" Resource use efficiency in vegetables: Application of molecular breeding to bambara groundnut, an underutilised crop for low-input agriculture"

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


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

http://www.cropsforthefuture.org/

http://www.bamyield.org/

http://www.bambaragroundnut.org/

http://www.cff-unmc-dtp.com/

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)


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


BamYIELD

Progressing wellMaking some progressPlanned for 2016

Copyright CFF 2015


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


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


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


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

Copyright CFF 2015


Development of segregating populations


Breeding for photoperiod insensitivityPresidor Kendabie

12 hr14 hr16 hr

Kendabie et al., 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


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


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


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


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)


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)


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


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


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

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http://www.gapad.org/

" Resource use efficiency in vegetables: Application of molecular breeding to bambara groundnut, an underutilised crop for low-input agriculture"

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