Download - Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Transcript
Page 1: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Progress in Common Bean Breeding for Angular Leaf Spot Resistance

T.L.P.O. Souza1, M.C. Gonçalves-Vidigal2, B. Raatz3, C.M. Mukankusi4, A.F.B. Abreu1, L.C. Melo1, M.A. Pastor-Corrales5

Common Bean Disease Workshop on Angular Leaf Spot and Root RotsProtea Hotel Kruger Gate, Skukuza, South Africa

July 20-24, 2015

1Embrapa Arroz e Feijão, Santo Antonio de Goiás, GO, Brazil; 2Universidade Estadual de Maringá, Maringá, PR, Brazil; 3CIAT, Bean Program, Cali, Colombia; 4CIAT, Bean Program,

Kawanda, Uganda; 5ARS-USDA, Beltsville, MD, USA.

July 20, 2015

Page 2: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Angular Leaf Spot (ALS)

Sources: Sami; Rava; Schwartz.

Page 3: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

• ALS resistance genes- Named genes- Unnamed genes

• Major ALS resistance QTLs

• Molecular markers linked to resistance loci

• Genomic localization of resistance loci

• Breeding efforts to develop ALS resistant germplasm/cultivars- Africa (CIAT and partners)- Brazil (Embrapa/UFLA/UFV and partners)

Contents

Page 4: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesNamed genes

Three independent dominant ALS resistance genes have been named, mapped and officially accepted by the BIC Genetics Committee

Gene symbolR source Gene pool LG Reference

Official Original

Phg-1 Phg-1 AND 277 Andean (A) Pv01Carvalho et al. (1998)Queiroz et al. (2004)Gonçalves-Vidigal et al. (2011)

Phg-2 Phg-? Mexico 54 Mesoamerican (MA) Pv08Sartorato et al. (2000)Namayanja et al. (2006)Mahuku et al. (2011)

Phg-3 Phg-ON Ouro Negro Mesoamerican (MA) Pv04

Corrêa et al. (2001)Faleiro et al. (2003) Gonçalves-Vidigal et al. (2013)Sanglard et al. (2013)

Page 5: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Markers linked to ALS resistance genesNamed genes

R Gene LGLinked marker

Marker type

Distance (cM)

R SourceGene pool

Reference

Phg-1 Pv01

OPH13490 RAPD 5.5

AND 277 A

Carvalho et al. (1998)SH13520 SCAR 5.6 Queiroz et al. (2004)

CV542014450 STS 0.7Gonçalves-Vidigal et al. (2011)

TGA1.1570 STS 1.3

Phg-2 Pv08OPE04650 RAPD 11.8

Mexico 54 MASartorato et al. (2000), Namayanja et al. (2006)

OPN02890 RAPD 5.9Sartorato et al. (2000)

SN02890 SCAR 5.9

Phg-3 Pv04

OPM02460 RAPD 5.3

Ouro Negro MA

Corrêa et al. (2001)OPBA16 RAPD 10.4 Faleiro et al. (2003)SBA16560 SCAR 7.1

Queiroz et al. (2004)SM02460 SCAR 5.3SF101050 SCAR 7.8

Gonçalves-Vidigal et al. (2013)g2303350 STS 0.0

Page 6: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesNamed genes

AND 277 (gene Phg-1)

• Single dominant gene (Andean gene pool)- Carvalho et al. (1998): race 63-23 - Gonçalves-Vidigal et al. (2011): race 63-23

• Phg-1 + three dominant and independent genes (Caixeta et al. 2005): allelism tests using the races 31-17, 63-19 and 63-23

• Phg-1 and Co-14 are tightly linked (0.0 cM) to each other on Pv01(Gonçalves-Vidigal et al. 2011).

• Important resistance source used in Brazil and Southern Africa(Aggarwal et al. 2004; Ragagnin et al. 2009; Costa et al. 2010; Sanglard 2010; Rocha et al. 2012; Ddamulira 2014)

Page 7: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesNamed genes

Mexico 54 (gene Phg-2)

• Single dominant gene (Mesoamerican gene pool)- Sartorato et al. (2000): race 63-19- Namayanja et al. (2006): race 63-39

• Three dominant and independent genes (Caixeta et al. 2005): allelism tests using the races 31-17, 63-19, 63-23 and 63-39

• ALS R genes in Mexico 54 and BAT 332 are located in the same locus on Pv08 - Namayanja et al. (2006): race 63-39

• Important resistance source used in Brazil and Pan-Africa (Oliveira et al. 2005; Namayanja et al. 2006; Sanglard 2010; Ddamulira 2014)

Page 8: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesNamed genes

Ouro Negro (gene Phg-3)

• Single dominant gene (Mesoamerican gene pool)- Corrêa et al. (2001): race 63-39- Faleiro et al. (2003): races 31-55 and 63-31- Gonçalves-Vidigal et al. (2013): race 63-39

• Phg-3, Co-34 and Ur-14 are tightly linked to each other on Pv04(Faleiro et al. 2000, 2003; Souza et al. 2011; Gonçalves-Vidigal et al. 2013).

• Important resistance source used in Brazil(Ragagnin et al. 2009; Costa et al. 2010; Sanglard 2010; Rocha et al. 2012)

Page 9: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesUnnamed genes

R source R geneGene pool

LG Reference

Cornell 49-242 Phg-? MA?

(Pv08)a

Nietsche et al. (2000) – Single dominant gene

Caixeta et al. (2005) – Single dominant gene

Mahuku et al. (2011) – Single dominant gene

Sanglard et al. (2013) – Single dominant gene

MAR 2 Phg-? MA?

(Pv08)

Ferreira et al. (2000) – Single dominant gene

Caixeta et al. (2005) – Two dominant and independent genes

Sanglard et al. (2013) – Single dominant gene

BAT 332 Phg-? (Phg-22) MA?

(Pv08)

Caixeta et al. (2003) – Single dominant gene

Namayanja et al. (2006) – Single dominant gene (Phg-22): ALS R genes in Mexico 54 and BAT 332 are located in the same locus

Sanglard et al. (2013) – Single dominant gene

G10474 Phg-? MA?

(Pv08)Mahuku et al. (2004) – Single dominant gene

Mahuku et al. (2011) – Single dominant gene

G5686Phg-? (PhgG5686A)Phg-? (PhgG5686B)Phg-? (PhgG5686C)

APv04Pv04 Mahuku et al. (2009) – Three dominant and complementary genesPv09

G10909Phg-? (PhgG10909A)

Phg-? (PhgG10909B)MA

Pv04Mahuku et al. (2011) – Two dominant and complementary genes

Pv08aPhysical position inferred based on allelism tests, mapping info and markers sequences/BLAST search.

Page 10: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Markers linked to ALS resistance genesUnnamed genes

R gene LG Linked markerMarker

typeDistance

(cM)R source

Gene pool

Reference

Phg-??

(Pv08) a

OPE04650 RAPD 12.5Cornell 49-242 MA Nietsche et al. (2000)OPN02890 RAPD 3.2

SN02890 SCAR 3.2

Phg-??

(Pv08)OPE04500 RAPD 5.8 MAR 2 MA Ferreira et al. (2000)

Phg-? (Phg-22)?

(Pv08)OPAA07950 RAPD 5.1

BAT 332 MA Caixeta et al. (2003)OPAO950 RAPD 5.8

Phg-??

(Pv08)PF5330 SCAR 5.0 G10474 MA

Mahuku et al. (2004)

(Andean gene pool)

Phg-? (PhgG5686A)Phg-? (PhgG5686B)Phg-? (PhgG5686C)

Pv04Pv04

Pv-ag004270

Pv-ctt001120

Pv-at007150

SSRSSRSSR

0.017.112.1

G5686 A Mahuku et al. (2009)Pv09

Phg-? (PhgG10909A) Pv04 Pv-gaat001164 SSR 13.0

G10909 MA Mahuku et al. (2011)Phg-? (PhgG10909B) Pv08

PF13310

PF9260

SE04709

SCAR

SCAR

SCAR

4.9

7.4

9.9aPhysical position inferred based on allelism tests, mapping info and markers sequences/BLAST search.

Page 11: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesUnnamed genes

Cornell 49-242 (Phg-?)

• Single dominant gene (Mesoamerican gene pool)- Nietsche et al. (2000): race 31-17- Caixeta et al. (2005): races 63-23 and 31-17 - Mahuku et al. (2011): race 1-7- Sanglard et al. (2013): race 63-23

• OPE04650, OPN02890 and SN02890 markers linked to Phg-2 present in Mexico 54 (Sartorato et al. 2000) are also linked to the unnamed ALS R gene present in Cornell 49-242 (Nietsche et al. 2000)

• Gene position inferred based on mapping info: Pv08

• Resistance source used in Brazil(Nietsche et al. 2000; Sanglard 2010)

Page 12: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesUnnamed genes

Cornell 49-242 (Phg-?)

• ALS R genes in Cornell 49-242 (Phg-?) and Mexico 54 (Phg-2) are not allelic, once they segregate independently- Caixeta et al. (2005): allelism tests using the races 63-23 and 31-17

• ALS R genes in Cornell 49-242 (Phg-?) and Ouro Negro (Phg-3) are not allelic, once they segregate independently- Sanglard et al. (2013): allelism test using the race 63-23

• ALS R gene in AND 277 (Phg-1) is from the Andean gene pool and located on Pv01

• Physical position suggests that the ALS R gene present in Cornell 49-242 (Phg-?) isan allele of Phg-2

- Fine mapping (???)

- Additional allelism tests (???)

Page 13: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

MAR 2 (Phg-?)

• Single dominant gene (Mesoamerican gene pool)- Ferreira et al. (2000): race 63-39- Sanglard et al. (2013): race 63-23

• Two dominant and independent genes (Caixeta et al. 2005): allelism tests using the races 63-19, 63-23 and 63-39

• OPE04650 marker linked to Phg-2 present in Mexico 54 (Sartorato et al. 2000) is also linked to the unnamed ALS R gene present in MAR 2 (Ferreira et al. 2000)

• Gene position inferred based on mapping info: Pv08

• Resistance source used in Brazil(Oliveira et al. 2005; Sanglard 2010)

ALS resistance genesUnnamed genes

Page 14: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesUnnamed genes

• Caixeta et al. (2005) - Allelism tests using the races 63-19, 63-23 and 63-39- ALS R genes in MAR 2 (Phg-?) and Mexico 54 (Phg-2) are allelic: races 63-19 and 63-39- ALS resistance genes in MAR 2 (Phg-?) and Mexico 54 (Phg-2) are NOT allelic: race 63-23

• ALS R genes in MAR 2 (Phg-?) and Ouro Negro (Phg-3) are not allelic, once they segregate independently- Sanglard et al. (2013): allelism tests using the races 63-23 and 63-39

• ALS R gene in AND 277 (Phg-1) is from the Andean gene pool and located on Pv01

• Physical position suggests that the ALS R gene present in MAR 2 is an allele of Phg-2

MAR 2 (Phg-?)

Page 15: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesUnnamed genes

BAT 332 (Phg-?: Phg-22)

• Single dominant gene (Mesoamerican gene pool)- Caixeta et al. (2003): race 61-41- Namayanja et al. (2006): race 63-39- Sanglard et al. (2013): race 63-39

• ALS R genes in Mexico 54 and BAT 332 are located in the same locus - Namayanja et al. (2006): allelism test using the race 63-39

• Gene position inferred based on allelism test (Namayanja et al. 2006): Pv08

• Resistance source used in Brazil (Oliveira et al. 2005; Sanglard 2010)

• ALS R gene present in BAT 332 (Phg-?) = Phg-22

- Physical position

Page 16: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesUnnamed genes

G10474 (Phg-?)

• Single dominant gene (Mesoamerican gene pool)- Mahuku et al. (2004): race 63-63- Mahuku et al. (2011): race 7-7

• The SCAR marker PF5330 linked to the ALS R gene present in G10474 and those linked to PhgG10909B in G10909 were mapped close to each other on Pv08 (Mahuku et al. 2011)- PF5330 marker is limited to the Andean gene pool.

• Gene position inferred based on mapping info and markers sequences/BLAST search: Pv08

• Fine-mapping is ongoing to support the fully characterization of the ALS R gene present in G10474 (Phg-?)

Page 17: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesUnnamed genes

G5686 (Phg-?: PhgG5686A/PhgG5686B/PhgG5686C)

• Three dominant and complementary genes (Andean gene pool)- Mahuku et al. (2009): race 31-0

• Physical position (Mahuku et al. 2009)- PhgG5686A: Pv04- PhgG5686B: Pv04- PhgG5686C: Pv09

• Major ALS R genes identified in G5686 by Mahuku et al. (2009) were later considered as quantitative ALS R loci by further QTL stuidies(Oblessuc et al. 2012; Keller et al. 2015)- PhgG5686A ALS4.1GS.UD

- PhgG5686B ALS4.2GS

- PhgG5686C ALS9.1GS

Page 18: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

ALS resistance genesUnnamed genes

G10909 (Phg-?: PhgG10909A/PhgG10909B)

• Two dominant and complementary genes (Mesoamerican gene pool)- Mahuku et al. (2011): race 63-63

• Physical position- PhgG10909A: Pv04- PhgG10909B : Pv08

• Allelism tests showed that the ALS R genes in G10909 were different from those in the Mesoamerican cultivars Mexico 54, MAR 2, G10474 and Cornell 49-242 (Mahuku et al. 2011)

• The G10909 ALS R gene resistant to the race 7-35 (PhgG10909B ) co-segregateswith the G10474 R gene – they are on the same locus or closely linked(Mahuku et al. 2011)

Page 19: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Major ALS resistance QTLs

a Named according to Miklas et al. (2010).

QTLa LG MarkerMarker

typeDistance

(cM)R Source

Gene pool

Reference

ALS10.1DG.UC Pv10

GATS11b – IAC137

SSR

13.4

CAL 143 A

Oblessuc et al. (2012)

GATS11b 6.0 Oblessuc et al. (2012, 2013, 2015)

ATA220 0.6Oblessuc et al. (2013)

PvM127 0.6

ALS4.2GS.UC Pv04 PvBR92 SSR 4.0Oblessuc et al. (2012)

ALS5.2UC Pv05 Pv-att006 SSR -

ALS4.1GS.UD Pv044M437

Marker50MAS_ALS4b

SNP (HRM)- G5686 A Keller et al. (2015)SNP (Tm)

SNO (LGC)

QTL studies support the quantitative nature of ALS resistance(Lopez et al. 2003; Teixeira et al. 2005; Mahuku et al. 2009; Mahuku et al. 2011)

Page 20: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Major ALS resistance QTLs

CAL 143 (ALS10.1DG,UC/ALS4.2GS,UC/ALS5.2UC)• Andean gene pool

• Effects of the ALS R QTLs in CAL 143 (Oblessuc et al. 2012)- ALS10.1DG.UC (Pv10): 16%–22% (major effects, significant in all experiments)- ALS4.2GS.UC (Pv04): 10.8% (natural infection in the field)- ALS5.2UC (Pv05): 9.4% (inoculated conditions in the greenhouse)

• Genealogy of CAL 143: Cargabello x AND 277- Caixeta et al. (2005) identified three major independent R genes in AND 277 by allelism tests using the races 31-17, 63-19 and 63-23, in addition to Phg-1.

Page 21: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Major ALS resistance QTLs

G5686 (ALS4.1GS,UD)

• Andean gene pool

• PhgG5686A (Pv04) ALS4.1GS.UD (Oblessuc et al. 2012; Keller et al. 2015)

• Effect of the QTL (Keller et al. 2012)- ALS4.1GS.UD (Pv04): 75% (inoculated conditions in the greenhouse – race 31-0)

Other QTL studies for ALS resistance are ongoing

Page 22: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Representation of ALS resistance lociPv01

Phg-1 (AND 277)

- - // - -

Co-14

(AND 277)(MDRK)

(Kaboon)(Perry Marrow)

(Widusa)

Co-14 (Pitanga)

Ur-9 (PC-50)

Co-xCo-w

(Jalo EEP558)- - // - -

Page 23: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Pv04

Phg-3 (Ouro Negro)

Co-34

(Ouro Negro)(Mexico 222)(Mexico 227)

(BAT 93/PI207262)

Ur-14 (Ouro Negro)

Ur-5 (Mexico 309)

Co-yCo-z

(Jalo EEP558)

Phg-?PhgG10909A(G10909)

ALS4.1GS,UD (G5686)ALS4.2GS,UC (CAL 143/G5686)

Phg-?PhgG5686APhgG5686B(G5686)

Representation of ALS resistance loci

- - // - -

- - // - -

Page 24: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Pv05

ALS5.2UC (CAL 143)

Representation of ALS resistance loci

- - // - -

- - // - -

Page 25: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Pv08

Phg-2 (Mexico 54)

Co-4 (TO)

(SEL 1308)(PI207262)

Ur-13(Redlands Pioneer)

(Kranskop)

Phg-? (Cornell 49-242)

Phg-?PhgG10909B (G10909)

Phg-? (MAR 2)

Phg-? Phg-22 (BAT 332)

Phg-? (G10474)

Representation of ALS resistance loci

- - // - -

- - // - -

- - // - -

Page 26: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Pv09

ALS9.1GS (G5686)Phg-?

PhgG5686C (G5686)

Representation of ALS resistance loci

- - // - -

- - // - -

Page 27: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Pv10

ALS10.1DG,UC (CAL 143)

Representation of ALS resistance loci

- - // - -

- - // - -

Page 28: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Representation of ALS resistance loci

Page 29: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Source: Ferreira, Campa & Kelly (2013).

Linkage groups showing anthracnose race-specific resistance genes directly mapped using different common bean genotypes

Page 30: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Highlights

• There are effective major loci controlling ALS resistance- Mesoamerican gene pool: Pv04 and Pv08- Andean gene pool: Pv01, Pv04 and Pv10

• QTL studies support the quantitative nature of ALS resistance

• Classical genetic analysis based on allelism tests are still important and necessary but presents limitations

• Direct or indirect mapping using info from molecular markers linked to known ALS R genes and QTLs is recommended to support the characterization of new ALS R loci

• Need and opportunity to develop specific SNP based markers- Lobaton et al. (in preparation) - G5686 and G10474

Page 31: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesAfrica – Identification of ALS resistance sources

• Resistance sources to a wide spectrum of Andean and Mesoamerican P. griseolaraces from Africa have been identified, under both field and screenhouse conditions (Pastor-Corrales et al. 1998; Stenglein et al. 2003; Mahuku et al., 2003, 2004, 2009; Wagara et al., 2011; Ddamulira et al., 2014)

- MEX 54, MAR 1, MAR 3, G5686, G10909, G4691, G 10613, G19833 and G10474

• Ddamulira et al. (2014): Screening with races 1:6, 21:39 and 17:39 of Mesoamerican origin and 61:63 of Andean origin

- U00297 (Ugandan landrace)- U0074- U351- U1-9

Page 32: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesAfrica – Identification of ALS resistance sources

• ECABREN/NDFRC selected bean genotypes were separately inoculated with 44 P. griseola races under greenhouse conditions:

- None of the genotypes was resistant to all races

- 13 genotypes were resistant (1-3) or moderately resistant (4-6) to at least 40 of the races

- Small-seeded genotypes ECAB 0754 and ECAB 0617 were resistant or moderately resistant to all races, except 33-39 and 58-18, respectively

- ECAB 0754 exhibited the highest level of resistance, with a mean disease severity of 1.1%.

All the resistant or moderately resistant genotypes were of the small-seeded bean types which are commercially less popular

Page 33: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesAfrica – Development of ALS resistance germplasm

The breeding strategy adopted by CIAT Uganda in developing ALS resistance germplasm has been three fold:

i. to introgress the gene Phg-2 (Mexico 54) into commercial susceptible varieties

ii. to combine ALS resistance with resistance to other diseases, in particular root rot and BCMV/BCMNV

iii. to pyramid the different ALS resistance genes into a single commercial variety

Page 34: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Combined crosses No. of lines evaluated

FieldALS (1-9 scale)

ScreenhousePythium (1-9 scale)

2 2.1-3.9 >3.9 1 1.1-3.9 >3.9

(CAL 96 x RWR 719) x (CAL 96 x MEX 54) 43 4 36 3 0 15 28

(CAL 96 x SCAM 80 CM/15) x (CAL 96 x MEX 54) 15 4 9 2 0 3 12

(CAL 96 x MLB 49-89 A) x (CAL 96 x MEX 54) 46 4 32 10 1 15 30

Total 104 12 77 15 1 33 70

Reaction of 104 lines from different crosses to combine ALS and Pythium root rot resistance

(Field and screenhouse conditions, Kawanda, 2006)

Breeding efforts to develop resistant varietiesAfrica – Development of ALS resistance germplasm

Lines resistant to both diseases have been selected

Page 35: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesAfrica – Development of ALS resistance germplasm

PedigreeNo. of families positive for:

SPE04(gene Phg-2)

SW13(gene I)

SPE04 and SW13

(CAL 96 x RW 719) x (CAL 96 x MEX 54) 35 11 16(CAL 96 x MLB-49-89A ) x (CAL 96 x MEX 54) 65 9 14(CAL 96 x SCAM 80CM/15) x (CAL 96 x MEX 54) 22 2 1Total 122 22 31

F5 progenies screened with the SCAR markers SPE04 and SW13

Page 36: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesAfrica – Gene pyramiding

Resistance sources (Ddamulira, 2014)

• Phg-1 (AND 277)

• Phg-2 (Mexico 54)

• Phg-? (G5686 – ALS4.1GS,UD)

Two popular susceptible varieties:

K132 and Kanyebwa

Page 37: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Highlights

• Important ALS resistance sources have been indentified and the inheritance of their resistance characterized

• Marker-assisted selection combined to phenotypic selection based on field and greenhouse screening is showing to be a promissory strategy to enhance the development of ALS R germplasm for Africa

Page 38: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Gene pyramiding

Resistance sources

• Phg-1 (AND 277)

• Phg-2 (Mexico 54)

• Phg-3 (Ouro Negro)

• Phg-? (Cornell 49-242)

• Phg-? (MAR 2)

• Phg-? (BAT 332)

Page 39: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Gene pyramiding

Source: Oliveira et al. (2005).

Phg-2 (Mexico 54)Phg-? (MAR 2/BAT 332)

Page 40: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Gene pyramiding

Source: Ragagnin et al. (2009).

Phg-1/Co-14 (AND 277)Phg-3/Co-34/Ur-14 (Ouro Negro)

Page 41: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Gene pyramiding

Source: Costa et al. (2010).

Black-seeded variety“Diamante Negro”

Phg-1/Co-14 (AND 277)Phg-3/Co-34/Ur-14 (Ouro Negro)

Page 42: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Gene pyramiding

Source: Rocha et al. (2012).

Phg-1/Co-14 (AND 277)Phg-3/Co-34/Ur-14 (Ouro Negro)

Page 43: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Gene pyramiding

Source: Sanglard (2010).

Phg-1/Co-14 (AND 277)Phg-3/Co-34/Ur-14 (Ouro Negro)

Phg-2 (Mexico 54)Phg-?

(Cornell 49-242)(MAR 2)

(BAT 332)

X

“Carioca” seeded background

cv. Rudácv. Pérola

Page 44: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Highlights

• Pyramiding effective Andean and Mesoamerican ALS R genes into a same variety is a likely strategy to provide wide and lasting resistance, as well as stack major genes and QTLs

• This strategy assisted by molecular markers is showing to be promissory to develop carioca-seeded elite germplasm resistant to ALS but presents limitations for cultivar development in Brazil

• The use of backcrossing as the only breeding strategy to stack target ALS R loci into a same elite line can not be a competitive approach for cultivar development, once the market demand can considerably diverge and the original recurrent parent could become obsolete regarding to other desirable agronomic traits

Page 45: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Multiple crosses and multisite field screening

- High yielding- High grain quality (“carioca”)- Adapted to mechanical harvesting- Resistance to ALS

cv. BRS Sublime(CNFC 10429)

- Genealogy: EMP 250 / 4 / A 769 /// A 429 / XAN 252 // V 8025 / PINTO UI 114 - Origin: CIAT, Cali, Colombia

Line YLD (Kg/ha) ALS (1-9)BRS Estilo 2,269.1 5.8BRS Sublime 2,532.9 2.7Perola 2,082.3 5.2

JOINT ANALYSIS19 Intermediate Field Trials (2006-2009)

Page 46: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Multiple crosses and multisite field screening

- High yielding- High grain quality (“carioca”)- Adapted to mechanical harvesting- Resistance to ALS

cv. BRS Sublime(CNFC 10429)

Line YLD (Kg/ha) ALS (1-9)BRS Estilo 1,959.5 5.2BRS Sublime 2,110.0 2.6Perola 2,036.9 4.6

JOINT ANALYSIS29 Final Field Trials (2009-2012)

Page 47: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Recurrent selection

Source: Borém & Miranda (2009).

Page 48: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Breeding efforts to develop resistant varietiesBrazil – Recurrent selection

Recombination of SelectedProgenies

Development ofProgenies

Evaluation ofProgenies

Source: Modified from Borém & Miranda (2009).

Page 49: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Source: Arantes et al. (2010).

Breeding efforts to develop resistant varietiesMinas Gerais, Brazil – Recurrent selection

• 7 carioca-seeded lines:Carioca MG, CI-140, CI-128, ANPAT 8.12, IAPAR 81, ESAL 693 and Pérola

• 10 ALS R sources:AN 512561, AND 277, Ouro Negro, CNC, CAL 143, MAR 2, MAR 1, G 5686, MA 4137 and Jalo

Base population - Partial diallel involving:

Page 50: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Source: Arantes et al. (2010).

Breeding efforts to develop resistant varietiesMinas Gerais, Brazil – Recurrent selection

Genetic gain after eight cycles of phenotypic recurrent selection for ALS resistance

Page 51: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Cycle

Lavras Lambari Patos de Minas Mean

ALS

(1-9)

YLD

(Kg/ha)

ALS

(1-9)

YLD

(Kg/ha)

ALS

(1-9)

YLD

(Kg/ha)

ALS

(1-9)

YLD

(Kg/ha)

1

4.9

(4.3-6.3) 2,403

6.2

(4.7-6.3) 2,517

4.1

(3.2-6.0) 1,873

5.1

(3.8-6.2) 2,264

2

4.6

(3.7-5.3) 2,260

5.6

(4.3-5.7) 2,800

4.3

(3.3-5.2) 2,350

4.8

(3.4-5.2) 2,470

3

4.2

(2.3-5.0) 2,047

3.7

(2.3-4.7) 2,530

3.2

(2.0-4.2) 1,970

3.7

(2.3-4.3) 2,182

4

3.8

(2.3-4.7) 2,463

3.9

(3.3-5.3) 3,140

3.3

(2.0-4.4) 2,605

3.7

(2.5-5.0) 2,736

5

4.6

(4.3-5.7) 2,542

4.9

(4.3-6.0) 2,430

3.9

(2.8-4.7) 2,305

4.5

(3.5-5.7) 2,426

6

4.2

(3.0-5.7) 2,402

5.3

(4.3-7.0) 2,687

3.8

(2.6-5.2) 2,135

4.4

(3.5-5.8) 2,408

7

3.8

(3.7-5.7) 2,683

4.0

(2.7-5.3) 2,940

3.5

(2.5-5.1) 2,183

3.8

(2.6-5.2) 2,602

Mean 4.3 2,400 4.8 2,720 3.7 2,203 4.3 2,441

Carioca MG 3.7 3,017 5.7 2,483 4.7 2,133 4.7 2,544

Pérola 5.3 2,542 6.3 2,617 5.0 1,592 5.6 2,250

Minas Gerais, Brazil – Recurrent selection

Page 52: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Central Brazil – Recurrent selectionProgenies (C0S2:4) AY (Kg/ha) ALS (1-9) AP (1-9) RL (1-9)SRCMA.127 1,736 2.0 5.0 4.5SRCMA.23 1,943 2.5 6.0 3.5SRCMA.26 2,977 2.5 6.0 5.5SRCMA.320 2,052 2.5 5.5 4.0BRS SUBLIME 1,733 3.0 5.5 4.5SRCMA.147 1,250 3.0 5.0 3.0SRCMA.216 1,636 3.0 5.0 4.0SRCMA.285 1,784 3.0 6.0 4.0SRCMA.162 2,065 3.5 7.0 6.5SRCMA.28 1,565 3.5 6.5 7.5SRCMA.29 1,565 3.5 7.0 7.0SRCMA.34 1,976 3.5 5.5 4.0SRCMA.75 1,564 3.5 5.0 4.0SRCMA.186 1,997 4.0 5.5 4.0SRCMA.198 2,141 4.0 5.5 6.0SRCMA.218 1,856 4.0 6.0 5.5SRCMA.229 2,396 4.0 5.0 4.0SRCMA.31 2,180 4.0 6.0 5.0SRCMA.314 1,849 4.0 6.5 5.5SRCMA.339 1,551 4.0 7.0 7.0SRCMA.73 1,943 4.0 5.0 4.5SRCMA.100 1,923 4.5 6.5 7.5SRCMA.241 1,744 4.5 5.5 4.5SRCMA.1 1,714 5.0 5.5 5.5SRCMA.206 1,951 5.5 4.5 4.0BRS HORIZONTE 1,234 9.0 5.0 3.0Mean (55 progenies) 1,800 5.0 5.6 4.8Mean (24 progenies) 1,859 3.8 5.7 4.9Mean (10 progenies) 1,857 3.0 5.6 4.7CV(%) 16.8 22.4 11.1 26.3F-value 6.55 3.8 2.4 2.4

Sources:Silva et al. (2015);

Melo et al. (in preparation)

JOINT ANALYSISThree Field Trials

(2013)

Genitors:1. MA-1-15-132. 2003200393. CNFC 107554. MA-1-2-10-15. CNFN 102846. MA-1-8-97. 2032003308. CF 220249

Page 53: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

• Recurrent selection can be used as a breeding strategy to accumulate the greatest number of major and minor ALS R genes/QTLs distributed in different parents into a same elite line

• The use of recurrent selection assisted by molecular markers as a breeding strategy to combine different target alleles into a same progeny presenting other desirable agronomic traits and still using this and other superior progenies to form a promissory new base population is been adopted by the Embrapa/UFLA breeding program

• This strategy could be very useful to develop high agronomic performing and modern common bean cultivars harboring multipleALS R loci (major and minor genes)

Highlights

Page 54: Progress in Common Bean Breeding for Angular Leaf Spot ...arsftfbean.uprm.edu/bean/.../BDW-Day1-Thiago-Livio.pdf · Progress in Common Bean Breeding for Angular Leaf Spot Resistance

Thank you!Thiago SouzaCommon Bean Breeding and GeneticsEmbrapa Rice and BeansSanto Antônio de Goiás, GO, [email protected]+55 (62) 3533-2129