Advances in Legume Breeding for Better Livelihoods of ... ... Advances in Legume Breeding for Better

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  • Feb 2017

    Advances in Legume Breeding for Better Livelihoods of Smallholder Farmers in sub-Saharan Africa Chris 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.org ICRISAT’s scientific information: http://EXPLOREit.icrisat.org

    *Correspondence: c.ojiewo@cgiar.org

    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 Reference Chickpea 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 Reference Chickpea ~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. 2016 Bertioli 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 Reference Chickpea 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. 2013 Pigeonpea Cytoplasmic male sterility (CMS) systems Saxena et al. 2015 Cowpea Resistance to insect pests Fatokun 2002 Lentil 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 Reference Chickpea 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. 2014 Sabbavarapu 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. 2010 Sujay 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. 2012 Lucas 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. 2010 Young et al. 1998 Keller 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 Others Groundnut Rosette, 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 (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)