaluated for heat
• We evaluated for drought and are repeating
2014: Pollen Viability in Interspecifics with
Tepary
with and without Heat Stress
Q40
RepMasked
MINI 300
MAF 0.01
Variants Group select
G40001W_sen Vs G19833W-G10474W
G19833W p. vulgaris
G40001W P. acutifolious
AM
INB
G40001 WGS
G40001 WGS _sen
G40001 GBS
G40035 GBS
G40036 GBS
P. acutifolious
introgression into
P. vulgaris
AM236
AM300
AM235
Chr01 Chr08Chr02 Chr03 Chr09 Chr10 Chr11Chr04 Chr05
AM235
AM269
AM235
AM51
AM235
AM114
AM94
AM94
AM300
AM120
AM122
AM125
AM126
AM129
AM131
AM134
AM41
AM94
AM236
AM300
AM235
AM150
AM236
AM292
AM78
AM105
AM236
AM292
AM114
AM105
AM116
AM236
AM50
AM51
AM114
AM236
AM120
AM150
AM64
AM125
AM126
AM134
AM133
AM131
AM122
AM120
AM7
AM8
AM111
AM29
AM285
AM272
AM277
AM113
AM104
AM276
AM150
AM300
AM39
AM80
AM174
AM29
AM89
AM273
AM8
AM132
AM126
AM1
AM51
AM292
AM202
AM79
AM41
AM120
AM125
AM129
AM132
AM51
AM13
Chr06
AM101
AM235
Chr07
AM150
AM78
AM273
AM275
AM276
AM268
AM282
AM269
AM1v
AM236
AM235
AM78
AM41
AM14
AM280
AM104
AM116
AM129
AM125
AM126
AM120
AM202
AM132
AM79
AM78
AM89
AM73
AM13
AM202
AM116
AM120
AM122
AM125
AM275
AM129
AM132
AM300
AM134
AM29
AM174
AM1
AM292
AM248
AM276
AM279
AM202
AM202
AM48
AM51
AM94
AM113
AM65
AM202
AM202
AM13
AM292
AM88
AM7
AM94
AM65
AM66
AM78
AM120
AM122
AM125
AM129
AM126
AM134
AM133
AM150
AM235
AM41
INB811
INB834
INB825
INB818
INB852
INB840
INB835
INB832
INB826
INB811
INB825
INB834
INB841
INB844
INB849
INB851
INB853
INB870
INB871
INB856
INB857
INB858
INB850
Phaseolus acutifolious introgression regions in P. vulgaris at AM and INB interspecific cross populations
= INB lines P. acutfolious introgression blocks
= AM lines P. acutfolious introgression blocks
AM120
AM122
AM125
AM300
Phaseolus acutifolious introgression on INB 841, MAGIC Parent P08 and VAX lines
P. acutifolious alleles
P. vulgaris and P. coccineous alleles
#CHROM POS Gene pos code Protein Domains #CHROM POS Gene pos code Protein domains
Chr08 58841149TA=FivePrimeUTR PAC:27153086 Chr08 59386906TA=Synonymous Phvul.008G291100 BR-signaling kinase 1
Chr08 58842950TA=Synonymous Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59386969TA=Synonymous Phvul.008G291100 BR-signaling kinase 1
Chr08 58843028TA=Synonymous Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59387023TA=Synonymous Phvul.008G291100 BR-signaling kinase 1
Chr08 58844144TA=Missense Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59387027TA=Missense Phvul.008G291100 BR-signaling kinase 1
Chr08 58846878TA=Missense Phvul.008G282700 cytochrome c oxidase 15 Chr08 59414987TA=Intron PAC:27156131
Chr08 58861011TA=Synonymous Phvul.008G282900 CCCH-type zinc fingerfamily protein with RNA-binding domain Chr08 59415015TA=Intron PAC:27156131
Chr08 58915717TA=Missense Phvul.008G283700 Neutral/alkaline non-lysosomal ceramidase Chr08 59418163TA=Synonymous Phvul.008G291500 isocitrate dehydrogenase 1
Chr08 58955990TA=Synonymous Phvul.008G284100 Transducin/WD40 repeat-like superfamily protein Chr08 59418238TA=Downstream PAC:27156131
Chr08 58977912TA=Missense Phvul.008G284300 F-box family protein Chr08 59421145TA=Missense Phvul.008G291600 Phosphoglycerate mutase family protein
Chr08 59021428TA=Missense Phvul.008G284900 Nucleoporin, Nup133/Nup155-like Chr08 59422596TA=Missense Phvul.008G291700 C2H2-like zinc finger protein
Chr08 59026184TA=Synonymous Phvul.008G284900 Nucleoporin, Nup133/Nup155-like Chr08 59422817TA=Synonymous Phvul.008G291700 C2H2-like zinc finger protein
Chr08 59059770TA=Intron PAC:27155480 Chr08 59429661TA=Missense Phvul.008G291800 Plant regulator RWP-RK family protein
Chr08 59059940TA=Intron PAC:27155480 Chr08 59453220TA=Intron PAC:27153741
Chr08 59060035TA=Synonymous Phvul.008G285400 HEAT SHOCK PROTEIN 89.1 Chr08 59459148TA=Synonymous Phvul.008G292000 Protein kinase superfamily protein
Chr08 59104120TA=Missense Phvul.008G286000 GRAS family transcription factor Chr08 59459160TA=Synonymous Phvul.008G292000 Protein kinase superfamily protein
Chr08 59104256TA=Synonymous Phvul.008G286000 GRAS family transcription factor Chr08 59462633TA=Intron PAC:27155306
Chr08 59112952TA=Synonymous Phvul.008G286200 DGCR14-related Chr08 59462641TA=Intron PAC:27155306
Chr08 59113009TA=Synonymous Phvul.008G286200 DGCR14-related Chr08 59464515TA=Intron PAC:27155306
Chr08 59120580TA=Synonymous Phvul.008G286400 Phototropic-responsive NPH3 family protein Chr08 59466377TA=Intron PAC:27155306
Chr08 59185195TA=Intron PAC:27155851 Chr08 59479372TA=Missense Phvul.008G292300 homoserine kinase
Chr08 59185202TA=Intron PAC:27155851 Chr08 59479376TA=Synonymous Phvul.008G292300 homoserine kinase
Chr08 59185207TA=Intron PAC:27155851 Chr08 59479390TA=Missense Phvul.008G292300 homoserine kinase
Chr08 59186244TA=Missense Phvul.008G287400 Chr08 59479407TA=Missense Phvul.008G292300 homoserine kinase
Chr08 59186348TA=FivePrimeUTR PAC:27155851 Chr08 59484931TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2
Chr08 59214540TA=Intron PAC:27154413 Chr08 59484932TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2
Chr08 59303118TA=Intron PAC:27154734 Chr08 59484948TA=Synonymous Phvul.008G292400 tonoplast monosaccharide transporter2
Chr08 59303144TA=Intron PAC:27154734 Chr08 59485055TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2
Chr08 59310941TA=Missense Phvul.008G289500 PHE ammonia lyase 1 Chr08 59485104TA=Synonymous Phvul.008G292400 tonoplast monosaccharide transporter2
Chr08 59310946TA=Synonymous Phvul.008G289500 PHE ammonia lyase 1 Chr08 59492351TA=Upstream PAC:27155451
Chr08 59310959TA=Missense Phvul.008G289500 PHE ammonia lyase 1 Chr08 59492372TA=Upstream PAC:27155451
Chr08 59311750TA=Synonymous Phvul.008G289500 PHE ammonia lyase 1 Chr08 59492379TA=Upstream PAC:27155451
Chr08 59312560TA=Synonymous Phvul.008G289500 PHE ammonia lyase 1 Chr08 59492380TA=Upstream PAC:27155451
Chr08 59348281TA=Synonymous Phvul.008G290500 PHE ammonia lyase 1 Chr08 59616761TA=Intron PAC:27153582
Chr08 59374770TA=Missense Phvul.008G291000 UDP-Glycosyltransferase superfamily protein Chr08 59630997TA=Missense Phvul.008G293100 SEC7-like guanine nucleotide exchange family protein
Chr08 59374916TA=Synonymous Phvul.008G291000 UDP-Glycosyltransferase superfamily protein Chr08 59631051TA=Missense Phvul.008G293100 SEC7-like guanine nucleotide exchange family protein
Chr08 59374932TA=Missense Phvul.008G291000 UDP-Glycosyltransferase superfamily protein Chr08 59650036TA=Synonymous Phvul.008G293200 FAR1-related sequence 9
SNPs gene location on the P. acutifolious introgression at INB841 interspecific line (Chr 08 58’724.703 – 59’187. 803) 500kbp
Thanks
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding

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Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding

  • 1. Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding j.d.lobaton@cigar.org b.raatz@cgiar.org June 2016 Lima, Peru Juan David Lobaton, Tamara Miller Juanita Gil, Alvaro Soler, Jorge Duitama, Paul Gepts and Bodo Raatz
  • 5. Population structure Variants detection SNPs , small /large indels, SNVs and translocations Population genetics SNPs Phylogenetics Genotyping Chips SNP selection
  • 6. Andean Ref G19833 P. coccineus G35346 P. acutifolious G40001 G5686 Mesoamerican MD_23-24 AFR_298 AND_665 VAX_1 G10474SEA_5
  • 8. Reads, Overall SNPs and coding SNPs
  • 11. Phaseolus sp. WGS SNPs neighbor join distance dendogram
  • 12. 2. Rice O. sativa Nipponbare 3. Bean P. vulgaris G19833 4. Bean P. coccineous G35346 – G 36106
  • 13. 4. Bean P. vulgaris G19833 3. Rice O. sativa Nipponbare 5. Bean P. acutifolious G40001 – G40020
  • 14. Phaseolus vulgaris WGS SNPs neighbor join distance dendogram Mesoamerican Andean
  • 18. SNPs Markers for Angular Leaf spot (ALS) resistance ALS is caused by the fungus Phaeoisariopsis griseola, is considered a serious disease of beans in many regions Marker PF5 in red was the previous SCAR marker for ALS resistance. With WGS we were Able to saturate the ALS QTL Region with a total Of 23 SNPs markers. In this set 5 SNPs had been selected for the CIAT breeding program (highlighted in blue). G5686
  • 19. Resistance allele Susceptibility allele Heterozygous ALS_SNP_C08_58703505 SNP marker tagging ALS resistance on chromosome 8. SNP selected from WGS and GBS data specific for G10474 and MD23-24 (WGS), MAB348 and MAB349 (GBS). All Andean and other Meso (WGS) have the reference allele.
  • 20. Indel markers for Mesoamerican Andean differentiation AFR_298 AND_696 G5686 G10474 SEA_5 VAX_1
  • 21. Indel markers for Mesoamerican Andean differentiation 5'-3' EXORIBONUCLEASE 2-RELATED AFR_298 AND_696 G5686 G10474 SEA_5 VAX_1 AND_696 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) Chro11 10’159701 1500bp
  • 22. G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) G19833 AFR_298 G5686 G10474 SEA_5 VAX_1 (-c) Chro1 Chro1 Chro1 Chro1 Chro3 Chro4 Chro4 Chro5 Chro8 Chro8 Chro8 Chro9 Chro9 Chro9 Chro10 Chro11 Genome deletions
  • 24. Mesoamerican-Andean introgression blocks 50 SNPs window analysis
  • 25. Chr01 Chr08Chr02 Chr03 Chr09 Chr10 Chr11Chr04 Chr05 179.140 Chr06 Chr07 180.401 22’423.90 2 2’016.825 Mesoamerican introgression regions in Andean G19833 line = Mesoamerican introgression blocks On G19833 line (bp) 171.674 293.050 1”429.941 502.790 152.288 120.527 490.960 456.284 28.106 258.426 1’288.778 676.174 837.932 139.819
  • 26. INB 841: A unique introgression line • Resulted from a cross among several introgression lines from a previous project • Selected originally under drought • Expressed resistance to wilting under intense mid-season drought • May have rapid pod elongation • Has been an excellent parent…progeny express: • Heat resistance • Resistance to wilting • Uniform and stable maturity • We have RILs of INB 841 x RCB 293 • Tim has evaluated for heat • We evaluated for drought and are repeating
  • 27. 2014: Pollen Viability in Interspecifics with Tepary with and without Heat Stress
  • 28. Q40 RepMasked MINI 300 MAF 0.01 Variants Group select G40001W_sen Vs G19833W-G10474W G19833W p. vulgaris G40001W P. acutifolious AM INB G40001 WGS G40001 WGS _sen G40001 GBS G40035 GBS G40036 GBS P. acutifolious introgression into P. vulgaris
  • 29. AM236 AM300 AM235 Chr01 Chr08Chr02 Chr03 Chr09 Chr10 Chr11Chr04 Chr05 AM235 AM269 AM235 AM51 AM235 AM114 AM94 AM94 AM300 AM120 AM122 AM125 AM126 AM129 AM131 AM134 AM41 AM94 AM236 AM300 AM235 AM150 AM236 AM292 AM78 AM105 AM236 AM292 AM114 AM105 AM116 AM236 AM50 AM51 AM114 AM236 AM120 AM150 AM64 AM125 AM126 AM134 AM133 AM131 AM122 AM120 AM7 AM8 AM111 AM29 AM285 AM272 AM277 AM113 AM104 AM276 AM150 AM300 AM39 AM80 AM174 AM29 AM89 AM273 AM8 AM132 AM126 AM1 AM51 AM292 AM202 AM79 AM41 AM120 AM125 AM129 AM132 AM51 AM13 Chr06 AM101 AM235 Chr07 AM150 AM78 AM273 AM275 AM276 AM268 AM282 AM269 AM1v AM236 AM235 AM78 AM41 AM14 AM280 AM104 AM116 AM129 AM125 AM126 AM120 AM202 AM132 AM79 AM78 AM89 AM73 AM13 AM202 AM116 AM120 AM122 AM125 AM275 AM129 AM132 AM300 AM134 AM29 AM174 AM1 AM292 AM248 AM276 AM279 AM202 AM202 AM48 AM51 AM94 AM113 AM65 AM202 AM202 AM13 AM292 AM88 AM7 AM94 AM65 AM66 AM78 AM120 AM122 AM125 AM129 AM126 AM134 AM133 AM150 AM235 AM41 INB811 INB834 INB825 INB818 INB852 INB840 INB835 INB832 INB826 INB811 INB825 INB834 INB841 INB844 INB849 INB851 INB853 INB870 INB871 INB856 INB857 INB858 INB850 Phaseolus acutifolious introgression regions in P. vulgaris at AM and INB interspecific cross populations = INB lines P. acutfolious introgression blocks = AM lines P. acutfolious introgression blocks AM120 AM122 AM125 AM300
  • 30. Phaseolus acutifolious introgression on INB 841, MAGIC Parent P08 and VAX lines P. acutifolious alleles P. vulgaris and P. coccineous alleles
  • 31. #CHROM POS Gene pos code Protein Domains #CHROM POS Gene pos code Protein domains Chr08 58841149TA=FivePrimeUTR PAC:27153086 Chr08 59386906TA=Synonymous Phvul.008G291100 BR-signaling kinase 1 Chr08 58842950TA=Synonymous Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59386969TA=Synonymous Phvul.008G291100 BR-signaling kinase 1 Chr08 58843028TA=Synonymous Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59387023TA=Synonymous Phvul.008G291100 BR-signaling kinase 1 Chr08 58844144TA=Missense Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59387027TA=Missense Phvul.008G291100 BR-signaling kinase 1 Chr08 58846878TA=Missense Phvul.008G282700 cytochrome c oxidase 15 Chr08 59414987TA=Intron PAC:27156131 Chr08 58861011TA=Synonymous Phvul.008G282900 CCCH-type zinc fingerfamily protein with RNA-binding domain Chr08 59415015TA=Intron PAC:27156131 Chr08 58915717TA=Missense Phvul.008G283700 Neutral/alkaline non-lysosomal ceramidase Chr08 59418163TA=Synonymous Phvul.008G291500 isocitrate dehydrogenase 1 Chr08 58955990TA=Synonymous Phvul.008G284100 Transducin/WD40 repeat-like superfamily protein Chr08 59418238TA=Downstream PAC:27156131 Chr08 58977912TA=Missense Phvul.008G284300 F-box family protein Chr08 59421145TA=Missense Phvul.008G291600 Phosphoglycerate mutase family protein Chr08 59021428TA=Missense Phvul.008G284900 Nucleoporin, Nup133/Nup155-like Chr08 59422596TA=Missense Phvul.008G291700 C2H2-like zinc finger protein Chr08 59026184TA=Synonymous Phvul.008G284900 Nucleoporin, Nup133/Nup155-like Chr08 59422817TA=Synonymous Phvul.008G291700 C2H2-like zinc finger protein Chr08 59059770TA=Intron PAC:27155480 Chr08 59429661TA=Missense Phvul.008G291800 Plant regulator RWP-RK family protein Chr08 59059940TA=Intron PAC:27155480 Chr08 59453220TA=Intron PAC:27153741 Chr08 59060035TA=Synonymous Phvul.008G285400 HEAT SHOCK PROTEIN 89.1 Chr08 59459148TA=Synonymous Phvul.008G292000 Protein kinase superfamily protein Chr08 59104120TA=Missense Phvul.008G286000 GRAS family transcription factor Chr08 59459160TA=Synonymous Phvul.008G292000 Protein kinase superfamily protein Chr08 59104256TA=Synonymous Phvul.008G286000 GRAS family transcription factor Chr08 59462633TA=Intron PAC:27155306 Chr08 59112952TA=Synonymous Phvul.008G286200 DGCR14-related Chr08 59462641TA=Intron PAC:27155306 Chr08 59113009TA=Synonymous Phvul.008G286200 DGCR14-related Chr08 59464515TA=Intron PAC:27155306 Chr08 59120580TA=Synonymous Phvul.008G286400 Phototropic-responsive NPH3 family protein Chr08 59466377TA=Intron PAC:27155306 Chr08 59185195TA=Intron PAC:27155851 Chr08 59479372TA=Missense Phvul.008G292300 homoserine kinase Chr08 59185202TA=Intron PAC:27155851 Chr08 59479376TA=Synonymous Phvul.008G292300 homoserine kinase Chr08 59185207TA=Intron PAC:27155851 Chr08 59479390TA=Missense Phvul.008G292300 homoserine kinase Chr08 59186244TA=Missense Phvul.008G287400 Chr08 59479407TA=Missense Phvul.008G292300 homoserine kinase Chr08 59186348TA=FivePrimeUTR PAC:27155851 Chr08 59484931TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2 Chr08 59214540TA=Intron PAC:27154413 Chr08 59484932TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2 Chr08 59303118TA=Intron PAC:27154734 Chr08 59484948TA=Synonymous Phvul.008G292400 tonoplast monosaccharide transporter2 Chr08 59303144TA=Intron PAC:27154734 Chr08 59485055TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2 Chr08 59310941TA=Missense Phvul.008G289500 PHE ammonia lyase 1 Chr08 59485104TA=Synonymous Phvul.008G292400 tonoplast monosaccharide transporter2 Chr08 59310946TA=Synonymous Phvul.008G289500 PHE ammonia lyase 1 Chr08 59492351TA=Upstream PAC:27155451 Chr08 59310959TA=Missense Phvul.008G289500 PHE ammonia lyase 1 Chr08 59492372TA=Upstream PAC:27155451 Chr08 59311750TA=Synonymous Phvul.008G289500 PHE ammonia lyase 1 Chr08 59492379TA=Upstream PAC:27155451 Chr08 59312560TA=Synonymous Phvul.008G289500 PHE ammonia lyase 1 Chr08 59492380TA=Upstream PAC:27155451 Chr08 59348281TA=Synonymous Phvul.008G290500 PHE ammonia lyase 1 Chr08 59616761TA=Intron PAC:27153582 Chr08 59374770TA=Missense Phvul.008G291000 UDP-Glycosyltransferase superfamily protein Chr08 59630997TA=Missense Phvul.008G293100 SEC7-like guanine nucleotide exchange family protein Chr08 59374916TA=Synonymous Phvul.008G291000 UDP-Glycosyltransferase superfamily protein Chr08 59631051TA=Missense Phvul.008G293100 SEC7-like guanine nucleotide exchange family protein Chr08 59374932TA=Missense Phvul.008G291000 UDP-Glycosyltransferase superfamily protein Chr08 59650036TA=Synonymous Phvul.008G293200 FAR1-related sequence 9 SNPs gene location on the P. acutifolious introgression at INB841 interspecific line (Chr 08 58’724.703 – 59’187. 803) 500kbp