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Ramulifho E, Rey C. A Coiled-Coil Nucleotide-Binding Domain Leucine-Rich Repeat Receptor Gene MeRPPL1 Plays a Role in the Replication of a Geminivirus in Cassava. Viruses 2024; 16:941. [PMID: 38932233 PMCID: PMC11209366 DOI: 10.3390/v16060941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Disease resistance gene (R gene)-encoded nucleotide-binding leucine-rich repeat proteins (NLRs) are critical players in plant host defence mechanisms because of their role as receptors that recognise pathogen effectors and trigger plant effector-triggered immunity (ETI). This study aimed to determine the putative role of a cassava coiled-coil (CC)-NLR (CNL) gene MeRPPL1 (Manes.12G091600) (single allele) located on chromosome 12 in the tolerance or susceptibility to South African cassava mosaic virus (SACMV), one of the causal agents of cassava mosaic disease (CMD). A transient protoplast system was used to knock down the expression of MeRPPL1 by clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9). The MeRPPL1-targeting CRISPR vectors and/or SACMV DNA A and DNA B infectious clones were used to transfect protoplasts isolated from leaf mesophyll cells from the SACMV-tolerant cassava (Manihot esculenta) cultivar TME3. The CRISPR/Cas9 silencing vector significantly reduced MeRPPL1 expression in protoplasts whether with or without SACMV co-infection. Notably, SACMV DNA A replication was higher in protoplasts with lower MeRPPL1 expression levels than in non-silenced protoplasts. Mutagenesis studies revealed that protoplast co-transfection with CRISPR-MeRPPL1 silencing vector + SACMV and transfection with only SACMV induced nucleotide substitution mutations that led to altered amino acids in the highly conserved MHD motif of the MeRPPL1-translated polypeptide. This may abolish or alter the regulatory role of the MHD motif in controlling R protein activity and could contribute to the increase in SACMV-DNA A accumulation observed in MeRPPL1-silenced protoplasts. The results herein demonstrate for the first time a role for a CNL gene in tolerance to a geminivirus in TME3.
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Affiliation(s)
- Elelwani Ramulifho
- Plant Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2001, South Africa;
- Germplasm Development, Agricultural Research Council, Small Grain Institute, Bethlehem 9700, South Africa
| | - Chrissie Rey
- Plant Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2001, South Africa;
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Ntui VO, Tripathi JN, Kariuki SM, Tripathi L. Cassava molecular genetics and genomics for enhanced resistance to diseases and pests. MOLECULAR PLANT PATHOLOGY 2024; 25:e13402. [PMID: 37933591 PMCID: PMC10788594 DOI: 10.1111/mpp.13402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
Cassava (Manihot esculenta) is one of the most important sources of dietary calories in the tropics, playing a central role in food and economic security for smallholder farmers. Cassava production is highly constrained by several pests and diseases, mostly cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). These diseases cause significant yield losses, affecting food security and the livelihoods of smallholder farmers. Developing resistant varieties is a good way of increasing cassava productivity. Although some levels of resistance have been developed for some of these diseases, there is observed breakdown in resistance for some diseases, such as CMD. A frequent re-evaluation of existing disease resistance traits is required to make sure they are still able to withstand the pressure associated with pest and pathogen evolution. Modern breeding approaches such as genomic-assisted selection in addition to biotechnology techniques like classical genetic engineering or genome editing can accelerate the development of pest- and disease-resistant cassava varieties. This article summarizes current developments and discusses the potential of using molecular genetics and genomics to produce cassava varieties resistant to diseases and pests.
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Affiliation(s)
| | | | | | - Leena Tripathi
- International Institute of Tropical AgricultureNairobiKenya
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Rajabu CA, Dallas MM, Chiunga E, De León L, Ateka EM, Tairo F, Ndunguru J, Ascencio-Ibanez JT, Hanley-Bowdoin L. SEGS-1 a cassava genomic sequence increases the severity of African cassava mosaic virus infection in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1250105. [PMID: 37915512 PMCID: PMC10616593 DOI: 10.3389/fpls.2023.1250105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023]
Abstract
Cassava is a major crop in Sub-Saharan Africa, where it is grown primarily by smallholder farmers. Cassava production is constrained by Cassava mosaic disease (CMD), which is caused by a complex of cassava mosaic begomoviruses (CMBs). A previous study showed that SEGS-1 (sequences enhancing geminivirus symptoms), which occurs in the cassava genome and as episomes during viral infection, enhances CMD symptoms and breaks resistance in cassava. We report here that SEGS-1 also increases viral disease severity in Arabidopsis thaliana plants that are co-inoculated with African cassava mosaic virus (ACMV) and SEGS-1 sequences. Viral disease was also enhanced in Arabidopsis plants carrying a SEGS-1 transgene when inoculated with ACMV alone. Unlike cassava, no SEGS-1 episomal DNA was detected in the transgenic Arabidopsis plants during ACMV infection. Studies using Nicotiana tabacum suspension cells showed that co-transfection of SEGS-1 sequences with an ACMV replicon increases viral DNA accumulation in the absence of viral movement. Together, these results demonstrated that SEGS-1 can function in a heterologous host to increase disease severity. Moreover, SEGS-1 is active in a host genomic context, indicating that SEGS-1 episomes are not required for disease enhancement.
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Affiliation(s)
- Cyprian A. Rajabu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Mary M. Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Evangelista Chiunga
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Elijah M. Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Fred Tairo
- Tanzania Agricultural Research Institute-Mikocheni, Dar Es Salaam, Tanzania
| | - Joseph Ndunguru
- Tanzania Agricultural Research Institute-Mikocheni, Dar Es Salaam, Tanzania
| | - Jose T. Ascencio-Ibanez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Chaowongdee S, Malichan S, Pongpamorn P, Paemanee A, Siriwan W. Metabolic profiles of Sri Lankan cassava mosaic virus-infected and healthy cassava (Manihot esculenta Crantz) cultivars with tolerance and susceptibility phenotypes. BMC PLANT BIOLOGY 2023; 23:178. [PMID: 37020181 PMCID: PMC10074701 DOI: 10.1186/s12870-023-04181-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Cassava mosaic disease (CMD) of cassava (Manihot esculenta Crantz) has expanded across many continents. Sri Lankan cassava mosaic virus (SLCMV; family Geminiviridae), which is the predominant cause of CMD in Thailand, has caused agricultural and economic damage in many Southeast Asia countries such as Vietnam, Loas, and Cambodia. The recent SLCMV epidemic in Thailand was commonly found in cassava plantations. Current understanding of plant-virus interactions for SLCMV and cassava is limited. Accordingly, this study explored the metabolic profiles of SLCMV-infected and healthy groups of tolerant (TME3 and KU50) and susceptible (R11) cultivars of cassava. Findings from the study may help to improve cassava breeding, particularly when combined with future transcriptomic and proteomic research. RESULTS SLCMV-infected and healthy leaves were subjected to metabolite extraction followed by ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS/MS). The resulting data were analyzed using Compound Discoverer software, the mzCloud, mzVault, and ChemSpider databases, and published literature. Of the 85 differential compounds (SLCMV-infected vs healthy groups), 54 were differential compounds in all three cultivars. These compounds were analyzed using principal component analysis (PCA), hierarchical clustering dendrogram analysis, heatmap analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Chlorogenic acid, DL-carnitine, neochlorogenic acid, (E)-aconitic acid, and ascorbyl glucoside were differentially expressed only in TME3 and KU50, with chlorogenic acid, (E)-aconitic acid, and neochlorogenic acid being downregulated in both SLCMV-infected TME3 and KU50, DL-carnitine being upregulated in both SLCMV-infected TME3 and KU50, and ascorbyl glucoside being downregulated in SLCMV-infected TME3 but upregulated in SLCMV-infected KU50. Furthermore, 7-hydroxycoumarine was differentially expressed only in TME3 and R11, while quercitrin, guanine, N-acetylornithine, uridine, vorinostat, sucrose, and lotaustralin were differentially expressed only in KU50 and R11. CONCLUSIONS Metabolic profiling of three cassava landrace cultivars (TME3, KU50, and R11) was performed after SLCMV infection and the profiles were compared with those of healthy samples. Certain differential compounds (SLCMV-infected vs healthy groups) in different cultivars of cassava may be involved in plant-virus interactions and could underlie the tolerance and susceptible responses in this important crop.
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Affiliation(s)
- Somruthai Chaowongdee
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok, 10900, Thailand
| | - Srihunsa Malichan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Pornkanok Pongpamorn
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Atchara Paemanee
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Wanwisa Siriwan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
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Sheat S, Winter S. Developing broad-spectrum resistance in cassava against viruses causing the cassava mosaic and the cassava brown streak diseases. FRONTIERS IN PLANT SCIENCE 2023; 14:1042701. [PMID: 36778712 PMCID: PMC9909537 DOI: 10.3389/fpls.2023.1042701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/02/2023] [Indexed: 06/18/2023]
Abstract
Growing cassava in Africa requires resistance against the viruses causing cassava mosaic disease (CMD) and the viruses causing cassava brown streak disease (CBSD). A dominant CMD2 resistance gene from a West African cassava landrace provides strong resistance against the cassava mosaic viruses. However, resistance against cassava brown streak viruses is limited to cassava varieties that show tolerance to the disease. A recently identified cassava germplasm that cannot be infected with cassava brown streak viruses provides a new source of the resistance required to protect cassava from CBSD. We present a synopsis of the status of virus resistance in cassava and report on the research to combine resistance against CBSD and CMD. We improve the lengthy and erratic screening for CBSD resistance by proposing a virus infection and screening protocol for the viruses causing CBSD and CMD, which allows a rapid and precise assessment of cassava resistance under controlled conditions. Using this approach, we classified the virus responses of cassava lines from Africa and South America and identified truly virus-resistant clones that cannot be infected with any of the known viruses causing CBSD even under the most stringent virus infections. A modification of this protocol was used to test seedlings from cassava crosses for resistance against both diseases. A broad-spectrum resistance was identified in a workflow that lasted 9 months from seed germination to the identification of virus resistance. The workflow we propose dramatically reduces the evaluation and selection time required in a classical breeding workflow to reach the advanced field trial stage in only 9 months by conducting selections for virus resistance and plant multiplication in parallel. However, it does not bypass field evaluations; cassava resistance assessment prior to the field limits the evaluation to candidates with virus resistance defined as the absence of symptoms and the absence of the virus. The transfer of our virus screening workflow to cassava breeding programs enhances the efficiency by which resistance against viruses can be selected. It provides a precise definition of the plant's resistance response and can be used as a model system to tackle resistance in cassava against other diseases.
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Amoakon WJL, Combala M, Pita JS, Mutuku JM, N'Zué B, Otron DH, Yéo EF, Kouassi NK, Sié R. Phenotypic screening and molecular characterization of cassava mosaic disease resistance in Côte d'Ivoire cassava germplasm. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.1052437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Cassava is the staple food crop for hundreds of millions of people in Africa. In Côte d'Ivoire, it is a main source of calories for over 26 million people. However, cassava mosaic disease (CMD), caused by cassava mosaic geminiviruses (CMGs) threaten its production. The development, adoption, and use of CMD resistant varieties remain a key CMD management strategy. Therefore, 610 accessions from the Côte d'Ivoire national cassava germplasm maintained by Centre National de Recherche Agronomique (CNRA) research stations in the cities of Man and Bouaké were characterized to assess their resistance to CMD. We found 72 accessions which were symptomless at both sites. Thirty five out of these 72 accessions were infected by African cassava mosaic virus (ACMV) without any CMD symptoms and 37 were virus free. None of the 72 symptomless accessions were infected by East African cassava mosaic Cameroon virus (EACMCMV). The remaining 538 accessions were CMD infected and displayed clear CMD symptoms. The promising 72 accessions (10 locals and 62 improved) were then tested for the presence of resistance genes, CMD1, CMD2 or CMD3. Except for 2 accessions for which no resistance gene was found, the remaining 70 accessions contained one or more resistance genes. Genotyping of the 69 symptomless accessions revealed that 56 were unique genotypes and 13 were potential duplicates. Accessions were structured in three groups with the variabilities at the individual's level. These findings reveal the existence of potential tolerant/resistant cassava accessions in CNRA's germplasm, which can contribute to CMD control and the increase of cassava production in Côte d'Ivoire.
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Nandudu L, Kawuki R, Ogbonna A, Kanaabi M, Jannink JL. Genetic dissection of cassava brown streak disease in a genomic selection population. FRONTIERS IN PLANT SCIENCE 2023; 13:1099409. [PMID: 36714759 PMCID: PMC9880483 DOI: 10.3389/fpls.2022.1099409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Introduction Cassava brown streak disease (CBSD) is a major threat to food security in East and central Africa. Breeding for resistance against CBSD is the most economical and sustainable way of addressing this challenge. Methods This study seeks to assess the (1) performance of CBSD incidence and severity; (2) identify genomic regions associated with CBSD traits and (3) candidate genes in the regions of interest, in the Cycle 2 population of the National Crops Resources Research Institute. Results A total of 302 diverse clones were screened, revealing that CBSD incidence across growing seasons was 44%. Severity scores for both foliar and root symptoms ranged from 1.28 to 1.99 and 1.75 to 2.28, respectively across seasons. Broad sense heritability ranged from low to high (0.15 - 0.96), while narrow sense heritability ranged from low to moderate (0.03 - 0.61). Five QTLs, explaining approximately 19% phenotypic variation were identified for CBSD severity at 3 months after planting on chromosomes 1, 13, and 18 in the univariate GWAS analysis. Multivariate GWAS analysis identified 17 QTLs that were consistent with the univariate analysis including additional QTLs on chromosome 6. Seventy-seven genes were identified in these regions with functions such as catalytic activity, ATP-dependent activity, binding, response to stimulus, translation regulator activity, transporter activity among others. Discussion These results suggest variation in virulence in the C2 population, largely due to genetics and annotated genes in these QTLs regions may play critical roles in virus initiation and replication, thus increasing susceptibility to CBSD.
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Affiliation(s)
- Leah Nandudu
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
- Root crops Department National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Robert Kawuki
- Root crops Department National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Alex Ogbonna
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Michael Kanaabi
- Root crops Department National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Jean-Luc Jannink
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Ithaca, NY, United States
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Esuma W, Eyoo O, Gwandu F, Mukasa S, Alicai T, Ozimati A, Nuwamanya E, Rabbi I, Kawuki R. Validation of KASP markers associated with cassava mosaic disease resistance, storage root dry matter and provitamin A carotenoid contents in Ugandan cassava germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:1017275. [PMID: 36507387 PMCID: PMC9727383 DOI: 10.3389/fpls.2022.1017275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The intrinsic high heterozygosity of cassava makes conventional breeding ineffective for rapid genetic improvement. However, recent advances in next generation sequencing technologies have enabled the use of high-density markers for genome-wide association studies, aimed at identifying single nucleotide polymorphisms (SNPs) linked to major traits such as cassava mosaic disease (CMD) resistance, dry matter content (DMC) and total carotenoids content (TCC). A number of these trait-linked SNPs have been converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers for downstream application of marker assisted selection. METHODS We assayed 13 KASP markers to evaluate their effectiveness in selecting for CMD, DMC and TCC in 1,677 diverse cassava genotypes representing two independent breeding populations in Uganda. RESULTS Five KASP markers had significant co-segregation with phenotypes; CMD resistance (2), DMC (1) and TCC (2), with each marker accounting for at least 30% of the phenotypic variation. Markers located within the chromosomal regions for which strong marker-trait association loci have been characterised (chromosome 12 markers for CMD, chromosome 1 markers for DMC and TCC) had consistently superior ability to discriminate the respective phenotypes. DISCUSSION The results indicate varying discriminatory abilities of the KASP markers assayed and the need for their context-based use for MAS, with PSY2_572 particularly effective in selecting for high TCC. Availing the effective KASP markers on cost-effective genotyping platforms could facilitate practical implementation of marker-assisted cassava breeding for accelerated genetic gains for CMD, DMC and provitamin A carotenoids.
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Affiliation(s)
- Williams Esuma
- National Crops Resources Research Institute, Kampala, Uganda
| | - Oscar Eyoo
- National Crops Resources Research Institute, Kampala, Uganda
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Francisca Gwandu
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Settumba Mukasa
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | - Titus Alicai
- National Crops Resources Research Institute, Kampala, Uganda
| | - Alfred Ozimati
- National Crops Resources Research Institute, Kampala, Uganda
- College of Natural Sciences, Department of Plant Sciences, Microbiology and Biotechnology, Makerere University, Kampala, Uganda
| | | | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Oyo, Nigeria
| | - Robert Kawuki
- National Crops Resources Research Institute, Kampala, Uganda
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Sharma KK, Palakolanu SR, Bhattacharya J, Shankhapal AR, Bhatnagar-Mathur P. CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects. Front Genet 2022; 13:999207. [PMID: 36276961 PMCID: PMC9582247 DOI: 10.3389/fgene.2022.999207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022] Open
Abstract
Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.
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Affiliation(s)
- Kiran K. Sharma
- Sustainable Agriculture Programme, The Energy and Resources Institute (TERI), India Habitat Center, New Delhi, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, Telangana, India
| | - Aishwarya R. Shankhapal
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- International Maize and Wheat Improvement Center (CIMMYT), México, United Kingdom
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Lim YW, Mansfeld BN, Schläpfer P, Gilbert KB, Narayanan NN, Qi W, Wang Q, Zhong Z, Boyher A, Gehan J, Beyene G, Lin ZJD, Esuma W, Feng S, Chanez C, Eggenberger N, Adiga G, Alicai T, Jacobsen SE, Taylor NJ, Gruissem W, Bart RS. Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses. Nat Commun 2022; 13:3933. [PMID: 35798722 PMCID: PMC9262879 DOI: 10.1038/s41467-022-31414-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/16/2022] [Indexed: 11/28/2022] Open
Abstract
Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for this loss of resistance, whole genome sequencing and genetic variant analysis was performed and the CMD2 locus was fine-mapped to a 190 kilobase interval. Collectively, these data indicate that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism in DNA polymerase δ subunit 1 (MePOLD1) located within this region. Virus-induced gene silencing of MePOLD1 in a CMD-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional candidate resistance alleles within MePOLD1. Genetic variation of MePOLD1, therefore, could represent an important genetic resource for resistance breeding and/or genome editing, and elucidating mechanisms of resistance to geminiviruses.
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Affiliation(s)
- Yi-Wen Lim
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Ben N Mansfeld
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Pascal Schläpfer
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Kerrigan B Gilbert
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Narayanan N Narayanan
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Qi Wang
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Adam Boyher
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Jackson Gehan
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Getu Beyene
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Zuh-Jyh Daniel Lin
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Williams Esuma
- Root Crops Program, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Christelle Chanez
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Nadine Eggenberger
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Universitätsstrasse 2, 8092, Zürich, Switzerland
| | - Gerald Adiga
- Root Crops Program, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Titus Alicai
- Root Crops Program, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute University of California Los Angeles, Los Angeles, CA, USA
| | - Nigel J Taylor
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Wilhelm Gruissem
- Institute of Molecular Plant Biology, Department of Biology, ETH Zürich, Universitätsstrasse 2, 8092, Zürich, Switzerland.
- Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung City, 40227, Taiwan.
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.
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Amelework AB, Bairu MW. Advances in Genetic Analysis and Breeding of Cassava ( Manihot esculenta Crantz): A Review. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11121617. [PMID: 35736768 PMCID: PMC9228751 DOI: 10.3390/plants11121617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 05/30/2023]
Abstract
Cassava (Manihot esculenta Crantz) is the sixth most important food crop and consumed by 800 million people worldwide. In Africa, cassava is the second most important food crop after maize and Africa is the worlds' largest producer. Though cassava is not one of the main commodity crops in South Africa, it is becoming a popular crop among farming communities in frost-free areas, due to its climate-resilient nature. This necessitated the establishment of a multi-disciplinary research program at the Agricultural Research Council of South Africa. The objective of this review is to highlight progress made in cassava breeding and genetic analysis. This review highlights the progress of cassava research worldwide and discusses research findings on yield, quality, and adaptability traits in cassava. It also discusses the limitations and the prospects of the cassava R&D program towards development of the cassava industry in South Africa.
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Affiliation(s)
- Assefa B. Amelework
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, South Africa;
| | - Michael W. Bairu
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, South Africa;
- Faculty of Natural & Agricultural Sciences, School of Agricultural Sciences, Food Security and Safety Focus Area, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
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12
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Lyons JB, Bredeson JV, Mansfeld BN, Bauchet GJ, Berry J, Boyher A, Mueller LA, Rokhsar DS, Bart RS. Current status and impending progress for cassava structural genomics. PLANT MOLECULAR BIOLOGY 2022; 109:177-191. [PMID: 33604743 PMCID: PMC9162999 DOI: 10.1007/s11103-020-01104-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/08/2020] [Indexed: 05/26/2023]
Abstract
KEY MESSAGE We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.
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Affiliation(s)
- Jessica B. Lyons
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720 USA
| | - Jessen V. Bredeson
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
| | - Ben N. Mansfeld
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | | | - Jeffrey Berry
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | - Adam Boyher
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
| | | | - Daniel S. Rokhsar
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720 USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720 USA
- DOE Joint Genome Institute, Walnut Creek, CA USA
- Chan-Zuckerberg BioHub, 499 Illinois, San Francisco, CA 94158 USA
| | - Rebecca S. Bart
- Donald Danforth Plant Science Center (DDPSC), St. Louis, MO 63132 USA
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13
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Rabbi IY, Kayondo SI, Bauchet G, Yusuf M, Aghogho CI, Ogunpaimo K, Uwugiaren R, Smith IA, Peteti P, Agbona A, Parkes E, Lydia E, Wolfe M, Jannink JL, Egesi C, Kulakow P. Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava. PLANT MOLECULAR BIOLOGY 2022; 109:195-213. [PMID: 32734418 PMCID: PMC9162993 DOI: 10.1007/s11103-020-01038-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/20/2020] [Indexed: 05/05/2023]
Abstract
More than 40 QTLs associated with 14 stress-related, quality and agro-morphological traits were identified. A catalogue of favourable SNP markers for MAS and a list of candidate genes are provided. Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5130 clones developed at the International Institute of Tropical Agriculture-Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type) were investigated. We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.
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Affiliation(s)
- Ismail Yusuf Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria.
| | - Siraj Ismail Kayondo
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | | | - Muyideen Yusuf
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Cynthia Idhigu Aghogho
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Kayode Ogunpaimo
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Ruth Uwugiaren
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Ikpan Andrew Smith
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Prasad Peteti
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Afolabi Agbona
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
| | - Ezenwaka Lydia
- National Root Crops Research Institute (NRCRI), PMB 7006, Umudike, 440221, Nigeria
| | - Marnin Wolfe
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14850, USA
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14850, USA
- United States Department of Agriculture - Agriculture Research Service, Ithaca, NY, 14850, USA
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
- National Root Crops Research Institute (NRCRI), PMB 7006, Umudike, 440221, Nigeria
- Global Development Department, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14850, USA
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, 200001, Oyo State, Nigeria
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14
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Qi W, Lim YW, Patrignani A, Schläpfer P, Bratus-Neuenschwander A, Grüter S, Chanez C, Rodde N, Prat E, Vautrin S, Fustier MA, Pratas D, Schlapbach R, Gruissem W. The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. Gigascience 2022; 11:giac028. [PMID: 35333302 PMCID: PMC8952263 DOI: 10.1093/gigascience/giac028] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/11/2022] [Accepted: 02/22/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome. FINDINGS Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20-30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in <2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding. CONCLUSIONS The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity.
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Affiliation(s)
- Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1202, Geneva, Switzerland
| | - Yi-Wen Lim
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Andrea Patrignani
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Pascal Schläpfer
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Anna Bratus-Neuenschwander
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Simon Grüter
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christelle Chanez
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, F-31320, Castanet Tolosan, France
| | - Elisa Prat
- INRAE, CNRGV French Plant Genomic Resource Center, F-31320, Castanet Tolosan, France
| | - Sonia Vautrin
- INRAE, CNRGV French Plant Genomic Resource Center, F-31320, Castanet Tolosan, France
| | | | - Diogo Pratas
- Department of Electronics, Telecommunications and Informatics and Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Virology, University of Helsinki, Haartmaninkatu 3, 00014 Helsinki, Finland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
- Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung 40227, Taiwan
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15
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Fathima AA, Sanitha M, Tripathi L, Muiruri S. Cassava (
Manihot esculenta
) dual use for food and bioenergy: A review. Food Energy Secur 2022. [DOI: 10.1002/fes3.380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Anwar Aliya Fathima
- Department of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Chennai India
| | - Mary Sanitha
- Department of Bioinformatics Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences Chennai India
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA) Nairobi Kenya
| | - Samwel Muiruri
- International Institute of Tropical Agriculture (IITA) Nairobi Kenya
- Department of Plant Sciences Kenyatta University Nairobi Kenya
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16
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Peng Y, Dallas MM, Ascencio-Ibáñez JT, Hoyer JS, Legg J, Hanley-Bowdoin L, Grieve B, Yin H. Early detection of plant virus infection using multispectral imaging and spatial-spectral machine learning. Sci Rep 2022; 12:3113. [PMID: 35210452 PMCID: PMC8873445 DOI: 10.1038/s41598-022-06372-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/21/2022] [Indexed: 02/06/2023] Open
Abstract
Cassava brown streak disease (CBSD) is an emerging viral disease that can greatly reduce cassava productivity, while causing only mild aerial symptoms that develop late in infection. Early detection of CBSD enables better crop management and intervention. Current techniques require laboratory equipment and are labour intensive and often inaccurate. We have developed a handheld active multispectral imaging (A-MSI) device combined with machine learning for early detection of CBSD in real-time. The principal benefits of A-MSI over passive MSI and conventional camera systems are improved spectral signal-to-noise ratio and temporal repeatability. Information fusion techniques further combine spectral and spatial information to reliably identify features that distinguish healthy cassava from plants with CBSD as early as 28 days post inoculation on a susceptible and a tolerant cultivar. Application of the device has the potential to increase farmers' access to healthy planting materials and reduce losses due to CBSD in Africa. It can also be adapted for sensing other biotic and abiotic stresses in real-world situations where plants are exposed to multiple pest, pathogen and environmental stresses.
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Affiliation(s)
- Yao Peng
- Department of Electrical and Electronic Engineering, University of Manchester, Manchester, UK
| | - Mary M Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - José T Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - J Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, USA
| | - James Legg
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Bruce Grieve
- Department of Electrical and Electronic Engineering, University of Manchester, Manchester, UK
| | - Hujun Yin
- Department of Electrical and Electronic Engineering, University of Manchester, Manchester, UK.
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17
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Codija ED, Olasanmi B, Agre PA, Uwugiaren R, Ige AD, Rabbi IY. Selection for resistance to cassava mosaic disease in African cassava germplasm using single nucleotide polymorphism markers. S AFR J SCI 2022. [DOI: 10.17159/sajs.2022/11607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Cassava mosaic disease (CMD) is one of the main constraints that hamper cassava production. Breeding for varieties that are CMD resistant is a major aim in cassava breeding programmes. However, the use of the conventional approach has its limitations, including a lengthy growth cycle and a low multiplication rate of planting materials. To increase breeding efficiency as well as genetic gain of traits, SNP markers can be used to screen and identify resistant genotypes. The objective of this study was to predict the performance of 145 cassava genotypes from open-pollinated crosses for CMD resistance using molecular markers. Two SNP markers (S12_7926132 and S14_4626854), previously converted into Kompetitive allele-specific PCR (KASP) assays, as well as CMD incidence and severity scores, were used for selection. About 76% of the genotypes were revealed to be resistant to CMD based on phenotypic scores, while over 24% of the total population were found to be susceptible. Significant effects were observed for alleles associated with marker S12_7926132 while the other marker had non-significant effects. The predictive accuracy (true positives and true negatives) of the major CMD2 locus on chromosome 12 was 77% in the population used in this study. Our study provides insight into the potential use of marker-assisted selection for CMD resistance in cassava breeding programmes.
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Affiliation(s)
- Esperance D. Codija
- Pan African University Life and Earth Sciences Institute (including Health and Agriculture), University of Ibadan, Ibadan, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Bunmi Olasanmi
- Pan African University Life and Earth Sciences Institute (including Health and Agriculture), University of Ibadan, Ibadan, Nigeria
- Department of Agronomy, University of Ibadan, Ibadan, Nigeria
| | - Paterne A. Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ruth Uwugiaren
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Adenike D. Ige
- Pan African University Life and Earth Sciences Institute (including Health and Agriculture), University of Ibadan, Ibadan, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ismail Y. Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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18
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Genome-wide association study of cassava starch paste properties. PLoS One 2022; 17:e0262888. [PMID: 35061844 PMCID: PMC8782291 DOI: 10.1371/journal.pone.0262888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 01/09/2022] [Indexed: 11/21/2022] Open
Abstract
An understanding of cassava starch paste properties (CSPP) can contribute to the selection of clones with differentiated starches. This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h2) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r2 <0.1) for most chromosomes, except chromosome 17, which exhibited an extensive LD. Thirteen SNPs were found to be significantly associated with CSPP, on chromosomes 3, 8, 17, and 18. Only the BreDow trait had no associated SNPs. The regional marker-trait associations on chromosome 18 indicate a LD block between 2907312 and 3567816 bp and that SNP S18_3081635 was associated with SetBack, FinalVis, and Cold-PVisc (all three GWAS methods) and with Hot-PVisc (MLM), indicating that this SNP can track these four traits simultaneously. The variance explained by the SNPs ranged from 0.13 to 0.18 for SetBack, FinalVis, and Cold-PVisc and from 0.06 to 0.09 for PeakVisc and Hot-PVisc. The results indicated additive effects of the genetic control of Cold-PVisc, FinalVis, Hot-PVisc, and SetBack, especially on the large LD block on chromosome 18. One transcript encoding the glycosyl hydrolase family 35 enzymes on chromosome 17 and one encoding the mannose-p-dolichol utilization defect 1 protein on chromosome 18 were the most likely candidate genes for the regulation of CSPP. These results underline the potential for the assisted selection of high-value starches to improve cassava root quality through breeding programs.
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19
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Uchendu K, Njoku DN, Paterne A, Rabbi IY, Dzidzienyo D, Tongoona P, Offei S, Egesi C. Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava. FRONTIERS IN PLANT SCIENCE 2021; 12:770434. [PMID: 34975953 PMCID: PMC8719520 DOI: 10.3389/fpls.2021.770434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.
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Affiliation(s)
- Kelechi Uchendu
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | - Agre Paterne
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Samuel Offei
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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20
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A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz). Sci Rep 2021; 11:23520. [PMID: 34876620 PMCID: PMC8651776 DOI: 10.1038/s41598-021-02794-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022] Open
Abstract
Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions. In this study, we carried out 3’RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Uganda for 5 tissue types, providing population-based transcriptomics resources to the research community in a web-based queryable cassava expression atlas. Differential expression and weighted gene co-expression network analysis were performed to detect 8820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant–pathogen interaction pathway, several previously identified CMD resistance genes, and two peroxidase family proteins different from the CMD2 gene. Present research work represents a novel resource towards understanding complex traits at expression and molecular levels for the development of resistant and high-yielding cassava varieties, as exemplified with CMD.
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21
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Zárate‐Chaves CA, Gómez de la Cruz D, Verdier V, López CE, Bernal A, Szurek B. Cassava diseases caused by Xanthomonas phaseoli pv. manihotis and Xanthomonas cassavae. MOLECULAR PLANT PATHOLOGY 2021; 22:1520-1537. [PMID: 34227737 PMCID: PMC8578842 DOI: 10.1111/mpp.13094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 05/27/2023]
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) and X. cassavae (Xc) are two bacterial pathogens attacking cassava. Cassava bacterial blight (CBB) is a systemic disease caused by Xpm, which might have dramatic effects on plant growth and crop production. Cassava bacterial necrosis is a nonvascular disease caused by Xc with foliar symptoms similar to CBB, but its impacts on the plant vigour and the crop are limited. In this review, we describe the epidemiology and ecology of the two pathogens, the impacts and management of the diseases, and the main research achievements for each pathosystem. Because Xc data are sparse, our main focus is on Xpm and CBB.
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Affiliation(s)
| | | | - Valérie Verdier
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
| | - Camilo E. López
- Manihot Biotec, Departamento de BiologíaUniversidad Nacional de ColombiaBogotáColombia
| | - Adriana Bernal
- Laboratorio de Interacciones Moleculares de Microorganismos AgrícolasDepartamento de Ciencias BásicasUniversidad de los AndesBogotáColombia
| | - Boris Szurek
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
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22
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Aimone CD, De León L, Dallas MM, Ndunguru J, Ascencio-Ibáñez JT, Hanley-Bowdoin L. A New Type of Satellite Associated with Cassava Mosaic Begomoviruses. J Virol 2021; 95:e0043221. [PMID: 34406866 PMCID: PMC8513466 DOI: 10.1128/jvi.00432-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/10/2021] [Indexed: 12/29/2022] Open
Abstract
Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is coinoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus-resistant Arabidopsis thaliana accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in A. thaliana. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of an SEGS-2-encoded protein that may also be encoded by the cassava genome. IMPORTANCE Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world's cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought, and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance.
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Affiliation(s)
- Catherine D. Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Mary M. Dallas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | | | - José T. Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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Aimone CD, Lavington E, Hoyer JS, Deppong DO, Mickelson-Young L, Jacobson A, Kennedy GG, Carbone I, Hanley-Bowdoin L, Duffy S. Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation. J Gen Virol 2021; 102:001622. [PMID: 34310272 PMCID: PMC8491896 DOI: 10.1099/jgv.0.001622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/05/2021] [Indexed: 01/06/2023] Open
Abstract
Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5' intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.
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Affiliation(s)
- Catherine D. Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Erik Lavington
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - David O. Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Alana Jacobson
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - George G. Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
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Ewa F, Asiwe JNA, Okogbenin E, Ogbonna AC, Egesi C. KASPar SNP genetic map of cassava for QTL discovery of productivity traits in moderate drought stress environment in Africa. Sci Rep 2021; 11:11268. [PMID: 34050196 PMCID: PMC8163807 DOI: 10.1038/s41598-021-90131-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/27/2021] [Indexed: 11/23/2022] Open
Abstract
Cassava is an important staple in Sub-Sahara Africa. While its production has rapidly expanded to the dry savannahs of the continent, productivity is low in this ecology due to drought by farmers, extending the growth cycle from 12 months to 18, and sometimes 24 months to ensure better harvests. Yield is a complex trait and often difficult to manipulate for genetic gain in conventional breeding. Unfortunately, the dearth of molecular tools for decades has hampered molecular breeding (MB) to improve cassava productivity. This study was conducted to explore KASpar SNPs to generate more molecular tools to enhance genetic dissection of elite African germplasm for improved cassava productivity in dry environments of Africa where molecular resources are highly limited for crop improvement. To aid molecular genetic analysis of traits, a linkage map covering 1582.8 cM with an average resolution of 3.69 cM was constructed using 505 polymorphic SNP markers distributed over 21 linkage groups. Composite interval mapping using 267 F1 progeny in initial QTL mapping identified 27 QTLs for productivity traits in the dry savannah of Nigeria. The availability of KASPar SNPs are anticipated to improve the implementation of MB for the development of high performing drought-tolerant cassava varieties in Africa.
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Affiliation(s)
- Favour Ewa
- Department of Plant Production, Soil Science and Agricultural Engineering, School of Agriculture and Environmental Sciences, University of Limpopo, Sovenga, South Africa.
| | - Joseph N A Asiwe
- Department of Plant Production, Soil Science and Agricultural Engineering, School of Agriculture and Environmental Sciences, University of Limpopo, Sovenga, South Africa
| | | | - Alex C Ogbonna
- Department of Plant Breeding and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Chiedozie Egesi
- Cassava Breeding Unit, International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Ogbonna AC, Braatz de Andrade LR, Mueller LA, de Oliveira EJ, Bauchet GJ. Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1343-1362. [PMID: 33575821 PMCID: PMC8081687 DOI: 10.1007/s00122-021-03775-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.
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Affiliation(s)
- Alex C Ogbonna
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | - Lukas A Mueller
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
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26
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Ogbonna AC, Braatz de Andrade LR, Mueller LA, de Oliveira EJ, Bauchet GJ. Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1343-1362. [PMID: 33575821 DOI: 10.1101/2020.07.13.200816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/11/2021] [Indexed: 05/25/2023]
Abstract
Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.
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Affiliation(s)
- Alex C Ogbonna
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | - Lukas A Mueller
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
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27
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Marker-assisted selection complements phenotypic screening at seedling stage to identify cassava mosaic disease-resistant genotypes in African cassava populations. Sci Rep 2021; 11:2850. [PMID: 33531574 PMCID: PMC7854622 DOI: 10.1038/s41598-021-82360-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
Cassava mosaic disease (CMD) is a serious threat to cassava production in sub-Saharan Africa. The use of genomic-assisted selection at the seedling trial stage would help to reduce the time for release, breeding cost, and resources used, hence increase selection efficiency in cassava breeding programs. Five cassava populations were screened for resistance to CMD during the seedling evaluation trial at 1, 3, and 5 months after planting using a scale of 1–5. The genotypes in the five populations were also screened using six molecular markers linked to the CMD2 gene. The correlation between the phenotypic and marker data was estimated. Based on Cassava Mosaic Disease Severity Score (CMDSS), between 53 and 82% of the progenies were resistant across the populations with an average of 70.5%. About 70% of the progenies were identified to be resistant to the disease across the populations with a range of 62–80% using the marker data. With both marker data and CMDSS combined, 40–60% of the progenies in each population, with an average of 52%, were identified to be resistant to CMD. There was a fairly significant correlation between the marker data and CMDSS in each cassava population with correlation coefficients ranging from 0.2024 to 0.3460 suggesting that novel genes not associated to the markers used might be involved in the resistance to CMD. The resistant genotypes identified in this study with potential for other desirable traits were selected for evaluation at the advanced trial stage thereby shortening the period required for the breeding program.
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28
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Ogbonna AC, Braatz de Andrade LR, Rabbi IY, Mueller LA, Jorge de Oliveira E, Bauchet GJ. Large-scale genome-wide association study, using historical data, identifies conserved genetic architecture of cyanogenic glucoside content in cassava (Manihot esculenta Crantz) root. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:754-770. [PMID: 33164279 PMCID: PMC7898387 DOI: 10.1111/tpj.15071] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/18/2020] [Accepted: 10/28/2020] [Indexed: 05/11/2023]
Abstract
Manihot esculenta (cassava) is a root crop originating from South America that is a major staple in the tropics, including in marginal environments. This study focused on South American and African germplasm and investigated the genetic architecture of hydrogen cyanide (HCN), a major component of root quality. HCN, representing total cyanogenic glucosides, is a plant defense component against herbivory but is also toxic for human consumption. We genotyped 3354 landraces and modern breeding lines originating from 26 Brazilian states and 1389 individuals were phenotypically characterized across multi-year trials for HCN. All plant material was subjected to high-density genotyping using genotyping by sequencing. We performed genome-wide association mapping to characterize the genetic architecture and gene mapping of HCN. Field experiments revealed strong broad- and narrow-sense trait heritability (0.82 and 0.41, respectively). Two major loci were identified, encoding for an ATPase and a MATE protein, and contributing up to 7 and 30% of the HCN concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for the domestication of sweet and bitter cassava. Fine genomic characterization revealed: (i) the major role played by vacuolar transporters in regulating HCN content; (ii) the co-domestication of sweet and bitter cassava major alleles are dependent upon geographical zone; and (iii) the major loci allele for high HCN in M. esculenta Crantz seems to originate from its ancestor, M. esculenta subsp. flabellifolia. Taken together, these findings expand our insights into cyanogenic glucosides in cassava roots and its glycosylated derivatives in plants.
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Affiliation(s)
- Alex C. Ogbonna
- Cornell University135 Plant Science BuildingIthacaNY14850USA
- Boyce Thompson Institute533 Tower RdIthacaNY14853USA
| | | | - Ismail Y. Rabbi
- International Institute of Tropical AgriculturePMB 5320, Oyo RoadIbadanOyo State200001Nigeria
| | - Lukas A. Mueller
- Cornell University135 Plant Science BuildingIthacaNY14850USA
- Boyce Thompson Institute533 Tower RdIthacaNY14853USA
| | - Eder Jorge de Oliveira
- Embrapa Mandioca e FruticulturaRua Embrapa s/nº, Caixa Postal 007Cruz das AlmasBACEP: 44380‐000Brazil
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Mbanjo EGN, Rabbi IY, Ferguson ME, Kayondo SI, Eng NH, Tripathi L, Kulakow P, Egesi C. Technological Innovations for Improving Cassava Production in Sub-Saharan Africa. Front Genet 2021; 11:623736. [PMID: 33552138 PMCID: PMC7859516 DOI: 10.3389/fgene.2020.623736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.
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Affiliation(s)
| | | | | | | | - Ng Hwa Eng
- CGIAR Excellence in Breeding Platform, El Batan, Mexico
| | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute, Umudike, Nigeria
- Department of Global Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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Igwe DO, Anyanwu CB, Afiukwa CA, Nnamani CV, Nweke FN, Ude GN, Ubi BE. Phenotypic and molecular screenings for determination of cassava mosaic disease (CMD) status in farmers' fields in Ebonyi State, Nigeria. Mol Biol Rep 2021; 48:227-240. [PMID: 33301051 PMCID: PMC7727096 DOI: 10.1007/s11033-020-06039-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/27/2020] [Indexed: 12/02/2022]
Abstract
African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) are among the major constraints to cassava productivity within tropical and sub-tropical regions, including Ebonyi State, Nigeria. Thus, virus indexing has become imperative to determine the status of cassava mosaic disease (CMD) in Ebonyi State, to implement appropriate preventive and control strategies. Seventy-eight cassava accessions obtained from different locations of Ebonyi State were phenotypically scored, using scales 1-5 depending on CMD symptomatic expressions, followed by multiplex-PCR and sequencing for validation. 11% of cassava accessions cultivated in Afikpo were resistant (RE) to ACMV compared to 8% of moderately-resistant (MR) accessions in Izzi and 55% of tolerant (TO) ACMV accessions in Ebonyi. 100% of cassava accessions in Onicha and 66% in Afikpo South were susceptible (SU) and highly susceptible (HS) to ACMV, respectively. With multiplex-PCR, 97.4% (ACMV) and 2.6% (EACMV) were positive. Dunn's multiple comparison tests of CMD mean incidence demonstrated differences (P < 0.05), except between RE and MR, and TO and MR. More transitions (A/G, C/T) compared to transversions (A/T, G/T), were detected, with nonsynonymous mutations (Leucine/Isoleucine; Valine/Isoleucine; Arginine/Lysine; Methionine/Isoleucine), and good bit-scores (91.13-99.07% identites; e-values of 7.00e-148-0.00e+00). Phylogeny resolved the sequences into five major groups. DNA sequencing validated the detected ACMV and EACMV species. This study revealed variants of ACMV and low adoption of RE and MR cassava accessions in the farmers' fields. The findings will guide in getting disease-free and resistant varieties as planting materials to significantly mitigate the CMD spread in Ebonyi State, Nigeria.
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Affiliation(s)
- David Okeh Igwe
- Department of Biotechnology, Ebonyi State University, Abakaliki, Ebonyi, Nigeria.
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA.
| | | | | | - Catherine Veronica Nnamani
- Plant Taxonomy and Conservation Biology Research Unit, Department of Applied Biology, Presco Campus, Ebonyi State University, Abakaliki, Nigeria
| | - Friday Nwalo Nweke
- Biology/Microbiology/Biotechnology, Faculty Science, Federal University, Ndufu-Alike Ikwo (FUNAI), Ikwo, Ebonyi, Nigeria
| | - George Nkem Ude
- Department of Natural Sciences, Bowie State University, Bowie, USA
| | - Benjamin Ewa Ubi
- Department of Biotechnology, Ebonyi State University, Abakaliki, Ebonyi, Nigeria
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Elegba W, McCallum E, Gruissem W, Vanderschuren H. Efficient Genetic Transformation and Regeneration of a Farmer-Preferred Cassava Cultivar From Ghana. FRONTIERS IN PLANT SCIENCE 2021; 12:668042. [PMID: 34140963 PMCID: PMC8204248 DOI: 10.3389/fpls.2021.668042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 05/04/2023]
Abstract
Cassava is an important staple crop that provides food and income for about 700 million Africans. Cassava productivity in Africa is limited by viral diseases, mainly cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). Genetic barriers such as high heterozygosity, allopolyploidy, poor seed set, and irregular flowering constrain the development of virus-resistant cassava varieties via conventional breeding. Genetic transformation represents a valuable tool to circumvent several challenges associated with the development of virus resistance and other valuable agronomic traits in cassava. The implementation of genetic transformation in many local African cultivars is limited either by the difficulty to produce friable embryogenic callus (FEC), low transformation, and/or regeneration efficiencies. Here, we report the successful induction of organized embryogenic structures (OES) in 11 farmer-preferred cultivars locally grown in Ghana. The production of high quality FEC from one local cultivar, ADI 001, facilitated its genetic transformation with high shoot regeneration and selection efficiency, comparable to the model cassava cultivar 60444. We show that using flow cytometry for analysis of nuclear ploidy in FEC tissues prior to genetic transformation ensures the selection of genetically uniform FEC tissue for transformation. The high percentage of single insertion events in transgenic lines indicates the suitability of the ADI 001 cultivar for the introduction of virus resistance and other useful agronomic traits into the farmer-preferred cassava germplasm in Ghana and Africa.
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Affiliation(s)
- Wilfred Elegba
- Plant Biotechnology, Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Biotechnology and Nuclear Agriculture Research Institute, GAEC, Legon, Ghana
- *Correspondence: Wilfred Elegba, ;
| | - Emily McCallum
- Plant Biotechnology, Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wilhelm Gruissem
- Plant Biotechnology, Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Hervé Vanderschuren
- Plant Biotechnology, Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- Plant Genetics, TERRA Research and Teaching Centre, Gembloux Agro BioTech, University of Liège, Gembloux, Belgium
- Hervé Vanderschuren,
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Sessou AF, Kahia JW, Houngue JA, Ateka EM, Dadjo C, Ahanhanzo C. In vitro propagation of three mosaic disease resistant cassava cultivars. BMC Biotechnol 2020; 20:51. [PMID: 32993601 PMCID: PMC7526170 DOI: 10.1186/s12896-020-00645-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/15/2020] [Indexed: 11/22/2022] Open
Abstract
Background Cassava is a staple food for over 800 million people globally providing a cheap source of carbohydrate. However, the cultivation of cassava in the country is facing to viral diseases, particularly cassava mosaic disease (CMD) which can cause up to 95% yield losses. With aim to supply farmers demand for clean planting materials, there is need to accelerate the production of the elite cultivars by use of tissue culture in order to cope with the demand. Methods Nodal explants harvested from the greenhouse grown plants were sterilised using different concentrations of a commercial bleach JIK (3.85% NaOCl) and varying time intervals. Microshoots induction was evaluated using thidiazuron (TDZ), benzyl amino purine (BAP), and kinetin. Rooting was evaluated using different auxins (Naphthalene acetic acid NAA and Indole-3-butyricacid IBA). PCR-based SSR and SCAR markers were used to verify the presence of CMD2 gene in the regenerated plantlets. Results The highest level of sterility in explants (90%) was obtained when 20% Jik was used for 15 min. The best cytokinin for microshoots regeneration was found to be kinetin with optimum concentrations of 5, 10 and 20 μM for Agric-rouge, Atinwewe, and Agblehoundo respectively. Medium without growth regulators was the best for rooting the three cultivars. A survival rate of 100, 98, and 98% was recorded in the greenhouse for Agric-rouge, Atinwewe, and Agblehoundo respectively and the plantlets appeared to be morphologically normal. The SSR and SCAR analysis of micropropagated plants showed a profile similar to that of the mother plants indicating that the regenerated plantlets retained the CMD2 gene after passing through in vitro culture, as expected with micropropagation. Conclusion The nodal explants was established to be 20% of Jik (3.85% NaOCl) with an exposure time of 15 min. Kinetin was proved to be the best cytokinins for microshoot formation with the optimum concentration of 5, 10 and 20 μM for Agric-rouge, Atinwewe, and Agblehoundo respectively. The protocol developed during this study will be useful for mass propagation of the elite cassava cultivars.
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Affiliation(s)
- Amitchihoué Franck Sessou
- Department of Genetics and Biotechnology, Faculty of Sciences and Techniques, University of Abomey-Calavi, Abomey-Calavi, Benin. .,Institute of Basic Sciences, Technology and Innovation, Pan African University, P. O. Box 62000-00200, Nairobi, Kenya.
| | - Jane W Kahia
- Coffee Research Institute, P.O. Box 4, Ruiru, Kenya
| | - Jerome Anani Houngue
- Department of Genetics and Biotechnology, Faculty of Sciences and Techniques, University of Abomey-Calavi, Abomey-Calavi, Benin.
| | - Elijah Miinda Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | - Colombe Dadjo
- Institute of Basic Sciences, Technology and Innovation, Pan African University, P. O. Box 62000-00200, Nairobi, Kenya
| | - Corneille Ahanhanzo
- Department of Genetics and Biotechnology, Faculty of Sciences and Techniques, University of Abomey-Calavi, Abomey-Calavi, Benin
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Gaffney J, Tibebu R, Bart R, Beyene G, Girma D, Kane NA, Mace ES, Mockler T, Nickson TE, Taylor N, Zastrow-Hayes G. Open access to genetic sequence data maximizes value to scientists, farmers, and society. GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT 2020. [DOI: 10.1016/j.gfs.2020.100411] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Genetic analysis and QTL mapping for multiple biotic stress resistance in cassava. PLoS One 2020; 15:e0236674. [PMID: 32756600 PMCID: PMC7406056 DOI: 10.1371/journal.pone.0236674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/09/2020] [Indexed: 11/19/2022] Open
Abstract
In Sub-Saharan Africa cassava (Manihot esculenta Crantz) is one of the most important food crops where more than 40% of the population relies on it as their staple carbohydrate source. Biotic constraints such as viral diseases, mainly Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD), and arthropod pests, particularly Cassava Green Mite (CGM), are major constraints to the realization of cassava’s full production potential in Africa. To address these problems, we aimed to map the quantitative trait loci (QTL) associated with resistance to CBSD foliar and root necrosis symptoms, foliar CMD and CGM symptoms in a full-sib mapping population derived from the genotypes AR40-6 and Albert. A high-density linkage map was constructed with 2,125 SNP markers using a genotyping-by-sequencing approach. For phenotyping, clonal evaluation trials were conducted with 120 F1 individuals for two consecutive field seasons using an alpha-lattice design at Chambezi and Naliendele, Tanzania. Previously identified QTL for resistance to CBSD foliar symptoms were corroborated, and a new putative QTL for CBSD root necrosis identified (qCBSDRNc14AR) from AR40-6. Two QTL were identified within the region of the previously recognized CMD2 locus from this population in which both parents are thought to possess the CMD2 locus. Interestingly, a minor but consistent QTL, qCGM18AR, for CGM resistance at 3 months after planting stage was also detected and co-localized with a previously identified SSR marker, NS346, linked with CGM resistance. Markers underlying these QTL may be used to increase efficiencies in cassava breeding programs.
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Sonnewald U, Fernie AR, Gruissem W, Schläpfer P, Anjanappa RB, Chang SH, Ludewig F, Rascher U, Muller O, van Doorn AM, Rabbi IY, Zierer W. The Cassava Source-Sink project: opportunities and challenges for crop improvement by metabolic engineering. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1655-1665. [PMID: 32502321 DOI: 10.1111/tpj.14865] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/22/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Cassava (Manihot esculenta Crantz) is one of the important staple foods in Sub-Saharan Africa. It produces starchy storage roots that provide food and income for several hundred million people, mainly in tropical agriculture zones. Increasing cassava storage root and starch yield is one of the major breeding targets with respect to securing the future food supply for the growing population of Sub-Saharan Africa. The Cassava Source-Sink (CASS) project aims to increase cassava storage root and starch yield by strategically integrating approaches from different disciplines. We present our perspective and progress on cassava as an applied research organism and provide insight into the CASS strategy, which can serve as a blueprint for the improvement of other root and tuber crops. Extensive profiling of different field-grown cassava genotypes generates information for leaf, phloem, and root metabolic and physiological processes that are relevant for biotechnological improvements. A multi-national pipeline for genetic engineering of cassava plants covers all steps from gene discovery, cloning, transformation, molecular and biochemical characterization, confined field trials, and phenotyping of the seasonal dynamics of shoot traits under field conditions. Together, the CASS project generates comprehensive data to facilitate conventional breeding strategies for high-yielding cassava genotypes. It also builds the foundation for genome-scale metabolic modelling aiming to predict targets and bottlenecks in metabolic pathways. This information is used to engineer cassava genotypes with improved source-sink relations and increased yield potential.
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Affiliation(s)
- Uwe Sonnewald
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, Erlangen, 91058, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland
- Advanced Plant Biotechnology Center, Institute of Biotechnology, National Chung Hsing University, Xingda Road, South District, Taichung City, 402, Taiwan
| | - Pascal Schläpfer
- Department of Biology, Plant Biotechnology, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland
| | - Ravi B Anjanappa
- Department of Biology, Plant Biotechnology, ETH Zurich, Universitaetstrasse 2, Zurich, 8092, Switzerland
| | - Shu-Heng Chang
- Advanced Plant Biotechnology Center, Institute of Biotechnology, National Chung Hsing University, Xingda Road, South District, Taichung City, 402, Taiwan
| | - Frank Ludewig
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, Erlangen, 91058, Germany
| | - Uwe Rascher
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Leo-Brandt-Str, Jülich, 52425, Germany
| | - Onno Muller
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Leo-Brandt-Str, Jülich, 52425, Germany
| | - Anna M van Doorn
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Leo-Brandt-Str, Jülich, 52425, Germany
| | - Ismail Y Rabbi
- International Institue for Tropical Agriculture, Oyo Road, Ibadan, Oyo State, 200001, Nigeria
| | - Wolfgang Zierer
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, Erlangen, 91058, Germany
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Kaya HB, Akdemir D, Lozano R, Cetin O, Sozer Kaya H, Sahin M, Smith JL, Tanyolac B, Jannink JL. Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). Sci Rep 2019; 9:18764. [PMID: 31822760 PMCID: PMC6904458 DOI: 10.1038/s41598-019-55338-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 11/05/2019] [Indexed: 01/08/2023] Open
Abstract
Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.
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Affiliation(s)
- Hilal Betul Kaya
- Department of Bioengineering, Faculty of Engineering, Manisa Celal Bayar University, Manisa, Turkey.
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
| | - Deniz Akdemir
- Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY, USA
| | - Roberto Lozano
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
| | | | | | | | - Jenny L Smith
- National Clonal Germplasm Repository, USDA-ARS, One Shields Avenue, Davis, CA, USA
| | - Bahattin Tanyolac
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Jean-Luc Jannink
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
- USDA ARS, Robert W. Holley Center for Agriculture & Health, Ithaca, NY, USA
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Kuon JE, Qi W, Schläpfer P, Hirsch-Hoffmann M, von Bieberstein PR, Patrignani A, Poveda L, Grob S, Keller M, Shimizu-Inatsugi R, Grossniklaus U, Vanderschuren H, Gruissem W. Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars. BMC Biol 2019; 17:75. [PMID: 31533702 PMCID: PMC6749633 DOI: 10.1186/s12915-019-0697-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022] Open
Abstract
Background Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown. Results We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars. Conclusions The genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars. Electronic supplementary material The online version of this article (10.1186/s12915-019-0697-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joel-E Kuon
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland.
| | - Weihong Qi
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Pascal Schläpfer
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Matthias Hirsch-Hoffmann
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | | | - Andrea Patrignani
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lucy Poveda
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefan Grob
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Miyako Keller
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Hervé Vanderschuren
- AgroBioChem Department, University of Liège, Passage des Déportés 2, Gembloux, Belgium
| | - Wilhelm Gruissem
- Department of Biology, Institute of Molecular Plant Biology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland. .,Advanced Plant Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan.
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Sheat S, Fuerholzner B, Stein B, Winter S. Resistance Against Cassava Brown Streak Viruses From Africa in Cassava Germplasm From South America. FRONTIERS IN PLANT SCIENCE 2019; 10:567. [PMID: 31134114 PMCID: PMC6523400 DOI: 10.3389/fpls.2019.00567] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/15/2019] [Indexed: 05/13/2023]
Abstract
Cassava brown streak disease (CBSD) is a severe virus disease of cassava and prevalent in the eastern regions of Africa. The disease is characterized by distinct vein chlorosis and streak symptoms on leaves and stems and necrosis of storage roots. This necrosis can encompass large areas of the root, rendering it inedible so that the entire cassava harvest can be lost. African cassava varieties are susceptible to either of the two viruses causing the disease, cassava brown streak virus (CBSV) and Uganda cassava brown streak virus, and while there are less sensitive varieties, all cassava eventually succumb to the disease. The lack of CBSD resistance in African cassava varieties prompted this search for new sources of virus resistance in the diversity of South American cassava germplasm held in the collection at International Center for Tropical Agriculture, Columbia. Our search for CBSD resistance in South American cassava germplasm accessions revealed that most of the 238 South American cassava lines infected with CBSV established systemic virus infections with moderate to severe disease symptoms on leaves and stems. Fifteen cassava accessions did not become virus infected, remained free of symptoms, and CBSV was undetected by qRT-PCR. When tuberous roots of those lines were examined, necrotic tissue was found in eight lines and CBSV was detected. The remaining seven cassava accessions remained clear of symptoms on all tissues and organs and were virus free. A broad spectrum of virus resistance also including other virus isolates was confirmed for the breeding lines DSC167 and DSC118. While detailed infection experiments with other cassava lines selected for resistance are still ongoing, this indicates that the resistance identified may also hold against a broader diversity of CBSVs. Taken together, we present the results of a comprehensive study on CBSV resistance and susceptibility in cassava germplasm accessions from South America. The virus resistance in cassava germplasm identified provides compelling evidence for the invaluable contribution of germplasm collections to supply the genetic resources for the improvement of our crops.
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Affiliation(s)
| | | | | | - Stephan Winter
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Houngue JA, Zandjanakou-Tachin M, Ngalle HB, Pita JS, Cacaï GHT, Ngatat SE, Bell JM, Ahanhanzo C. Evaluation of resistance to cassava mosaic disease in selected African cassava cultivars using combined molecular and greenhouse grafting tools. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2019; 105:47-53. [PMID: 31007373 PMCID: PMC6472601 DOI: 10.1016/j.pmpp.2018.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 05/14/2023]
Abstract
Cassava mosaic disease (CMD) threatens cassava (Manihot esculenta) production in Africa. A total of 24 selected cultivars were screened against CMD using combined molecular and greenhouse grafting tools. Disease severity was recorded for 10 weeks after inoculation and the molecular markers associated with CMD2 were detected by PCR. CMD severity significantly differed (P < 0.0001) among cultivars. Twelve cultivars were morphologically resistant and eight of these possessed CMD2 and four did not. These results suggest that there are several CMD-resistant cassava cultivars that could be recommended for on-farm production and for conservation and breeding programs.
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Affiliation(s)
- Jerome Anani Houngue
- Central Laboratory of Plant Biotechnology and Plant Breeding, Department of Genetics and Biotechnology, Faculty of Science and Technique, University of Abomey-Calavi, Benin
- Laboratory of Genetics and Plant Breeding, Department of Plant Biology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
- International Institute of Tropical Agriculture (IITA), Nkolbisson, Yaoundé, Cameroon
| | - Martine Zandjanakou-Tachin
- Laboratory of Molecular Plant Pathology, School of Horticulture and Green Space, National University of Agriculture, Porto-Novo, Benin
| | - Hermine Bille Ngalle
- Laboratory of Genetics and Plant Breeding, Department of Plant Biology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Justin S. Pita
- Laboratory of Plant Physiology, Université Félix Houphouët-Boigny, Cote d’Ivoire
| | - Gilles Habib Todjro Cacaï
- Central Laboratory of Plant Biotechnology and Plant Breeding, Department of Genetics and Biotechnology, Faculty of Science and Technique, University of Abomey-Calavi, Benin
| | - Sergine E. Ngatat
- International Institute of Tropical Agriculture (IITA), Nkolbisson, Yaoundé, Cameroon
| | - Joseph Martin Bell
- Laboratory of Genetics and Plant Breeding, Department of Plant Biology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Corneille Ahanhanzo
- Central Laboratory of Plant Biotechnology and Plant Breeding, Department of Genetics and Biotechnology, Faculty of Science and Technique, University of Abomey-Calavi, Benin
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Kumar V, Paillard S, Fopa-Fomeju B, Falentin C, Deniot G, Baron C, Vallée P, Manzanares-Dauleux MJ, Delourme R. Multi-year linkage and association mapping confirm the high number of genomic regions involved in oilseed rape quantitative resistance to blackleg. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1627-1643. [PMID: 29728747 DOI: 10.1007/s00122-018-3103-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/20/2018] [Indexed: 05/02/2023]
Abstract
A repertoire of the genomic regions involved in quantitative resistance to Leptosphaeria maculans in winter oilseed rape was established from combined linkage-based QTL and genome-wide association (GWA) mapping. Linkage-based mapping of quantitative trait loci (QTL) and genome-wide association studies are complementary approaches for deciphering the genomic architecture of complex agronomical traits. In oilseed rape, quantitative resistance to blackleg disease, caused by L. maculans, is highly polygenic and is greatly influenced by the environment. In this study, we took advantage of multi-year data available on three segregating populations derived from the resistant cv Darmor and multi-year data available on oilseed rape panels to obtain a wide overview of the genomic regions involved in quantitative resistance to this pathogen in oilseed rape. Sixteen QTL regions were common to at least two biparental populations, of which nine were the same as previously detected regions in a multi-parental design derived from different resistant parents. Eight regions were significantly associated with quantitative resistance, of which five on A06, A08, A09, C01 and C04 were located within QTL support intervals. Homoeologous Brassica napus genes were found in eight homoeologous QTL regions, which corresponded to 657 pairs of homoeologous genes. Potential candidate genes underlying this quantitative resistance were identified. Genomic predictions and breeding are also discussed, taking into account the highly polygenic nature of this resistance.
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Affiliation(s)
- Vinod Kumar
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Sophie Paillard
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | | | - Cyril Falentin
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Cécile Baron
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | - Patrick Vallée
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France
| | | | - Régine Delourme
- IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France.
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de Souza LM, dos Santos LHB, Rosa JRBF, da Silva CC, Mantello CC, Conson ARO, Scaloppi EJ, Fialho JDF, de Moraes MLT, Gonçalves PDS, Margarido GRA, Garcia AAF, Le Guen V, de Souza AP. Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree ( Hevea brasiliensis). FRONTIERS IN PLANT SCIENCE 2018; 9:815. [PMID: 30018620 PMCID: PMC6037771 DOI: 10.3389/fpls.2018.00815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr.de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation.
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Affiliation(s)
- Livia M. de Souza
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Luciano H. B. dos Santos
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - João R. B. F. Rosa
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Carla C. da Silva
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Camila C. Mantello
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- The John Bingham Laboratory, National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - André R. O. Conson
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Erivaldo J. Scaloppi
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute of Campinas, Votuporanga, Brazil
| | - Josefino de F. Fialho
- Centro de Pesquisa Agropecuária dos Cerrados (Cpac), Embrapa Cerrados, Empresa Brazileira de Pesquisa Agropecuária, Planaltina, Brazil
| | - Mario Luiz T. de Moraes
- Departamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, Brazil
| | - Paulo de S. Gonçalves
- Center of Rubber Tree and Agroforestry Systems, Agronomic Institute of Campinas, Votuporanga, Brazil
| | - Gabriel R. A. Margarido
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
| | - Antonio A. F. Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, Brazil
| | - Vincent Le Guen
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France
| | - Anete P. de Souza
- Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas, Campinas, Brazil
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Chauhan RD, Beyene G, Taylor NJ. Multiple morphogenic culture systems cause loss of resistance to cassava mosaic disease. BMC PLANT BIOLOGY 2018; 18:132. [PMID: 29940871 PMCID: PMC6020238 DOI: 10.1186/s12870-018-1354-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/17/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Morphogenic culture systems are central to crop improvement programs that utilize transgenic and genome editing technologies. We previously reported that CMD2-type cassava (Manihot esculenta) cultivars lose resistance to cassava mosaic disease (CMD) when passed through somatic embryogenesis. As a result, these plants cannot be developed as products for deployment where CMD is endemic such as sub-Saharan Africa or the Indian sub-continent. RESULT In order to increase understanding of this phenomenon, 21 African cassava cultivars were screened for resistance to CMD after regeneration through somatic embryogenesis. Fifteen cultivars were shown to retain resistance to CMD through somatic embryogenesis, confirming that the existing transformation and gene editing systems can be employed in these genetic backgrounds without compromising resistance to geminivirus infection. CMD2-type cultivars were also subjected to plant regeneration via caulogenesis and meristem tip culture, resulting in 25-36% and 5-10% of regenerated plant lines losing resistance to CMD respectively. CONCLUSIONS This study provides clear evidence that multiple morphogenic systems can result in loss of resistance to CMD, and that somatic embryogenesis per se is not the underlying cause of this phenomenon. The information described here is critical for interpreting genomic, transcriptomic and epigenomic datasets aimed at understanding CMD resistance mechanisms in cassava.
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Affiliation(s)
| | - Getu Beyene
- Donald Danforth Plant Science Center, St. Louis, MO USA
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Díaz Tatis PA, Herrera Corzo M, Ochoa Cabezas JC, Medina Cipagauta A, Prías MA, Verdier V, Chavarriaga Aguirre P, López Carrascal CE. The overexpression of RXam1, a cassava gene coding for an RLK, confers disease resistance to Xanthomonas axonopodis pv. manihotis. PLANTA 2018; 247:1031-1042. [PMID: 29453662 DOI: 10.1007/s00425-018-2863-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/24/2018] [Indexed: 05/27/2023]
Abstract
The overexpression of RXam1 leads to a reduction in bacterial growth of XamCIO136, suggesting that RXam1 might be implicated in strain-specific resistance. Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) is a prevalent disease in all regions, where cassava is cultivated. CBB is a foliar and vascular disease usually controlled through host resistance. Previous studies have found QTLs explaining resistance to several Xam strains. Interestingly, one QTL called XM5 that explained 13% of resistance to XamCIO136 was associated with a similar fragment of the rice Xa21-resistance gene called PCR250. In this study, we aimed to further identify and characterize this fragment and its role in resistance to CBB. Screening and hybridization of a BAC library using the molecular marker PCR250 as a probe led to the identification of a receptor-like kinase similar to Xa21 and were called RXam1 (Resistance to Xam 1). Here, we report the functional characterization of susceptible cassava plants overexpressing RXam1. Our results indicated that the overexpression of RXam1 leads to a reduction in bacterial growth of XamCIO136. This suggests that RXAM1 might be implicated in strain-specific resistance to XamCIO136.
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Affiliation(s)
- Paula A Díaz Tatis
- Laboratorio Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá, Colombia
- Grupo de Ciencias Biológicas y Químicas, Departamento de Biología, Universidad Antonio Nariño, Cra1 #47a15, Bogotá, Colombia
| | - Mariana Herrera Corzo
- Laboratorio Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá, Colombia
- Programa de Biología y Mejoramiento de la Palma de Aceite, Cenipalma, Dir: Km 137 via Pto Araujo-La lizama, Bogotá, Colombia
| | - Juan C Ochoa Cabezas
- Laboratorio Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá, Colombia
- Department of Integrative Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | - Adriana Medina Cipagauta
- Plataforma de Transformación Genética, Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, Palmira, Colombia
| | - Mónica A Prías
- Plataforma de Transformación Genética, Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, Palmira, Colombia
| | - Valerie Verdier
- Institute de Recherche pour le Développement (IRD), CIRAD, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394, Montpellier, France
| | - Paul Chavarriaga Aguirre
- Plataforma de Transformación Genética, Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, Palmira, Colombia
| | - Camilo E López Carrascal
- Laboratorio Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Cra30 #45-03, Bogotá, Colombia.
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Zhang S, Chen X, Lu C, Ye J, Zou M, Lu K, Feng S, Pei J, Liu C, Zhou X, Ma P, Li Z, Liu C, Liao Q, Xia Z, Wang W. Genome-Wide Association Studies of 11 Agronomic Traits in Cassava ( Manihot esculenta Crantz). FRONTIERS IN PLANT SCIENCE 2018; 9:503. [PMID: 29725343 PMCID: PMC5917017 DOI: 10.3389/fpls.2018.00503] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.
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Affiliation(s)
- Shengkui Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Cheng Lu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Meiling Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kundian Lu
- Wuming Agricultural Technology Extension Center, Nanning, China
| | - Subin Feng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinli Pei
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chen Liu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xincheng Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ping’an Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhaogui Li
- Wuming Agricultural Technology Extension Center, Nanning, China
| | - Cuijuan Liu
- Hepu Institute of Agricultural Science, Beihai, China
| | - Qi Liao
- Hepu Institute of Agricultural Science, Beihai, China
| | - Zhiqiang Xia
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Zhiqiang Xia, Wenquan Wang,
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Zhiqiang Xia, Wenquan Wang,
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Lentz EM, Kuon JE, Alder A, Mangel N, Zainuddin IM, McCallum EJ, Anjanappa RB, Gruissem W, Vanderschuren H. Cassava geminivirus agroclones for virus-induced gene silencing in cassava leaves and roots. PLANT METHODS 2018; 14:73. [PMID: 30154909 PMCID: PMC6109987 DOI: 10.1186/s13007-018-0340-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/16/2018] [Indexed: 05/08/2023]
Abstract
AIM We report the construction of a Virus-Induced Gene Silencing (VIGS) vector and an agroinoculation protocol for gene silencing in cassava (Manihot esculenta Crantz) leaves and roots. The African cassava mosaic virus isolate from Nigeria (ACMV-[NOg]), which was initially cloned in a binary vector for agroinoculation assays, was modified for application as VIGS vector. The functionality of the VIGS vector was validated in Nicotiana benthamiana and subsequently applied in wild-type and transgenic cassava plants expressing the uidA gene under the control of the CaMV 35S promoter in order to facilitate the visualization of gene silencing in root tissues. VIGS vectors were targeted to the Mg2+-chelatase gene in wild type plants and both the coding and promoter sequences of the 35S::uidA transgene in transgenic plants to induce silencing. We established an efficient agro-inoculation method with the hyper-virulent Agrobacterium tumefaciens strain AGL1, which allows high virus infection rates. The method can be used as a low-cost and rapid high-throughput evaluation of gene function in cassava leaves, fibrous roots and storage roots. BACKGROUND VIGS is a powerful tool to trigger transient sequence-specific gene silencing in planta. Gene silencing in different organs of cassava plants, including leaves, fibrous and storage roots, is useful for the analysis of gene function. RESULTS We developed an African cassava mosaic virus-based VIGS vector as well as a rapid and efficient agro-inoculation protocol to inoculate cassava plants. The VIGS vector was validated by targeting endogenous genes from Nicotiana benthamiana and cassava as well as the uidA marker gene in transgenic cassava for visualization of gene silencing in cassava leaves and roots. CONCLUSIONS The African cassava mosaic virus-based VIGS vector allows efficient and cost-effective inoculation of cassava for high-throughput analysis of gene function in cassava leaves and roots.
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Affiliation(s)
- Ezequiel Matias Lentz
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Joel-Elias Kuon
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Adrian Alder
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Nathalie Mangel
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Ima M. Zainuddin
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Emily Jane McCallum
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Ravi Bodampalli Anjanappa
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
| | - Hervé Vanderschuren
- Department of Biology, Plant Biotechnology, ETH Zurich-LFW, E56.1, Universitaetstrasse 2, 8092 Zurich, Switzerland
- Plant Genetics Lab, TERRA Research and Teaching Centre, Gembloux Agro BioTech, University of Liège, Gembloux, Belgium
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Rabbi IY, Udoh LI, Wolfe M, Parkes EY, Gedil MA, Dixon A, Ramu P, Jannink JL, Kulakow P. Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content. THE PLANT GENOME 2017; 10:10.3835/plantgenome2016.09.0094. [PMID: 29293815 PMCID: PMC7822061 DOI: 10.3835/plantgenome2016.09.0094] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
Cassava is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Primary selection objectives in cassava breeding include dry matter content and micronutrient density, particularly provitamin A carotenoids. These traits are negatively correlated in the African germplasm. This study aimed at identifying genetic markers associated with these traits and uncovering whether linkage and/or pleiotropy were responsible for observed negative correlation. A genome-wide association mapping using 672 clones genotyped at 72,279 single nucleotide polymorphism (SNP) loci was performed. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness were identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that colocated with the 24.1 Mbp peak for carotenoids was identified. Haplotypes at these loci explained 70 and 37% of the phenotypic variability for root yellowness and dry matter content, respectively. Evidence of megabase-scale linkage disequilibrium (LD) around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid () and starch biosynthesis ( and ) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate the genetic architecture of carotenoids and dry matter in cassava and provide an opportunity to accelerate breeding of these traits.
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Affiliation(s)
- Ismail Y. Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
- Corresponding author ()
| | - Lovina I. Udoh
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Marnin Wolfe
- Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY 14853
| | - Elizabeth Y. Parkes
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Melaku A. Gedil
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Alfred Dixon
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Punna Ramu
- Institute of Genomic Diversity, Cornell Univ., Ithaca, NY 14853
| | - Jean-Luc Jannink
- Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY 14853
- USDA-ARS, R.W. Holley Center for Agriculture and Health, Ithaca, NY 14853
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
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Wolfe MD, Carpio DPD, Alabi O, Ezenwaka LC, Ikeogu UN, Kayondo IS, Lozano R, Okeke UG, Ozimati AA, Williams E, Egesi C, Kawuki RS, Kulakow P, Rabbi IY, Jannink JL. Prospects for Genomic Selection in Cassava Breeding. THE PLANT GENOME 2017; 10:10.3835/plantgenome2017.03.0015. [PMID: 29293806 PMCID: PMC7822052 DOI: 10.3835/plantgenome2017.03.0015] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Cassava ( Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: cross-validation within populations, cross-population prediction and cross-generation prediction. We also evaluated the impact of increasing the training population (TP) size by phenotyping progenies selected either at random or with a genetic algorithm. Cross-validation results were mostly consistent across programs, with nonadditive models predicting of 10% better on average. Cross-population accuracy was generally low (mean = 0.18) but prediction of cassava mosaic disease increased up to 57% in one Nigerian population when data from another related population were combined. Accuracy across generations was poorer than within-generation accuracy, as expected, but accuracy for dry matter content and mosaic disease severity should be sufficient for rapid-cycling GS. Selection of a prediction model made some difference across generations, but increasing TP size was more important. With a genetic algorithm, selection of one-third of progeny could achieve an accuracy equivalent to phenotyping all progeny. We are in the early stages of GS for this crop but the results are promising for some traits. General guidelines that are emerging are that TPs need to continue to grow but phenotyping can be done on a cleverly selected subset of individuals, reducing the overall phenotyping burden.
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Affiliation(s)
- Marnin D. Wolfe
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- Corresponding authors (, )
| | - Dunia Pino Del Carpio
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- Corresponding authors (, )
| | - Olumide Alabi
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | | | - Ugochukwu N. Ikeogu
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- National Root Crops Research Inst., Umudike, Umuahia, Nigeria
| | | | - Roberto Lozano
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
| | - Uche G. Okeke
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | - Alfred A. Ozimati
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- National Crops Resources Research Inst., Namulonge, Uganda
| | - Esuma Williams
- National Crops Resources Research Inst., Namulonge, Uganda
| | - Chiedozie Egesi
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
- National Root Crops Research Inst., Umudike, Umuahia, Nigeria
- International Programs, College of Agriculture and Life Sciences, Cornell Univ., Ithaca, NY
| | | | - Peter Kulakow
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | - Ismail Y. Rabbi
- International Inst. for Tropical Agriculture, Ibadan, Oyo, Nigeria
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, Cornell Univ., Ithaca, NY
- USDA-ARS, R.W. Holley Center for Agriculture and Health, Ithaca, NY
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48
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Masumba EA, Kapinga F, Mkamilo G, Salum K, Kulembeka H, Rounsley S, Bredeson JV, Lyons JB, Rokhsar DS, Kanju E, Katari MS, Myburg AA, van der Merwe NA, Ferguson ME. QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2069-2090. [PMID: 28707249 PMCID: PMC5606945 DOI: 10.1007/s00122-017-2943-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 06/25/2017] [Indexed: 05/17/2023]
Abstract
KEY MESSAGE QTL consistent across seasons were detected for resistance to cassava brown streak disease induced root necrosis and foliar symptoms. The CMD2 locus was detected in an East African landrace, and comprised two QTL. Cassava production in Africa is compromised by cassava brown streak disease (CBSD) and cassava mosaic disease (CMD). To reduce costs and increase the precision of resistance breeding, a QTL study was conducted to identify molecular markers linked to resistance against these diseases. A bi-parental F1 mapping population was developed from a cross between the Tanzanian farmer varieties, Namikonga and Albert. A one-step genetic linkage map comprising 943 SNP markers and 18 linkage groups spanning 1776.2 cM was generated. Phenotypic data from 240 F1 progeny were obtained from two disease hotspots in Tanzania, over two successive seasons, 2013 and 2014. Two consistent QTLs linked to resistance to CBSD-induced root necrosis were identified in Namikonga on chromosomes II (qCBSDRNFc2Nm) and XI (qCBSDRNc11Nm) and a putative QTL on chromosome XVIII (qCBSDRNc18Nm). qCBSDRNFc2Nm was identified at Naliendele in both seasons. The same QTL was also associated with CBSD foliar resistance. qCBSDRNc11Nm was identified at Chambezi in both seasons, and was characterized by three peaks, spanning a distance of 253 kb. Twenty-seven genes were identified within this region including two LRR proteins and a signal recognition particle. In addition, two highly significant CMD resistance QTL (qCMDc12.1A and qCMDc12.2A) were detected in Albert, on chromosome 12. Both qCMDc12.1A and qCMDc12.2A lay within the range of markers reported earlier, defining the CMD2 locus. This is the first time that two loci have been identified within the CMD2 QTL, and in germplasm of apparent East African origin. Additional QTLs with minor effects on CBSD and CMD resistance were also identified.
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Affiliation(s)
- E A Masumba
- Sugarcane Research Institute, P. O. Box 30031, Kibaha, Tanzania
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
- IITA, P.O. Box 30709-00100, Nairobi, Kenya
| | - F Kapinga
- Naliendele Agricultural Research Institute, P. O. Box 509, Mtwara, Tanzania
| | - G Mkamilo
- Naliendele Agricultural Research Institute, P. O. Box 509, Mtwara, Tanzania
| | - K Salum
- Ukiriguru Agricultural Research Institute, P. O. Box 1433, Mwanza, Tanzania
| | - H Kulembeka
- Ukiriguru Agricultural Research Institute, P. O. Box 1433, Mwanza, Tanzania
| | | | - J V Bredeson
- Molecular and Cell Biology Department, University of California, Berkeley, CA, USA
| | - J B Lyons
- Molecular and Cell Biology Department, University of California, Berkeley, CA, USA
| | - D S Rokhsar
- Molecular and Cell Biology Department, University of California, Berkeley, CA, USA
| | - E Kanju
- International Institute of Tropical Agriculture (IITA), P.O. Box 2066, Dar es Salaam, Tanzania
| | | | - A A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - N A van der Merwe
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
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49
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Nzuki I, Katari MS, Bredeson JV, Masumba E, Kapinga F, Salum K, Mkamilo GS, Shah T, Lyons JB, Rokhsar DS, Rounsley S, Myburg AA, Ferguson ME. QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii. FRONTIERS IN PLANT SCIENCE 2017; 8:1168. [PMID: 28785268 PMCID: PMC5519584 DOI: 10.3389/fpls.2017.01168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/19/2017] [Indexed: 05/24/2023]
Abstract
Genetic mapping of quantitative trait loci (QTL) for resistance to cassava brown streak disease (CBSD), cassava mosaic disease (CMD), and cassava green mite (CGM) was performed using an F1 cross developed between the Tanzanian landrace, Kiroba, and a breeding line, AR37-80. The population was evaluated for two consecutive years in two sites in Tanzania. A genetic linkage map was derived from 106 F1 progeny and 1,974 SNP markers and spanned 18 chromosomes covering a distance of 1,698 cM. Fifteen significant QTL were identified; two are associated with CBSD root necrosis only, and were detected on chromosomes V and XII, while seven were associated with CBSD foliar symptoms only and were detected on chromosomes IV, VI, XVII, and XVIII. QTL on chromosomes 11 and 15 were associated with both CBSD foliar and root necrosis symptoms. Two QTL were found to be associated with CMD and were detected on chromosomes XII and XIV, while two were associated with CGM and were identified on chromosomes V and X. There are large Manihot glaziovii introgression regions in Kiroba on chromosomes I, XVII, and XVIII. The introgression segments on chromosomes XVII and XVIII overlap with QTL associated with CBSD foliar symptoms. The introgression region on chromosome I is of a different haplotype to the characteristic "Amani haplotype" found in the landrace Namikonga and others, and unlike some other genotypes, Kiroba does not have a large introgression block on chromosome IV. Kiroba is closely related to a sampled Tanzanian "tree cassava." This supports the observation that some of the QTL associated with CBSD resistance in Kiroba are different to those observed in another variety, Namikonga.
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Affiliation(s)
- Inosters Nzuki
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of PretoriaPretoria, South Africa
- International Institute of Tropical AgricultureNairobi, Kenya
| | | | - Jessen V. Bredeson
- Molecular and Cell Biology Department, University of California, BerkeleyBerkeley, CA, United States
| | | | | | - Kasele Salum
- Lake Zone Agricultural Research and Development InstituteMwanza, Tanzania
| | | | - Trushar Shah
- International Institute of Tropical AgricultureNairobi, Kenya
| | - Jessica B. Lyons
- Molecular and Cell Biology Department, University of California, BerkeleyBerkeley, CA, United States
| | - Daniel S. Rokhsar
- Molecular and Cell Biology Department, University of California, BerkeleyBerkeley, CA, United States
| | | | - Alexander A. Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of PretoriaPretoria, South Africa
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50
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Soto Sedano JC, Mora Moreno RE, Mathew B, Léon J, Gómez Cano FA, Ballvora A, López Carrascal CE. Major Novel QTL for Resistance to Cassava Bacterial Blight Identified through a Multi-Environmental Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:1169. [PMID: 28725234 PMCID: PMC5496946 DOI: 10.3389/fpls.2017.01169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/19/2017] [Indexed: 05/31/2023]
Abstract
Cassava, Manihot esculenta Crantz, has been positioned as one of the most promising crops world-wide representing the staple security for more than one billion people mainly in poor countries. Cassava production is constantly threatened by several diseases, including cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam), it is the most destructive disease causing heavy yield losses. Here, we report the detection and localization on the genetic map of cassava QTL (Quantitative Trait Loci) conferring resistance to CBB. An F1 mapping population of 117 full sibs was tested for resistance to two Xam strains (Xam318 and Xam681) at two locations in Colombia: La Vega, Cundinamarca and Arauca. The evaluation was conducted in rainy and dry seasons and additional tests were carried out under controlled greenhouse conditions. The phenotypic evaluation of the response to Xam revealed continuous variation. Based on composite interval mapping analysis, 5 strain-specific QTL for resistance to Xam explaining between 15.8 and 22.1% of phenotypic variance, were detected and localized on a high resolution SNP-based genetic map of cassava. Four of them show stability among the two evaluated seasons. Genotype by environment analysis detected three QTL by environment interactions and the broad sense heritability for Xam318 and Xam681 were 20 and 53%, respectively. DNA sequence analysis of the QTL intervals revealed 29 candidate defense-related genes (CDRGs), and two of them contain domains related to plant immunity proteins, such as NB-ARC-LRR and WRKY.
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Affiliation(s)
- Johana C. Soto Sedano
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de ColombiaBogotá, Colombia
| | - Rubén E. Mora Moreno
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de ColombiaBogotá, Colombia
| | - Boby Mathew
- Institute of Crop Science and Resource Conservation-Plant Breeding, University of BonnBonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation-Plant Breeding, University of BonnBonn, Germany
| | - Fabio A. Gómez Cano
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de ColombiaBogotá, Colombia
- Institute of Crop Science and Resource Conservation-Plant Breeding, University of BonnBonn, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation-Plant Breeding, University of BonnBonn, Germany
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