Complex genetic structure of African cassava and genetic architecture of key traits

Ismail Y. RabbiIITA

Ibadan – Nigeria2014 Annual RTB Meeting

Team members and funding acknowledgements

IITAPeter Kulakow, Melaku Gedil, Elizabeth Parkes, Lava Kumar, Nzola Mahungu, Rachid Hanna, Pheneas Ntewaruhunga, Edward Kanju, Morag Ferguson,

Cornell UniversityJean-Luc Jannink, Martha Hamblin, Charlotte Acharya,Delphine Ly, Puna Ramu,

US DoE-JGI and UC BerkeleyDan Rokhsar,Simon Prochnik, Jessen Bredesen, Cindy Ha

CIATLuis-Augusto Becerra

Funding: CRP-RTB/HarvestPlus/BMGF and DFID

National ProgramsNRCRI – Chiedozie EgesiNaCCRI – Robert Kawuki, Yona Baguma,

Objective: increase genetic gain through use of molecular markers in cassava breeding

• Limited use of markers in cassava research.

• Advances in next-generation sequencing should change (and is changing) this situation.

Technical overview

Application of GBS in cassava improvement research areas

1. Understanding genetic diversity and population structure for targeted breeding strategy (e.g. heterotic grouping and hybrid breeding)

2. Development of genomic resources (e.g. snp markers, annotated reference genomes, genetic linkage maps).

3. Determining genetic architecture of target traits (e.g. disease resistance, nutrition).

4. Genomic selection for accelerated breeding.

Population structure and genetic diversity of African cassava

• Very little is known about the population structure, levels of diversity, and ancestry of African cassava.

• Such information is required for targeted breeding strategy (e.g. heterotic grouping and hybrid breeding).

• Most historical studies relied on at most few dozen markers and limited germplasm set.

Populations genotyped so far

Population N Description

IITA improved varieties 1055 Improved genotypes cloned since 1970s

IITA-GRC 278 IITA genebank’s core collection

NRCRI 383 National Root Crops Research Institute (Nigeria)

IITA regional breeding 543 Breeding germplasm/landraces from DRC, Tanzania, Ghana, Malawi, Zambia, Cameroon

IITA landrace collection 809 Landraces assembled from sub-Saharan Africa since early 1980’s

CIAT* 285

Total 3353

*** Sequencing just completed, analysis in progress

60326 SNP loci from ApekI GBS

Population structure/ancestry of African cassava

West Africa, East Africa, Central Africa

• Admixture analysis detected about nine subpopulation (divergent founders).

• Most clones derive their ancestry from more than two subpopulations

• Improved varieties typically show more ancestries (expected?)

Identification of genetic duplicates: Reduce cost of germplasm maintenance

Zambia

DRC

Cameroon

Ghana

Tanzania

IITA GRC

Duplicate distance threshold

04/13/2023

Application of GBS in cassava improvement

1. Understanding genetic diversity and population structure for targeted breeding strategy (e.g. heterotic grouping and hybrid breeding)

2. Development of genomic resources (e.g. snp markers, annotated reference genomes, genetic linkage maps).

3. Determining genetic architecture of target traits (e.g. disease resistance, nutrition).

4. Genomic selection for accelerated breeding.

Mapping populations genotypedthrough RTB/other projects

Population Cross N Genotyping

IITA_MP1 TMSI961089AxTMEB117 205 IGD

IITA_MP2 TMEB117 x TMSI961089A 207 IGD

IITA_MP3* TMS I011412 x TMS4(2)1425

177 IGD, Berkeley

IITA_MP4* TMS30001 x I961089A 271 Berkeley

IITA_MP5* TMSI961089A x TMS30001

243 Berkeley

IITA_MP6 I011371xTMEB117 300 Berkeley

* Contributed to the cassava consensus map consortium

High-density GBS SNP maps

PstI (GACGTC); 770 SNPs ApekI (GCWGC); 6756 SNPs

IITA_MP1 IITA_MP3Crop Science Vol. 54 (2014) Virus Research (2014)

Improvement of reference genome using high-density linkage maps

• High-quality genome assembly needed for QTL, GS, GWAS, genetic transformation.

• Current cassava genome is assembled into 12977 pieces (scaffolds).

• 10 high-density GBS SNP maps used to anchor the cassava reference genome.

• 71.9% of the assembled genome has been placed on the 18 cassava chromosomes.

• Work done as part of the cassava genetic map consortium

04/13/2023

Application of GBS in cassava improvement

1. Understanding genetic diversity and population structure for targeted breeding strategy (e.g. heterotic grouping and hybrid breeding)

2. Development of genomic resources (e.g. snp markers, annotated reference genomes, genetic linkage maps).

3. Determining genetic architecture of target traits (e.g. disease resistance, nutrition).

a. QTL mapping using bi-parental populations

4. Genomic selection for accelerated breeding.

QTL mapping in bi-parental populations

• Mapping population: – Full-sib F1 populations derived from pairs of non-inbred parents

• Phenotyping (>2 years):– Susceptibility to Cassava Mosaic Disease – Carotenoid accumulation (b-carotene) in storage roots– Anthocyanin pigmentations– Number of harvested roots – root weight per plot.

• Genotyping: – GBS using PstI Restriction enzyme (n = 770 SNPs)

• Data analysis: – Genetic map – Joinmap®– Phenotype data analysis - R/lme4 – QTL mapping using R/qtl

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Rabbi et al. Crop Science vol. 54:

QTL mapping in bi-parental populations

Major locus underlying carotenoid accumulation in cassava roots

Phytoene synthase II

Rabbi et al. Crop Science vol. 54:

High-resolution mapping of the CMD2 locus

Resistant parent Susceptible parent

Narrow genetic base for major gene resistance to CMD?

0

10

20

30

40

50

-Log

10(P

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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Linkage group

S5214_780931R2 = 0.74

a

0 30 60 90 120 1500

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20

30

40

50

IITA TMS 011412Moving average (IITA TMS 011412)IITA TMS 4(2)1425scaffold 5214

Position (cM)

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b

a. Genome-wide scan for linkage between CMD resistance and 6756 SNPs across 18 cassava linkage groups.

b. A detailed view of the of linkage group 16

Rabbi et al. Virus Research 2014 DOI: 10.1016/j.virusres.2013.12.028

Anchoring previously-mapped resistance loci

All markers linked to dominant, major gene resistance to CMD from different genetic backgrounds occur in same chromosome!

Linkage group 16

04/13/2023

Application of GBS in cassava improvement

1. Understanding genetic diversity and population structure for targeted breeding strategy (e.g. heterotic grouping and hybrid breeding)

2. Development of genomic resources (e.g. snp markers, annotated reference genomes, genetic linkage maps).

3. Determining genetic architecture of target traits (e.g. disease/pest resistance, plant morphology, nutrition)

b. Genome-wide association

4. Genomic selection for accelerated breeding.

What next?

• So far, most of the applications of GBS SNPs relate to germplasm characterization and QTL discovery.

• Next step is to change gears to ‘applications’ by using the discovered information in the crops’ improvement.– Heterotic pattern/grouping (on-going)– Genomic selection and MAS

• www.nextgencassava.org• www.cassavabase.org

Team members and funding acknowledgements

IITAPeter Kulakow, Melaku Gedil, Elizabeth Parkes, Lava Kumar, Nzola Mahungu, Rachid Hanna, Pheneas Ntewaruhunga, Edward Kanju, Morag Ferguson,

Cornell UniversityJean-Luc Jannink, Martha Hamblin, Charlotte Acharya,Delphine Ly, Puna Ramu,

US DoE-JGI and UC BerkeleyDan Rokhsar,Simon Prochnik, Jessen Bredesen, Cindy Ha

CIATLuis-Augusto Becerra

Funding: CRP-RTB/HarvestPlus/BMGF and DFID

National ProgramsNRCRI – Chiedozie EgesiNaCCRI – Robert Kawuki, Yona Baguma,

Also, check out our poster on tracking of cassava varieties in farmers fields

Thank you !!!