Genetic diversity assessment of east African finger millet and cost- effective development of new SSR markers Santie de Villiers, Kassahun Tesfaye, Emmarold Mneney, Mathews Dida, Patrick Okori, Vincent Njunge, Annis Saiyiorri, Santosh Deshpande, Katrien Devos, Davis Gimode, Dagnachew Lule, Isaac Dramadri, Ismail Mohamed and Damaris Odeny First Bio-Innovate Regional Scientific Conference United Nations Conference Centre (UNCC-ECA) Addis Ababa, Ethiopia, 25-27 February 2013
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Genetic diversity assessment of east African finger millet and cost-effective development of new SSR markers
Presented by Santie de Villiers, Kassahun Tesfaye, Emmarold Mneney, Mathews Dida, Patrick Okori, Vincent Njunge, Annis Saiyiorri, Santosh Deshpande, Katrien Devos, Davis Gimode, Dagnachew Lule, Isaac Dramadri, Ismail Mohamed and Damaris Odeny at the First Bio-Innovate Regional Scientific Conference, Addis Ababa, Ethiopia, 25-27 February 2013
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Genetic diversity assessment of east African finger millet and cost-effective
development of new SSR markers
Santie de Villiers, Kassahun Tesfaye, Emmarold Mneney, Mathews Dida, Patrick Okori, Vincent Njunge, Annis Saiyiorri, Santosh Deshpande, Katrien Devos, Davis Gimode, Dagnachew Lule, Isaac Dramadri, Ismail Mohamed and Damaris Odeny
First Bio-Innovate Regional Scientific ConferenceUnited Nations Conference Centre (UNCC-ECA)
Addis Ababa, Ethiopia, 25-27 February 2013
ICRISAT: Santie de Villiers, Vincent Njunge, Annis Saiyiorri, Santosh Deshpande, Davis Gimode, Damaris Odeny
AAU: Kassahun Tesfaye, Dagnachew Lule
MARI: Emmarold Mneney, Ismail Mohamed
Makerere: Patrick Okori, Isaac Dramadri
Maseno: Mathews Dida
UGA: Katrien Devos
Project Partners
Combined abstracts
‘Genetic diversity assessment of east African finger millet germplasm using SSR genotyping’
and‘Employing next generation sequencing technology for
cost-effective development of new SSR markers for finger millet’
Outline
• Microsatellite genotyping for genetic diversity assessment
• Generation of new molecular tools for marker assisted breeding
• Capacity building• Challenges and opportunities
Molecular markers• Characters which inheritance can be followed at
morphological, biochemical or DNA level.• We use markers to obtain information about the genetics of
traits of interest• Examples
– Morphological trait (such as seed or flower color)– Protein (storage or structural proteins and isozymes)– Identifiable piece of DNA sequence
• Found at specific locations of the genome and transmitted by the standard laws of inheritance from one generation to the next
• Can be used to identify and track particular genes in an experimental cross
Finger milletMicrosatellite genotyping for to determine
genetic relatedness or diversityOptimised sampling strategy
• Single sample per accession• Bulked samples of 3 to 5 individuals, leaves or DNA
Finger millet is >95% inbred, very little variation expected at DNA level
Single or bulked samples can be used
Genotyping markers optimization• Tested 83 available UGEP markers; 57 worked well• Identified set of 20 - 30 SSRs• Ranked according to:Polymorphic information content (PIC) No of alleles at each locus and how well representedEase to work with• 20 markers previously selected by GCP are not the best for
African germplasm; only 2 fall within the 20 best markers• Publication
Optimised SSR markers for genotypingMarker Name Primer F Primer R Allele No Availability PIC GCP
– Analysed 1307 cultivated accessions (from Bio-Innovate and HOPE projects)
– Used 20 SSR markers, generated > 26 000 data points– Wild germplasm (106 accessions) data being finalised
Post-graduate students at ICRISAT-Nairobi (3 months)Ethiopia (Dagnachew Lule), Uganda (Isaac Dramadri) and
Tanzania (Ismail Mohamed)– DNA extraction– Genotyping– Data analysis– Training course (CAPACITATE)
Publication write-up
Diversity assessment continuedResults
All data sets <10% missing data; Analysed with genetic diversity software (PowerMarker, DARwin, Arlequin, STRUCTURE)Combined data: PIC ranged from 0.47 to 0.95 (mean 0.81)
Publication strategyCultivated for each country Wild germplasm across countries
5/6 from BioInnovate, 2 from HOPE
Genetic diversity resultsEthiopia Kenya
Tanzania Uganda
Developing additional molecular tools for marker-assisted breeding
SSR markers – status and potential– Only 82 published SSR markers available– Basic genetic map with 32 SSRs (Dida et al, 2007)– Need more markers, mapped – Used next-generation sequencing (NGS) to
identify more SSRs in finger millet• Ecogenics (Switzerland): Roche 454 seq after SSR
enrichment (KNE 755, KNE 796 and E. indica)• UGA: Illumina MiSeq with Covaris random sheared and
Pst1 digested libraries of KNE 755 and KNE796
SSR marker developmentFrom Roche 454 data, 178 new SSRs identified–Validated in laboratory (MSc student, KU)–63 polymorphic (12 did not work well), 15 monomorphic, 100 did not work/work well
–PIC ranged from 0.12 - 0.77; mean 0.67
Total NGS data assembled and run through MISA to identify SSRs:–KNE796 - 1552 SSRs; KNE755 - 1845 SSRs–SNP markers to be identified from NGS data
Outputs achieved• Optimized FM sampling, DNA extraction and
genotyping protocol, prepared publication• Trained students (2 PhD, 2 MSc in molecular
marker applications; 1 MSc in Bioinformatics• 1408 samples (cultivated and wild)
genotyped and 6 publications under preparation
• > 3000 new SSRs identified; 178 validated• 63 new SSR markers developed; potentially
1000s more
Challenges• Cost of validating SSRs
– $16 per primer pair, validation– 1000s new primer pairs identified
• Mapping of new and potential SSR markers
• General lack of genomic resources for finger millet