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TLI 2012: Groundnut research pogress report
 

TLI 2012: Groundnut research pogress report

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    TLI 2012: Groundnut research pogress report TLI 2012: Groundnut research pogress report Presentation Transcript

    • Objective 1: Improve groundnut productivity for marginal environments from Sub-Saharan Africa Report Year 2EMBRAPA- UGA – ICRISAT – ISRA-Senegal – Malawi Nat. Prog. – Tanzania Nat. Prog Addis Ababa 8 May 2012
    • Confirm disease/drought resistance/tolerance sources – Activity 1 Assess new diversityMilestone 1 Confirmation of disease resistance and drought tolerance of at least 10 new genotypesMilestone 2 Two new sources of disease resistance - new genetic material for breeding (either CSSL, AB line, synthetics)Milestone 3 Chromosome segments from wild donor for disease and/or drought (CSSL Ad xAi – Fleur11)Milestone 4 Pre-breeding material incorporating wild favourable alleles for future MARS.Milestone 5 8 available synthetics tested for disease resistance; 1–2 AB-QTL populations with one synthetic amphidiploids.Milestone 6 Database of phenotyping data for drought / knowledge of key traits for drought adaptation.Milestone 7 A sub-set of 10 tolerant lines for TLII breeding / PVS trials.
    • 60 lines for drought New sources of resis- Confirmed tolerant Confirmed sensitive tance to diseaseICG 12879 47-10 Rust: ICGV 02194, ICG 11426,ICGV 02189 ICG 14482 ICGV 01276, ICGV 02286, and55-437 ICG 2772 ICG 02446ICG 3140 ICG 5663ICG 4729 JL24 Rosette: ICG 14705, ICG 13099,ICG 3584 ICG 1834 ICG 9449, and ICG 15405ICGV 02038 ICG 12625ICGV 02266 ICG 8106 ELS in ESA; ICG 6022, ICGICGV 96466 ICGV 99001 405, ICG 14466, ICG 6057, ICGICGV 97183 Trial on-going in 9449 and ICG 12509ICG 4750 Senegal / India /ICG 11088 Niger ELS in WCA: ICG 6703; ICG Repeat in Niger / Senegal 10036, ICG 10384 ICG 9449, ICG 12509, and ICG 11219 On-going PVS trials in Mali
    • Profile of water use from flowering to maturity Sensitive Tolerant Arrows indicates Re-wateringTolerant lines develop a smaller canopyWork on going to assess variation / test with modeling (obj 5) Ratnakumar & Vadez 2011 - FPB
    • Relationship between TE and yield 16 14 R² = 0.65 Post RainyPod Yield - WS 12 10 season 8 6 4 2 0 0.00 0.50 1.00 1.50 2.00 2.50 3.00 -2 Transpiration Efficiency 12 R² = 0.03 Rainy Pod yield - WS 10 8 season 6 4 2 0 0.00 0.50 1.00 1.50 2.00 2.50 3.00 Transpiration Efficiency TE effect depends on season
    • Marker assisted AB-QTL population development A. ipaensis (BB) x A. duranensis (AA) F1 (AB) sterile colchicineFleur11(AABB) x AiAd (AABB) fertile F1 Genetic map AB-QTL (BC2F3, BC3F2) BC4F1 CSSL (BC4F3)
    •    – – – – – – BC3F2)Foncéka et al. 2012 Pod width Seed size Pod morphology Days to flowering Plant architecture Seed morphology Yield components AB-QTL Analysis 27 traits recorded: Two water regimes 142 families (BC2F3 & a01 a06 Stress tolerance indices Pn_ww Pw_ww b06 Shw_ww GH_ww Activity 1 – milestone 3 Hw_wl b01 Pb_wl Pb_ww Pmat_wl Pwi_wl a02 Pwi_ww HI_wl Ss_ww HI_ww STI-Tb Hw_wl Swi_wl Hw_ww Tb_wl Pb_wl Pb_ww Pod weight Pc_ww Pod number a07 STI-Hw GH_ww Hsw_wl b02 Hsw_ww Pb_wl Hpw_wl Pb_ww Hpw_ww Pc_ww Hsw_wl Pc_ww Hsw_ww PH_ww Pb_wl Pl_ww Pwi_wl Pwi_wl Pwi_ww Pwi_ww Ss_wl Sl_wl Ss_ww Sl_ww STI-Hpw Ss_wl STI-Hsw Ss_ww Swi_wl STI-Hsw Swi_ww STI-Pn STI-Sn Swi_wl Swi_wl a03 Swi_ww GH_ww Swi_ww b03 b07 Pmat_ww DFL a04 a08 Pb_ww PH_ww Pc_ww Pl_wl b04 Pwi_ww GH_ww Sl_ww PH_ww Pod length involved in drought adaptation b08 Seed length a05 PH_ww Hw_wl Pn_ww Sn_ww a09 Pb_ww STI-Hw Pc_ww STI-Pn Pl_wl STI-Pw Sl_ww STI-Sw STI-Tb Chromosome segments from wild donor Tb_wl b09 Tb_ww b05 indices a10 GH_ww Pc_ww Hpw_wl Pwi_wl Stress tol. Pod width Hpw_ww Pwi_ww Pwi_wl Pod number Pwi_ww b11 Seed number STI-Hpw b10 Pb_ww GH_ww Sw_ww Pc_ww PH_ww Swi_wl Pmat_wl Swi_ww
    • Chromosome segments from wild donor involved in drought adaptationActivity 1 – milestone 3CSSL Population AiAd x Fleur11: phenotyping – Two years characterization in Senegal (2011 & 2012 ongoing) • Yield and yield components • Morphology and phenology • Two water regimes / 6 rep/trtMapping of new QTLs and validation of previously identified QTLs
    • Chromosome segments from wild donor involved in disease resistance Activity 1 – milestone 2CSSL Population AiAd x Fleur11: distribution• Seeds multiplication /distribution: – Icrisat Niger – Icrisat Malawi – Icrisat India – Embrapa (ongoing)• Ongoing multiplication in Senegal / India
    • Development of new AB-QTL populations Activity 1 – milestone 5• Amphidiploids from ICRISAT ICRISAT identity number Cross ISATGR 1212 A. duranensis x A. ipaensis AAxBB ISATGR 278-18 A. duranensis x A. batizocoi AAxBB ISATGR 10B A. magna x A. valida BBxBB ISATGR 9A A. batizocoi x A. cardenasii BBxAA ISATGR 5B A. magna x A. batizocoi BBxBB ISATGR 265-5A A. kempff mercadoi x A. hoehnei AAxAA ISATGR 90B A. kempff mercadoi x A. stenosperma AAxAA ISATGR 34B A. batizocoi x A. duranensis BBxAA ISATGR 206 A. duranensis x A. valida AAxBB ISATGR 52B A. valida x A. duranensis BBxAA• Succesful germination: • ISATGR 278-18 • ISATGR 52B • ISATGR 206• Successful hybridization with Fleur11 • ISATGR 278-18: 22 BC1 plants produced. BC2 development ongoing. • ISATGR 206: Hybridation ongoing
    • Activity 2 Develop SNP markers for cultivated groundnutMilestone 8 One suitable method to identify SNPs. Genome-wide resource of SNPs useable towards a broadly applicableMilestone 9 SNP, from an exploration of at least 8+8 contrasting genotypes.
    • Simple and flexible genotyping-by-sequencing requiring minimal infrastructure 1. Digest total genomic DNA of individual samples with pre-selected restriction enzyme 2. Ligate to sample-specific adaptors that include bar codes 3. Pool, then size-select all at once 4. Sequence pool -- map reads, call SNPs, infer genotypes Steps 1-3 require minimal infrastructure (gel electrophoresis, waterbath, UV illuminator, refrigeration) Flexible to low polymorphism rates (via sequencing depth) Presently piloting in diploid and polyploid genomes with and without reference sequences
    • Activity 3 Map disease resistance QTLs Anchor these QTL to the physical mapMilestone 10 4 populations phenotyped (1 per disease) for disease resistance QTLs for resistance to major groundnut diseases - QTL flankingMilestone 11 markers deposited in MBP database. 25 additional SSR markers in strategic regions of the groundnutMilestone 12 genome containing disease resistance QTLs
    • Consensus map with QTLs for LLS and rust resistance Common QTLs for LLS and rust Major QTL Major QTL for LLS for rustMolecular Breed 2012, DOI 10.1007/s11032-011-9661-z.
    • Stable QTLs identified for LLS and rust resistance Major QTLs detected in two or more than two out of 6 environmentsQTLs Linkage Marker interval No. of R² (%) group environmentsLate leaf spot (LLS) resistanceQTLR4-LLS01 AhXII GM1573-pPGPseq8D09 6 10.27-62.34QTLR4-LLS02 AhXV GM2009-GM1536 2 12.49-67.98QTLR4-LLS03 AhXV GM1536-GM2301/GM2079 2 10.83-17.37QTLR4-LLS05 AhV IPAHM356-GM1577 4 10.81-15.34QTLR4-LLS09 AhXVIII TC11F12-TC2G05 3 3.39-8.5QTLR5-LLS01 AhXV GM2009-GM1536 2 7.58-49.64QTLR5-LLS02 AhVIII GM2504-GM2746 2 9.79-22.46Rust resistanceQTLR4-Rust01 AhXV GM2009-GM1536 6 10.68-82.27QTLR4-Rust02 AhXV GM1536-GM2301/GM2079 6 12.43-62.35QTLR4-Rust03 AhXV IPAHM103-GM1954 6 23.12-82.96QTLR4-Rust05 AhII TC1B02-pPGSseq18E07 2 2.54-3.29QTLR5-Rust01 AhXV GM2009-GM1536 7 17.57-66.05QTLR5-Rust02 AhXV IPAHM103-GM1954 6 17.42-78.96QTLR5-Rust03 AhV RN16F05-GM1988 2 15.07-29.02 Molecular Breed 2012, DOI 10.1007/s11032-011-9661-z.
    • INTROGRESSION OF DISEASE RESISTANCES BY BACKCROSSING Starting pointA. hypogaea IAC-Runner-886susceptible agronomically adaptedSynthetic amphidiploidresistant unadapted phenotype Runner-886 Amphidiploid end of season LS damage pod types more resistant (not as resistant as new synthetics)
    • We can see introgression of resistance in BC1F2 A. hypogaeacv IAC Runner-886 BC-111
    • Field evaluations of BC1F2s Resistance %DLA10.00 8.00 6.00 Productivity x resistance 4.00 2.00 90.00 0.00 80.00 AixAd BC-6 BC-92 BC-174 BC-16 BC-15 BC-70 BC-13 BC-37 BC-33 BC-146 BC-125 BC-135 BC-203 BC-145 BC-138 BC-122 BC-152 BC-170 70.00 60.00 50.00 40.00 Productivity (g) Productivity 30.00 %DLA *10 Productivity 20.00 150.00 10.00 100.00 0.00 BC-6 BC-30 BC-5 BC-3 BC-36 BC-33 BC-77 BC-15 BC-13 BC-157 BC-136 BC-138 BC-203 BC-156 BC-170 BC-111 BC-145 AixAd 50.00 0.00 AixAd BC-6 BC-195 BC-85 BC-36 BC-16 BC-15 BC-136 BC-150 BC-196 BC-170 BC-135 BC-146 Resistance is not inversely related to productivity – low linkage drag
    • Map constructionRIL (F5/F6) mapPop. developmentPhenotypingEMBRAPA and UnB,BrazilGenotypingKazusa, Japan1228 SSR markersAlso contributions fromUniversity of Georgia Runner-886 x AiAdICRISAT AABBDiploid AA and BB mapsof similar densityalso produced
    • Identification of highly informative SSR markers S. PIC value Genomic SSRs Genic SSRs Total markers No. range Number (%) Number (%) Number (%) 1 0.10-0.20 51 19.6 284 37.4 335 32.8 2 0.21-0.30 55 21.2 196 25.8 251 24.6 3 0.31-0.40 35 13.5 146 19.2 181 17.7 4 0.41-0.50 29 11.2 62 8.2 91 8.9 5 0.51-0.60 24 9.2 44 5.8 68 6.7 6 0.61-0.70 39 15.0 15 1.9 52 5.3 7 0.71-0.80 21 8.1 11 1.4 32 3.1 8 0.81-0.90 6 2.3 2 0.3 8 0.8 Total markers 260 760 1020• Availability of sequence information for 946 novel polymorphic SSR markers• Identification of 199 highly informative SSRs with PIC >0.50
    • Parental screening of parental genotypes for disease resistance Parental screening for Malawi : Six populations Niamey : One populationPopulations Markers Poly. Disease Locations screened markers resistanceICGV 93437 X ICGV 94114 510 36 Rust resistance MalawiICGV 93437 X ICGVSM 95342 510 30 Rust resistance MalawiCG7 X ICGVSM 90704 510 63 GRD MalawiCHALIMBANA X ICGVSM 90704 510 9 GRD MalawiICGV 93437 X ICGV 95714 510 24 ELS MalawiROBUT 33-1 X ICGV 95714 510 31 ELS MalawiICGV 86124 X ICG 7878 510 62 ELS NiameyGRD : Groundnut rosette diseaseELS : Early leaf spot
    • Rust Resistance Adapted No. of Progenies Locations Source parent ICGV-SM JL 24 295 Malawi 94114 ICGV-SM ICGV 93437 188 Malawi and 95342 TanzaniaELS Resistance Source Adapted parent No. of Progenies Location ICGV-SM 95714 ICGV 93437 139 Malawi ICGV-SM 95714 Robut-33-1 187 MalawiRosette Resistance Source Adapted parent No. of Progenies F Generation ICGV-SM 90704 CG 7 242 F6 ICGV-SM 90704 Chalimbana 320 F6
    • DNA extraction and SSR genotyping of parental genotypes from Mali• DNA extracted from fresh leaves of 5 parental lines in 5 populations developed for resistance to ELS – Fleur 11 x ICG 7878 (1polymorhic SSR) – 55-437 x ICG7878 (6 polymorphic SSRs – JL24 x ICG 7878 (1 polymorphic SSR) – 47-10 x ICG 7877 (10 polymorphic SSRs) – ICG 86124 x ICG 7878 (16 polymorphic SSRs• To be advanced to F5:6 in 2012 crop season for further phenotyping and genotyping
    • Use MABC to introgress disease resistance QTLActivity 4 New breeding population for drought and disease towards MARSMilestone 14 4 populations advanced to RILs - Multi-location disease phenotyping.Milestone 15 8 MABC materials introgressed with rust and rosette disease resistance QTLs in four FMPV backgrounds and transferred to TLII breeders in Year 4Milestone 16 4 breeding products from MABC with enhanced attributes available for testing and selection by NARS.Milestone 17 5 advanced backcross breeding materials with disease resistance tested in PVS trials.Milestone 18 PVS trials of 10–20 new sources of disease resistance and drought tolerance (TLII)Milestone 19 At least 4 new crosses (one per disease) developed and QTL identified for each disease between FMPV lines and new sources of disease resistance.Milestone 20 At least 4 new crosses developed between advanced BC lines in FMPV background and new sources of drought tolerance from Activity 4, Phase I.Milestone 21 Relevance of F4-family phenotyping for drought-related traits tested in at least one segregating population.Milestone 22 Polymorphism information content (PIC) of lines involved in crossing available
    • Five genetic maps maps for 4x groundnutDetails of different TAG 24 ICGS 76 ICGS 44 TAG 24 TG 26 linkage maps x x x x x ICGV 86031 CSMG 84-1 ICGS 76 GPBD 4 GPBD 4 (RIL-1) (RIL-2) (RIL-3) (RIL-4) (RIL-5)Marker loci mapped 191 119 83 188 181Linkage groups 22 18 16 20 20Marker loci/LG 2-19 2-14 2-10 2-17 2-15Avg. marker loci/LG 8 7 5 9 8Total map distance (cM) 1785 888 2203 1922 1964Avg. distance/LG (cM) 81.15 59.2 110.1 96.1 85.4Avg. inter-locus distance 9.54 11.88 15.47 10.23 9.9(cM)TAG 2009, 118:729-739; TAG 2011 122:1119-1132;TAG 2010, 121:971-984; Mol Breeding 2012, DOI 10.1007/s11032-011-9661-z;Field Crops Res 2011, 122:49-59; Mol Breeding 2012, DOI 10.1007/s11032-011-9660-0.
    • Eleven 4X- genetic maps used for consensus mapMaps Linkage Polymorphic Mapped Map Map References groups loci loci length density (cM) (cM)RIL-1 22 211 191 1785.4 9.35 Varshney et al. 2009b; Ravi et al. 2011RIL-2 20 128 119 2208.2 18.56 Gautami et al. 2012 PLoS ONE 2012, submittedRIL-3 15 87 82 831.4 10.14 Gautami et al. 2012RIL-4 20 209 188 1922.4 10.23 Khedikar et al. 2010; Sujay et al. 2012RIL-5 21 209 181 1963 10.85 Sarvamangala et al. 2011; Sujay et al. 2012RIL-6 19 146 132 793.1 6.01 Hong et al. 2010RIL-7 21 124 109 503.1 4.62 Hong et al. 2010RIL-8 13 64 46 357.4 7.76 Hong et al. 2010RIL-9 26 261 233 1304.9 5.6 Qin et al. 2012RIL-10 22 183 173 917.45 5.3 Qin et al. 2012BC1F1-11 21 339 332 847.4 2.53 Foncéka et al. 2009Consensus map 20 - 897 3,863.6 4.42 -RIL-1: TAG 24 x ICGV 86031; RIL-2: ICGS 76 x CSMG 84-1; RIL-3: ICGS 44 x ICGS 76; RIL-4: TAG 24 x ICGV 86031;RIL-5: TG 26 x GPBD 4; RIL-6: Yueyou 13 × Zhenzhuhei; RIL-7: Yueyou 13 × Fu 95-5; RIL-8: Yueyou 13 × J11;RIL-8: Tifrunner × GT-C20; RIL-10: SunOleic 97R × NC94022; RIL-11: Fleur11 × AiAd (synthetic amphidiploid)
    • High density reference consensus genetic map LG_AhXX LG_AhXV PLoS ONE 2012, submitted LG_AhXVI LG_AhXVII LG_AhXIX LG_AhIX LG_AhXIV LG_AhII LG_AhXVIII LG_AhVI LG_AhXILG_AhI LG_AhVIII LG_AhVII LG_AhXII LG_AhXIII LG_AhIII LG_AhIV LG_AhX LG_AhV Marker loci mapped 897 Total map distance (cM) 3863.6 Map density (cM) 4.42
    • Consensus QTL map for drought tolerance traits Mol Breed 2012, DOI 10.1007/s11032-011-9660-0. Cluster 4 Cluster 2 Cluster 5 Cluster 3 Cluster 1 Cluster 9 Cluster 10 Cluster 7 Cluster 8 Cluster 6 Cluster 13 Cluster 14Cluster 11Cluster 12 Cluster 15 Cluster 16
    • How yield and traits QTL co-map in cultivated groundnut ? QTL cluster for: Yield Transpiration Growth
    • How yield and traits QTL co-map in cultivated groundnut ? QTL cluster for: Leaf expansion Leaf area Leaf conductance
    • Development of new crosses for drought Number of surviving F1 plants during 2011-12 postrainyS.No Female Parent Male Parent season 1 ICGS 44 JL 24 41 2 55-437 JL 24 35 3 ICGV 91114 ICG 1834 63 4 ICGV 44 ICG 1834 45 5 ICGV 97182 ICG 1834 65 6 Fluer 11 ICG 1834 32 7 ICGV 01232 ICG 1834 61 8 ICG 434 ICG 1834 65 9 ICGV 91114 ICG 13787 28 10 ICGV 02189 ICG 4598 55 11 55-437 ICG 2772 45 12 55-437 ICGV 99001 65 22 crosses made / 12 currently advanced. F2 seeds harvested.
    • QTLs/markers for rustA major QTL for rust in groundnut (PVE upto 82.96%) Environments: ER-I Rainy 2004, ER-II Rainy 2005, ER-III Post-rainy 2007, ER-IV Rainy 2007, ER-V Rainy 2008. Stages: LR-I: scored at 70 DAS, LR-II: scored at 80 DAS, LR-III: scored at 90 DAS, LR-IV: scored at 105 DAS, LR-V: scored at 113 DAS, LR-VI: scored at 120 DAS, IP: incubation period, LP: latent period, IT: infection type.TAG 2010, 121:971-984; Molecular Breed 2012, DOI 10.1007/s11032-011-9661-z
    • Marker-assisted selection (MAS) for rust resistance ICGV 91114, Post Rainy 2008-09 JL 24, TAG 24 × GPBD 4 Recurrent Parent (RP) Donor Parent (DP) Rainy 2009 RP × F1 Backcrossing Post Rainy 2009-10 RP × BC1F1Completed FG selection-heterozygote Backcrossing Rainy 2010 RP × BC2F1 FG selection-heterozygote Backcrossing Selfing Post Rainy FG selection- BC3F1 BC2F2 FG selection-homozygote 2010-11 heterozygote Selfing Selfing FG selection- Rainy 2011 BC3F2 BC2F3 Screened for rust homozygote Selection based on disease reaction, agronomic and yield performance
    • Screening of introgressionlines for rust resistance
    • A review on Arachis genomics published in reputed journal “ Biotechnology Advances” in collaboration with several GCP partners• This article provides current updates on accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms• These developments leading to identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits• Translation of information developed through use of genomics tools for improvement of disease resistance and oil quality traits in groundnut
    • Strengthen capacity of NARS partnersActivity 5Milestone At least 2 NARS partners empowered to breed groundnut varieties with multiple23 attributes.Milestone 3 scientists and 3 technicians trained in drought phenotyping and in the24 logistics of fast advancement of breeding populations.Milestone 1 scientist and 1 technician from Malawian and Malian national programmes25 trained in DNA extraction and use of simple markers.
    • Activity 5: Capacity building• Mamary Traore, Msc student under TLII in Mali trained in phenotyping for foliar disease resistance• 2 PhD students at WACCI (Usman Alhassan- Nigeria and Aboudoulay Adama- Niger) in groundnut breeding supported by TLI to participate in the 2-day training in IB filed book and data management (TLI)• Groundnut breeders from Burkina Faso (1), Ghana (1), Mali (1), Niger (2), Nigeria (1) and Senegal (1), supported by TLII to attend the IB Field Book and data management training
    • Activity 6 Management and storage of dataMilestone 26 Marker genotyping data for groundnut reference collection - At least 4 populations stored in public database and linked to the MBP.Milestone 27 Phenotyping data of reference collection over 6 sites (India, Niger, Mali, Senegal, Tanzania and Malawi) and 6 years; RIL and MABC lines analysed and data stored in public database - Data from TLII trials added to this database.
    • Data provided to Bioinformatics unit•Most data delivered or close to be
    • In summaryMajor progresses with the genomic tools (maps, markers)Progress continues on drought adaptation mechanismsQTLs for disease resistance getting harnessed: QTL introgression of rust / LLS resistance BC work with AiAd Synthetic x cultivated populations AB-QTL populationsWild relatives have a big stake there
    • Thank you