Theme 1:Comparative andApplied Genomics (CAG)Rajeev VarshneyTheme Leader, GCP
QTL*cp488892 *cp491181*cp678132 *cp680434*cp6814250.0*OG905182 *OG9054747.8*OG938507 *OG927619*CaESTContig3 *OG9010158.1*O...
- Assembly of genomics and germplasmresources- Development of comparative maps andframework genetic markers for targetcrop...
 Large-scale molecular markers including SSR, SNPand DArT markers for less-studied crops Genetic maps with moderate mark...
 Cloning of AltSB (SbMATE1) and Pup1 in sorghum andrice and diagnostic markers Molecular markers associated with traits ...
Comparative Genomics Challenge Initiative(PDC: Leon Kochian USDA/ARS & Cornell Uni)• This CI takes advantage of previous G...
• Rice:QTL mapping and GWAS for Al-tolerance (G7009.07, Susan McCouch);cloning and characterization of Pup1 and disseminat...
• Pup1 major tolerance gene is a constitutive enhancer of root growth• Acts upstream of genes with key function in root gr...
Genotyping and Phenotyping ofSorghum Association Panel• Initially genotyped with Illumina 1536 SNP chip by M Hamblin• Curr...
GWAS of Rice 3D Root Architecture Traits• Have completed phenotyping rice for 3-D RSA traits undercontrol conditions in ge...
Breeding value of AltSB0.001.002.003.00Control (-Al) TT ttYield(tons/ha)Allelic substitution effect:100 RILs BR007 x SC283...
 Establish network for genomics community forenhanced discussions in the area ofdevelopment and application of genomic to...
Consensus: AGN is a GREAT initiative, it would encourage newbreeders also to have access and provide all help toimplement...
Suggestions:A broader survey about requirements of tools,resources on portals may be conducted Some basic information ab...
Comparative genomicsvsspecies specific genomics research Excellent for understanding the genomeevolution, gene function a...
Challenges/ Opportunities Data management and sharing (continuous discussions Analysis of large scale datasets especiall...
 Utilization of developed genomic resources Assemble large scale informative SNPs for breedingapplications Accelerated ...
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GRM 2011: Theme 1 -- Comparative genomics

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GRM 2011: Theme 1 -- Comparative genomics

  1. 1. Theme 1:Comparative andApplied Genomics (CAG)Rajeev VarshneyTheme Leader, GCP
  2. 2. 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*cp171561*cp172966 *cp677302*cp67675334.5*Ca22434 *OG89761935.7*OG90696936.1*OG90389838.2*cp489035 *cp173466*cp48922239.4*cp68164939.6*cp68192039.8*CaM078742.7*OG89823144.1*Ts4547.5*X60755 *U7148.8*FENR50.1*G6PD54.1*ACONc54.3*PGMb61.1*OG89569073.2*OG896172 *OG89587177.3*TA3R-TA23L82.2*OG901744 *OG901711112.9*Ca21567 *cp350602118.9*OG898271 *OG919502122.3*H1D24 *H1C092*CaM0539 *H5B04125.28Genetic mapTechnologyinterventionGeneticsof traitKnowledge-basedbreedingUses or develops genomic tools and technologies and evaluatesmultidisciplinary approaches to better understand gene functionand interaction to improve knowledge of gene system acrosscrops for enabling knowledge-based breedingNot technology driven;Demand driven tech use
  3. 3. - Assembly of genomics and germplasmresources- Development of comparative maps andframework genetic markers for targetcrops- Assignment of genes and pathways tophenotypes- Validation of genes and pathwaysFour objectives
  4. 4.  Large-scale molecular markers including SSR, SNPand DArT markers for less-studied crops Genetic maps with moderate marker density available Cost-effective SNP genotyping platform i.e.GoldenGate assays, KASPar assays for a number ofcrops Transcriptomic resources for chickpea, pigeonpea,sweetpotato, cowpea, cassava Physical maps for cassava, cowpea Mutant collections in common bean, potatoes Utilization of mutant collections in rice for functionanalysisProgress updates- i
  5. 5.  Cloning of AltSB (SbMATE1) and Pup1 in sorghum andrice and diagnostic markers Molecular markers associated with traits of interest tobreeders in cowpea, chickpea Gene expression analysis for drought tolerance in rice Bioinformatic tools for comparative genomicsanalysis Gene expression analysis for selected transcriptionfactors in wheat for drought tolerance Allele discovery for drought tolerance in sorghum andrice Bioinformatic tools for gene expression analysis ISMU pipeline for analysis of NGS data…Progress updates- ii
  6. 6. Comparative Genomics Challenge Initiative(PDC: Leon Kochian USDA/ARS & Cornell Uni)• This CI takes advantage of previous GCP projectswhere two genes AltSB (SbMATE1) and Pup1 haveeither already been cloned.Rice PUP1 Sorghum AltSBClonehomologsClonehomologsMaize Sorghum Maize RiceVerify role inP efficiencyVerify role in AltoleranceP EfficientMaizeP EfficientSorghumProducts for breeding programsin developing countriesAl TolerantMaizeAl TolerantRiceProducts for breeding programsin developing countriesPyramid P Eff & Al Tol
  7. 7. • Rice:QTL mapping and GWAS for Al-tolerance (G7009.07, Susan McCouch);cloning and characterization of Pup1 and dissemination of breedinglinesto NARS partners (G7010.03.04, Sigrid Heuer)• Maize:Cloning and characterization of Al-tolerance(G7010.03.02, Claudia Guimaraes);Cloning and characterization of Pup1 (G7010.03.01, Leon Kochian);breeding for Al-tolerance and P-efficiency (G7010.03.05, Sam Gudu)• Sorghum:Cloning and characterization of P-efficiency(G7009.03, Jura Magalhaes)breeding for Al-tolerance and P-efficiency (G7010.03.03, EvaWeltzein)Comparative genomics RI
  8. 8. • Pup1 major tolerance gene is a constitutive enhancer of root growth• Acts upstream of genes with key function in root growth and stress response• Final set of Pup1 gene/allele specific markers available• Development of Pup1-breeding lines by MABC completed• First field data confirm beneficial effect of Pup1• Seed increase ongoing at IRRI and ICABIOGRAD• Mapping of Al-tolerance in rice is underwaySigrid Heuer, IRRI
  9. 9. Genotyping and Phenotyping ofSorghum Association Panel• Initially genotyped with Illumina 1536 SNP chip by M Hamblin• Currently being genotyped by sequencing by Ed Buckler andSharon Mitchell as part of their NSF BREAD grant .-Developed multiplexing approach to sequence multiplesamples in one lane of Illumina High-Seq.- Developed a bioinformatics pipeline for SNP ID- Hope to add 100,000 to 200,000 SNPs to each member ofassociation panel.• Have phenotyped entire panel for Al tolerance – waiting forgenotyping to be completed to conduct GWAS on Al tolerance.• Have phenotyped the IGD part of the panel (converted lines) forP efficiency at Embrapa.•Will soon phenotype panel for P efficiency and root architecture inlow P soils in greenhosse at CornellLeon Kochian, USDA/ARS & Cornell Uni
  10. 10. GWAS of Rice 3D Root Architecture Traits• Have completed phenotyping rice for 3-D RSA traits undercontrol conditions in gel-based media. Phenotyped theMcCouch’s NSF-TV rice diversity panel (500 lines) and alsobi-parental mapping population (168 lines).• That involved phenotyping approximately 2000 individualplants in gellan gum cylinders.• Roots imaged at 3, 6, 9, & 12 days afterplanting to include dynamicgrowth parameters.• Randy is in Taiwan for the summerwhere he as nearly completes 3Dreconstructions and quantificationof his 20 RSA traits.• GWAS analysis will be completedin Fall with 950k SNP chip.Leon Kochian, USDA/ARS & Cornell Uni
  11. 11. Breeding value of AltSB0.001.002.003.00Control (-Al) TT ttYield(tons/ha)Allelic substitution effect:100 RILs BR007 x SC283 r=0.28 (P=0.0047):nutrient sol. vs. field Drought x Al tt  TT 0.5 - 1 ton/haChr 3Map position (cM)-log10(p)0 50 100 150 200 250024681012GyGy_floRnrgAltSB• Background SNP markers• Association pipeline for Altolerance• Assessment of AltSB onacid soils (grain yieldadvantage)Jura Magalhaes, EMBRAPA
  12. 12.  Establish network for genomics community forenhanced discussions in the area ofdevelopment and application of genomic tools Develop user friendly portal that will presentinformation on tools, resources developed byGCP or available in public domain to offer one-stop shop solution to the breeding community Broker-access to economically pricedgenotyping and sequencing servicesAgricultural Genomics Network(AGN)
  13. 13. Consensus: AGN is a GREAT initiative, it would encourage newbreeders also to have access and provide all help toimplement molecular breeding.AGN will keep the existing GCP community vibrant andactive in post-GCP era! Markers of choice for breeding applications:SNPs (also SSRs in some cases!) Genotyping through outsourcing is preferred andaccepted solution by NARS breedersDiscussions on AGN
  14. 14. Suggestions:A broader survey about requirements of tools,resources on portals may be conducted Some basic information about molecular breedingtogether with tutorials may be kept on portal Helpdesk to respond on genomics related questions intime is URGENTLY required.Portal can be in wiki style Sustainability is an important issue in post-GCP era.Discussions on AGN
  15. 15. Comparative genomicsvsspecies specific genomics research Excellent for understanding the genomeevolution, gene function and trait mechanism Applied aspects- few examples? Cloning of one gene in one species- how usefulthis is for the other species? Pup1 and Al-tolerance in cereals? Development of diploid genome physical mapfor applications in 4x groundnuts? Species specific genomic resourcedevelopment is no more an expensive and timeconsuming task?
  16. 16. Challenges/ Opportunities Data management and sharing (continuous discussions Analysis of large scale datasets especially NGS data(working with international players/Theme 3) Outsourcing vs. in-house work to generate data in cost-effective and timely fashion (BGI collaboration) Conversion of genomics research platform in breedingapplication platforms (KASar assays in collaborationwith Theme 2/ IBP) Capacity building – an important component ofGenomics Integrated Breeding Services
  17. 17.  Utilization of developed genomic resources Assemble large scale informative SNPs for breedingapplications Accelerated activities of Comparative Genomics CItowards identifying diagnostic markers for Al-toleranceand P-uptake in targeted cereals Publication of large scale datasets Engage CGIAR community by implementing AGN underGIBSPerspectivesThank you !

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