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