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Ferguson ME, Eyles RP, Garcia-Oliveira AL, Kapinga F, Masumba EA, Amuge T, Bredeson JV, Rokhsar DS, Lyons JB, Shah T, Rounsley S, Mkamilo G. Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources. Front Plant Sci 2023; 14:1270963. [PMID: 38023930 PMCID: PMC10655247 DOI: 10.3389/fpls.2023.1270963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope® in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions.
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Affiliation(s)
- Morag E. Ferguson
- Cassava Breeding, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Rodney P. Eyles
- Cassava Breeding, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Fortunus Kapinga
- Cassava Breeding, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Cassava Breeding, Naliendele Agricultural Research Institute, Mtwara, Tanzania
| | - Esther A. Masumba
- Cassava Breeding, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Cassava Breeding, Sugarcane Research Institute, Kibaha, Tanzania
| | - Teddy Amuge
- Cassava Breeding, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Cassava Breeding, National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda
| | - Jessen V. Bredeson
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA, United States
| | - Daniel S. Rokhsar
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA, United States
| | - Jessica B. Lyons
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA, United States
| | - Trushar Shah
- Bioinformatics, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Steve Rounsley
- Seeds & Traits R&D, Dow AgroSciences, Indianapolis, IN, United States
| | - Geoffrey Mkamilo
- Cassava Breeding, Naliendele Agricultural Research Institute, Mtwara, Tanzania
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Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Sci Rep 2017; 7:9747. [PMID: 28852026 PMCID: PMC5575035 DOI: 10.1038/s41598-017-09617-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/21/2017] [Indexed: 12/13/2022] Open
Abstract
A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of 'translational elongation', 'translation factor activity', 'ribosomal subunit' and 'phosphorelay signal transduction', were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga's resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding.
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Affiliation(s)
- T Amuge
- National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - D K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - M S Katari
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - A A Myburg
- Genetics Department, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - S L Goldman
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - M E Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya.
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Shi S, Zhang X, Mandel MA, Zhang P, Zhang Y, Ferguson M, Amuge T, Rounsley S, Liu Z, Xiong Z. Variations of five eIF4E genes across cassava accessions exhibiting tolerant and susceptible responses to cassava brown streak disease. PLoS One 2017; 12:e0181998. [PMID: 28771520 PMCID: PMC5542559 DOI: 10.1371/journal.pone.0181998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022] Open
Abstract
Cassava (Manihot esculenta) is an important tropical subsistence crop that is severely affected by cassava brown streak disease (CBSD) in East Africa. The disease is caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Both have a (+)-sense single-stranded RNA genome with a 5' covalently-linked viral protein, which functionally resembles the cap structure of mRNA, binds to eukaryotic translation initiation factor 4E (eIF4E) or its analogues, and then enable the translation of viral genomic RNA in host cells. To characterize cassava eIF4Es and their potential role in CBSD tolerance and susceptibility, we cloned five eIF4E transcripts from cassava (accession TMS60444). Sequence analysis indicated that the cassava eIF4E family of proteins consisted of one eIF4E, two eIF(iso)4E, and two divergent copies of novel cap-binding proteins (nCBPs). Our data demonstrated experimentally the coding of these five genes as annotated in the published cassava genome and provided additional evidence for refined annotations. Illumina resequencing data of the five eIF4E genes were analyzed from 14 cassava lines tolerant or susceptible to CBSD. Abundant single nucleotide polymorphisms (SNP) and biallelic variations were observed in the eIF4E genes; however, most of the SNPs were located in the introns and non-coding regions of the exons. Association studies of non-synonymous SNPs revealed no significant association between any SNP of the five eIF4E genes and the tolerance or susceptibility to CBSD. However, two SNPs in two genes were weakly associated with the CBSD responses but had no direct causal-effect relationship. SNPs in an intergenic region upstream of eIF4E_me showed a surprising strong association with CBSD responses. Digital expression profile analysis showed differential expression of different eIF4E genes but no significant difference in gene expression was found between susceptible and tolerant cassava accessions despite the association of the intergenic SNPs with CBSD responses.
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Affiliation(s)
- Shanshan Shi
- Institute of Tropical biology and biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Xiuchun Zhang
- Institute of Tropical biology and biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - M. Alejandra Mandel
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yuliang Zhang
- Institute of Tropical biology and biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Morag Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Teddy Amuge
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Steve Rounsley
- Genus plc, DeForest, Wisconsin, United States of America
| | - Zhixin Liu
- Institute of Tropical biology and biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- * E-mail: (ZX); (ZL)
| | - Zhongguo Xiong
- School of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (ZX); (ZL)
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Kawuki RS, Kaweesi T, Esuma W, Pariyo A, Kayondo IS, Ozimati A, Kyaligonza V, Abaca A, Orone J, Tumuhimbise R, Nuwamanya E, Abidrabo P, Amuge T, Ogwok E, Okao G, Wagaba H, Adiga G, Alicai T, Omongo C, Bua A, Ferguson M, Kanju E, Baguma Y. Eleven years of breeding efforts to combat cassava brown streak disease. Breed Sci 2016; 66:560-571. [PMID: 27795681 PMCID: PMC5010303 DOI: 10.1270/jsbbs.16005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/07/2016] [Indexed: 05/05/2023]
Abstract
Cassava (Manihot esculenta Crantz) production is currently under threat from cassava brown streak disease (CBSD), a disease that is among the seven most serious obstacles to world's food security. Three issues are of significance for CBSD. Firstly, the virus associated with CBSD, has co-evolved with cassava outside its center of origin for at least 90 years. Secondly, that for the last 74 years, CBSD was only limited to the low lands. Thirdly, that most research has largely focused on CBSD epidemiology and virus diversity. Accordingly, this paper focuses on CBSD genetics and/or breeding and hence, presents empirical data generated in the past 11 years of cassava breeding in Uganda. Specifically, this paper provides: 1) empirical data on CBSD resistance screening efforts to identify sources of resistance and/or tolerance; 2) an update on CBSD resistance population development comprising of full-sibs, half-sibs and S1 families and their respective field performances; and 3) insights into chromosomal regions and genes involved in CBSD resistance based on genome wide association analysis. It is expected that this information will provide a foundation for harmonizing on-going CBSD breeding efforts and consequently, inform the future breeding interventions aimed at combating CBSD.
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Affiliation(s)
- Robert Sezi Kawuki
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Tadeo Kaweesi
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Williams Esuma
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Anthony Pariyo
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Ismail Siraj Kayondo
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Alfred Ozimati
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Vincent Kyaligonza
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Alex Abaca
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Joseph Orone
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Robooni Tumuhimbise
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Ephraim Nuwamanya
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Philip Abidrabo
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Teddy Amuge
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Emmanuel Ogwok
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Geoffrey Okao
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Henry Wagaba
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Gerald Adiga
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Titus Alicai
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Christopher Omongo
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Anton Bua
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
| | - Morag Ferguson
- International Institute of Tropical Agriculture (IITA), C/o International Livestock Research Institute (ILRI),
P.O. Box 30709, Nairobi 00100,
Kenya
| | - Edward Kanju
- International Institute of Tropical Agriculture (IITA),
P.O. Box 34441, Dar es Salaam,
Tanzania
| | - Yona Baguma
- National Crops Resources Research Institute,
9 km Gayaza-Zirobwe Road, P.O. Box 7084, Kampala,
Uganda
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