Breeding for resistance to BCMV and BCMNV Phillip Miklas, John Hart, Tim Porch and Jim Beaver

Bean common mosaic virus

Bean common mosaic necrosis virus

BCMV and BCMNV - breeding for resistance

• Persistent global disease problem

• Seed borne • Alternate weed/plant hosts • Spread by aphids

Genetic resistance is the key for control of BCMV and BCMNV

Host x Pathogen Interaction

• BCMV – 5 pathogroups (1, 2, 4, 5, 7) – B serotype • BCMNV – 2 pathogroups (3, 6) – A serotype

Five resistance loci

I gene bc-u bc-1, bc-12

bc-2, bc-22

bc-3

Review paper: Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus: Relationships, Biology, and Prospects for Control

Elizabeth A. Worrall, Francis O. Wamonje, Gerardine Mukeshimana, Jagger J.W. Harvey, John P. Carr, Neena Mitter

Advances in Virus Research # 2015 Elsevier Inc. http://dx.doi.org/10.1016/bs.aivir.2015.04.002 - 46 pages 1

ARTICLE IN PRESS

Viruses separated based on I gene reaction

Potyvirus Host

group BCMV BCMNV

No i gene + mosaic + mosaic

I gene - no symptom

- HR hypersensitive

response

- = resistant reaction, and + = susceptible reactio-

Typical compatible ( + ) susceptible interaction between host & BCMV = mosaic symptoms

Host (non i gene) x pathogen interaction

Host Resistance BCMV BCMNV group genes VII VI

0 none + +

1 bc-u + +

2 bc-u, bc-1 + +

3 bc-u, bc-12 + +

4 bc-u, bc-2 - +

6 bc-u, bc-22 + -

7 bc-u, bc-3 - - - = resistant reaction, and + = susceptible reaction-

Host Resistance BCMV BCMNV group genes VII VIII VI

0 none + + +

1 bc-u + + +

2 bc-u, bc-1 + - +

3 bc-u, bc-12 + - +

4 bc-u, bc-2 - + +

6 bc-u, bc-22 + - -

7 bc-u, bc-3 - + - - = resistant reaction, and + = susceptible reaction-

Host (non i gene) x pathogen interaction new pathogroup (Karasev – BIC 2015)

• 72% of 250 accessions primarily from Africa were susceptible to Pathogroup VI

• 78% of 83 accessions from North America had I gene or I gene protected resistance

Host (I gene) x pathogen interaction Host Resistance BCMV BCMNV

group genes VII III VIa VIb

8 I - dead dead dead

9 I, bc-1 - - dead dead

10 I, bc-12 - - VN = vein necrosis dead

11 I, bc-u, bc-22 - Local lesion LL LL

12 I, bc-3 - - - -

dead = Top Necrosis or Black Root response

Protected I gene against Pathogroup VI strain NL-3

I gene only

I gene + bc-12

I gene protected by bc-12 HR restricted to the 1o leaf (Vein Necrosis)

Inoculated by pathogroup VI strain NL-3

I gene protected by bc-22 (bc-u gene necessary) HR restricted to 1o leaf (Local lesion)

Inoculated by pathogroup VI strain NL-3

I gene protected by bc-3 No symptoms

Inoculated by pathogroup VI strain NL-3

Pyramiding I + bc-3 genes

• Cross I-gene x bc-3 screen F2 pop screened with BCMNV NL-3 strain

R Genes F2 phenotypes None mosaic I only necrosis bc-3 only no symptoms I + bc-3 no symptoms*

Kelly, J.D., L. Afanador & S.D. Haley, 1995. Pyramiding genes for resistance to bean common mosaic virus. Euphytica 82: 207–212.

I gene DNA marker

• Haley, Afanador & Kelly, 1994. W13 RAPD for the I gene. Phytopathology 84: 157–160.

• Melotto, Afanador & Kelly, 1996. SW13 SCAR marker. Genome 39: 1216–1219.

• Vandemark and Miklas. 2005. qPCR for co-dominant interpretation of SW13. Phytopathology 95:499-505.

• Vallejos et al. 2006 molecular characterization of the I locus. Genetics 172:1229–1242.

Phgp 0.1 cm Bng 045 0.2 cm 7 TIR-NBS-LRR genes (I gene)

SW13 SCAR

SNP CAPS

Bello et al. 2014. In silico bulked segregant analysis for development of markers linked to I gene. BMC Genomics 15:903

I gene DNA marker on Pv02

Phgp 0.1 cm Bng 045 0.2 cm 7 TIR-NBS-LRR genes (I gene)

SW13 SCAR

SNP CAPS SNP

Hart et al. (unpublished) ~ 40,000 GBS SNPs and ~ 1000 genotypes

I gene DNA marker - Association Mapping

MAS for the bc-12 gene for resistance to BCMV on Pv03

Miklas, Larsen, Riley, and Kelly. 2000. Potential MAS for bc-12 resistance to BCMV in common bean. Euphytica 116:211-219.

RAPD SCAR Gene Pool Specificity restricts MAS

bc-3 gene DNA marker on Pv06 • Haley, Afanador & Kelly, 1994. Selection for monogenic resistance traits with

coupling- and repulsion-phase RAPD markers. Crop Sci 34: 1061–66. AD19, S13

• Miklas, Afanador, Kelly. 1996. Recombination-facilitated RAPD marker-assisted selection for disease resistance in dry bean. Crop Sci. 36:86-90. S13, AD19

• Johnson, W.C., P. Guzman, D. Mandala, A.B.C. Mkandawire, S. Temple, R.L. Gilbertson & P. Gepts, 1997. Molecular tagging of the bc-3 gene for introgression into Andean common bean. Crop Sci 37: 248–254. ROC11 co-dominant marker and repulsion marker ROC20

• Mukeshimana, et al. & Kelly, 2005. Markers linked to the bc-3 gene

conditioning resistance to bean common mosaic potyviruses in dry bean. Euphytica 144: 291–299.

new AFLP and RAPD flanking markers

bc-3 gene DNA marker • Naderpour et al. 2010. Potyviral resistance derived from cultivars of Phaseolus

vulgaris carrying bc-3 is associated with the homozygotic presence of a mutated eIF4E allele Molecular Plant Pathology 11: 255–263. CAPS marker – candidate gene eIF4E

bc-3 and some bc-32 = 381 bp and 160 bp fragments Bc-3 = 541 bp fragment

• Hart, J.P., and P.D. Griffiths. 2013. A series of eIF4E alleles at the Bc-3 locus are associated with recessive resistance to Clover yellow vein virus in common bean. Theor. Appl. Genet. 126:2849–2863.

single nonsynonymous SNP KASP SNP assay bc-3 – blue Hets – green Bc-3 or bc-32 – red • B. Raatz – KASP marker (10,000 samples))

Recommendations • Combine I and bc-3

• Does bc-3 have negative effect on yield? • Combine I and bc-12 • Does I gene have a negative effect on seed color?

• Use KASP or CAPs for MAS backcrossing of bc-3 and I genes into susceptible cultivars

• Confirm presence of I gene using KASP or CAPS markers. • Phenotype your lines with HG VI strain – NL-3

Kelly, J.D., 1997. A review of varietal response to bean common potyvirus in Phaseolus vulgaris. Plant Varieties Seeds 10: 1–6.

• Monitor/Type strains using a small set of Host Group cultivars

(contact Miklas) or PCR primers (literature) or ELISA (kits or self)

• Fund Bean Virologist position(s)