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Science-based approaches for efficient conservation and use of genetic resources

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11-14 February 2019. Jodhpur, India. The 13th International Conference on Dryland Development
13 February: Satellite Symposium Dryland Agrobiodiversity for Adaptation to Climate Change
Conservation and use of agrobiodiversity in CWANA drylands, Ahmed Amri (see picture), ICARDA, Morocco Head of ICARDA's Genetic Resources Unit, which runs the GRU seed bank in Rabat.

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Science-based approaches for efficient conservation and use of genetic resources

  1. 1. International Center for Agricultural Research in the Dry Areas icarda.org cgiar.org A CGIAR Research Center Science-based approaches for efficient conservation and use of genetic resources Ahmed Amri on behalf of ICARDA colleagues ✓ Increasing population ✓ Land degradation ✓ Water scarcity ✓ Loss of agrobiodiversity ✓ Climate change
  2. 2. icarda.org 2 Crop Improvement and Food Security “ a situation that exists when all people, at all times, have physical, social and economic access to sufficient, safe and nutritious food that meets their daily healthy life style” 1. Availability: production …. 2. Access: reflect the demand side… 3. Utilization: make good use of food to which they have access; dietary quality associated with malnutrition Food is the moral right of all who are born into this world Dr. Norman Borlaug Dr. N. Borlaug: (ICARDA, May 2005) “There are many good genes in the wild species and we should use them more in breeding” Hessian Fly Resistant
  3. 3. icarda.org 3 Approaches for conservation and use of genetic resources • How to add novel diversity to existing collections? • How to efficiently mine the collections? • Strengthening pre-breeding
  4. 4. Gap analysis to add novel diversity for landraces 4 Scope: ICARDA, CIAT, and Crop Trust will develop methods to understand and map existing diversity and determine coverage and gaps of 22 ex situ collections for crop landraces and forages, using data from Genesys and other sources. • The Crop Trust to run crop diversity trees • CIAT to run spatial gap analysis • ICARDA to run trait gap analysis. Diversity tree for barley landraces Gap classes for Naked Barley
  5. 5. Aegilops, Avena, Hordeum, Secale and Triticum species Sources: Katherine Whitehouse, Holly Vincent, Ahmed Amri and Nigel Maxted (2012) and Maxted et al (2010) Cicer, Lathyrus, Lens, Medicago, Pisum and Vicia species Mapping of species richness for priority species
  6. 6. 6 Performance Measures k-NN SVM RF Accuracy 0.885 0.882 0.895 95% CI (0.87, 0.899) (0.866, 0.896) (0.881, 0.908) No Information Rate 0.831 0.831 0.831 P-Value [Acc > NIR] 0.00 0.00 0.00 Kappa 0.578 0.54 0.614 Sensitivity 0.625 0.546 0.649 Specificity 0.938 0.95 0.945 True Positive 205 179 213 False Positive 101 81 89 True Negative 1515 1535 1527 False Negative 123 149 115 Landraces gap analysis: Map of predicted probability for frost tolerance in Barley Modeling metrics for frost
  7. 7. Crop No of accs. Crop No of accs. Barley 30,214 Pisum spp. 6,132 Bread wheat 15,053 Trifolium spp. 5,936 Durum wheat 20,505 Vicia spp. 6,562 Primitive wheat 1,195 Faba bean 10,034 Aegilops spp. 5,157 Chickpea 15,195 Wild Triticum 1,962 Lentil 13,978 Wild Hordeum 2,575 Wild Cicer 554 Not mandate cereals 195 Wild Lens 619 Lathyrus spp. 4,451 Range & Pasture 7,406 Medicago annual 9,136 Others 50 Total 156,909 Regeneration of 600 strains of rhizobium Total taxa Perennial Cross-pollinated 718 > 100 > 130 % unique accessions 45 % landraces and native species 85 % characterized 78 % safe duplicated 98 % stored in Svalbard 60 Collections held in-trust by ICARDA Syria: Active and base collections (250,000) Second level Safety duplication at Svalbard Safety duplication Lebanon: Collections of faba bean, Lathyrus, forage and range species and crop wild relatives (75,000) Morocco: Collections of cultivated species of barley, wheat, lentil and chickpea (45,000 acc.) Safety duplication
  8. 8. 0 5000 10000 15000 20000 25000 1st Qtr USA India Morocco Australia Ethiopia Mexico Tunisia Syria Turkey Italy Russia Great Britain Canada Jordan Iran Top 15 country recipients of material NARS Universities CGIAR centers Genebanks Regional organizations Commercial companies Main users ICARDA distributes more than 20,000 accessions on average annually
  9. 9. User define a trait and set size No data available Data available Data assembly Filtering to mimic selection pressure Subset formation maximizing environmental diversity Data assembly Machine learning algorithms Metrics for validation Trait prediction for unobserved accessions → assign a probability to an accession Evaluation Evaluation • Environnement • Trait (disease score) FIGS subset Filtering Modeling FIGS approach links adaptive traits, environments (and associated selection pressures) with genebank accessions (e.g. landraces and crop wild relatives) Focused Identification of Germplasm Strategy: Definition and pathways
  10. 10. Trait Barl ey Brea d whe at Chic kpea Duru m whe at Faba bean Lenti l Pea AB x x Acid x Asco chyt a x BGM x x Botr ytis x Bruc hid x BYD V x Chill x Cold x x CR x CSN x Drou ght x x x x x Fros t x x Fusa rium x Heat x x x x Heat Cool x Hess ian Fly x HotC old x Leaf Min er x Leaf Rust x x Low pH x x x x LR x Net Blotc h x pH x Phos phor ousU seEf ficie ncy x Phyt opht hora x x Pod Bore r x Pow dery Mild ew x x PUE x Rust x RW A x Salin ity x x x Salt x x x Scal d x Sept oria x Spot Blotc h x Ste m Gall x Ste m Rust x x x Sun Pest x Sunn Pest x TurA fglrn x Viru s x x WB x Wet Dry x 10 Crop Trait Barley BYDV CSN Drought Frost Heat Leaf Rust NA Net Blotch pH Powdery Mildew Salinity Scald Stem Gall Stem Rust Bread wheat CR Drought Frost Heat Cold Hessian Fly Low pH LR Phosphorous Use Efficiency Powdery Mildew RWA Septoria Spot Blotch Stem Rust Sun Pest Durum wheat Hot Leaf Rust Low pH Salt Stem Rust Sunn Pest Drought Crop Trait Chickpea AB BGM Chill Cold Drought Fusarium Heat Leaf Miner Low pH Pod Borer Salinity Virus Faba bean Acid Botrytis Bruchid Cold Drought Heat Low pH Phytophthora Rust Salt Lentil AB Ascochyta BGM Drought Phytophthora Salt Virus Pea Salinity FIGS subsets developed and shared with partners • Up to know more than 80 FIGS subsets were formed and shared with users. • Confirmed traits include salinity (all crops), all rusts (barley), Sunn pest (wheat), spot and net blotch (barley)… • Only traits not yet found using FIGS are resistance to gall midge in barley and resistance to ascochyta blight in chickpea
  11. 11. Verified under controlled conditions 534 accessions screened at ICARDA Two QTLs have been identified on 5B and 6A for Sunn Pest 8 landrace accessions from Afghanistan and 2 from Tajikistan identified as resistant at juvenile stage 3 Mapping populations developed and phenotyped during three years. Genetic analysis finalized. Entomology: Sunn Pest example FIGS Outcomes
  12. 12. Screening of NB-FIGS with Net blotch and Spot blotch 1 17 12 24 9 0 5 10 15 20 25 30 #ofbarleyaccessions §Infection responses Response of NB-FIGS subset to Net Blotch Immune Resistant Medium Resistant Medium susceptible 0 2 15 28 38 0 10 20 30 40 Numberof accessions ¥Infection responses Response of NB-FIGS to Spot Blotch Immune Resistant Medium Resistant NB- FIGS subset seems to be specific to NB Focused Identification of Germplasm Strategy: Specificity of FIGS sets 95 11 23 54 36 30 23 21 0 10 20 30 40 50 60 70 80 90 100 0 <50 >50-<100 >100-< 200 >200-< 400 >400-< 800 >800-< 1500 >1500 95 / 293 Immu ne 183/293 Slow rusting
  13. 13. icarda.org 13 Value of genetic resources in lentil improvement Trait of interest CWR screened Donors identified Fusarium wilt 435 ILWLs76, 79 37, 113, 138 Salinity tolerance 100 ILWL297, ILWL368, ILWL371, ILWL417, IG136670 Earliness 285 ILWL 118 Fe and Zn contents 285 ILWL74, IG135395, IG 135403 Orobanche 31 ILWL367, ILWL240 Lens orientalis derivative lines
  14. 14. Assessment of Lathyrus germplasm for ODAP content and Resistance to Orobanche 0.087 0.045 0.335 0.133 0.024 0.045 0.093 0.093 0.093 0.049 0.030 0.086 0.229 0.162 0.105 0.131 0.096 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4
  15. 15. Performance of some improved lines developed from wide crosses under Moroccan conditions
  16. 16. • Synthetics have exponentially increased genetic diversity in wheat 1. Yield under drought and irrigated conditions 2. Multiple disease • Leaf, stem, and yellow rusts • Yellow Leaf Spot (= tan spot) resistance • Nematode resistance • Septoria tritici blotch resistance 3. Salinity tolerance 4. Pre-harvest sprouting tolerance 5. Insect pests tolerance • After introducing a novel DD genome (Ae. tauschii), now work starting on using novel AABB genome (. dicoccoides and T. dicoccum) in new synthetics. Genotype YR respo nse Yield (t/ha) % of Arrehane KAUZ/PASTOR/3/ALTAR 84/AEGILOPSSQUARROSA (TAUS)//OPATA 5R 6.93 131 TINAMOU-3/BANA-4 40MS 6.59 125 NESSER/SERI/3/SHUHA-2//NS732/HER 40MS 6.51 123 MUNIA//CHEN/ALTAR 84/3/CHEN/AEGILOPS SQUARROSA (TAUS)//BCN/4/MARCHOUCH-8 10MR 6.37 121 NESSER/SERI//TEVEE-1/SHUHA-6 15MR 6.33 120 KAUZ/PASTOR/3/ALTAR 84/AEGILOPSSQUARROSA (TAUS)//OPATA 5R 6.32 120 YEBROUD'S'//DOVE'S'/SERI/3/SAFI-1 10MR 6.17 117 SHUHA-4/FLORKWA-4//HUBARA-3 5MR 6.07 115 KAUZ/PASTOR/3/ALTAR 84/AEGILOPSSQUARROSA (TAUS)//OPATA 10MR 6.05 115 TEVEE-1/SHUHA-6//MASSIRA 5R 5.99 114 CHILERO-1/STAR'S'//SHUHA-2/FOW-2 15MR 5.93 112 NESSER/SERI/3/SHUHA-2//NS732/HER 10MR 5.92 112 NESSER/SERI//TEVEE-1/SHUHA-6 40MS 5.92 112 MUNIA//CHEN/ALTAR 84/3/CHEN/AEGILOPS SQUARROSA (TAUS)//BCN/4/MARCHOUCH-8 5R 5.87 111 KAUZ/PASTOR/3/ALTAR 84/AEGILOPSSQUARROSA (TAUS)//OPATA 10MR 5.70 108 QIMMA-12/PASTOR-6//QIMMA-12 30MS 5.65 107 KARAWAN-1/TALLO 3//REGRAG-1 5R 5.64 107 ALTAR 84/AE.SQUARROSA (219)//SERI/3/MASSIRA 5R 5.63 107 ALTAR 84/AE.SQUARROSA (219)//SERI/3/MASSIRA 5R 5.62 107 KARAWAN-1/TALLO 3//JADIDA-2 5R 5.58 106 Arrehane (check) 15MR 5.27 100 Useful traits transferred from synthetic hexaploid wheat
  17. 17. T. boeoticum New genetic diversity for wheat derived from wide crosses T. urartu T. dicoccoides yellow rust resistance leaf rust resistance earliness high productive tillering spike productivity plant productivity plant height drought tolerance Sunn pest resistance Russian wheat aphid resistance Septoria tritici resistance Ae. speltoides Cham5 Cham5*3/T. baeoticum 500647 Cham5*4/Ae. speltoides 401293 Cham5*3/T. baeoticum 500647 Cham5*3/T. dicoccoides 601116 Cham5*4/Ae. speltoides 401293 Cham5*3/T. baeoticum 500647 Cham5*4/Ae. speltoides 401293 Cham5*3/T. urartu 500649 Cham5*4/Ae. speltoides 401293 Cham5*3/T. baeoticum 500647 Cham5*3/T. baeoticum 500647 Cham5*4/Ae. speltoides 401293 Cham5*3/T. urartu 500529 Cham5*3/T. baeoticum 500647 Cham5*3/T. baeoticum 500647 Cham5*4/Ae. speltoides 401293 Cham5*3/T. baeoticum 500647 Pedigree 6.40 6.20 6.00 5.80 5.60 5.40 5.20 5.00 Grainyield(t/ha) High-yielding lines derived from wild crosses - season 2004/2005
  18. 18. icarda.org 18 Value of wild relatives in durum wheat improvement Germplasm 1,000-Kernel weight (g) Grain protein content (%) SDS sedimentation test (ml) Yellow index (b*) Average Max Average Max Average Max Average Max Varieties 44.8 c 47.5 b 14.9 a 15.6 b 35.4 a 46.8 a 20.7 a 22.7 a Elites 47.3 b 48.4 b 14.7 a 14.9 c 24.6 b 29.6 b 17.4 b 18.2 c Wide cross 51.9 a 56.6 a 15.0 a 16.1 a 34.4 a 44.0 a 18.3 b 20.2 b Grand Mean 50.1 14.9 33.3 18.6 LSD 2.3 0.6 5.9 1.0 1 Wide-crosses (WC) obtained by “top-crossing” with wild relatives have better yield potential + stability, and good end-use quality Wide crosses of durum wheat reveal good disease resistance, yield stability, and industrial quality across Mediterranean sites. Zaim et al. 2017. Field Crop Research, 214:219-227.
  19. 19. icarda.org 19 Releases of « wide » varieties • Among 125 varieties released, 8% were derived from CWR, and 30% by landraces • Lately, wild relatives are becoming even more common • Omrabi (Jori/Haurani) has been released in 15 countries and is in the pedigree of 17 cultivars 0 2 4 6 8 10 Numberofreleases CWR Landraces
  20. 20. icarda.org 20 Genetic diversity for breeding Cluster ID N Allelle segr. (%) Common Rare 1. Middle East 11 0.13 0.00 2. T. abyssinicum 18 0.42 0.01 3. Mediterranean 26 0.65 0.06 4. C. and S. Asia 27 0.84 0.62 5. ‘Om Rabi’ 13 0.19 0.00 6. Italian 26 0.46 0.01 7. Exchange 58 0.58 0.04 8. Developed 30 0.43 0.01 9. ICARDA 119 0.51 0.03 10. CIMMYT 42 0.44 0.21 Kabbaj et al. 2017. Frontiers in Plant Sciences, 8:1277.
  21. 21. Using high density DartSeq markers for a better conservation and use of genebank accessions Mis-classified accessions Tunisian durum landraces Different diversity: New genepool
  22. 22. 22 Focused Identification of Germplasm Strategy: Enhancement with genotyping
  23. 23. New ICARDA Strategy 2017-2026
  24. 24. Conservation and sustainable use of Agrobiodiversity Status and threats assessed Awareness increase and information sharing Appropriate policies and legislations Low-cost technologies for in situ conservation/ management Collection and ex situ Conservation/management Alternative sources of income Add value technologies Improvement of income/ Livelihoods of custodians Regional and international collaboration Benefit sharing and funding Actions for complementary actions for effective in situ and ex situ conservation of genetic resources
  25. 25. icarda.org 25 • IPM of Cactus Cochineal: Good progrees since September 2016: • Through surveys, the initial pest distribution data and map. • Out of 320 cactus ecotypes tested, eight were found resistant to the cochineal. These resistant ecotypes have been registered in the Moroccan catalogue. • Three bio-insecticides were identified with high level of efficiency against the cochineal. • Cryptolaeumus montrozieri identified as a potential predator. Diversification and intensification of farming systems

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