association mapping mines qtls underlying cassava … · 2016-03-01 · association mapping...
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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
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• 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.
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CBSD: A threat….
Herrera Campo et al., (2011) Food Security, 3:329-345
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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
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Virus – Plant relations……Plant resistance
Forms
Virus
Resistance
Disease
Resistance
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Experiences with Molecular markers in cassava
Breeding Material
QTL mappingFine 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
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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
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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 MappingFine Mapping
& Gene Discovery
Recurrent & Genomic selection
Identify genetic variants explain differences in phenotype among individuals in a study population
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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
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Score Root Symptom Description Pictorial
1 No symptoms on storage roots
2less than 5% of storage root
tissue is necrotic
35-10% of storage root tissue is
necrotic
4
10-50% of storage root tissue is
necrotic
5More than 75% of storage root
tissue is necrotic
CBSD Root Severity Scoring Scale
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Association mapping data sets
• Genotyped 429 using the GBS pipeline
• ≈ 36,000 SNPs at a 0.05% MAF
• Analysis• Used Gapit package under R
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Population structure & Kinship?
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CBSD root Incidence
What do GWAS results say….CBSD root Severity
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CBSD _3MAP Severity
What do GWAS results say….
CBSD_3MAP Incidence
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What do GWAS results say….
CBSD_6MAP Incidence
CBSD _6MAP Severity
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Top ten SNPs…..
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Genomic predictions……
Allelic variation in a breeders’ population captured
Breeding success measured as prediction
accuraciesMarker effects
estimated simultaneously
Shortening the breeding cycle
Breeding Material
QTL mappingFine Mapping
& Gene Discovery
Recurrent & Genomic selection
GWAS meets GS
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Genomic Prediction for CBSD….
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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.
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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.
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Thanks for listening