" Resource use efficiency in vegetables: Application of molecular breeding to bambara groundnut, an underutilised crop for low-input agriculture" presentation by Sean Mayes, Crops for the Future, Semenyih, Malaysia

1. 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 Future
Biotechnology and Crop Genetics Theme
sean.mayes@cffresearch.org/sean.mayes@nottingham.ac.uk Copyright CFF 2015

2. © Copyright CFF - 2015
Major crops have helped to secure food supplies and will continue to play
a 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

3. An alternative to trying to reintroduce resource use efficiency into
major 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

4. - Not for profit company without shareholders
- Guarantors: Government of Malaysia
University of Nottingham
- International remit dedicated to quantitative and
comparative 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 active
Sep 2015: HQ completes and opens
Research partners world-wide 49 Ha Field Research Centre in old oil palm
Copyright CFF 2015

5. Copyright CFFRC - 2014
Current Programmes
SAGEPLUS
FoodPLUS
FishPLUS
BamYIELD
CropBASE
BamYIELD Research and Field Partner Network
www.cropsforthefuture.org; www.bamyield.org
www.bambaragroundnut.org; www.cff-unmc-dtp.com
Copyright CFF 2015

6. Outputs
Outcome
Problem Statement Problem Statement Problem Statement Problem Statement Problem Statement
Biotechnology & Crop Genetics
Breeding & Agronomy
Agrometeorology & Ecophysiology
Nutrition & Bioproducts
Social, Economic & Policy
FishPLUS
FoodPLUS
BamYIELD
CropBASE
SAGEPLUS
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 from
all disciplinary Themes.
Many programmes have CFF-UNMC-DTP PhD studentships attached to them to tackle more
fundamental aspects of the problem (50 PhD students to date; 20 more expected by 2017)

7. © 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
Drawbacks
Photoperiod sensitive
Variability within landraces
Lack of commercial varieties
Limited markets & value added
products
Opportunities
• Food security
• Income generation
• Product development
• Human dietary diversification
• Animal feed
Copyright CFF 2015

8. © Copyright CFF - 2015Copyright CFF 2015

9. © Copyright CFF - 2015
BamYIELD
Progressing well
Making some progress
Planned for 2016
Copyright CFF 2015

10. Copyright CFFRC - 2014
Biotech. and Crop Genetics
SNP100015426|F|0-250.0
bgPabg-597086-17.0
bgPabg-593892-18.5
SNP100024750|F|0-2011.6
SNP100034475|F|0-6313.6
SNP100009818|F|0-5115.0
SNP100016201|F|0-5516.5
SNP100025248|F|0-2418.8
SNP100010701|F|0-4520.9
SNP100030004|F|0-3123.1
SNP100018718|F|0-2324.9
SNP100007045|F|0-2829.2
DQ10002386933.9
SNP100031337|F|0-1636.5
SNP100009992|F|0-1738.6
SNP100030036|F|0-2939.8
SNP100032264|F|0-1741.6
SNP100028074|F|0-644.4
SNP100027856|F|0-945.9
SNP100031378|F|0-1546.8
bgPabg-596774-148.3
DQ10002381148.8
DQ10000940849.2
SNP100027558|F|0-3449.4
SNP100027153|F|0-4450.1
SNP100006188|F|0-5551.3
SNP100009979|F|0-2155.1
SNP100027142|F|0-4156.2
SNP100028068|F|0-2057.5
bgPabg-593965-158.4
SNP100035761|F|0-6359.2
SNP100003688|F|0-5760.9
SNP100028865|F|0-4262.3
SNP100022041|F|0-3563.7
DQ10004380164.1
SNP100015620|F|0-965.5
SNP100029678|F|0-3468.9
SNP100011727|F|0-2271.5
SNP100020429|F|0-6371.9
SNP100021699|F|0-5475.5
SNP100030946|F|0-1676.3
SNP100025104|F|0-5278.1
SNP100021988|F|0-3481.5
SNP100005817|F|0-5482.2
SNP100021970|F|0-5984.4
DQ10002009785.2
DQ10001797186.2
SNP100020997|F|0-3890.5
GH-19-B2-D9-194.0
PRIMER26-196.5
mBam3co7-1101.0
SNP100030604|F|0-62102.2
SNP100006888|F|0-36107.1
SNP100018662|F|0-49116.9
SNP100031948|F|0-40128.7
DQ100010829130.9
DQ100010742131.5
DQ100011481 SNP100033358|F|0-38132.4
SNP100034020|F|0-65134.8
1
Copyright CFF 2015

11. 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 groups
Molosiwa et al., 2015; Siise et al., 2015
Genetic diversity of germplasm
Copyright CFF 2015

12. © Copyright CFF - 2015
Genetic maps
SNP100015426|F|0-250.0
bgPabg-597086-17.0
bgPabg-593892-18.5
SNP100024750|F|0-2011.6
SNP100034475|F|0-6313.6
SNP100009818|F|0-5115.0
SNP100016201|F|0-5516.5
SNP100025248|F|0-2418.8
SNP100010701|F|0-4520.9
SNP100030004|F|0-3123.1
SNP100018718|F|0-2324.9
SNP100007045|F|0-2829.2
DQ10002386933.9
SNP100031337|F|0-1636.5
SNP100009992|F|0-1738.6
SNP100030036|F|0-2939.8
SNP100032264|F|0-1741.6
SNP100028074|F|0-644.4
SNP100027856|F|0-945.9
SNP100031378|F|0-1546.8
bgPabg-596774-148.3
DQ10002381148.8
DQ10000940849.2
SNP100027558|F|0-3449.4
SNP100027153|F|0-4450.1
SNP100006188|F|0-5551.3
SNP100009979|F|0-2155.1
SNP100027142|F|0-4156.2
SNP100028068|F|0-2057.5
bgPabg-593965-158.4
SNP100035761|F|0-6359.2
SNP100003688|F|0-5760.9
SNP100028865|F|0-4262.3
SNP100022041|F|0-3563.7
DQ10004380164.1
SNP100015620|F|0-965.5
SNP100029678|F|0-3468.9
SNP100011727|F|0-2271.5
SNP100020429|F|0-6371.9
SNP100021699|F|0-5475.5
SNP100030946|F|0-1676.3
SNP100025104|F|0-5278.1
SNP100021988|F|0-3481.5
SNP100005817|F|0-5482.2
SNP100021970|F|0-5984.4
DQ10002009785.2
DQ10001797186.2
SNP100020997|F|0-3890.5
GH-19-B2-D9-194.0
PRIMER26-196.5
mBam3co7-1101.0
SNP100030604|F|0-62102.2
SNP100006888|F|0-36107.1
SNP100018662|F|0-49116.9
SNP100031948|F|0-40128.7
DQ100010829130.9
DQ100010742131.5
DQ100011481 SNP100033358|F|0-38132.4
SNP100034020|F|0-65134.8
1
3 populations with genetic maps so far, segregating for different traits
1. Photoperiod sensitivity
2. 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

13. Copyright CFFRC - 2013
Developing translational methodology…
171 spaced markers (+/- and SNP), 7.8 cM/marker, 1,341 cM
Genetic framework map
with Pv syntenic blocks
within and cross-species alignment
Manuscript in preparation
Copyright CFF 2015

14. © 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

15. Breeding and agronomy
Copyright CFF 2015

16. © Copyright CFF - 2015
Development of segregating populations

17. © Copyright CFF - 2015
Breeding for photoperiod insensitivity
Presidor Kendabie
12 hr14 hr16 hr
Kendabie et al., 2015

18. © Copyright CFF - 2015
Genetic variation
Differences 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
Ankpa4
12 hours 14 hours 16 hours
UniswaRedDipC
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

19. © 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

20. © Copyright CFF - 2015
Analysisscheme
Gene expression changes associated with sub-
optimal growth temperatures
Presented as a gene network with a series of
modules with clustered gene ontologies
Cold tolerance in bambara groundnut
Genetic variation

21. © 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 sales
for cash farmers
Sponsored seed provision
for poor farmers
Delivery from breeding to farmers

22. 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)

23. © 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)

24. 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

25. 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 products
for Malaysia

26. © Copyright CFF - 2015
Acknowledgements:
Funding:
European Framework Programmes
DFID, UK
Government of Malaysia
CFF, Malaysia
University of Nottingham and UNMC
Kirkhouse Trust
Genetic diversity analysis:
Florian Stadler, TUM, Germany
Odireleng Molosiwa, UoN
Genetic mapping, QTL & eQTL:
Rakhi Basu, UoN
Nariman Ahmad, UoN
Hui Hui Chai, UoN
John Peter Hammond, Reading Uni, UK
Sequence analysis:
Martin Blythe, Deep Seq, Nottingham
Joanna Moreton, Deep Seq
Wai Kuan Ho, CFF
Single Genotype Lines:
Presidor Kendabie
Katie Mayes
DArTseq development:
Dr Andrzej Kilian, DArT Pty Ltd., Australia
Gene Networks:
Suresh Bonthala, UoN
Jamie Twycross, UoN
CropStore Database
Prof Graham King
Crop Yield Mapping
Prof Asha Karunaratne
CFF:
Sean Mayes
Aryo Feldman
Razlin Azman Halimi
Advina Julkifle
Miang Hoon Lim
Sayed Azam-Ali
Sue Walker
Festo Massawe

27. 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 teff
Biological 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 bambara
groundnut (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

28. Diversifying Agriculture – new species or more use of minor species
www.gapad.org