" resource use efficiency in vegetables: application of molecular breeding to bambara...
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Copyright CFFRC - 2014
Resource use efficiency in vegetables: Application of molecular breeding to bambara groundnut, an underutilised crop for low-input agriculture
Dr Sean Mayes, Crops for the FutureBiotechnology and Crop Genetics [email protected]/[email protected]
Copyright CFF 2015
© Copyright CFF - 2015
Major crops have helped to secure food supplies and will continue to playa major part in any future solutions to food security
However, a major adjustment is needed to reduce the intensity of inputs in the face of climate change and improve resource use efficiency , with a focus on introduction of genes from relatives, ancestors and alien species
KWS wheat trials,Thriplow, UK.
e.g. Quan et al., 2016
An alternative to trying to reintroduce resource use efficiency intomajor crops which have lost it, is to re-examine underutilised crops,many of which have always been grown under low input systems
Copyright CFF 2015
- Not for profit company without shareholders
- Guarantors: Government of MalaysiaUniversity of Nottingham
- International remit dedicated to quantitative andcomparative research on underutilised crops for food, feed, fuel and materialsHQ next to the UoN Malaysian Campus
June 2011: (initial 7 years funding for staff and infrastructure, opened by Malaysian PM)Feb 2013: Doctoral Training Partnership begins (currently 50 PhDs; 30 more expected by 2017)June 2014: Field Research Station opened and activeSep 2015: HQ completes and opens
Research partners world-wide 49 Ha Field Research Centre in old oil palm
Copyright CFF 2015
Copyright CFFRC - 2014
Current Programmes
SAGEPLUS
FoodPLUS
FishPLUS
BamYIELD
CropBASE
BamYIELD Research and Field Partner Network
www.cropsforthefuture.org; www.bamyield.orgwww.bambaragroundnut.org; www.cff-unmc-dtp.com
Copyright CFF 2015
Outputs
Outcome
Problem Statement Problem Statement Problem Statement Problem Statement Problem Statement
Biotechnology & Crop Genetics
Breeding & Agronomy
Agrometeorology & Ecophysiology
Nutrition & Bioproducts
Social, Economic & Policy
Fish
PLU
S
Foo
dP
LUS
Bam
YIE
LD
Cro
pB
ASE
SAG
EPLU
S
Projects
CFFPLUS DTP Studentships
Outcome Outcome Outcome Outcome
Outputs Outputs Outputs Outputs
Impact Impact Impact Impact Impact
Projects and Programmes begin with a problem statement and receive input fromall disciplinary Themes.
Many programmes have CFF-UNMC-DTP PhD studentships attached to them to tackle morefundamental aspects of the problem (50 PhD students to date; 20 more expected by 2017)
© Copyright CFF - 2015
Why Bambara groundnut?
Strengths:• Drought tolerance• Grows in semi- arid and tropical environments• Nitrogen fixing• Fast growing (4-5 months)• 3rd most important nutrient legume in sub-Saharan Africa
DrawbacksPhotoperiod sensitive Variability within landracesLack of commercial varietiesLimited markets & value added products
Opportunities• Food security• Income generation• Product development• Human dietary diversification• Animal feed
Copyright CFF 2015
© Copyright CFF - 2015Copyright CFF 2015
© Copyright CFF - 2015
BamYIELD
Progressing wellMaking some progressPlanned for 2016
Copyright CFF 2015
Copyright CFFRC - 2014
Biotech. and Crop Genetics
SNP100015426|F|0-250.0bgPabg-597086-17.0bgPabg-593892-18.5SNP100024750|F|0-2011.6SNP100034475|F|0-6313.6SNP100009818|F|0-5115.0SNP100016201|F|0-5516.5SNP100025248|F|0-2418.8SNP100010701|F|0-4520.9SNP100030004|F|0-3123.1SNP100018718|F|0-2324.9SNP100007045|F|0-2829.2DQ10002386933.9SNP100031337|F|0-1636.5SNP100009992|F|0-1738.6SNP100030036|F|0-2939.8SNP100032264|F|0-1741.6SNP100028074|F|0-644.4SNP100027856|F|0-945.9SNP100031378|F|0-1546.8bgPabg-596774-148.3DQ10002381148.8DQ10000940849.2SNP100027558|F|0-3449.4SNP100027153|F|0-4450.1SNP100006188|F|0-5551.3SNP100009979|F|0-2155.1SNP100027142|F|0-4156.2SNP100028068|F|0-2057.5bgPabg-593965-158.4SNP100035761|F|0-6359.2SNP100003688|F|0-5760.9SNP100028865|F|0-4262.3SNP100022041|F|0-3563.7DQ10004380164.1SNP100015620|F|0-965.5SNP100029678|F|0-3468.9SNP100011727|F|0-2271.5SNP100020429|F|0-6371.9SNP100021699|F|0-5475.5SNP100030946|F|0-1676.3SNP100025104|F|0-5278.1SNP100021988|F|0-3481.5SNP100005817|F|0-5482.2SNP100021970|F|0-5984.4DQ10002009785.2DQ10001797186.2SNP100020997|F|0-3890.5GH-19-B2-D9-194.0PRIMER26-196.5mBam3co7-1101.0SNP100030604|F|0-62102.2SNP100006888|F|0-36107.1SNP100018662|F|0-49116.9SNP100031948|F|0-40128.7DQ100010829130.9DQ100010742131.5DQ100011481 SNP100033358|F|0-38132.4SNP100034020|F|0-65134.8
1
Copyright CFF 2015
SSR-based genetic diversity analysis (PCA)
DArT microarray analysis
Clear differentiation between West and South+East African accessions
Crosses to introduce new variation could be made between agro-ecologically matched accessions but from different breeding groupsMolosiwa et al., 2015; Siise et al., 2015
Genetic diversity of germplasm
Copyright CFF 2015
© Copyright CFF - 2015
Genetic maps
SNP100015426|F|0-250.0bgPabg-597086-17.0bgPabg-593892-18.5SNP100024750|F|0-2011.6SNP100034475|F|0-6313.6SNP100009818|F|0-5115.0SNP100016201|F|0-5516.5SNP100025248|F|0-2418.8SNP100010701|F|0-4520.9SNP100030004|F|0-3123.1SNP100018718|F|0-2324.9SNP100007045|F|0-2829.2DQ10002386933.9SNP100031337|F|0-1636.5SNP100009992|F|0-1738.6SNP100030036|F|0-2939.8SNP100032264|F|0-1741.6SNP100028074|F|0-644.4SNP100027856|F|0-945.9SNP100031378|F|0-1546.8bgPabg-596774-148.3DQ10002381148.8DQ10000940849.2SNP100027558|F|0-3449.4SNP100027153|F|0-4450.1SNP100006188|F|0-5551.3SNP100009979|F|0-2155.1SNP100027142|F|0-4156.2SNP100028068|F|0-2057.5bgPabg-593965-158.4SNP100035761|F|0-6359.2SNP100003688|F|0-5760.9SNP100028865|F|0-4262.3SNP100022041|F|0-3563.7DQ10004380164.1SNP100015620|F|0-965.5SNP100029678|F|0-3468.9SNP100011727|F|0-2271.5SNP100020429|F|0-6371.9SNP100021699|F|0-5475.5SNP100030946|F|0-1676.3SNP100025104|F|0-5278.1SNP100021988|F|0-3481.5SNP100005817|F|0-5482.2SNP100021970|F|0-5984.4DQ10002009785.2DQ10001797186.2SNP100020997|F|0-3890.5GH-19-B2-D9-194.0PRIMER26-196.5mBam3co7-1101.0SNP100030604|F|0-62102.2SNP100006888|F|0-36107.1SNP100018662|F|0-49116.9SNP100031948|F|0-40128.7DQ100010829130.9DQ100010742131.5DQ100011481 SNP100033358|F|0-38132.4SNP100034020|F|0-65134.8
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3 populations with genetic maps so far, segregating for different traits 1. Photoperiod sensitivity2. Growth habit (domesticated x domesticated)3. Growth habit (domesticated x wild)
Composite linkage groups consisting of DArT, SSR and DArTseq markers; manuscript submitted to Genome
DipC (domesticated)‘bunched’
‘less-sensitive to photoperiod’
Tiga Necaru (domesticated)‘semi-spreading’
VSSP11 (wild)‘spreading’
ancestor
Ankpa4 (domesticated)‘sensitive to photoperiod’
Copyright CFF 2015
Copyright CFFRC - 2013
Developing translational methodology…
171 spaced markers (+/- and SNP), 7.8 cM/marker, 1,341 cM
Genetic framework mapwith Pv syntenic blocks
within and cross-species alignment
Manuscript in preparation
Copyright CFF 2015
© Copyright CFF - 2015
By focusing on trait of interest eg. peduncle length
Peduncle length QTL
LOD
Gp9 high dense map
Generating links from bambara groundnut maps to sequenced genomes permits the likely genes underlying the corresponding position in the major or model species to be identified as candidate gene orthologues for the traits in bambara groundnut
Breeding and agronomy
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© Copyright CFF - 2015
Development of segregating populations
© Copyright CFF - 2015
Breeding for photoperiod insensitivityPresidor Kendabie
12 hr14 hr16 hr
Kendabie et al., 2015
© Copyright CFF - 2015
Genetic variationDifferences in yield formation at three daylengths
Qualitative short day:Ankpa 4
Quantitative short day:Tiga Necaru, Lun T, Getso and Gresik
Quantitative long day:IITA-686 and DodR
Less-sensitive types:Dip C, Uniswa Red and S19-3
An
kpa
4
12 hours 14 hours 16 hours
Un
isw
aR
edD
ip C
Name Origin
Ankpa 4 Nigeria
Dip C Botswana
DodR Tanzania
Getso Nigeria
Gresik Indonesia
IITA-686 Tanzania
Lun T Sierra Leone
S19-3 Namibia
Tiga Necaru Mali
Uniswa Red Swaziland
© Copyright CFF - 2015
Investigating responses to drought in bambara groundnut
Soil water content; PR2 probe
Tiga Necaru x DipC; F5 n=73; soybean Microarray and DArT seq
Genetic variation
Chai et al., 2015; Yusuf et al., 2015
© Copyright CFF - 2015
An
alys
is s
chem
e
Gene expression changes associated with sub-optimal growth temperaturesPresented as a gene network with a series of modules with clustered gene ontologies
Cold tolerance in bambara groundnutGenetic variation
© Copyright CFF - 2014
Germplasm screening: photoperiod sensitivity of bambara groundnut accessions could be affecting yield and preventing its growth in North Africa and the Southern Mediterranean
Other traits under analysis: drought tolerance, morphology, disease R
3. Field/farmer evaluation
2. Line purification / improved varieties
. 1. FACE/controlled field environments
Joint venture seed companies (under discussion) - Malaysia
- South Africa - Tanzania
Genetic analysis and introgression of climate resilience traits into locally adapted germplasm
in CE
Commercial salesfor cash farmers
Sponsored seed provisionfor poor farmers
Delivery from breeding to farmers
Copyright CFFRC - 2013
Agrometeorology & Ecophysiology
• Model predictions for crop growth in Malaysia for 2 African landraces: Uniswa Red and S19-3 with CropBASE colleagues
• Provide baseline data for future field experiments for proof of concept
Climate and growth modelling using BG
Uniswa Red (Swaziland; sub-humid) S19-3(Namibia; arid)
© Copyright CFF - 2015
Nutrition and Bioproducts
In collaboration with a local snack company
‘Boiled’ snack in Kedah & Thailand
‘Fried’ snack in Indonesia BG tortilla chips (with rice flour, 90% BG), Keropok (with tapioca and rice
flour, 20% BG), BG tortilla chips (with tapioca flour, 90% BG) and murukku
(with rice flour, 50% BG)
Copyright CFFRC - 2013
Socio, Economics and Policy
1) Value Chain research in Indonesia
- Assessment of co-operative model set up for BG cultivation, and production of raw material for direct commissioning of processing by the farmers, socio-economic impact on local community
2) End user research in Africa
- Acceptance of local community towards BG as a crop, and as a food source (Ghana, Nigeria and Tanzania)
- Understanding consumption, utilisation, marketing constraints
Improving livelihood of local communities
Copyright CFFRC - 2013
Yield predictions based on actual and predicted climate in Malaysia (tonnes) 2010 and 2050 – UniSwa Red landrace
International research and development programme
2010 2050
A potential new crop for Malaysia
Indonesian ‘Kacang Bogor’
Malaysian prototype testing (with Mamee DD)
Example productsfor Malaysia
© Copyright CFF - 2015
Acknowledgements:
Funding: European Framework ProgrammesDFID, UKGovernment of MalaysiaCFF, MalaysiaUniversity of Nottingham and UNMCKirkhouse Trust
Genetic diversity analysis:Florian Stadler, TUM, GermanyOdireleng Molosiwa, UoN
Genetic mapping, QTL & eQTL:Rakhi Basu, UoNNariman Ahmad, UoNHui Hui Chai, UoNJohn Peter Hammond, Reading Uni, UK
Sequence analysis:Martin Blythe, Deep Seq, NottinghamJoanna Moreton, Deep SeqWai Kuan Ho, CFF
Single Genotype Lines:Presidor KendabieKatie Mayes
DArTseq development:Dr Andrzej Kilian, DArT Pty Ltd., Australia
Gene Networks:Suresh Bonthala, UoNJamie Twycross, UoN
CropStore DatabaseProf Graham King
Crop Yield MappingProf Asha Karunaratne
CFF:Sean MayesAryo Feldman Razlin Azman HalimiAdvina JulkifleMiang Hoon LimSayed Azam-Ali Sue WalkerFesto Massawe
Xie Q, Mayes, S. and Sparkes, D.L. (2015). Spelt as a genetic resource for yield component improvement in bread wheat. Crop Science doi:10.2135/cropsci2014.12.0842
Chai, H.H., Massawe, F. and Mayes, S (2015) Effects of mild drought stress on the morpho-physiological characteristics of a Bambara groundnut segregating population, Euphytica DOI 10.1007/s10681-015-1581-2
Bonthala, V.S., Mayes, K., Moreton, J., Blythe, M., Wright, V., May, S., Massawe, F., Mayes, S. and Twycross, J (2016) Identification of gene modules associated with low temperatures response in bambara groundnut by network-based analysis. PLoS One.11(2): e0148771. doi:10.1371/journal.pone.0148771
Mayes, S., Ho, W.K., Kendabie, K., Chai, H.H., Aliyu, S., Feldman, A., Halimi, R.A., Massawe, F. and Azam-Ali, S (2015) Applying molecular genetics to underutilised species – problems and opportunities Malaysian Applied Biotechnology 44(4); 1-8.
Musa, M., Al-Shareef, I., Mayes, S., Massawe, F. and Singh, A. (in press) Nitrogen Fixation and N-balance Studies on Bambara Groundnut (Vigna subterranea L. Verdc) Landraces Grown on Tropical Acidic Soils of Malaysia Communications in Soil Science and Plant Analysis
Chai, H.H., Massawe, F. and Mayes, S (2015) Effects of mild drought stress on the morpho-physiological characteristics of a Bambara groundnut segregating population, Euphytica DOI 10.1007/s10681-015-1581-2
Cheng, A., Mayes, S., Dalle, G., Demissew, S. and Massawe, F. (2015) Diversifying crops for food and nutrition security – a case of teffBiological Reviews doi: 10.1111/brv.12225
Abberton, M., Batley, J., Bentley, A., Bryant, J., Cai, H., Cockram, J., Costa de Oliveira, A., Cseke, L., Dempewolf, H., De Pace, C., Edwards, D., Gepts, P., Greenland, A., Hall, A., Henry, R., Hori, K., Howe, G., Hughes, S., Humphreys, M., Lightfoot, D., Marshall, A., Mayes, S.,Nguyen, H., Ogbonnaya, F., Ortiz, R., Paterson, A., Tuberosa, R., Valliyodan, B., Varshney, R. and Yano, M. (2015) Global agricultural intensification during climate change: a role for genomics. The Plant Biotechnology Journal DOI: 10.1111/pbi.12467
Kendabie, K., Massawe, F. and Mayes, S. (2015) Developing genetic mappingresources from landrace-derived genotypes that differ for photoperiod sensitivity in bambara groundnut (Vigna subterranea L.) Aspects of Applied Biology 124;124, Breeding Plants to Cope with Future Climate Change pp 49 - 56
Muhammad, YY, Mayes S & Massawe F (2015) Effects of short term water deficit stress on physiological characteristics of bambaragroundnut (Vigna subterranea L. Verdc) South African Journal of Plant and Soil DOI:10.1080/02571862.2015.1056847
Molosiwa O, Aliyu S, Stadler F, Mayes K, Massawe F, Kilian A & Mayes S (2015). SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces Genetic Resources and Crop Evolution DOI 10.1007/s10722-015-0226-6
Aliyu S, Massawe FJ & Mayes S (2015) Beyond landraces: Developing improved germplasm resources for underutilized species - a case for Bambara groundnut Biotechnology and Genetic Engineering Reviews;30:127-41
Diversifying Agriculture – new species or more use of minor species
www.gapad.org