Association Mapping Identifies QTLs Underlying Cassava Brown Streak Disease Resistance

Transcription

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 18 th 24 th 2016

2 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 Considerable genome diversity within isolates of a species CBSV>UCBSV Winter et. al.

3 CBSD: A threat. Herrera Campo et al., (2011) Food Security, 3:

4 CBSD: Successful colonization. Re-emerges in the SSA region in 2001 Resistance sources unadapted & 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 Bi-parental mapping 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

7 QTL studies in cassava.. Trait / study Markers used Key findings CBB (Jorge et al. 1999) CMD (Akano et al. 2002) Productivity (Fregene et al. 1997) 68 RFLPs 120QTLs (8 in female + 4 in male) 186 SSRs 1 SSR linked to a QTL (SSRY28) 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:

8 Are Association approaches complimentary? Breeding Material QTL Mapping Fine Mapping & Gene Discovery Recurrent & Genomic selection Association mapping Identify genetic variants explain differences in phenotype among individuals in a study population 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 bypasses the need for bi-parental mapping populations

9 Association mapping data sets Year NaCRRI Kasese Lira 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

10 CBSD Root Severity Scoring Scale Score Root Symptom Description Pictorial 1 No symptoms on storage roots less than 5% of storage root tissue is necrotic 5-10% of storage root tissue is necrotic 10-50% of storage root tissue is necrotic More than 75% of storage root tissue is necrotic

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 What do GWAS results say. CBSD root Severity CBSD root Incidence

14 What do GWAS results say. CBSD _3MAP Severity CBSD_3MAP Incidence

15 What do GWAS results say. CBSD _6MAP Severity CBSD_6MAP Incidence

16 Top ten SNPs..

17 Genomic predictions Breeding Material QTL mapping Fine Mapping & Gene Discovery Recurrent & Genomic selection GWAS meets GS Allelic variation in a breeders population captured Breeding success measured as prediction accuracies Marker effects estimated simultaneously Shortening the breeding cycle

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.

21 Thanks for listening