Characterization of Genetic Diversity of Conserved Germplasm        A major component of IITA’s Research Portfolio        ...
1. Why to assess genetic diversity?-From domestication to selection to improvement, farmers have relied on genetic variati...
2. How IITA does it?1. Morphological characterization: morphological and agronomical descriptors2. Molecular characterizat...
Morphological characterization  Bambara groundnut: 391 accessions  characterized using 39 descriptors                     ...
Germplasm characterizationCrops            Number        Characterization                 descriptorsCowpea           46  ...
Assessment of genetic diversity of yam germplasm with DNA markers-Yam (Dioscorea sp): multi-species, polyploid and vegetat...
D. alata (red)                                                                     D. bulbifera (purple)                  ...
Assessment of genetic diversity of cowpea germplasm with DNA markers-Cowpea (Vigna unguiculata L. ) plays an important nut...
Diverse geographical origins covered in Sub-Saharan Africa              Nigeria, Niger, Cameroon, Ghana,Senegal, Zambia, M...
Genetic diversity in yard-long bean      (Vigna unguiculata subspecies unguiculata cv-gr sesquipedalis)-50 accessions anal...
Molecular analysis of genetic diversity of Maize Sample study in a collaborative GCP funded project (IITA, France, Kenya, ...
Caribbean - Cuba                               2                            Central America - Guatemala                   ...
Molecular analysis of genetic diversity in bananas (banana & plantain)-Bananas (Musa spp.) are major food crops in tropica...
EMS treatment to induced mutations in vitro                             The most preferred cultivars                      ...
Analysis of somaclonal variations in IITA germplasm-Genetic integrity is of primary importance in germplasm conservation, ...
Characterization of somaclonal variations in banana germplasm                                                      2nd rou...
IITA participates to international efforts to generate genomic resourcesuseful for diversity analysis, mapping and functio...
Characterization of germplasm by Cytogenetics-Two flow cytometers (Nigeria and Uganda)-Ploidy analysis in yam, cassava, ba...
Acknowledgments:-Morphological description of Germplasm: Dr. Dumet D.-Molecular analysis of Yam : Dr. Asiedu R.-Analysis o...
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Characterization of Genetic Diversity of Conserved Germplasm

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Why to assess genetic diversity? How IITA does it: Morphological characterization, Molecular characterization,Cytogenetic characterization.

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Characterization of Genetic Diversity of Conserved Germplasm

  1. 1. Characterization of Genetic Diversity of Conserved Germplasm A major component of IITA’s Research Portfolio Outline 1. Why to assess genetic diversity? 2. How IITA does it? 3. Case studies Crops: - Yam - Cowpea - Bananas (Banana & Plantain) - Bambara groundnut - Maize - African yam bean By Irie Vroh Bi
  2. 2. 1. Why to assess genetic diversity?-From domestication to selection to improvement, farmers have relied on genetic variation for thousands of years.-Genetic diversity gives species the ability to adapt to changing environments,including new pests, new diseases and new climatic conditions.-Efficient conservation of germplasm depends on the understandingof the available diversity.-Efficient utilization of germplasm by breeders depends on the understandingof the extent, nature and structure of the available genetic diversity.Conservation of a diversity in crop species, varieties and wild relativesand efficient utilization are key to our survival Need to assess and understand crop genetic diversity
  3. 3. 2. How IITA does it?1. Morphological characterization: morphological and agronomical descriptors2. Molecular characterization: Molecular markers (Biotech Ibadan & BECA, Nairobi) -Simple Sequence Repeat (SSR) -Amplified Fragment Length Polymorphism (AFLP) -Single Nucleotide Polymorphism (SNP) -Diversity Array Technology (DArT) -IITA uses available DNA markers -IITA in collaboration with partners participates in developing new molecular markers -Molecular analyses are performed in house or outsourced3. Cytogenetic characterization : ploidy analysis
  4. 4. Morphological characterization Bambara groundnut: 391 accessions characterized using 39 descriptors Bananas: ~200 accessions characterized with 50 descriptorsAfrican yam bean: 152 accessionsCharacterized using 62 descriptors
  5. 5. Germplasm characterizationCrops Number Characterization descriptorsCowpea 46 Completed Core/MinicoreBambara 39 Completed CoreYam 125 Completed CoreCassava 42 Partial In progressSoybean 6 PartialWild vigna 70 Partial In progressBananas 50 Completed coreMaize 0 Started
  6. 6. Assessment of genetic diversity of yam germplasm with DNA markers-Yam (Dioscorea sp): multi-species, polyploid and vegetatively propagated-Over 90% of world yam production comes from West and Central Africa-Farmers continue to grow local landraces that are low in productivity-IITA holds >3000 landrace accessions from several African countries-Identification of suitable diverse parents is key to breeding-A core subset of 391 accessions characterized by IITA based onmorphological characteristics-The core collection comprising six economically important species.-Analysis of the core for inter- and intra-specific variability using 23 SSR markers
  7. 7. D. alata (red) D. bulbifera (purple) D. cayenensis (yellow) D. dumentorum (ash) D. esculenta (blue) D. rotundata (green) -Results generally consistent with established taxonomical relationships -High level of genetic variation in core germplasm -Greater resolution of genetic relationships among and within species Valuable information for trait mapping and breeding in yamFigure 1. Genetic diversity tree of 342 yam accessions baseon SSR data using unweighted neighbour- joining analysis
  8. 8. Assessment of genetic diversity of cowpea germplasm with DNA markers-Cowpea (Vigna unguiculata L. ) plays an important nutritional role in tropicaland subtropical regions (e.g. Sub-Saharan Africa)-High protein content “~20%” (cowpea is recognized as the poor man’s meat)-Cowpea forage is also used to feed livestock-IITA maintains 15,000 accessions of cowpea-A core collection of 2000 accessions was selected basedon morphological characterization-Subsets of the core collection were analyzed further using molecular markersto make a mini core of more than 300 accessions-Subsets of the mini core are often drawn for further analyses
  9. 9. Diverse geographical origins covered in Sub-Saharan Africa Nigeria, Niger, Cameroon, Ghana,Senegal, Zambia, Malawi, Swaziland, Chad, Tanzania, Keyna, Mozambique, Zimbabwe, Congo, Botswana48 wild cowpeas assessed using 12 SSR markers Gel electrophoregram of SSR primer VM27 showing amplifications with forty eight wild cowpeaFrom the analysis of number of alleles, marker polymorphic information content (PIC)and clustering:-Three subspecies, dekindtiana, pubescens and rhomboidea were recognized-Others were recognized as varieties of dekindtiana except mensensis-Southern Africa region is a likely center of diversity of wild cowpeas-Nine SNP markers were also used to assess the diversity of the subset
  10. 10. Genetic diversity in yard-long bean (Vigna unguiculata subspecies unguiculata cv-gr sesquipedalis)-50 accessions analyzed with 16 SSR primers-68 polymorphic bands produced-Accessions of yard-long-bean from India showed the highest level of genetic diversity-The results support the suggestion that India is a likely center of diversity Development of genomic resources for diversity analysis, mapping and marker assisted breeding in cowpea IITA in collaboration with UCR, GCP and others
  11. 11. Molecular analysis of genetic diversity of Maize Sample study in a collaborative GCP funded project (IITA, France, Kenya, China, India, Indonesia, Thailand, Vietnam, and Philippines)Objective 1: Assess the global maize diversity (previous studies targetedLatin and North American and European germplasm only)Objective 2: Compare genotyping procedures from different laboratories-237 landraces (Asia, Africa and Latin America). 10 teosinte accessions(Northern and Central America) and six CIMMYT maize lines were used- 80 African landraces provided by IITA and analyzed with 51 SSR markers-The diversity within maize landraces was extensive- Up to 36% of alleles were unique to teosintes
  12. 12. Caribbean - Cuba 2 Central America - Guatemala Central America - Mexico Eastern Africa - Ethiopia Eastern Africa - Kenya Eastern Africa - Malawi Eastern Africa - Somalia 1.5 Eastern Africa - Uganda Eastern Africa - Zambia Eastern Africa - Zimbabwe Eastern Asia - China Eastern Asia - Japan Middle Africa - Angola Middle Africa - Chad 1 Middle Africa - Congo North America - Canada North America - USA Northern Africa - Algeria Northern Africa - Egypt Northern Africa - Morocco 0.5 Northern Africa - Sudan Oceania - Australia South America - Argentina South America - Bolivia South America - Brazil South America - Chilie 0 South America - Colombia-2 -1.5 -1 -0.5 0 0.5 1 1.5 2 South America - Ecuador South America - Paraguay South America - Peru South America - Peru South America - Venezuela -0.5 South-Eastern Asia - Indonesia South-Eastern Asia - Philippines South-Eastern Asia - Thailand South-Eastern Asia - Vietnam Southern Africa - South Africa Southern Asia - Afghanistan Southern Asia - India -1 Southern Asia - Nepal Southern Asia - Pakistan Teosinte Western Africa - Benin Western Africa - Burkina Faso Western Africa - Ghana -1.5 Western Africa - Guinea Western Africa - Mali Western Africa - Niger Comparison to data gathered from collaborators indicated that data from IITA was of good quality
  13. 13. Molecular analysis of genetic diversity in bananas (banana & plantain)-Bananas (Musa spp.) are major food crops in tropical and subtropical regions-Major cultivars are triploid (AAA, AAB and ABB genomes) with high sterility levels-Wild species are highly diverse genetically and fertile-IITA maintains cultivated and wild accessions (in vitro and field germplasm)-Diversity analysis in the wild diploids to group and use the most diverse -Done with SSR analysis-Diversity analysis in the triploid landraces for association mapping -Done with SSR and AFLP markers-Diversity in mapping populations (also conserved in vitro) -Done with SSR, AFLP, DArT and SNP markers Markers specific to Musa genomes A genome B genome Reproducible PCR markers differentiating the A from the B genome in a diversity panel
  14. 14. EMS treatment to induced mutations in vitro The most preferred cultivars are evolutionary dead endPlantain Agbagba (AAB) Cooking banana Bluggoe (ABB) -Meristems treated with various concentrations of EMS -Duration of treatment from 2 hours to 72 hours -In vitro culture of meristems and acclimatation EMS treated plants transferred to the field for evaluation of phenotypes and agronomic traits Collaboration with IAEA?
  15. 15. Analysis of somaclonal variations in IITA germplasm-Genetic integrity is of primary importance in germplasm conservation, plant breeding,and in the adoption of new varieties-IITA conserves vegetatively propagated crops in its in vitro Genbank-The germplasm is maintained over years and distributed to national and internationalrequesters-Unexpected variations can occur during in vitro propagation (somaclonal)to generate off-types with or without agronomic value-It is critical to track those variations and to possibly link them to traits
  16. 16. Characterization of somaclonal variations in banana germplasm 2nd round amplification of variant band by PCR -In vitro culture & -Appropriate molecular techniques Sequencing-Potential functions of the variation assessed-Sequences registered in public genomic databasesExamples:GenBank Acc# ET165586 to ET165601 (US_NCBI)-Plants tagged & transferred to the field to linkgenomic variations to phenotypes-Applying the procedure to other IITA Sequence of a variant fragment in Bluggoe (ABB genome)mandate crops (e.g. Yam)
  17. 17. IITA participates to international efforts to generate genomic resourcesuseful for diversity analysis, mapping and functional genomics Cowpea • Over 40,000 ESTs sequenced from cowpea drought differential cDNA libraries • 17,000 unique contiguous and single sequences yielded • Over 5000 potential new markers identified – 3226 single nucleotide polymorphisms – 1806 microsatelite markers • Microarray chip under manufacture Bananas • 5494 ESTs sequenced from musa drought differential cDNA libraries, combined with existing consortia data • 32,000 unique contiguous and single sequences yielded • Over 30000 potential new markers identified – 28800 single nucleotide polymorphisms – 1937 microsatelite markers Participation to generating DArT arrays in IITA mandate crops -Bananas -Yam
  18. 18. Characterization of germplasm by Cytogenetics-Two flow cytometers (Nigeria and Uganda)-Ploidy analysis in yam, cassava, bananas, Cowpea and other orphan crops-Throughtput of 100 samples a day CV-Accessions File # Ploidy CV-Accessions File # Ploidy D. rotundata 907 4x Balbisiana-selfed2 310 2x D. rotundata 927 4x Balbisiana-selfed3 317 2x D. rotundata 929 4x Balbisiana-selfed4 301 2x D. cayenensis 908 8x Balbisiana-selfed5 320 2x D. cayenensis 909 8x Balbisiana-selfed6 389 2x D. cayenensis 910 8x Balbisiana-selfed7 302 2x D. cayenensis 911 8x Balbisiana-selfed8 330 2x D. cayenensis 912 8x Balbisiana-selfed9 303 2x D. cayenensis 916 8x Balbisiana-selfed10 340 2x
  19. 19. Acknowledgments:-Morphological description of Germplasm: Dr. Dumet D.-Molecular analysis of Yam : Dr. Asiedu R.-Analysis of Bananas: Dr. Vroh B. I.-Cowpea analysis by SSR markers: Dr Fatokun C.-Maize analysis by SSR markers: Dr. Hearnes S.-Cytogenetics-ploidy analysis: Dr. Vroh B. I.-Generating genomic resources (Cowpea, bananas): Dr. Hearnes S.-Participating to DArT markers activities: Dr. Vroh B. I. -Several Donors -Several collaborators (NARS, ARIs) -Several students and national partners trained (List available with scientists mentioned above) THANK YOU

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