Germplasm Conservation, Evaluation and Gene Discovery

Transcription

1 Germplasm Conservation, Evaluation and Gene Discovery Andreas Ebert November Headquarters 2012 GLOBAL STRATEGIC PLANNING

2 Theme Germplasm 2012 GLOBAL STRATEGIC PLANNING Goal: Biodiversity of vegetable genetic resources is preserved and its utilization for food and nutritional security is enhanced Purpose: Vegetable germplasm collected, conserved and distributed; collection evaluated to identify accessions with desirable traits; their genes identified, characterized, and introgressed using classical and molecular technologies Germplasm Traits Genes - Acquisition/Conserv. - Regen. /Characteriz. - Documentation - Distribution - Safety duplication - Screening - Introgression - QTL Mapping - Characterization - Isolation - Engineering - IPR - Capacity Building 2

3 Theme Outputs and Output/Outcome Coordinators 1. Germplasm collection, conservation and distribution - Andreas Ebert 2. Germplasm characterization and analysis - Roland Schafleitner 3. Trait-based characterization & screening of germplasm - Srinivasan Ramasamy 4. Trait Introgression and QTL mapping - Roland Schafleitner 5. Gene characterization and functional analysis - Roland Schafleitner 6. IPR strategy on germplasm, transgenics and genes - Andreas Ebert 7. Building capacity in germplasm and gene research - Andreas Ebert 3

4 4 Global Theme Germplasm Meeting at HQ, November 2012

5 Pre-meeting Field Trip 11 November 2012 Tsengwen Reservoir Fire & Water Meditation Garden

6 Staff changes in Theme Germplasm Marilyn Belarmino Genetic Resources Support Scientist RCA-Arusha 5 January June 2012 Tsvetelina Stoilova Scientist Genetic Resources RCA-Arusha 16 January 2013

7 Output 1 Vegetable genetic resources collected, conserved and distributed Outcome and impact in

8 No. of accessions / breeding lines 1200 Worldwide Seed distribution by seed country distribution and within AVRDC in in GLOBAL STRATEGIC PLANNING Total: 4565 (2622 genebank accessions; 1943 breeding lines) as of 31/10/ Breeding GRSU

9 NGOs 2% Bangladesh Proj. 1% Priv. comp./individ. 1% Universities 9% AVRDC-HQ 15% AVRDC-RC 6% Seed companies 30% NARES 36% Seed distribution by recipient category in 2012

10 Germplasm use at HQ in 2012 (667 accessions) GRSU

11 GLOBAL STRATEGIC PLANNING External seed distribution (# of lines) 18,000 17,000 16,000 15,000 14,000 13,000 12,000 11,000 10,000 9,000 8,000 7,000 6,000 5,000 4,000 3,000 2,000 1,000 0 All crops Capsicum Tomato Introduction of handling & shipping fees

12 Seed handling charges threatening impact Many clients (12% in 2011; 17.9% in 2012) simply interrupt communication with AVRDC staff once informed that payment for seed shipment is necessary or indicate that they have no means to pay the fees. We may consider (again) to forego seed charges for the first materials (genebank accessions and breeding lines combined) per institution and year, if the seed request is coming from clients in the public sector living in the 49 least developed countries (LDC). This would have helped 6 countries (7 requests) in 2012: Cambodia, Ethiopia, Mali, Mozambique, Nepal, Uganda. Momina Aragaw, Researcher, Ethiopia (21 Nov. 2012): I am from Amhara Agricultural Research Institute (Adet Agric. Res. Center). No money to pay for you. How can U help me? Thanks more!!

13 Safety duplication of AVRDC germplasm Duplication Site Crops # of acc. National Plant Genetic Resources Center (NPGRC), Taichung, Taiwan (1993 to present) National Plant Genetic Resources Laboratory, Philippines (08/1982) Nat. Vegetable Res. Station Wellesbourne, UK ( ) Nat. Inst. Agrobiol. Sciences (NIAS), Japan ( ) Mungbean, soybean, pepper, tomato, etc. 26,954 Mungbean, tomato 9,407 Brassica 371 Brassica 357 NIAS, Japan ( ) Southeast Asian soybeans 2,389 Nat. Germplasm Resources Lab., Beltsville, USA ( ) Southeast Asian soybeans 2,389 Svalbard Global Seed Vault, Norway (02/ / / /2012) National Agrobiodiversity Center, RDA, Korea (05/ / /2012) All major AVRDC collections included All major AVRDC collections included 12,769 12,819 (21.5%)

14 Vegetable Introduction Number VINo All passport and characterization data do now have a VI number in AVGRIS (S. Chou!) Physical relabeling of all seed packets is in progress!

15 Transfer of germplasm to new facility From Nov to Feb. 2012: Support from other AVRDC units to transfer germplasm 1221 accessions redried and repacked!

16 Transfer of germplasm to new facility (2) From April 2012 to date: Support from young, temporary staff to transfer germplasm 2164 accessions (93,683 small + 81,855 large packets) re-dried and re-packed! In addition, 3,827 mungbean acc. /17,380 packets of treated seed re-packed!

17 Output 2 Germplasm characterized to enhance understanding and utilization of biodiversity in the vegetable germplasm collections Outcome and impact 17

18 Characterization and evaluation of bitter gourd germplasm at ESEA TOT 4234 TOT 4296 TOT 4333 TOT 4383 TOT 4533 TOT 4548 TOT 4622 TOT 4705 TOT 5521 TOT 5850 TOT TOT 6851 TOT TOT TOT 2377 TOT TOT P H O T O D O C U M E N T A T I O N

19 Usefulness of S. pimpinellifolium core collection (75 acc.) Genotype No. Accession No. Other code Country of origin Remarks 8 VI PI Peru High yield under salt stress 25 VI PI Peru High yield under salt stress 26 VI PI Venezuela High survival score under salt stress 42 VI PI Mexico High survival score under salt stress 72 VI LA1547 Ecuador High survival score under salt stress 75 VI LA1606 Peru High survival score under salt stress 86 VI LA1384 Peru High yield under salt stress 39 VI PI Mexico LB resistance* * Merk et al. (2012) Selective genotyping to identify late blight resistance genes in an accession of the tomato wild species Solanum pimpinellifolium. Euphytica DOI /s

20 Molecular and morphological characterization, genetic relationship and diversity analysis of Abelmoschus germplasm collection 165 genotypes genotyped Further 100 genotypes will be genotyped before the end of the year Phylogenetic tree established for 165 genotypes Combined phylogenetic tree for 265 genotypes will be produced for 2012 COA report Outcomes/impacts Genomic resources (gene sequences, markers) available for Abelmoschus Markers in use at Known You Seed Co., Kaohsiung for variety identification

21 Output 3 Trait-based characterization and screening to enhance vegetable germplasm for effective use of important horticultural traits in the development of new vegetable cultivars Outcome and impact 21

22 AVRDC genebank selections for further use in breeding TOT 1843 TOT 7098 TOT 7308 Completely powdery mildew resistant bitter gourd line from GRSU TOT 1513 TOT

23 Bacterial wilt screening - results of tomato cv. Namib grafted on AVRDC eggplant and other rootstocks in Honduras 2012** Rootstock I.D.* Rootstock type Source Mortality (%) at 102 DAT Yield mt/ha VI045276/S00022 Eggplant AVRDC, Taiwan 1.5 a a VI046103/S00019 Eggplant AVRDC, Taiwan 3.0 a a VI034845/S00003 Eggplant AVRDC, Taiwan 4.0 a a VI045571/S00021 Eggplant AVRDC, Taiwan 4.5 a a Control cv. Namib - Rogers/Syngenta, USA 31.5 ab a Emperador Tomato Rijk Zwaan, Netherlands 43.0 b a 1098 Eggplant Seminis, USA 46.1 b a Tomato Rijk Zwaan, Netherlands 63.6 b a * Rootstocks presumably resistant to Ralstonia solanacearum (bacterial wilt) ** Field trial conducted at CEDEH-FHIA, Comayagua, 2012

24 Brassica germplasm screening for resistance to white rust (Albugo macrospora)* (Sakata Seed Corp., Japan; 2009 data; 73 acc.) AVRDC code (old/new) Country of origin Resista nce (%) AVRDC code (old/new) Country of origin Resista nce (%) B00001 / VI USA 100 B00708 / VI China 14.3 B00083 / VI Malaysia 9.1 B00842 / VI Mauritius 27.3 B00104 / VI Thailand 10 B00857 / VI Nepal 50 B00585 / VI India 40 B00858 / VI Nepal 100 B00587 / VI India 100 TB00364 / VI Thailand 63.6 B00588 / VI India 100 TB00564 / VI Indonesia 18.2 B00589 / VI India 81.8 TB00570 / VI Indonesia 10 B00590 / VI India 12.5 TB00686 / VI Lao PDR 100 B00591 / VI India 25 TB00692 / VI Vietnam 100 B00592 / VI India 11.1 TB00694 / VI Vietnam 100 B00593 / VI India 100 TB00765 / VI Bangladesh 9.1 B00707 / VI China 20 TB00767 / VI Bangladesh 18.2 *Spraying seedlings with suspensions of zoosporandia

25 Genebank accessions selected as elite vegetable (and grain) soybean lines 25

26 New varieties submitted to SVTC in CAC in 2012 Armenia: hot pepper Al Tsayhik, Artsiv; Azerbaijan: sweet pepper "Humay" (ISPNO8-1), "Firuz" (AVPPO910), "Shams" (AVPPO911); Georgia: hot pepper 0907 and sweet pepper 0504, and tomato 3078S ; Kazakhstan: pattypan squash VI / TOT7863; basil VI / TOT5925; Kyrgyzstan: sweet pepper , VI / С05483, АVРР0701, АVРР0408 and hot pepper РР , РР ; Tajikistan: mungbean Dubara, Marvorid, Muattar ; Turkmenistan: cucumber "Ashkhabad" (09WVC-18); Uzbekistan: eggplant "Kuvončh" (VI / S00219). squash "Gayrat" (09WVC S-3).

27 New varieties submitted to SVTC in CAC in 2012 VI032170

28 Cucurbit germplasm and breeding lines confirmed for resistance to Squash leaf curl Philippine virus Taiwan isolate (Begomovirus) Cucurbita moschata (seed from selfed apparently resistant plants in earlier screening) SqLCPHV infection Lines Original Source Symptomless plants / total plants (%) PCR + / symptomless plants Virus infec. (%) 3001 VI /24 (58.3) 3/10 17/24 (70.8) 3002 VI /21 (42.9) 2/12 11/21 (52.4) 3005 VI /22 (0) 5/22 5/22 (22.7) 3006 VI /21 (33.3) 11/14 18/21 (85.7) 3007 PK /24 (25) 6/18 12/24 (50) 3008 PK /22 (0) 18/22 18/22 (81.8) 3010 PK /23 (8.7) 19/21 21/23 (91.3) S CK 24/24 (100) NT 24/24 (100)

29 Purified pepper lines resistant to Phytophthora blight deposited at GRSU VI No. Mycol. No. Weight (g) VI C /Pcres,93m/17E,97s5/rf,02s2 5.0 VI C01175/Pcres,95m/17E,96m/97s1/rf,98s6/rf,02s4 2.0 VI C01176/Pc res,?87m/14,96m/17e,97s5/rf,98s6/rf,02s VI C02227/Pc res,92m/17e,97s3/rf,98s1/rf,02s VI C02289/Pc res,92m/17e,96m/97s1/rf,98s1/rf,02s1 3.0 VI C03289/Pc res,92m/17e,96m/rf,02s2 3.0 VI Fidel/Pc17E,97s2/rf,98s2/rf,02s1 3.0 VI TC05415/Pc33E6,08S2/151,09s2 10.0

30 Okra accessions screened for resistance to aphid

31 Advanced screening of okra for aphid resistance at AVRDC Cameroon (Feb - May 2012) Accessions AUIPC Resistance category EVODOULA MR VI MR VI MR VI MR VI056457/TOT MR VI MR VI046559/TOT MR VI051114/TOT6599* R VI036213/TOT3145* R VI033805/TOT2769* 87.9 R *3 out of 367 accessions confirmed as resistant to aphid

32 Output 4 Specialized genetic materials, molecular tools, and methods developed to enable the development of new varieties more rapidly Outcome and impact 32

33 Flavonoids in Tomato Flavonoids are a group of polyphenolic secondary metabolites that include chalcones, flavanones, anthocyanins, flavonols, others High flavonoid consumption associated with lower incidence of some cancers, heart disease Rutin (quercetin-3-rutinoside) is the major flavonoid in tomato fruit Flavonol: quercetin Glycoside: rutinose Rutin (quercetin rutinoside)

34 High Rutin Introgression Line LA3984 High rutin content mainly confined to skin No association with negative fruit or horticultural traits Possible introduction of a new allele for chalcone isomerase from S. habrochaites. otest chalcone isomerase candidate gene for co-segregation with high rutin LA3984 Introgression could extend below TES1325 (42.5 cm). Develop more markers to delimit introgression. Selected high rutin F 4 lines undergoing selection for horticultural traits and generation advance

35 Output 6 IPR strategy on germplasm, transgenics and genes implemented Outcome and impact 35

36 IPR - MTA concluded with Seminis (Oct. 2012) 17 lines of Allium cepa x Allium fistulosum progeny (F5, F9, F10 and several backcrosses (F3-F5) transferred to Seminis (November 2012) Seminis shall attempt to increase seed of each line for 5 years and share 50% of the seed produced with AVRDC. Seminis shall test lines for reactions to stemphylium leaf blight, fusarium basal rot and pink root and share the results annually with AVRDC. If Seminis succeeds in introgressing resistance to stemphylium leaf blight, fusarium basal rot and pink root into A. cepa within 8 years, Seminis shall provide AVRDC with an A. cepa donor line. AVRDC shall have a non-exclusive royalty-free worldwide license to use such line.

37 Output 7 Capacity in germplasm conservation, evaluation, characterization, and gene discovery developed Outcome and impact 37

38 International Training Course for ASEAN countries in Korea, KOICA/RDA, 6-26 May 2012 Topic: Agricultural Genetic Resources Management for ASEAN Countries Participants: 19 trainees from 7 ASEAN countries (Cambodia, Indonesia, Laos, Malaysia, Philippines, Thailand, Vietnam) A. Ebert served as lecturer and mentor from 7-12 May 2012

39 Innovative work done/planned Opportunities 39

40 GENESYS we can work together to fly further SINGER shut down on 24 Nov. 2012

41 Better access to data - Dynamic Interface Data Providers Genebanks Researchers Breeders Others Data Users Pre breeders Breeders Academics Non research A global system for data access

42 Crop Trait Information Network National variety trials Crop genetic Resource Collections Seeds of Discovery CTIN Users: Breeders Pre-Breeders Curators Researchers Others GENESYS Portal CGIAR International Nurseries CGIAR Breeding Programs Current Global Pre-Breeding Research FIGS Trait Mining National Breeding Programs International Phenotyping Molecular Information Programs Systems Courtesy P Brennan

43 Developing a core collection of mungbean germplasm at AVRDC 7640 mungbean entries (5111 accessions) Phenotypic characterization (1984 Spring) 9 quantitative and 13 qualitative traits Core set accessions of 6379 acc. (23.4%) Molecular characterization using 25 SSR markers 43 Refined core set

44 Conduct fine mapping of QTLs of bacterial wilt resistance in tomato and develop markers for MAS Innovative work Planned: Fine-mapping of bacterial wilt QTL in tomato Opportunities Molecular breeding/marker assisted selection

45 Molecular Markers Polymorphic molecular markers may be scarce (mungbean) Reduction of sequencing costs offer new opportunities for obtaining polymorphic markers Genotyping by sequencing: Still too expensive for routine application Requires reference genome sequence information Alternative method: Restriction enzyme Associated DNA (RAD) Sequencing Sequencing of DNA surrounding restriction enzyme cutting sites Effective complexity reduction: 0.1 2% of whole genome sequence information is obtained Bioinformatics translates sequence information into molecular markers

46 RAD Sequencing RAD-Seq of mungbean Collaboration UC Davis AVRDC Establishing the methodology Choice of restriction enzyme Determine sequence coverage Work without reference sequence Optimization of AVRDC bioinformatics pipeline RAD-Seq of tropical tomato populations Sequencing outsourced SNP detection in-house Routine marker development by RAD-Seq on model crop Optimization of workflow Improving quality and cost efficiency RAD-Seq of pepper populations RAD-Seq application on large and complex genomes

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