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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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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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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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Anchoring a genetic map of an interspecific backcross two family to the genome builds of Elaeis. J Genet 2021. [DOI: 10.1007/s12041-020-01240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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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Ahn YK, Manivannan A, Karna S, Jun TH, Yang EY, Choi S, Kim JH, Kim DS, Lee ES. Whole Genome Resequencing of Capsicum baccatum and Capsicum annuum to Discover Single Nucleotide Polymorphism Related to Powdery Mildew Resistance. Sci Rep 2018; 8:5188. [PMID: 29581444 PMCID: PMC5980001 DOI: 10.1038/s41598-018-23279-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 03/06/2018] [Indexed: 11/08/2022] Open
Abstract
The present study deals with genome wide identification of single-nucleotide polymorphism (SNP) markers related to powdery mildew (PM) resistance in two pepper varieties. Capsicum baccatum (PRH1- a PM resistant line) and Capsicum annuum (Saengryeg- a PM susceptible line), were resequenced to develop SNP markers. A total of 6,213,009 and 6,840,889 SNPs for PRH1 and Saengryeg respectively have been discovered. Among the SNPs, majority were classified as homozygous type SNPs, particularly in the resistant line. Moreover, the SNPs were differentially distributed among the chromosomes in both the resistant and susceptible lines. In total, 4,887,031 polymorphic SNP loci were identified between the two lines and 306,871 high-resolution melting (HRM) marker primer sets were designed. In order to understand the SNPs associated with the vital genes involved in diseases resistance and stress associated processes, chromosome-wise gene ontology analysis was performed. The results revealed the occurrence that SNPs related to diseases resistance genes were predominantly distributed in chromosome 4. In addition, 6281 SNPs associated with 46 resistance genes were identified. Among the lines, PRH1 consisted of maximum number of polymorphic SNPs related to NBS-LRR genes. The SNP markers were validated using HRM assay in 45 F4 populations and correlated with the phenotypic disease index.
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Affiliation(s)
- Yul-Kyun Ahn
- Department of Vegetable Crops, Korea National College of Agriculture and Fisheries, Jeonju, 54874, Republic of Korea.
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Sandeep Karna
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Busan, 46241, Republic of Korea
| | - Eun-Young Yang
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Sena Choi
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Jin-Hee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
| | - Eun-Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365, Republic of Korea
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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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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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Wang B, Guo X, Zhao P, Ruan M, Yu X, Zou L, Yang Y, Li X, Deng D, Xiao J, Xiao Y, Hu C, Wang X, Wang X, Wang W, Peng M. Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz). PLoS One 2017; 12:e0177456. [PMID: 28493955 PMCID: PMC5426748 DOI: 10.1371/journal.pone.0177456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/27/2017] [Indexed: 11/19/2022] Open
Abstract
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2.87 alleles per locus, gene diversity of 0.48 and polymorphic information content (PIC) of 0.41 on average. The genetic coefficient between every two lines was 0.37 on average, ranging from 0.21 to 0.82. According to our population structure analysis, these samples could be divided into three sub-populations showing obvious gene flow between them. We also performed water stress experiments using 100-day old cassava plants in two years and calculated the drought tolerance coefficients (DTCs) and used them as phenotypes for marker-trait association mapping. We found that 53 markers were significantly associated with these drought-related traits, with a contribution rate for trait variation of 8.60% on average, ranging between 2.66 and 28.09%. Twenty-four of these 53 associated genes showed differential transcription or protein levels which were confirmed by qRT-PCR under drought stress when compared to the control conditions in cassava. Twelve of twenty-four genes were the same differential expression patterns in omics data and results of qRT-PCR. Out of 33 marker-traits combinations on 24 loci, 34 were positive and 53 negative alleles according to their phenotypic effects and we also obtained the typical materials which carried these elite alleles. We also found 23 positive average allele effects while 10 loci were negative according to their allele effects (AAEs). Our results on molecular diversity, locus association and differential expression under drought can prove beneficial to select excellent materials through marker assisted selection and for functional genes research in the future.
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Affiliation(s)
- Bin Wang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xin Guo
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Pingjuan Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Mengbin Ruan
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaoling Yu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Liangping Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiling Yang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiao Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Deli Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Jixiang Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiwei Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Chunji Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xue Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaolin Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
- * E-mail:
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10
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Patil BL, Legg JP, Kanju E, Fauquet CM. Cassava brown streak disease: a threat to food security in Africa. J Gen Virol 2015; 96:956-68. [PMID: 26015320 DOI: 10.1099/vir.0.000014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cassava brown streak disease (CBSD) has emerged as the most important viral disease of cassava (Manihot esculenta) in Africa and is a major threat to food security. CBSD is caused by two distinct species of ipomoviruses, Cassava brown streak virus and Ugandan cassava brown streak virus, belonging to the family Potyviridae. Previously, CBSD was reported only from the coastal lowlands of East Africa, but recently it has begun to spread as an epidemic throughout the Great Lakes region of East and Central Africa. This new spread represents a major threat to the cassava-growing regions of West Africa. CBSD-resistant cassava cultivars are being developed through breeding, and transgenic RNA interference-derived field resistance to CBSD has also been demonstrated. This review aims to provide a summary of the most important studies on the aetiology, epidemiology and control of CBSD and to highlight key research areas that need prioritization.
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Affiliation(s)
- Basavaprabhu L Patil
- National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India
| | - James P Legg
- International Institute of Tropical Agriculture, PO Box 34441, Dar-Es-Salaam, Tanzania
| | - Edward Kanju
- International Institute of Tropical Agriculture, PO Box 34441, Dar-Es-Salaam, Tanzania
| | - Claude M Fauquet
- Centro Internacional de Agricultura Tropical, Apartado Aéreo 6713, Cali, Colombia
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11
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Ceballos H, Kawuki RS, Gracen VE, Yencho GC, Hershey CH. Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1647-67. [PMID: 26093610 PMCID: PMC4540783 DOI: 10.1007/s00122-015-2555-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 06/05/2015] [Indexed: 05/19/2023]
Abstract
Consolidates relevant molecular and phenotypic information on cassava to demonstrate relevance of heterosis, and alternatives to exploit it by integrating different tools. Ideas are useful to other asexually reproduced crops. Asexually propagated crops offer the advantage that all genetic effects can be exploited in farmers' production fields. However, non-additive effects complicate selection because, while influencing the performance of the materials under evaluation, they cannot be transmitted efficiently to the following cycle of selection. Cassava can be used as a model crop for asexually propagated crops because of its diploid nature and the absence of (known) incompatibility effects. New technologies such as genomic selection (GS), use of inbred progenitors based on doubled haploids and induction of flowering can be employed for accelerating genetic gains in cassava. Available information suggests that heterosis, non-additive genetic effects and within-family variation are relatively large for complex traits such as fresh root yield, moderate for dry matter or starch content in the roots, and low for defensive traits (pest and disease resistance) and plant architecture. The present article considers the potential impact of different technologies for maximizing gains for key traits in cassava, and highlights the advantages of integrating them. Exploiting heterosis would be optimized through the implementation of reciprocal recurrent selection. The advantages of using inbred progenitors would allow shifting the current cassava phenotypic recurrent selection method into line improvement, which in turn would allow designing outstanding hybrids rather than finding them by trial and error.
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Affiliation(s)
- Hernán Ceballos
- International Center for Tropical Agriculture (CIAT), Apartado Aéreo, 6713, Cali, Colombia,
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Patil BL, Legg JP, Kanju E, Fauquet CM. Cassava brown streak disease: a threat to food security in Africa. J Gen Virol 2015. [DOI: 10.1099/jgv.0.000014] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Basavaprabhu L. Patil
- National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India
| | - James P. Legg
- International Institute of Tropical Agriculture, PO Box 34441, Dar-Es-Salaam, Tanzania
| | - Edward Kanju
- International Institute of Tropical Agriculture, PO Box 34441, Dar-Es-Salaam, Tanzania
| | - Claude M. Fauquet
- Centro Internacional de Agricultura Tropical, Apartado Aéreo 6713, Cali, Colombia
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Soto JC, Ortiz JF, Perlaza-Jiménez L, Vásquez AX, Lopez-Lavalle LAB, Mathew B, Léon J, Bernal AJ, Ballvora A, López CE. A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes. BMC Genomics 2015; 16:190. [PMID: 25887443 PMCID: PMC4417308 DOI: 10.1186/s12864-015-1397-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/24/2015] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Cassava, Manihot esculenta Crantz, is one of the most important crops world-wide representing the staple security for more than one billion of people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding program represents a significant challenge. A reference genome sequence for cassava has been made recently available and community efforts are underway for improving its quality. Cassava is threatened by several pathogens, but the mechanisms of defense are far from being understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organization in the cassava genome. RESULTS A high dense genetic map of cassava containing 2,141 SNPs has been constructed. Eighteen linkage groups were resolved with an overall size of 2,571 cM and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred eighty nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map with 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on physical map of the corresponding sequencing scaffolds, unambiguous genetic localization was possible for 569 IRPs. CONCLUSIONS This is the first study reported so far of an integrated high density genetic map using SNPs with integrated genetic and physical localization of newly annotated immunity related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome sequencing consortium.
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Affiliation(s)
- Johana Carolina Soto
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Juan Felipe Ortiz
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia. .,Present address Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | - Laura Perlaza-Jiménez
- Laboratory of Mycology and Plant Pathology, Universidad de los Andes, Bogotá, Colombia. .,Present address Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
| | - Andrea Ximena Vásquez
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | | | - Boby Mathew
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Jens Léon
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Adriana Jimena Bernal
- Laboratory of Mycology and Plant Pathology, Universidad de los Andes, Bogotá, Colombia.
| | - Agim Ballvora
- INRES-Plant Breeding University of Bonn, Bonn, Germany.
| | - Camilo Ernesto López
- Manihot Biotec Laboratory, Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
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Pootakham W, Shearman JR, Ruang-areerate P, Sonthirod C, Sangsrakru D, Jomchai N, Yoocha T, Triwitayakorn K, Tragoonrung S, Tangphatsornruang S. Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz). PLoS One 2014; 9:e116028. [PMID: 25551642 PMCID: PMC4281258 DOI: 10.1371/journal.pone.0116028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/30/2014] [Indexed: 11/18/2022] Open
Abstract
Cassava (Manihot esculenta Crantz) is one of the most important crop species being the main source of dietary energy in several countries. Marker-assisted selection has become an essential tool in plant breeding. Single nucleotide polymorphism (SNP) discovery via transcriptome sequencing is an attractive strategy for genome complexity reduction in organisms with large genomes. We sequenced the transcriptome of 16 cassava accessions using the Illumina HiSeq platform and identified 675,559 EST-derived SNP markers. A subset of those markers was subsequently genotyped by capture-based targeted enrichment sequencing in 100 F1 progeny segregating for starch viscosity phenotypes. A total of 2,110 non-redundant SNP markers were used to construct a genetic map. This map encompasses 1,785 cM and consists of 19 linkage groups. A major quantitative trait locus (QTL) controlling starch pasting properties was identified and shown to coincide with the QTL previously reported for this trait. With a high-density SNP-based linkage map presented here, we also uncovered a novel QTL associated with starch pasting time on LG 10.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
| | - Jeremy R. Shearman
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
| | - Panthita Ruang-areerate
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
| | | | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand
- * E-mail:
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High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations. G3-GENES GENOMES GENETICS 2014; 5:133-44. [PMID: 25504737 PMCID: PMC4291464 DOI: 10.1534/g3.114.015008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400-500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selection-enhanced breeding of this important crop.
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Differences in Manioc Diversity Among Five Ethnic Groups of the Colombian Amazon. DIVERSITY 2014. [DOI: 10.3390/d6040792] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping. Sci Rep 2014; 4:7300. [PMID: 25466435 PMCID: PMC4252907 DOI: 10.1038/srep07300] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/17/2014] [Indexed: 11/09/2022] Open
Abstract
We describe methods for the assessment of amplified-fragment single nucleotide polymorphism and methylation (AFSM) sites using a quick and simple molecular marker-assisted breeding strategy based on the use of two restriction enzyme pairs (EcoRI-MspI and EcoRI-HpaII) and a next-generation sequencing platform. Two sets of 85 adapter pairs were developed to concurrently identify SNPs, indels and methylation sites for 85 lines of cassava population in this study. In addition to SNPs and indels, the simplicity of the AFSM protocol makes it particularly suitable for high-throughput full methylation and hemi-methylation analyses. To further demonstrate the ease of this approach, a cassava genetic linkage map was constructed. This approach should be widely applicable for genetic mapping in a variety of organisms and will improve the application of crop genomics in assisted breeding.
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18
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Allie F, Pierce EJ, Okoniewski MJ, Rey C. Transcriptional analysis of South African cassava mosaic virus-infected susceptible and tolerant landraces of cassava highlights differences in resistance, basal defense and cell wall associated genes during infection. BMC Genomics 2014; 15:1006. [PMID: 25412561 PMCID: PMC4253015 DOI: 10.1186/1471-2164-15-1006] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cassava mosaic disease is caused by several distinct geminivirus species, including South African cassava mosaic virus-[South Africa:99] (SACMV). To date, there is limited gene regulation information on viral stress responses in cassava, and global transcriptome profiling in SACMV-infected cassava represents an important step towards understanding natural host responses to plant geminiviruses. RESULTS A RNA-seq time course (12, 32 and 67 dpi) study, monitoring gene expression in SACMV-challenged susceptible (T200) and tolerant (TME3) cassava landraces, was performed using the Applied Biosystems (ABI) SOLiD next-generation sequencing platform. The multiplexed paired end sequencing run produced a total of 523 MB and 693 MB of paired-end reads for SACMV-infected susceptible and tolerant cDNA libraries, respectively. Of these, approximately 50.7% of the T200 reads and 55.06% of TME3 reads mapped to the cassava reference genome available in phytozome. Using a log2 fold cut-off (p<0.05), comparative analysis between the six normalized cDNA libraries showed that 4181 and 1008 transcripts in total were differentially expressed in T200 and TME3, respectively, across 12, 32 and 67 days post infection, compared to mock-inoculated. The number of responsive transcripts increased dramatically from 12 to 32 dpi in both cultivars, but in contrast, in T200 the levels did not change significantly at 67 dpi, while in TME3 they declined. GOslim functional groups illustrated that differentially expressed genes in T200 and TME3 were overrepresented in the cellular component category for stress-related genes, plasma membrane and nucleus. Alterations in the expression of other interesting genes such as transcription factors, resistance (R) genes, and histone/DNA methylation-associated genes, were observed. KEGG pathway analysis uncovered important altered metabolic pathways, including phenylpropanoid biosynthesis, sucrose and starch metabolism, and plant hormone signalling. CONCLUSIONS Molecular mechanisms for TME3 tolerance are proposed, and differences in patterns and levels of transcriptome profiling between T200 and TME3 with susceptible and tolerant phenotypes, respectively, support the hypothesis that viruses rearrange their molecular interactions in adapting to hosts with different genetic backgrounds.
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Affiliation(s)
- Farhahna Allie
- />School of Molecular and Cell Biology, University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein, Johannesburg, 2000 South Africa
| | - Erica J Pierce
- />School of Molecular and Cell Biology, University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein, Johannesburg, 2000 South Africa
| | - Michal J Okoniewski
- />Functional Genomics Center, Zurich, UNI ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Chrissie Rey
- />School of Molecular and Cell Biology, University of the Witwatersrand, 1 Jan Smuts Ave, Braamfontein, Johannesburg, 2000 South Africa
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19
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Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, Møller BL, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJCB, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, Jørgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, López-Lavalle LAB, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K, Peng M. Cassava genome from a wild ancestor to cultivated varieties. Nat Commun 2014; 5:5110. [PMID: 25300236 PMCID: PMC4214410 DOI: 10.1038/ncomms6110] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022] Open
Abstract
Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
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Affiliation(s)
- Wenquan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Binxiao Feng
- 1] Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China [2] Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Jingfa Xiao
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Zhiqiang Xia
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Xincheng Zhou
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Pinghua Li
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Weixiong Zhang
- 1] Department of Computer Science and Engineering and Department of Genetics, Washington University, Saint Louis, Missouri 63130, USA [2] Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Ying Wang
- South China Botanical Garden, CAS, Guangzhou 510650, China
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Peng Zhang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS, Shanghai 200032, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Gong Xiao
- South China Botanical Garden, CAS, Guangzhou 510650, China
| | - Jingxing Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Jun Yang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences of CAS, Shanghai 200032, China
| | - Songbi Chen
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Pablo D Rabinowicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Xin Chen
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Henan Ceballos
- International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Meiling Zou
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Luiz J C B Carvalho
- Brazilian Enterprise for Agricultural Research (EMBRAPA), Genetic Resources and Biotechnology, Brasilia 70770, Brazil
| | - Changying Zeng
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Jing Xia
- 1] Department of Computer Science and Engineering and Department of Genetics, Washington University, Saint Louis, Missouri 63130, USA [2] Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Shixiang Sun
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yuhua Fu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Haiyan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Cheng Lu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Mengbin Ruan
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China
| | - Zhicheng Wu
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China
| | - Hui Liu
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200433, China
| | - Rubini Maya Kannangara
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Kirsten Jørgensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Rebecca Louise Neale
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Maya Bonde
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Nanna Heinz
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Wenli Zhu
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Shujuan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Yang Zhang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Kun Pan
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Mingfu Wen
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Ping-An Ma
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Zhengxu Li
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Meizhen Hu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Wenbin Liao
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Wenbin Hu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Shengkui Zhang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Jinli Pei
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Anping Guo
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Jianchun Guo
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Jiaming Zhang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Zhengwen Zhang
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Jianqiu Ye
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Wenjun Ou
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Yaqin Ma
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Xinyue Liu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Kevin Galens
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Sandra Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jie Huang
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Jingjing Xue
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Feifei An
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Qingqun Yao
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Xiaojing Lu
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Martin Fregene
- International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | | | - Jiajie Wu
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Frank M You
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Meili Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Guojiang Wu
- South China Botanical Garden, CAS, Guangzhou 510650, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Peng Ling
- Citrus Research and Education Center (CREC), University of Florida, Gainesville, Florida 32611, USA
| | - Yeyuan Chen
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Qinghuang Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Guodao Liu
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Bin Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Biogeography and Bioresources in Arid Land, Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Urumqi 830011, China
| | - Kaimian Li
- Tropical Crop Genetic Resources Institute, CATAS, Danzhou 571700, China
| | - Ming Peng
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
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Ma JQ, Yao MZ, Ma CL, Wang XC, Jin JQ, Wang XM, Chen L. Construction of a SSR-based genetic map and identification of QTLs for catechins content in tea plant (Camellia sinensis). PLoS One 2014; 9:e93131. [PMID: 24676054 PMCID: PMC3968092 DOI: 10.1371/journal.pone.0093131] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/03/2014] [Indexed: 02/04/2023] Open
Abstract
Catechins are the most important bioactive compounds in tea, and have been demonstrated to possess a wide variety of pharmacological activities. To characterize quantitative trait loci (QTLs) for catechins content in the tender shoots of tea plant, we constructed a moderately saturated genetic map using 406 simple sequence repeat (SSR) markers, based on a pseudo-testcross population of 183 individuals derived from an intraspecific cross of two Camellia sinensis varieties with diverse catechins composition. The map consisted of fifteen linkage groups (LGs), corresponding to the haploid chromosome number of tea plant (2n = 2x = 30). The total map length was 1,143.5 cM, with an average locus spacing of 2.9 cM. A total of 25 QTLs associated with catechins content were identified over two measurement years. Of these, nine stable QTLs were validated across years, and clustered into four main chromosome regions on LG03, LG11, LG12 and LG15. The population variability explained by each QTL was predominantly at moderate-to-high levels and ranged from 2.4% to 71.0%, with an average of 17.7%. The total number of QTL for each trait varied from four to eight, while the total population variability explained by all QTLs for a trait ranged between 38.4% and 79.7%. This is the first report on the identification of QTL for catechins content in tea plant. The results of this study provide a foundation for further cloning and functional characterization of catechin QTLs for utilization in improvement of tea plant.
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Affiliation(s)
- Jian-Qiang Ma
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Ming-Zhe Yao
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Chun-Lei Ma
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Xin-Chao Wang
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Ji-Qiang Jin
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Xue-Min Wang
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
| | - Liang Chen
- Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, Zhejiang Province, China
- * E-mail:
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Sakurai T, Mochida K, Yoshida T, Akiyama K, Ishitani M, Seki M, Shinozaki K. Genome-wide discovery and information resource development of DNA polymorphisms in cassava. PLoS One 2013; 8:e74056. [PMID: 24040164 PMCID: PMC3770675 DOI: 10.1371/journal.pone.0074056] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/29/2013] [Indexed: 01/06/2023] Open
Abstract
Cassava (Manihot esculenta Crantz) is an important crop that provides food security and income generation in many tropical countries, and is known for its adaptability to various environmental conditions. Its draft genome sequence and many expressed sequence tags are now publicly available, allowing the development of cassava polymorphism information. Here, we describe the genome-wide discovery of cassava DNA polymorphisms. Using the alignment of predicted transcribed sequences from the cassava draft genome sequence and ESTs from GenBank, we discovered 10,546 single-nucleotide polymorphisms and 647 insertions and deletions. To facilitate molecular marker development for cassava, we designed 9,316 PCR primer pairs to amplify the genomic region around each DNA polymorphism. Of the discovered SNPs, 62.7% occurred in protein-coding regions. Disease-resistance genes were found to have a significantly higher ratio of nonsynonymous-to-synonymous substitutions. We identified 24 read-through (changes of a stop codon to a coding codon) and 38 premature stop (changes of a coding codon to a stop codon) single-nucleotide polymorphisms, and found that the 5 gene ontology terms in biological process were significantly different in genes with read-through single-nucleotide polymorphisms compared with all cassava genes. All data on the discovered DNA polymorphisms were organized into the Cassava Online Archive database, which is available at http://cassava.psc.riken.jp/.
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Affiliation(s)
- Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- RIKEN Biomass Engineering Program, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
| | - Takuhiro Yoshida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Kenji Akiyama
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Manabu Ishitani
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Kanagawa, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Kanagawa, Japan
- RIKEN Biomass Engineering Program, Tsurumi-ku, Yokohama, Kanagawa, Japan
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