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Similar to 2016. kayondo si. associatonn mapping identifies qt ls underlying cassava brown streak disease resistance
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2016. kayondo si. associatonn mapping identifies qt ls underlying cassava brown streak disease resistance
- 1. Association Mapping Identifies QTLs Underlying Cassava Brown Streak Disease Resistance Kayondo S.I , Dunia P.D.C., Ozimati A.A, Lozano R, Osingada F., Baguma Y., Vernon Gracen V.E, Offei S.K, Kawuki R.S., Jannink J.L The First World Congress on Root and Tuber Crops CBSD: A Thread to Africa Session Guangxi, Nanning China Jan 18th – 24th 2016
- 2. • Considerable genome diversity within isolates of a species CBSV>UCBSV Cassava Brown Streak Disease…. • Two monopartite +ssRNA viruses of genus Ipomovirus (Family Potyviridae) • Two major strains reported •Uganda cassava Brown Streak Virus •Cassava brown streak Virus Winter et. al.
- 3. CBSD: A threat…. Herrera Campo et al., (2011) Food Security, 3:329-345
- 4. CBSD: Successful colonization…. • Re-emerges in the SSA region in 2001 • Resistance sources un- adapted & rare but could be explored. • Reports of Quantitative (Multi-genic) inheritance of CBSD resistance • Phenotyping protocol still challenging
- 5. Virus – Plant relations…… Plant resistance Forms Virus Resistance Disease Resistance
- 6. Experiences with Molecular markers in cassava Breeding Material QTL mapping Fine Mapping & Gene Discovery Recurrent & Genomic selection QTL detection in bi-parental crosses Only allelic variation present in the two parents captured Best suited for traits with high heritability Complex hybrids from 2 heterozygous parents Bi-parental mapping
- 7. QTL studies in cassava….. Trait / study Markers used Key findings CBB (Jorge et al. 1999) 68 RFLPs 120QTLs (8 in female + 4 in male) CMD (Akano et al. 2002) 186 SSRs 1 SSR linked to a QTL (SSRY28) Productivity (Fregene et al. 1997) 250 markers 114 QTLs CBB (Wydra et al. 2004) 63 SSRs 11 QTLs identified CNP and dry matter (Kizito et al. 2007) 110 SSRs 2 QTLs for CNP & 6 QTLs for DMC Anthracnose 53 RAPDs 2 RAPDs (single Dominant gene) CBSD (Kanju et al.) 500 SSRs 3 Markers reported; EST-SSRY75, NS149 & SSR83 Ferguson et al. (2012) Theor. Appl. Genet. 124:685-695
- 8. Are Association approaches complimentary? Allelic variation in a breeders’ population captured Most current target traits are multi-genic Difficult to get statistical power to detect LD or association mapping by- passes the need for bi-parental mapping populations Association mapping Breeding Material QTL Mapping Fine Mapping & Gene Discovery Recurrent & Genomic selection Identify genetic variants explain differences in phenotype among individuals in a study population
- 9. Association mapping data sets • 429 accessions • Phenotyped 3 years (3trials) • Based on foliar and root phenotypes • 3MAP, 6MAP, 9MAP, 12MAP • Infector rows used to augment disease pressure (TME 204) • Standard and local checks Year NaCRRI Kasese Lira 2012 308 - - 2013 429 429 429 2014 429 429 429
- 10. Score Root Symptom Description Pictorial 1 No symptoms on storage roots 2 less than 5% of storage root tissue is necrotic 3 5-10% of storage root tissue is necrotic 4 10-50% of storage root tissue is necrotic 5 More than 75% of storage root tissue is necrotic CBSD Root Severity Scoring Scale
- 11. Association mapping data sets • Genotyped 429 using the GBS pipeline • ≈ 36,000 SNPs at a 0.05% MAF • Analysis • Used Gapit package under R
- 12. Population structure & Kinship?
- 13. CBSD root Incidence What do GWAS results say…. CBSD root Severity
- 14. CBSD _3MAP Severity What do GWAS results say…. CBSD_3MAP Incidence
- 15. What do GWAS results say…. CBSD_6MAP Incidence CBSD _6MAP Severity
- 16. Top ten SNPs…..
- 17. Genomic predictions…… Allelic variation in a breeders’ population captured Breeding success measured as prediction accuracies Marker effects estimated simultaneously Shortening the breeding cycle Breeding Material QTL mapping Fine Mapping & Gene Discovery Recurrent & Genomic selection GWAS meets GS
- 18. Genomic Prediction for CBSD….
- 19. Summary….… • We identified SNPs with strong association to CBSD resistance on chromosomes; 5 and 11 • Significant SNPs could be weighted for genome wide predictions for better accuracies in GS. • Fine mapping for gene discovery underway • Identify and validate key genes involved in resistant response to CBSD • Further evaluation of virus resistance based on virus titres could be complimentary • Stability of resistance across environments is being explored.
- 20. Project Members / Support • NEXTGEN/NaCRRI. • Dr. Baguma Yona • Dr. Kawuuki Robert • Dr. Titus Alicai • Osingada F. • Mukiibi D. • Adiga. G. • Kyaligonza V. • Kaweesi T. • Majara C. • Orone J. • WACCI • Prof. Vernon G. • Prof. Offei Samuel • Prof. Tongoona P. • Dr. Dzidzienyo D. • Cornell University • Dr. Hamblin M. T. (RIP) • Dr. Hale Tufan • Dr. Jean-Luc J. • Dr. Dunia P.D.C • Dr. Wolfe. M • Ozimati Alfred • Lozano R.