Role of genebank in pre breeding - UMR AGAP · A member of CGIAR consortium IITA Genetic Resources...

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


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


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


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.


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


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



ICG2381: ICG1668 0.667 ICG11088: ICG2925 0.643 ICG12625: ICG2925 0.762












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!

Role of genebank in pre breeding - UMR AGAP · A member of CGIAR consortium IITA Genetic Resources...

Documents

Transcript of Role of genebank in pre breeding - UMR AGAP · A member of CGIAR consortium IITA Genetic Resources...