Post on 08-Jan-2017
Sequencing of common bean genotypes provides a comprehensive resources for genetic introgression studies and molecular breeding
j.d.lobaton@cigar.orgb.raatz@cgiar.org
June 2016Lima, Peru
Juan David Lobaton, Tamara Miller
Juanita Gil, Alvaro Soler,
Jorge Duitama, Paul Gepts and
Bodo Raatz
Population structure
Variants detectionSNPs , 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
Reads, Overall SNPs and coding SNPs
P. co
ccin
eous
P. a
cutif
olio
us
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
SNPs Markers for Angular Leaf spot(ALS) resistanceALS 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 wereAble to saturate the ALS QTL Region with a totalOf 23 SNPs markers. In this set 5 SNPs had been selected for the CIAT breeding program (highlighted in blue).
G5686
Resistance alleleSusceptibility 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
G568
6G1
0474
SEA_
5VA
X_1
(-c)
Chro11 10’159701 1500bp
G198
33AF
R_29
8G5
686
G104
74
SEA_
5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5
VAX_
1(-c
)
G198
33AF
R_29
8G5
686
G104
74SE
A_5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5
VAX_
1(-c
)
G198
33AF
R_29
8G5
686
G104
74SE
A_5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5VA
X_1
(-c)
G198
33AF
R_29
8G5
686
G104
74SE
A_5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5VA
X_1
(-c)
G198
33AF
R_29
8G5
686
G104
74SE
A_5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5VA
X_1
(-c)
G198
33AF
R_29
8G5
686
G104
74SE
A_5
VAX_
1(-c
)G1
9833
AFR_
298
G568
6G1
0474
SEA_
5VA
X_1
(-c)
Chro1 Chro1 Chro1 Chro1
Chro3 Chro4 Chro4 Chro5
Chro8 Chro8 Chro8 Chro9
Chro9 Chro9 Chro10 Chro11
Genome deletions
AND_
696
Chr09
1Kbp
ladd
er
H2OVA
X_1
SEA_
5
G104
74
MD2
3-24
G568
6
G198
33
AFR_
298
Mesoamerican-Andean introgression blocks 50 SNPs window analysis
Chr01 Chr08 Chr02 Chr03 Chr09 Chr10 Chr11 Chr04 Chr05
179.140
Chr06 Chr07
180.401
22’423.902
2’016.825
Mesoamerican introgression regions in Andean G19833 line
= Mesoamerican introgression blocksOn G19833 line (bp)
171.674
293.050
1”429.941
502.790
152.288
120.527
490.960456.284
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
Q40RepMaskedMINI 300MAF 0.01Variants Group select
G40001W_sen Vs G19833W-G10474W
G19833W p. vulgaris
G40001W P. acutifolious
AM
INB
G40001 WGSG40001 WGS _senG40001 GBSG40035 GBSG40036 GBS
P. acutifolious introgression into P. vulgaris
AM236AM300AM235
Chr01 Chr08 Chr02 Chr03 Chr09 Chr10 Chr11 Chr04 Chr05
AM235AM269AM235AM51
AM235
AM114
AM94
AM94AM300AM120AM122AM125AM126AM129AM131AM134AM41
AM94
AM236AM300AM235AM150AM236AM292AM78AM105AM236AM292AM114AM105AM116AM236AM50AM51AM114AM236AM120AM150AM64AM125AM126AM134AM133AM131AM122AM120AM7AM8AM111AM29AM285AM272AM277AM113AM104AM276
AM150AM300AM39AM80AM174AM29AM89AM273AM8AM132AM126AM1
AM51
AM292AM202AM79AM41AM120AM125AM129AM132AM51
AM13
Chr06
AM101AM235
Chr07
AM150AM78AM273AM275AM276AM268AM282AM269AM1v
AM236AM235AM78AM41AM14AM280AM104AM116AM129AM125AM126AM120
AM202AM132AM79AM78AM89AM73
AM13
AM202AM116AM120AM122AM125AM275AM129AM132AM300AM134AM29AM174AM1AM292AM248AM276AM279
AM202
AM202AM48AM51AM94
AM113AM65
AM202
AM202AM13AM292AM88AM7AM94AM65AM66AM78
AM120AM122AM125AM129AM126AM134AM133AM150AM235AM41
INB811INB834INB825INB818INB852INB840INB835INB832INB826
INB811INB825INB834INB841INB844INB849INB851INB853INB870
INB871INB856INB857INB858INB850
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
AM120AM122AM125AM300
Phaseolus acutifolious introgression on INB 841, MAGIC Parent P08 and VAX linesP. acutifolious alleles
P. vulgaris and P. coccineous alleles
#CHROM POS Gene pos code Protein Domains #CHROM POS Gene pos code Protein domainsChr08 58841149TA=FivePrimeUTR PAC:27153086 Chr08 59386906TA=Synonymous Phvul.008G291100 BR-signaling kinase 1Chr08 58842950TA=Synonymous Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59386969TA=Synonymous Phvul.008G291100 BR-signaling kinase 1Chr08 58843028TA=Synonymous Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59387023TA=Synonymous Phvul.008G291100 BR-signaling kinase 1Chr08 58844144TA=Missense Phvul.008G282600 seed imbibition 1 Raffinose synthase Chr08 59387027TA=Missense Phvul.008G291100 BR-signaling kinase 1Chr08 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 1Chr08 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 proteinChr08 59021428TA=Missense Phvul.008G284900 Nucleoporin, Nup133/Nup155-like Chr08 59422596TA=Missense Phvul.008G291700 C2H2-like zinc finger proteinChr08 59026184TA=Synonymous Phvul.008G284900 Nucleoporin, Nup133/Nup155-like Chr08 59422817TA=Synonymous Phvul.008G291700 C2H2-like zinc finger proteinChr08 59059770TA=Intron PAC:27155480 Chr08 59429661TA=Missense Phvul.008G291800 Plant regulator RWP-RK family proteinChr08 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 proteinChr08 59104120TA=Missense Phvul.008G286000 GRAS family transcription factor Chr08 59459160TA=Synonymous Phvul.008G292000 Protein kinase superfamily proteinChr08 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 kinaseChr08 59185202TA=Intron PAC:27155851 Chr08 59479376TA=Synonymous Phvul.008G292300 homoserine kinaseChr08 59185207TA=Intron PAC:27155851 Chr08 59479390TA=Missense Phvul.008G292300 homoserine kinaseChr08 59186244TA=Missense Phvul.008G287400 Chr08 59479407TA=Missense Phvul.008G292300 homoserine kinaseChr08 59186348TA=FivePrimeUTR PAC:27155851 Chr08 59484931TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2Chr08 59214540TA=Intron PAC:27154413 Chr08 59484932TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2Chr08 59303118TA=Intron PAC:27154734 Chr08 59484948TA=Synonymous Phvul.008G292400 tonoplast monosaccharide transporter2Chr08 59303144TA=Intron PAC:27154734 Chr08 59485055TA=Missense Phvul.008G292400 tonoplast monosaccharide transporter2Chr08 59310941TA=Missense Phvul.008G289500 PHE ammonia lyase 1 Chr08 59485104TA=Synonymous Phvul.008G292400 tonoplast monosaccharide transporter2Chr08 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 proteinChr08 59374916TA=Synonymous Phvul.008G291000 UDP-Glycosyltransferase superfamily protein Chr08 59631051TA=Missense Phvul.008G293100 SEC7-like guanine nucleotide exchange family proteinChr08 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