Advances in Legume Breeding for Better Livelihoods of...
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Feb 2017 Advances in Legume Breeding for Better Livelihoods of Smallholder Farmers in sub-Saharan Africa Chris O Ojiewo 1 , Asnake Fikre 1 , Haile Desmae 2 , Babu N Motagi 3 , Ousmane Boukar 4 , Clare Mukankusi-Mugisha 5 , Emmanuel Monyo 6 , Rajeev K Varshney 7 1 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Ethiopia, 2 Mali, 3 Nigeria, 6 Kenya, 7 India; Addis Ababa, Ethiopia; 4 International Institute of Tropical Agriculture (IITA), Kano Station, Kano, Nigeria; 5 International Center for Tropical Agriculture (CIAT), Kampala, Uganda About ICRISAT: www.icrisat.org ICRISAT’s scienfic informaon: hp://EXPLOREit.icrisat.org *Correspondence: [email protected] Benefits of legumes • Intensify cropping systems as double, catch, relay and intercrops; • Provide ‘free’ nitrogen to soils through atmospheric nitrogen fixaon; • Act as break crops for disease and pest cycles; • Increase and diversify smallholder farmers’ incomes; • Increase household diet quality with plant proteins and micronutrients. The Problem Despite their many benefits, producvity of legumes in sub-Saharan Africa (SSA) is generally lower than world averages (Figure 1) due to: • Bioc stresses (diseases, pests, weeds) • Abioc stresses (heat, frost, drought, and salinity) • Edaphic factors (associated with soil nutrient deficits) Reference sets developed for assorted legumes and traits of agronomic importance idenfied for further crop improvement. Selected Legumes Important traits idenfied in reference collecons Reference Chickpea Drought, salinity, high temperature and herbicide tolerance, Fusarium wilt, Ascochyta blight and Botrys gray mold and pod borer resistance Upadhyaya et al. 2008 Groundnut Early-maturing groundnut (90 days) with high pod yield, large variability in pod/seed characteriscs, oil content and oil quality (oleic/linoleic rao), and grain Fe and Zn content; tolerance to drought, salinity and low temperature; resistance to root-knot nematode, and early/late leaf spot Gowda et al. 2013 Pigeonpea Early flowering, high number of pods, high 100-seed weight and high seed yield/plant Upadhyaya et al. 2011 Cowpea Striga resistance, agronomic traits Mahalakshmi et al. 2006 Use of genome resources for trait discovery. Selected Legumes Genome sequencing progress Reference Chickpea ~738-Mb draſt whole genome - 28,269 genes; disease resistance and agronomic traits Varshney et al. 2013 Groundnut Sub genome size ~2.7 Gb; disease resistance, enhanced pod and oil yield, tolerance to drought and heat, beer oil quality. Chen et al. 2016 Beroli et al. 2016 Pigeonpea Draſt pigeonpea genome sequence - 48,680 genes; drought tolerance agronomic traits Varshney et al. 2012 Cowpea Genome size ~620 Mbp; 298,848 cowpea genespace sequences (GSS) used to develop a database consisng of GSS annotaon and comparave genomics knowledge base, GSS enzyme and metabolic pathway knowledge base, and GSS simple sequence repeats (SSRs) Chen et al. 2007 Common Bean Sequenced genome size ~74 Mbp; two independent domescaon events confirmed Schmutz et al. 2010 Pre-breeding as a source of desired traits. Selected Legumes Desired traits from evaluaon of wild relaves and exoc landraces Reference Chickpea Resistance/tolerance to Phytophthora root rot, cyst nematode (Heterodera ciceri), root-lesion nematode (Pratylenchus spp.), pod borer (Helicoverpa armigera), Ascochyta blight, Botrys gray mold and low temperatures Gaur et al. 2010 Groundnut Resistance to disease and insect pests Sharma et al. 2013 Pigeonpea Cytoplasmic male sterility (CMS) systems Saxena et al. 2015 Cowpea Resistance to insect pests Fatokun 2002 Lenl Anthracnose and wilt resistance; drought tolerance Fiala et al. 2009 Deploying markers in breeding programs for developing improved lines in a cost- and me-effecve manner. Selected Legumes Phenotypic and molecular markers available for forward breeding Reference Chickpea Nine QTL clusters containing QTLs for several drought tolerance traits idenfied. Two novel QTLs explain 10.4–18.8% of phenotypic variaon for resistance to race 1 of Fusarium wilt caused by Fusarium oxysporum f. sp. ciceris and 6 QTLs explaining up to 31.9 % of phenotypic variaon for resistance to Ascochyta blight caused by Ascochyta rabiei Varshney et al. 2014 Sabbavarapu et al. 2013 Groundnut Rust QTL (QTLrust01), contribung 6.90–55.20% variaon idenfied. GM2009, GM1536, GM2301 and GM2079 new markers for QTLrust01 reported. Khedikar et al. 2010 Sujay et al. 2012 Cowpea E-ACT/M-CAA524, 61R and 61M2 gene markers available for use in introgression of Striga resistance into suscepble cowpea lines. Five QTLs represenng 9% of the cowpea genome idenfied to explain 11.5–18.1 % of the phenotypic variaon for heat tolerance and tagged with 48 transcript-derived SNP markers Ouedraogo et al. 2012 Lucas et al. 2013 Common Bean Potyviral resistance associated with the homozygoc presence of a mutated eIF4E allele. A random amplified polymorphic DNA (RAPD) molecular marker (OPH181200C) linked in resistance to race 73 of Colletotrichum lindemuthianum causing anthracnose in beans was idenfied. Three QTL regions responsible for angular leaf spot (ALS) resistance Naderpour et al. 2010 Young et al. 1998 Keller et al. 2015 • Released 177 improved variees of 6 legumes (groundnut, cowpea, chickpea, common bean, pigeonpea, soybean) in SSA and India between 2007-2016 under Tropical Legumes Projects (TLII/ TLIII; Figure 2) • Produced 601,284 tons of various seed classes (Breeders, basic, cerfied and QDS). • 2.245 million ha potenally planted with this amount of seed • With farm size of 0.2ha/farmer about 11,225,365 households reached • Some of these variety releases and their adopon are included in the CGIAR DIIVA (Diffusion and Impact of Improved Variees in Africa) project (Figure 3) while others are more recent. Conclusions and Prospects for Legume Breeding in SSA • Integrang genomics-assisted breeding approaches and rapid generaon advancement to reduce me required for culvar development • Improving targeng, speed, scale, efficiency, quality (control, precision, and accuracy) • Developing formal product profiles for key variees, priorizing traits and raonalizing resource allocaon • Increased throughput (more crosses, larger populaons, more plots at more sites and more generaons per year) • Use of modern high-throughput phenotyping and genotyping protocols and plaorms • Increased mechanizaon and automaon (plot threshers, seed cleaners and seed counters) • Broadening genec base by greater use of genec diversity, either natural or arficial • Improved experimental and stascal designs and methods, precision and accuracy of data handling (e.g. electronic data capture and barcoding) • Tracking pipeline metrics (#crosses, #lines/cross, #lines/evaluaon, yield trials) and trends (CV%, genec progress and genec gains) of the breeding program • Disseminaon models that are rapid and that support rapid varietal replacement. Figure 2. TLIII operates in 8 focus geographies and 4 crops down from 15 countries and 6 crops in TLII Figure 3. Variety release and adopon as summarized by the CGIAR DIIVA (Diffusion and Impact of Improved Variees in Africa) project data on selected crops in Sub-Saharan Africa (hp://www.as.cgiar.org/diiva). Figure 1. Global and SSA comparave figures on yield increase of selected legumes over the years. Priority challenges and traits for genec improvement of selected legumes in sub-Saharan Africa. Crop Constraints Bioc Abioc Others Groundnut Rosee, rust, early leaf spot, late leaf spot, aphids Drought Aflatoxin, oil content and quality Common bean Anthracnose, common bacterial blight, angular leaf spot, bean common mosaic (necroc) virus (BCM(N)V), bean stem maggots, bruchids Heat, drought, low phosphorus (P) and nitrogen (N) tolerance Symbioc nitrogen fixaon, cooking me and canning quality Chickpea Botrys gray mold, Ascochyta blight, Fusarium wilt, dry root rot, pod borer Drought, heat, cold Large-seeded, cooking me and quality Pigeonpea Fusarium wilt, and sterility mosaic disease, pod borer Terminal drought, waterlogging Grain quality and hybrids for different niches Soybean Rust, Cercospora leaf spot, bacterial pustule, and mosaic viruses Drought, low P tolerance Processing quality, symbioc nitrogen fixaon Cowpea Aphids, thrips, bacterial blight, Striga, alectra, and mosaic viruses Drought, low P tolerance, Pod quality, dual purpose The Solution • Genec resources (reference sets, pre-breeding, Mul-parent Advanced Generaon Inter-cross (MAGIC) and intraspecific mapping populaons) • Genomic resources (comprehensive genec maps, whole genome sequences, QTLs and trait- specific markers) • Integrated breeding approaches (high-throughput genotyping and phenotyping plaorms, MAS in pedigree breeding schemes, MABC and MARS) • Improved variees released and disseminated together • Innovave seed and associated technology disseminaon systems Results • Policy issues (less emphasis on legumes compared to staples)
Transcript of Advances in Legume Breeding for Better Livelihoods of...
Feb 2017
Advances in Legume Breeding for Better Livelihoods of Smallholder Farmers in sub-Saharan AfricaChris O Ojiewo1, Asnake Fikre1, Haile Desmae2, Babu N Motagi3, Ousmane Boukar4, Clare Mukankusi-Mugisha5, Emmanuel Monyo6, Rajeev K Varshney7 1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Ethiopia, 2Mali, 3Nigeria, 6Kenya, 7India; Addis Ababa, Ethiopia;4International Institute of Tropical Agriculture (IITA), Kano Station, Kano, Nigeria; 5International Center for Tropical Agriculture (CIAT), Kampala, Uganda
About ICRISAT: www.icrisat.orgICRISAT’s scientific information: http://EXPLOREit.icrisat.org
*Correspondence: [email protected]
Benefits of legumes• Intensify cropping systems as double, catch, relay
and intercrops; • Provide ‘free’ nitrogen to soils through
atmospheric nitrogen fixation; • Act as break crops for disease and pest cycles; • Increase and diversify smallholder farmers’
incomes; • Increase household diet quality with plant proteins
and micronutrients.
The Problem Despite their many benefits, productivity of legumes in sub-Saharan Africa (SSA) is generally lower than world averages (Figure 1) due to:
• Biotic stresses (diseases, pests, weeds)• Abiotic stresses (heat, frost, drought, and salinity) • Edaphic factors (associated with soil nutrient
deficits)
Reference sets developed for assorted legumes and traits of agronomic importance identified for further crop improvement.Selected Legumes Important traits identified in reference collections ReferenceChickpea Drought, salinity, high temperature and herbicide
tolerance, Fusarium wilt, Ascochyta blight and Botrytis gray mold and pod borer resistance
Upadhyaya et al. 2008
Groundnut Early-maturing groundnut (90 days) with high pod yield, large variability in pod/seed characteristics, oil content and oil quality (oleic/linoleic ratio), and grain Fe and Zn content; tolerance to drought, salinity and low temperature; resistance to root-knot nematode, and early/late leaf spot
Gowda et al. 2013
Pigeonpea Early flowering, high number of pods, high 100-seed weight and high seed yield/plant
Upadhyaya et al. 2011
Cowpea Striga resistance, agronomic traits Mahalakshmi et al. 2006
Use of genome resources for trait discovery.Selected Legumes Genome sequencing progress ReferenceChickpea ~738-Mb draft whole genome - 28,269 genes; disease
resistance and agronomic traits Varshney et al. 2013
Groundnut Sub genome size ~2.7 Gb; disease resistance, enhanced pod and oil yield, tolerance to drought and heat, better oil quality.
Chen et al. 2016Bertioli et al. 2016
Pigeonpea Draft pigeonpea genome sequence - 48,680 genes; drought tolerance agronomic traits
Varshney et al. 2012
Cowpea Genome size ~620 Mbp; 298,848 cowpea genespace sequences (GSS) used to develop a database consisting of GSS annotation and comparative genomics knowledge base, GSS enzyme and metabolic pathway knowledge base, and GSS simple sequence repeats (SSRs)
Chen et al. 2007
Common Bean Sequenced genome size ~74 Mbp; two independent domestication events confirmed
Schmutz et al. 2010
Pre-breeding as a source of desired traits.Selected Legumes Desired traits from evaluation of wild relatives and exotic landraces ReferenceChickpea Resistance/tolerance to Phytophthora root rot, cyst nematode
(Heterodera ciceri), root-lesion nematode (Pratylenchus spp.), pod borer (Helicoverpa armigera), Ascochyta blight, Botrytis gray mold and low temperatures
Gaur et al. 2010
Groundnut Resistance to disease and insect pests Sharma et al. 2013Pigeonpea Cytoplasmic male sterility (CMS) systems Saxena et al. 2015Cowpea Resistance to insect pests Fatokun 2002Lentil Anthracnose and wilt resistance; drought tolerance Fiala et al. 2009
Deploying markers in breeding programs for developing improved lines in a cost- and time-effective manner.Selected Legumes Phenotypic and molecular markers available for forward breeding ReferenceChickpea Nine QTL clusters containing QTLs for several drought tolerance traits
identified.Two novel QTLs explain 10.4–18.8% of phenotypic variation for resistance to race 1 of Fusarium wilt caused by Fusarium oxysporum f. sp. ciceris and 6 QTLs explaining up to 31.9 % of phenotypic variation for resistance to Ascochyta blight caused by Ascochyta rabiei
Varshney et al. 2014Sabbavarapu et al. 2013
Groundnut Rust QTL (QTLrust01), contributing 6.90–55.20% variation identified.GM2009, GM1536, GM2301 and GM2079 new markers for QTLrust01 reported.
Khedikar et al. 2010Sujay et al. 2012
Cowpea E-ACT/M-CAA524, 61R and 61M2 gene markers available for use in introgression of Striga resistance into susceptible cowpea lines.Five QTLs representing 9% of the cowpea genome identified to explain 11.5–18.1 % of the phenotypic variation for heat tolerance and tagged with 48 transcript-derived SNP markers
Ouedraogo et al. 2012Lucas et al. 2013
Common Bean
Potyviral resistance associated with the homozygotic presence of a mutated eIF4E allele.A random amplified polymorphic DNA (RAPD) molecular marker (OPH181200C) linked in resistance to race 73 of Colletotrichum lindemuthianum causing anthracnose in beans was identified.Three QTL regions responsible for angular leaf spot (ALS) resistance
Naderpour et al. 2010Young et al. 1998Keller et al. 2015
• Released 177 improved varieties of 6 legumes (groundnut, cowpea, chickpea, common bean, pigeonpea, soybean) in SSA and India between 2007-2016 under Tropical Legumes Projects (TLII/TLIII; Figure 2)
• Produced 601,284 tons of various seed classes (Breeders, basic, certified and QDS). • 2.245 million ha potentially planted with this amount of seed• With farm size of 0.2ha/farmer about 11,225,365 households reached• Some of these variety releases and their adoption are included in the CGIAR DIIVA (Diffusion and
Impact of Improved Varieties in Africa) project (Figure 3) while others are more recent.
Conclusions and Prospects for Legume Breeding in SSA • Integrating genomics-assisted breeding approaches and rapid generation advancement to
reduce time required for cultivar development• Improving targeting, speed, scale, efficiency, quality (control, precision, and accuracy)• Developing formal product profiles for key varieties, prioritizing traits and rationalizing resource
allocation • Increased throughput (more crosses, larger populations, more plots at more sites and more
generations per year)• Use of modern high-throughput phenotyping and genotyping protocols and platforms • Increased mechanization and automation (plot threshers, seed cleaners and seed counters) • Broadening genetic base by greater use of genetic diversity, either natural or artificial• Improved experimental and statistical designs and methods, precision and accuracy of data
handling (e.g. electronic data capture and barcoding) • Tracking pipeline metrics (#crosses, #lines/cross, #lines/evaluation, yield trials) and trends (CV%,
genetic progress and genetic gains) of the breeding program • Dissemination models that are rapid and that support rapid varietal replacement.
Figure 2. TLIII operates in 8 focus geographies and 4 crops down from 15 countries and 6 crops in TLII
Figure 3. Variety release and adoption as summarized by the CGIAR DIIVA (Diffusion and Impact of Improved Varieties in Africa) project data on selected crops in Sub-Saharan Africa (http://www.asti.cgiar.org/diiva).
Figure 1. Global and SSA comparative figures on yield increase of selected legumes over the years.
Priority challenges and traits for genetic improvement of selected legumes in sub-Saharan Africa.Crop Constraints
Biotic Abiotic OthersGroundnut Rosette, rust, early leaf spot,
late leaf spot, aphidsDrought Aflatoxin, oil content
and qualityCommon bean
Anthracnose, common bacterial blight, angular leaf spot, bean common mosaic (necrotic) virus (BCM(N)V), bean stem maggots, bruchids
Heat, drought, low phosphorus (P) and nitrogen (N) tolerance
Symbiotic nitrogen fixation, cooking time and canning quality
Chickpea Botrytis gray mold, Ascochyta blight, Fusarium wilt, dry root rot, pod borer
Drought, heat, cold Large-seeded, cooking time and quality
Pigeonpea Fusarium wilt, and sterility mosaic disease, pod borer
Terminal drought, waterlogging
Grain quality and hybrids for different niches
Soybean Rust, Cercospora leaf spot, bacterial pustule, and mosaic viruses
Drought, low P tolerance Processing quality, symbiotic nitrogen fixation
Cowpea Aphids, thrips, bacterial blight, Striga, alectra, and mosaic viruses
Drought, low P tolerance, Pod quality, dual purpose
The Solution• Genetic resources (reference sets, pre-breeding, Multi-parent Advanced Generation Inter-cross
(MAGIC) and intraspecific mapping populations)• Genomic resources (comprehensive genetic maps, whole genome sequences, QTLs and trait-
specific markers)• Integrated breeding approaches (high-throughput genotyping and phenotyping platforms, MAS
in pedigree breeding schemes, MABC and MARS) • Improved varieties released and disseminated together • Innovative seed and associated technology dissemination systems
Results
• Policy issues (less emphasis on legumes compared to staples)
