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Role of genebank in pre‐breeding
Presented inInternational Workshop on the promotion of Public‐Private
Partnerships for Pre‐breding
2‐4 Februray 2015
Agropolis International, Montpellier, France
Hari Upadhyaya and Michael Abberton, CGIAR
A member of CGIAR consortium www.iita.org
IITA Genetic Resources Center
Crops Number of accessions
Cowpea (Vigna unguiculata L.) 15,379
Soybean (Glycine max L. Merr) 4,841
Cassava (Manihot esculenta Crantz) 3,499
Yam (Dioscorea spp.) 3,156
Bambara groundnut (Vigna subterranea L. Verdc) 1,752
Maize (Zea Mays L.) 1,565
Miscellaneous legumes 558
Wild Vigna (Vigna species L.) 1,543
Banana/plantain (Musa spp.) 546
African yam bean [Sphenostylis stenocarpa (Hochst.) Harms] 456
Cowpea47%
Soybean15%
Cassava10%
Yam9%
Bambara Groundnut
5%
Maize5%
Legumes2%
Wild Vigna5%
Musa spp.2%
Afican yam bean>0%
IITA Genebank
Over 32,800 Accessions of African major food crops
A member of CGIAR consortium www.iita.org
Joint NGS and Evaluation studiesGBS and multi environment field evaluation of both breeders lines and accessions e.g. yam (complementary funding of RTB).Ranjana Bhattarcharjee
Genotypes for GBS Number Varieties from markets (Nigeria) 33Popular varieties 61IITA varieties 95TDr Core collection 470Nigeria 206Ghana 30Benin 33Cote d'Ivoire 26Burkina Faso 1Equitorial Guinea 1Togo 165Guinea 7Sierra Leone 1Yam Breeding 307Mapping populations 207Populations with target traits 100
A member of CGIAR consortium www.iita.org
Yam: Metabolomics5 species (D. alata, D. bulbifera, D. cayenensis, D. dumetorum, D. rotundata)
Ranjana Bhattarcharjee, Paul Fraser, Royal Holloway, University of London.
10mg lyophilised tissue
phase separation
polar
standard extraction
non-polar
GC-MS
LC-MS/MS (UP)LC-PDA/MS
Polar = up to ~500 features
Non-polar = up to ~300 features
A member of CGIAR consortium www.iita.org
Crop wild relatives-cowpea
Niyi Oyatomi, Christian Fatokun, Ousmane Boukar
Cowpea land races from geographical locations of resistant wild relatives are sources of resistance to S.gesnerioides.
A member of CGIAR consortium www.iita.org
Neglected and underutilised species• Bambara groundnut-collaboration with Crops
for the Future Research Centre GWAS Panel, DArT markers, QTL studies
• African Yam bean-diversity analysis and Symposium 2015
• Winged bean-diversity analyses
• PhD and MSc students
• Consultancy-Taro
A member of CGIAR consortium www.iita.org
Some considerations• Partnership between genebanks and breeders including
private sector
• Needs to be two way interaction including flexibility of genebanks with regard to genetic stocks, breeding lines etc
• Funding should not get in the way but encourage partnership and synergies
• Different needs for different crops-and different roles for genebanks.
Crop germplasmGlobal• 7.4 million accessions • >1750 genebanks , 2500 botanical
garden and 70000 protected areas• 25-30% unique• 10% wild crop relatives• 11% in CGIAR genebanks
ICRISAT• > 123,000 accessions from 144 countries• > 2800 wild accessions of 176 species from 82 countries• >1.42 million seed samples distributed to 147 countries • > 55,000 accessions restored to 9 countries• 108,000 safely duplicated at Svalbard Global Seed Vault• 830 cultivars released in 79 countries from germplasm and
breeding material• 266 elite germplasm notified with specific traits
Commodity group No. of accessions Wild species (%)
Landraces (%)
Breeding materials (%)
Advanced cultivars (%)
Others (%)
Cereals 3,157,578 5 29 15 8 43
Food legumes 1,069,897 4 32 7 9 49
Roots and tubers 204,408 10 30 13 10 37
Vegetables 502,889 5 22 8 14 51
Nuts, fruits and berries 423,401 7 13 14 21 45
Oil crops 181,752 7 22 14 11 47
Forages 651,024 35 13 3 4 45
Sugar crops 63,474 7 7 11 25 50
Fiber crops 169,969 4 18 10 10 57
Medicinal, aromatic, spice and stimultant crops
160,050 13 24 7 9 47
Industrial and ornamental plants 152,325 46 1 2 4 47
Others 262,993 29 4 2 2 64
Total/overall mean 6,998,760 10 24 11 9 46
Global germplasm holding in term of type of accessions
Global conservation and priorityWild species,
10%
Land races; 24%
Breeding material, 11%Advanced
cultivar, 9%
Others, 46%
• Over 60 000 CWR species worldwide
• Over 700 CWR species considered of highest priority, that comprise the primary and secondary genepools of the world’s most important (FAO 2010)
• 14 CWR species considered of very highest priority (Maxted & Kell, 2009)
Crop Samples received by NBPGR
Samples released for planting
Accessions registered
Sorghum 1705 1681 1285
Pearl millet 1113 1077 677Chickpea 360 360 334Pigeonpea 7 7 0Finger millet 1250 1250 819Total 4435 4375 3115
New germplasm through GCDT Regeneration Project
763; 70%
145; 13%
130; 12%51; 5%
HPS MPS
• Analysed 1,089 CWR species of 81 crops• 763 (70%) were classified as High Priority Species (HPS)
for further collection• 145 (13%) as Medium Priority Species (MPS)• 130 (12%) as Low Priority Species (LPS)• 51 (5%) as No Further Collecting Required (NFCR)
Priority category for conservationof crop wild relatives
http://www.cwrdiversity.org/conservation‐gaps/
• Significant gaps in collections evident within the great majority of crop genepools
• High priority species for collecting per crop genepoolreach up to 100% for banana and plantain
• 88% for sorghum• 86% for sweet potato
Priority category for conservationof crop wild relatives
• Crop genepools displaying the greatest absolute number of high priority species in need of collecting include cassava, eggplant, mango, breadfruit, potato, almond, apple, and sunflower.
• Very few germplasm lines used in China, USA and ICRISAT
• At ICRISAT only 132 germplasm lines from >15400 were used to develop 8279 advance varieties (ICGV) during 1986–2002
Limited use of germplasm
Upadhyaya et al., 2006; Plant Genetic Resources 4:25-35
Groundnut
• Robut 33-1(3096 times) and Chico (1180 times) most widely used
• Similar situation in other crops
• Trait specific genetically diverse parents for trait enhancement
• Agronomically superior or similar preferable - so that scope for exploitation of addictive genetic variance
• This would avoid unpredictable epistatic and dominance deviation variances
Needs of plant breeder
Crop Entire collection
Mini core number
% of entire
Traits used
Reference
Chickpea 16,991 211 1.24 16 Upadhyaya and Ortiz 2001; TAG 102:1292-1298
Groundnut 14,310 184 1.28 34 Upadhyaya et al. 2002; Crop Sci. 42: 2150-2156
Pigeonpea 12,153 146 1.20 16 Upadhyaya et al. 2006; Crop Sci. 46:2127-2132
Sorghum 22,473 242 1.08 21 Upadhyaya et al. 2009; Crop Sci. 49:1769-1780
Pearl millet 20,844 238 1.14 12 Upadhyaya et al. 2011: Crop Sci. 51 :217-223
Finger millet 5,940 80 1.34 18Upadhyaya et al. 2010: Crop Sci. 50: 1924-1931
Foxtail millet1,474 35 2.37 21
Upadhyaya et al. 2011; Field Crops Research 124:459-467
Mini core collections of germplasm at ICRISAT
• 28 abiotic stresses tolerant 3 of them yield 2-33% more than best control
• 30 biotic stresses resistant3 of them yield 4-9% more than best control
• 16 nutritional quality traits2 of them yield 2-27% more than best control
• 18 agronomic traits7 of them yield 1-13% more than best control
• 9 multiple traits (biotic, abiotic, agronomic and nutritional traits4 of them yield 3-33% more than best control
Identification of trait‐specific germplasm using groundnut mini core collection
Genetic diversity of multiple resistances in superior agronomic background in groundnut
Upadhyaya et al., 2014; Crop Sci. 54:679‐693
Identity Genetic diversity
Identity Genetic diversity
Identity Genetic diversity
ICG2381: ICG1668 0.667 ICG11088: ICG2925 0.643 ICG12625: ICG2925 0.762
ICG2925: ICG1668 0.405 ICG11088: ICG5475 0.833 ICG12625: ICG5475 0.929
ICG2925: ICG2381 0.667 ICG11088: ICG8285 0.675 ICG12625: ICG8285 0.800
ICG5475: ICG1668 0.786 ICG11426: ICG1668 0.786 ICG12625: ICG11088 0.738
ICG5475: ICG2381 0.857 ICG11426: ICG2381 0.690 ICG14482: ICG1668 0.725
ICG5475: ICG2925 0.738 ICG11426: ICG2925 0.667 ICG14482: ICG2381 0.650
ICG8285: ICG1668 0.350 ICG11426: ICG5475 0.929 ICG14482: ICG2925 0.650
ICG8285: ICG2381 0.650 ICG11426: ICG8285 0.800 ICG14482: ICG5475 0.875
ICG8285: ICG2925 0.550 ICG11426: ICG11088 0.643 ICG14482: ICG8285 0.684
ICG8285: ICG5475 0.775 ICG11426: ICG12625 0.762 ICG14482: ICG11088 0.600
ICG11088: ICG1668 0.690 ICG12625: ICG1668 0.810 ICG14482: ICG11426 0.600
ICG11088: ICG2381 0.667 ICG12625: ICG2381 0.786 ICG14482: ICG12625 0.700
Sources of multiple resistances in superior agronomic background in groundnut
Identity Resistances Yield (kg ha‐1) (3R+6PR pooled)
ICG 1668 Heat, LLS, PBND, BW 1626ICG 2381 Rust, A. flavus, O/L 1677
ICG 2925 Heat, LLS, Rust 1468
ICG 5475 Drought, Low temperature, Oil, O/L, Fe
1422
ICG 8285 Drought, Heat, Salinity 2083
ICG 11088 Drought, Low temperature 2506
ICG 12625 Drought, Low temperature, LLS, A. flavus, BW, Oil, O/L
1953
ICG 14482 PBND, Fe, Oil 1830
ICG 11426 ELS, LLS, Rust 2034
Upadhyaya et al., 2014; Crop Sci. 54:679‐693
• Evaluated 269 accessions from 20 wild Arachis species from six sections for 41 morphoagronomic, quality and drought related traits
• Significant differences between species and accessions for most of the traits
• Identified 20 accessions superior for multiple traits
Evaluation of wild Arachis species at ICRISAT
• A. duranensis showed maximum diversity for 20 of the 41 traits including flowering, primary branches, main stem thickness, plant width, SCMR and SLA
Evaluation of wild Arachis species
Upadhyaya et al., 2011; Euphytica 182:103‐115
• The other species with desirable traits were A pusilla (earliest flowering) and A. villosa (high SCMR at 60 and 80 days after sowing)
Cicer wild species relatives having resistance to biotic stresses
• Fusarium wilt: C. bijugum, C. judiacum, C. reticulatum, C. echinospermum, C. pinnatifidum, C. canariense, C. chorassanicum, C. cuneatum and C. montbreti(Infantino et al 1996, Croser et al. 2003, Rao et al.,2003)
• Cyst nematode: C. bijugum, C. pinnatifidum, and C. reticulatum (Sharma et al., 1994, Vito et al.,1996, Rao et al. 2003)
• Root-knot nematode: C judiacum, C. pinnatifidum, C. chorassanicum, and C. cuneatum (Sharma et al. 1994)
• Leaf miner: C. reticulatum, C. echinospermum, C. pinnatifidum, C. bijugum, C. chorassanicum, C. cuneatum and C. judiacum, (Croser et al. 2003)
• Bruchid: C. reticulatum, C. echinospermum, C. pinnatifidum, C. bijugum,, C. cuneatum and C. judiacum (Croser et al. 2003)
• Botrytis gray mold: C. pinnatifidum and C. bijugum ( Stevenson and Haware 1999, rao et al 2003)
• Ascochyta blight: C. reticulatum, C. echinospermum, C. pinnatifidum and C. bijugum, C judiacum, C. cuneatum and C. montbreti (Croser et al. 2003, Rao et al.,2003)
• Phytophthora: C. echinospermum (Croser et al. 2003, Knights et al 2003)
• Helicoverpa: Cicer bijugum, C. judaicum, C. pinnatifidum, C. reticulatum , C. microphyllum, C. pungens and C. canariense (Sharma et al.2003, 2007, Rai et al., 2003).
Pre‐breeding at ICRISAT Genebank
• Groundnut: Started in 1980 and on going
• Chickpea and pigeonpea : On going for < 20 years (cytoplasmic male sterility in pigeonpea)
• Pearl millet: On going (submitted proposal to GCDT
• Sorghum: On going as students thesis research
Lines developed through pre‐breeding at ICRISAT
Interspecific derivative
Beneficial trait Wild species/relative contributing gene(s) for resistance
Reference
ICGV 86699 Resistant to rust and late leaf spot
A. cardenasii Reddy et al. 1996
ICGV 87165 Resistant to rust and late leaf spot
A. cardenasii Moss et al. 1997
ICGV‐SM 86715 (Veronica)
Foliar disease resistant variety
A. cardenasii Moss et al. 1998
ICGV‐SM 85048 Foliar disease resistant variety
A. cardenasii Nigam et al. 1998
ICGVs 99001, 99004
Resistance to late leaf spot
Singh et al. 2003
ICGVs 99003, 99005
Resistance to rust Singh et al. 2003
Tetraploid synthetics involving AB genome
A. duranensis x A. ipaensis, A. duranensis x A. batizocoi, A. duranensis x A. hoehnei, A. valida x A. duranensis , A. ipaensis x A. duranensis , A. batizocoi x A. duranensis , A. valida x A. duranensis , A. kempff-mercadoi x A. hoehnei, A. batizocoi x A. cardenasii, A. valida x A. diogoi, A. magna x A. batizocoi, A. batizocoi x A. cardenasii
Tetraploid synthetics involving AA genome
A. kempff-mercadoi x A. stenosperma , A. duranensis x A. cardenasii
Tetraploid synthetics involving BB genome
A. trinitensis x A. hoehnei, A. magna x A. valida
New tetraploid synthetics at ICRISAT
Cultivated parent and BC2F1 progenies
Cultivated parent(ICGV 91114)
Wild parent Progeny Progeny
Variation for root length in cultivated x wild BC2F1 plants
Parents Root length (cm)
BC2 F1(range cm)
Superior plants
TMV 2 21 25-51 14
JL 24 14 25-48 8
GG 2 17 29-60 7
ICGV 91114 22 28-51 8
JUG 26 22 29-55 9
Amphidiploid 35 - -
Wild Arachis species for improving pod yield and seed size
Identity 3 season pooled pod yield (kg ha‐1)
3 season pooled100‐seed
weight (g)
SPAD SLA
2013‐14 mean % over best control
mean % over best control
2013R 2013R
ATY2‐E13 2456 13.3 88 23.5 54 184
ATY2‐E15 2416 11.5 93 31.0 56 178
ATY2‐E23 2704 24.8 78 9.9 53 178
ATY2‐E18 2615 20.7 84 18.3 55 182
ATY2‐E16 2740 26.4 79 10.8 54 186
TMV 2 2167 43 ‐ 43 202
Somnath 2128 71 ‐ 50 191
Wild Arachis species for improving seed size
Wild Cicer for improving agronomic traits
• Used C. reticulatum (2 acc.): 110-113 days to 50% flowering, 143-150 days to maturity, 12-16g 100-seed weight, 2-5 g plant yield, and 6-16% harvest index) as a parent
• Selected several progenies that˗ Flowered 8-21 days and matured 6-33
days earlier
˗ Produced 20-103% large seeds, 97-217% greater seed yield and 6-68% higher harvest index than the cultivated parents
02468
101214161820222426283032343638
5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100
105
110
115
120
125
130
135
140
145
150
155
160
165
170
175
180
Number of days / seed weight (g)
Plan
tsdf dm SDWT YLD
Cultivated parent: df (67); dm (128), SDWT (32g), YLD (17g)Wild parent: df (115), dm (>180), SDWT (16g), YLD (3g)
Wild Cicer for improving agronomic traits
ICC8261
ICC17160
BC4F2
BC4F2 Cultivated WildRoot Depth (cm)6 – 80 42 4251(>50cm) - -RLD (CM3)0.06-1.12 0.53 0.5963 (>1.0cm3) - -
Wild Cicer for drought tolerance
Conclusions• Role of genebanks is different for different crops in pre-
breeding
• CGIAR Genebanks are well endowed with PGR and collection already include genetic stocks, breeding lines and landrace; more materials to store will require additional funding
• However, wild and weedy relatives need to be collected more
• CGIAR genebanks are open to collaboration with private sector
• Wild relatives not only contribute in enhancing resistances to biotic and abiotic stresses but also for agronomic traits
• Sustainable funding for carry evaluation of wild relatives and pre-breeding activities in the public institutions particularly CGIAR genebanks is needed
Thanks!