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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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2
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Hohenfeld CS, de Oliveira SAS, Ferreira CF, Mello VH, Margarido GRA, Passos AR, de Oliveira EJ. Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance. Sci Rep 2024; 14:10587. [PMID: 38719851 PMCID: PMC11078935 DOI: 10.1038/s41598-024-60847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.
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Affiliation(s)
- Camila Santiago Hohenfeld
- Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N - 44036-900, Novo Horizonte, Feira de Santana, BA, Brazil
| | | | - Claudia Fortes Ferreira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, Cruz das Almas, BA, 44380-000, Brazil
| | - Victor Hugo Mello
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Adriana Rodrigues Passos
- Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N - 44036-900, Novo Horizonte, Feira de Santana, BA, Brazil
| | - Eder Jorge de Oliveira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, Cruz das Almas, BA, 44380-000, Brazil.
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3
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Mota APZ, Dossa K, Lechaudel M, Cornet D, Mournet P, Santoni S, Lopez D, Chaïr H. Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata. BMC Genomics 2024; 25:248. [PMID: 38443859 PMCID: PMC10916269 DOI: 10.1186/s12864-024-10135-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Quality traits are essential determinants of consumer preferences. Dioscorea alata (Greater Yam), is a starchy tuber crop in tropical regions. However, a comprehensive understanding of the genetic basis underlying yam tuber quality remains elusive. To address this knowledge gap, we employed population genomics and candidate gene association approaches to unravel the genetic factors influencing the quality attributes of boiled yam. METHODS AND RESULTS Comparative genomics analysis of 45 plant species revealed numerous novel genes absent in the existing D. alata gene annotation. This approach, adding 48% more genes, significantly enhanced the functional annotation of three crucial metabolic pathways associated with boiled yam quality traits: pentose and glucuronate interconversions, starch and sucrose metabolism, and flavonoid biosynthesis. In addition, the whole-genome sequencing of 127 genotypes identified 27 genes under selection and 22 genes linked to texture, starch content, and color through a candidate gene association analysis. Notably, five genes involved in starch content and cell wall composition, including 1,3-beta Glucan synthase, β-amylase, and Pectin methyl esterase, were common to both approaches and their expression levels were assessed by transcriptomic data. CONCLUSIONS The analysis of the whole-genome of 127 genotypes of D. alata and the study of three specific pathways allowed the identification of important genes for tuber quality. Our findings provide insights into the genetic basis of yam quality traits and will help the enhancement of yam tuber quality through breeding programs.
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Affiliation(s)
- Ana Paula Zotta Mota
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
- Université Côte d'Azur, Institut Sophia Agrobiotech, INRAE, CNRS, Sophia Antipolis, PACA, 06903, France
| | - Komivi Dossa
- UMR AGAP, CIRAD, 34398, Montpellier, France
- CIRAD, UMR AGAP Institut, 97170, Petit Bourg, Guadeloupe, France
| | - Mathieu Lechaudel
- UMR Qualisud, CIRAD, F97130, Capesterre-Belle-Eau, Guadeloupe, France
- QualiSud, Université Montpellier, Institut Agro, CIRAD, Avignon Université, Université de La Réunion, 34398, Montpellier, France
| | - Denis Cornet
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - Pierre Mournet
- UMR AGAP, CIRAD, 34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France
| | - David Lopez
- UMR AGAP, CIRAD, 34398, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France.
| | - Hana Chaïr
- UMR AGAP, CIRAD, 34398, Montpellier, France.
- AGAP, Univ Montpellier, CIRAD, INRAe, Montpellier SupAgro, Montpellier, France.
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Yang Y, Liu M, Huang Z. Genomic and Expression Analysis of Cassava ( Manihot esculenta Crantz) Chalcone Synthase Genes in Defense against Tetranychus cinnabarinus Infestation. Genes (Basel) 2024; 15:336. [PMID: 38540395 PMCID: PMC10970205 DOI: 10.3390/genes15030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
Cassava is susceptible to mites, especially Tetranychus cinnabarinus. Secondary metabolism products such as flavonoids play an important role as antimicrobial metabolites protecting plants against biotic stressors including fungal, pathogen, bacterial, and pest defense. The chalcone synthase (CHS) is the initial step of the phenylpropanoid pathway for producing flavonoids and is the gatekeeper of the pathway. Until recently, the CHS genes family has not been systematically studied in cassava. Thirty-nine CHS genes were identified from the cassava genome database. Based on phylogenetic and sequence composition analysis, these CHSs were divided into 3 subfamilies. Within the same subfamily, the gene structure and motif compositions of these CHS genes were found to be quite conserved. Duplication events, particularly segmental duplication of the cassava CHS genes, were identified as one of the main driving force of its expansion. Various cis-elements contained in the promoter might regulate the gene expression patterns of MeCHS. Protein-protein interaction (PPI) network analysis showed that MeCHS1 and MeCHS10 protein are more closely related to other family members. The expression of MeCHS genes in young leaves was higher than that in other tissues, and their expression varies even within the same tissue. Coincidentally, these CHS genes of most LAP subclasses were highly expressed in young leaves. The verified MeCHS genes showed consistent with the real-time reverse transcription quantitative PCR (RT-qPCR) and proteomic expression in protected and affected leaves respectively, indicating that these MeCHS genes play crucial roles in the response to T. cinnabarinus. This study is the first to comprehensively expatiate the information on MeCHS family members. These data will further enhance our understanding both the molecular mechanisms and the effects of CHS genes. In addition, the results will help to further clarify the effects on T. cinnabarinus and provide a theoretical basis for the potential functions of the specific CHS gene in resistance to mites and other biotic stress.
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Affiliation(s)
- Yanni Yang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China;
- College of Agronomy, Guangxi University, Nanning 530004, China
| | - Ming Liu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China;
| | - Zenghui Huang
- Nanning New Technology Entrepreneur Center, Nanning 530007, China;
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Solé-Gil A, López A, Ombrosi D, Urbez C, Brumós J, Agustí J. Identification of MeC3HDZ1/MeCNA as a potential regulator of cassava storage root development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111938. [PMID: 38072332 DOI: 10.1016/j.plantsci.2023.111938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023]
Abstract
The storage root (SR) of cassava is the main staple food in sub-Saharan Africa, where it feeds over 500 million people. However, little is known about the genetic and molecular regulation underlying its development. Unraveling such regulation would pave the way for biotechnology approaches aimed at enhancing cassava productivity. Anatomical studies indicate that SR development relies on the massive accumulation of xylem parenchyma, a cell-type derived from the vascular cambium. The C3HDZ family of transcription factors regulate cambial cells proliferation and xylem differentiation in Arabidopsis and other species. We thus aimed at identifying C3HDZ proteins in cassava and determining whether any of them shows preferential activity in the SR cambium and/or xylem. Using phylogeny and synteny studies, we identified eight C3HDZ proteins in cassava, namely MeCH3DZ1-8. We observed that MeC3HDZ1 is the MeC3HDZ gene displaying the highest expression in SR and that, within that organ, the gene also shows high expression in cambium and xylem. In-silico analyses revealed the existence of a number of potential C3HDZ targets displaying significant preferential expression in the SR. Subsequent Y1H analyses proved that MeC3HDZ1 can bind canonical C3HDZ binding sites, present in the promoters of these targets. Transactivation assays demonstrated that MeC3HDZ1 can regulate the expression of genes downstream of promoters harboring such binding sites, thereby demonstrating that MeC3HDZ1 has C3HDZ transcription factor activity. We conclude that MeC3HDZ1 may be a key factor for the regulation of storage root development in cassava, holding thus great promise for future biotechnology applications.
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Affiliation(s)
- Anna Solé-Gil
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de Valencia, Camino de Vera S/N, 46022 València, Spain
| | - Anselmo López
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de Valencia, Camino de Vera S/N, 46022 València, Spain
| | - Damiano Ombrosi
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de Valencia, Camino de Vera S/N, 46022 València, Spain
| | - Cristina Urbez
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de Valencia, Camino de Vera S/N, 46022 València, Spain
| | - Javier Brumós
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de Valencia, Camino de Vera S/N, 46022 València, Spain.
| | - Javier Agustí
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de Valencia, Camino de Vera S/N, 46022 València, Spain.
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6
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Yaqoob H, Tariq A, Bhat BA, Bhat KA, Nehvi IB, Raza A, Djalovic I, Prasad PVV, Mir RA. Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system. GM CROPS & FOOD 2023; 14:1-20. [PMID: 36606637 PMCID: PMC9828793 DOI: 10.1080/21645698.2022.2146952] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Domestication of orphan crops could be explored by editing their genomes. Genome editing has a lot of promise for enhancing agricultural output, and there is a lot of interest in furthering breeding in orphan crops, which are sometimes plagued with unwanted traits that resemble wild cousins. Consequently, applying model crop knowledge to orphan crops allows for the rapid generation of targeted allelic diversity and innovative breeding germplasm. We explain how plant breeders could employ genome editing as a novel platform to accelerate the domestication of semi-domesticated or wild plants, resulting in a more diversified base for future food and fodder supplies. This review emphasizes both the practicality of the strategy and the need to invest in research that advances our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help alleviate food scarcities in the challenge of future climate crises.
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Affiliation(s)
- Huwaida Yaqoob
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Arooj Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Kaisar Ahmad Bhat
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Jammu and Kashmir, India
| | - Iqra Bashir Nehvi
- Department of Clinical Biochemistry, SKIMS, Srinagar, Jammu and Kashmir, India
| | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China,Ali Raza College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - PV Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, Kansas, USA
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Jammu and Kashmir, India,CONTACT Rakeeb Ahmad MirDepartment of Biotechnology, School of Life Sciences, Central University of Kashmir, Jammu and Kashmir, India
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7
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Landi M, Shah T, Falquet L, Niazi A, Stavolone L, Bongcam-Rudloff E, Gisel A. Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta). Sci Data 2023; 10:887. [PMID: 38071206 PMCID: PMC10710486 DOI: 10.1038/s41597-023-02800-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions.
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Affiliation(s)
- Michael Landi
- Department of Animal Breeding and Genetics, Bioinformatics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
- International Institute of Tropical Agriculture, Nairobi, Kenya.
| | - Trushar Shah
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Adnan Niazi
- Department of Animal Breeding and Genetics, Bioinformatics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Livia Stavolone
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- Institute for Sustainable Plant Protection, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Bioinformatics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andreas Gisel
- International Institute of Tropical Agriculture, Ibadan, Nigeria.
- Institute for Biomedical Technologies, Consiglio Nazionale delle Ricerche, Bari, Italy.
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8
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Zheng L, Assane Hamidou A, Zhao X, Ouyang Z, Lin H, Li J, Zhang X, Luo K, Chen Y. Superoxide dismutase gene family in cassava revealed their involvement in environmental stress via genome-wide analysis. iScience 2023; 26:107801. [PMID: 37954140 PMCID: PMC10638475 DOI: 10.1016/j.isci.2023.107801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/29/2023] [Accepted: 08/29/2023] [Indexed: 11/14/2023] Open
Abstract
Superoxide dismutase (SOD) is a crucial metal-containing enzyme that plays a vital role in catalyzing the dismutation of superoxide anions, converting them into molecular oxygen and hydrogen peroxide, essential for enhancing plant stress tolerance. We identified 8 SOD genes (4 CSODs, 2 FSODs, and 2 MSODs) in cassava. Bioinformatics analyses provided insights into chromosomal location, phylogenetic relationships, gene structure, conserved motifs, and gene ontology annotations. MeSOD genes were classified into two groups through phylogenetic analysis, revealing evolutionary connections. Promoters of these genes harbored stress-related cis-elements. Duplication analysis indicated the functional significance of MeCSOD2/MeCSOD4 and MeMSOD1/MeMSOD2. Through qRT-PCR, MeCSOD2 responded to salt stress, MeMSOD2 to drought, and cassava bacterial blight. Silencing MeMSOD2 increased XpmCHN11 virulence, indicating MeMSOD2 is essential for cassava's defense against XpmCHN11 infection. These findings enhance our understanding of the SOD gene family's role in cassava and contribute to strategies for stress tolerance improvement.
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Affiliation(s)
- Linling Zheng
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Abdoulaye Assane Hamidou
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xuerui Zhao
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Zhiwei Ouyang
- HNU-ASU Joint International Tourism College, Hainan University, Haikou 570228, China
| | - Hongxin Lin
- Soil Fertilizer and Resources Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Junyi Li
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xiaofei Zhang
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Kai Luo
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
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9
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Selvakumar R, Jat GS, Manjunathagowda DC. Allele mining through TILLING and EcoTILLING approaches in vegetable crops. PLANTA 2023; 258:15. [PMID: 37311932 DOI: 10.1007/s00425-023-04176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023]
Abstract
MAIN CONCLUSION The present review illustrates a comprehensive overview of the allele mining for genetic improvement in vegetable crops, and allele exploration methods and their utilization in various applications related to pre-breeding of economically important traits in vegetable crops. Vegetable crops have numerous wild descendants, ancestors and terrestrial races that could be exploited to develop high-yielding and climate-resilient varieties resistant/tolerant to biotic and abiotic stresses. To further boost the genetic potential of economic traits, the available genomic tools must be targeted and re-opened for exploitation of novel alleles from genetic stocks by the discovery of beneficial alleles from wild relatives and their introgression to cultivated types. This capability would be useful for giving plant breeders direct access to critical alleles that confer higher production, improve bioactive compounds, increase water and nutrient productivity as well as biotic and abiotic stress resilience. Allele mining is a new sophisticated technique for dissecting naturally occurring allelic variants in candidate genes that influence important traits which could be used for genetic improvement of vegetable crops. Target-induced local lesions in genomes (TILLINGs) is a sensitive mutation detection avenue in functional genomics, particularly wherein genome sequence information is limited or not available. Population exposure to chemical mutagens and the absence of selectivity lead to TILLING and EcoTILLING. EcoTILLING may lead to natural induction of SNPs and InDels. It is anticipated that as TILLING is used for vegetable crops improvement in the near future, indirect benefits will become apparent. Therefore, in this review we have highlighted the up-to-date information on allele mining for genetic enhancement in vegetable crops and methods of allele exploration and their use in pre-breeding for improvement of economic traits.
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Affiliation(s)
- Raman Selvakumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
| | - Gograj Singh Jat
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India.
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Harenčár J, Vargas OM, Escalona M, Schemske DW, Kay KM. Genome assemblies and comparison of two Neotropical spiral gingers: Costus pulverulentus and C. lasius. J Hered 2023; 114:286-293. [PMID: 36928286 PMCID: PMC10212132 DOI: 10.1093/jhered/esad018] [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: 02/22/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The spiral gingers (Costus L.) are a pantropical genus of herbaceous perennial monocots; the Neotropical clade of Costus radiated rapidly in the past few million years into over 60 species. The Neotropical spiral gingers have a rich history of evolutionary and ecological research that can motivate and inform modern genetic investigations. Here, we present the first 2 chromosome-level genome assemblies in the genus, for C. pulverulentus and C. lasius, and briefly compare their synteny. We assembled the C. pulverulentus genome from a combination of short-read data, Chicago and Dovetail Hi-C chromatin-proximity sequencing, and alignment with a linkage map. We annotated the genome by mapping a C. pulverulentus transcriptome and querying mapped transcripts against a protein database. We assembled the C. lasius genome with Pacific Biosciences HiFi long reads and alignment to the C. pulverulentus genome. These 2 assemblies are the first published genomes for non-cultivated tropical plants. These genomes solidify the spiral gingers as a model system and will facilitate research on the poorly understood genetic basis of tropical plant diversification.
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Affiliation(s)
- Julia Harenčár
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Oscar M Vargas
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Douglas W Schemske
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Kathleen M Kay
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States
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Ezoe A, Iuchi S, Sakurai T, Aso Y, Tokunaga H, Vu AT, Utsumi Y, Takahashi S, Tanaka M, Ishida J, Ishitani M, Seki M. Fully sequencing the cassava full-length cDNA library reveals unannotated transcript structures and alternative splicing events in regions with a high density of single nucleotide variations, insertions-deletions, and heterozygous sequences. PLANT MOLECULAR BIOLOGY 2023; 112:33-45. [PMID: 37014509 DOI: 10.1007/s11103-023-01346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/27/2023] [Indexed: 05/09/2023]
Abstract
The primary transcript structure provides critical insights into protein diversity, transcriptional modification, and functions. Cassava transcript structures are highly diverse because of alternative splicing (AS) events and high heterozygosity. To precisely determine and characterize transcript structures, fully sequencing cloned transcripts is the most reliable method. However, cassava annotations were mainly determined according to fragmentation-based sequencing analyses (e.g., EST and short-read RNA-seq). In this study, we sequenced the cassava full-length cDNA library, which included rare transcripts. We obtained 8,628 non-redundant fully sequenced transcripts and detected 615 unannotated AS events and 421 unannotated loci. The different protein sequences resulting from the unannotated AS events tended to have diverse functional domains, implying that unannotated AS contributes to the truncation of functional domains. The unannotated loci tended to be derived from orphan genes, implying that the loci may be associated with cassava-specific traits. Unexpectedly, individual cassava transcripts were more likely to have multiple AS events than Arabidopsis transcripts, suggestive of the regulated interactions between cassava splicing-related complexes. We also observed that the unannotated loci and/or AS events were commonly in regions with abundant single nucleotide variations, insertions-deletions, and heterozygous sequences. These findings reflect the utility of completely sequenced FLcDNA clones for overcoming cassava-specific annotation-related problems to elucidate transcript structures. Our work provides researchers with transcript structural details that are useful for annotating highly diverse and unique transcripts and alternative splicing events.
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Affiliation(s)
- Akihiro Ezoe
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Satoshi Iuchi
- Experimental Plant Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Tetsuya Sakurai
- Multidisciplinary Science Cluster, Interdisciplinary Science Unit, Kochi University, Nankoku, Kochi, 783-8502, Japan
| | - Yukie Aso
- Experimental Plant Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hiroki Tokunaga
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, Okinawa, 907-0002, Japan
| | - Anh Thu Vu
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Satoshi Takahashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ishida
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Manabu Ishitani
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan.
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12
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Li R, Yuan S, Zhou Y, Wang S, Zhou Q, Ding Z, Wang Y, Yao Y, Liu J, Guo J. Comparative Transcriptome Profiling of Cassava Tuberous Roots in Response to Postharvest Physiological Deterioration. Int J Mol Sci 2022; 24:ijms24010246. [PMID: 36613690 PMCID: PMC9820078 DOI: 10.3390/ijms24010246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Cassava is one of the most versatile tuberous-root crops on Earth. However, the postharvest storage properties of cassava tuberous root mean that it is perishable through a process known as postharvest physiological deterioration (PPD), which seriously affects its starch quality. Therefore, a comprehensive understanding of the transcriptional regulatory activity of cassava against the PPD response is necessary in order to extract key molecular mechanisms related to PPD tolerance. In this study, we found that RYG1 tuberous roots showed delayed PPD compared to those of SC8. In addition, RYG1 roots maintained a more stable cell wall structure after storage than those of SC8. The transcriptome changes in tuberous roots were analyzed for both RYG1 and SC8 after 21 days of storage (SR and SS) compared to fresh (FR and FS) by the RNA-Seq method. The total number of differentially expressed genes (DEGs) in the various comparisons of these four samples ranged from 68 to 3847. Of these, a total of 2008 co-DEGs in SR vs. SS were shared by either SR vs. FR or SS vs. FS. GO and KEGG enrichment analysis revealed that upregulated co-DEGs in SR vs. SS were mainly enriched in photosynthesis, protein processing, hormone and cutin, suberine and wax biosynthesis. By contrast, the downregulated co-DEGs were mainly related to cell wall organization, starch and sucrose metabolism, galactose metabolism, phenylpropanoid biosynthesis, diterpenoid biosynthesis, cysteine and methionine metabolism and flavonoid biosynthesis. The protein-protein interaction (PPI) networks of the co-DEGs showed a complex interaction of genes in different pathways, and 16 hub genes were characterized to have a degree in excess of 15, among which eight genes were associated with photosynthesis. These results provide new information for the study of cassava resistance to PPD and lay a foundation for the further molecular breeding of storage-tolerant cassava varieties.
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Affiliation(s)
- Ruimei Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Shuai Yuan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yangjiao Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Shijia Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Qin Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Zhongping Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yajie Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yuan Yao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Jiao Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- Correspondence: (J.L.); (J.G.); Tel.: +86-898-6698-6031 (J.L.); +86-898-6696-2953 (J.G.)
| | - Jianchun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- Correspondence: (J.L.); (J.G.); Tel.: +86-898-6698-6031 (J.L.); +86-898-6696-2953 (J.G.)
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Amelework AB, Bairu MW, Marx R, Owoeye L, Laing M, Venter SL. On-Farm Multi-Environment Evaluation of Selected Cassava ( Manihot esculenta Crantz) Cultivars in South Africa. PLANTS (BASEL, SWITZERLAND) 2022; 11:3339. [PMID: 36501378 PMCID: PMC9740417 DOI: 10.3390/plants11233339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Cassava is an important starchy root crop grown globally in tropical and subtropical regions. The ability of cassava to withstand difficult growing conditions and long-term storability underground makes it a resilient crop, contributing to food and nutrient security. This study was conducted to evaluate the performance and adaptability of exotic cassava cultivars across different environments in South Africa and to recommend genotypes for cultivation. A total of 11 cassava cultivars were evaluated at six on-farm sites, using a randomized complete block design with three replications. There were highly significant (p < 0.001) variations between genotypes, environments, and their interaction for all yield and yield-related traits studied. This indicates the need to test the genotypes in multiple environments before effective selection and commercialization can be undertaken. MSAF2 and UKF4 showed the overall best performances for most of the traits, whilst UKF9 (49.5%) and P1/19 (48.5%) had the highest dry matter yield. UKF4 (102.7 t ha−1) had the highest yield and greatest root yield stability across environments. MSAF2 did not perform consistently across environments because it was highly susceptible to cassava mosaic disease (CMD). MSAF2 could be used as a donor parent to generate novel clones with large numbers of marketable roots, and high fresh root yields, if the other parent can provide effective resistance to CMD. Based on genotype and environmental mean, Mabuyeni (KwaZulu-Natal), Mandlakazi (Limpopo), and Shatale (Mpumalanga) were found to be better environments for cassava cultivation and testing. This study is a pioneer in cassava research using multiple environments in South Africa. It provides baseline information on the performance of currently available cassava clones, their adaptation to multiple sites, the identification of suitable test sites, and information on current genetic resources for a future breeding program.
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Affiliation(s)
- Assefa B. Amelework
- Agricultural Research Council, Vegetable, Industrial and Medicinal Plants, Private Bag X293, Pretoria 0001, South Africa
| | - Michael W. Bairu
- Agricultural Research Council, Vegetable, Industrial and Medicinal Plants, Private Bag X293, Pretoria 0001, South Africa
- Faculty of Natural & Agricultural Sciences, School of Agricultural Sciences, Food Security and Safety Niche Area, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Roelene Marx
- Agricultural Research Council, Vegetable, Industrial and Medicinal Plants, Private Bag X293, Pretoria 0001, South Africa
| | - Lawrence Owoeye
- Agricultural Research Council, Vegetable, Industrial and Medicinal Plants, Private Bag X293, Pretoria 0001, South Africa
| | - Mark Laing
- African Centre for Crop Improvement, School of Agriculture, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg 3209, South Africa
| | - Sonja L. Venter
- Agricultural Research Council, Vegetable, Industrial and Medicinal Plants, Private Bag X293, Pretoria 0001, South Africa
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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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15
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Ozimati AA, Esuma W, Manze F, Iragaba P, Kanaabi M, Ano CU, Egesi C, Kawuki RS. Utility of Ugandan genomic selection cassava breeding populations for prediction of cassava viral disease resistance and yield in West African clones. FRONTIERS IN PLANT SCIENCE 2022; 13:1018156. [PMID: 36507414 PMCID: PMC9728524 DOI: 10.3389/fpls.2022.1018156] [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: 08/12/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a staple crop for ~800 million people in sub-Saharan Africa. Its production and productivity are being heavily affected by the two viral diseases: cassava brown streak disease (CBSD) and cassava mosaic disease (CMD), impacting greatly on edible root yield. CBSD is currently endemic to central, eastern and southern Africa, if not contained could spread to West Africa the largest cassava producer and consumer in the continent. Genomic selection (GS) has been implemented in Ugandan cassava breeding for accelerated development of virus resistant and high yielding clones. This study leveraged available GS training data in Uganda for pre-emptive CBSD breeding in W. Africa alongside CMD and fresh root yield (FRW). First, we tracked genetic gain through the current three cycles of GS in Uganda. The mean genomic estimated breeding values (GEBVs), indicated general progress from initial cycle zero (C0) to cycle one (C1) and cycle two (C2) for CBSD traits and yield except for CMD. Secondly, we used foliar data of both CBSD and CMD, as well as harvest root necrosis and yield data to perform cross-validation predictions. Cross-validation prediction accuracies of five GS models were tested for each of the three GS cycles and West African (WA) germplasm as a test set. In all cases, cross-validation prediction accuracies were low to moderate, ranging from -0.16 to 0.68 for CBSD traits, -0.27 to 0.57 for CMD and -0.22 to 0.41 for fresh root weight (FRW). Overall, the highest prediction accuracies were recorded in C0 for all traits tested across models and the best performing model in cross-validation was G-BLUP. Lastly, we tested the predictive ability of the Ugandan training sets to predict CBSD in W. African clones. In general, the Ugandan training sets had low prediction accuracies for all traits across models in West African germplasm, varying from -0.18 to 0.1. Based on the findings of this study, the cassava breeding program in Uganda has made progress through application of GS for most target traits, but the utility of the training population for pre-emptive breeding in WA is limiting. In this case, efforts should be devoted to sharing Ugandan germplasm that possess resistance with the W. African breeding programs for hybridization to fully enable deployment of genomic selection as a pre-emptive CBSD breeding strategy in W. Africa.
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Affiliation(s)
- Alfred A. Ozimati
- National Crops Resources Research Institute, Kampala, Uganda
- Department of Plant Sciences, Microbiology and Biotechnology, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Williams Esuma
- National Crops Resources Research Institute, Kampala, Uganda
| | - Francis Manze
- National Crops Resources Research Institute, Kampala, Uganda
| | - Paula Iragaba
- National Crops Resources Research Institute, Kampala, Uganda
| | - Michael Kanaabi
- National Crops Resources Research Institute, Kampala, Uganda
| | - Chukwuka Ugochukwu Ano
- Plant Breeding and Genetics Section, College of Agricultare and Life Sciences, Cornell University, Ithaca NY, United States
| | - Chiedozie Egesi
- Plant Breeding and Genetics Section, College of Agricultare and Life Sciences, Cornell University, Ithaca NY, United States
- National Root Crops Research Institute, Umudike, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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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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17
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Bakare MA, Kayondo SI, Aghogho CI, Wolfe MD, Parkes EY, Kulakow P, Egesi C, Jannink JL, Rabbi IY. Parsimonious genotype by environment interaction covariance models for cassava ( Manihot esculenta). FRONTIERS IN PLANT SCIENCE 2022; 13:978248. [PMID: 36212387 PMCID: PMC9532941 DOI: 10.3389/fpls.2022.978248] [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: 06/25/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
The assessment of cassava clones across multiple environments is often carried out at the uniform yield trial, a late evaluation stage, before variety release. This is to assess the differential response of the varieties across the testing environments, a phenomenon referred to as genotype-by-environment interaction (GEI). This phenomenon is considered a critical challenge confronted by plant breeders in developing crop varieties. This study used the data from variety trials established as randomized complete block design (RCBD) in three replicates across 11 locations in different agro-ecological zones in Nigeria over four cropping seasons (2016-2017, 2017-2018, 2018-2019, and 2019-2020). We evaluated a total of 96 varieties, including five checks, across 48 trials. We exploited the intricate pattern of GEI by fitting variance-covariance structure models on fresh root yield. The goodness-of-fit statistics revealed that the factor analytic model of order 3 (FA3) is the most parsimonious model based on Akaike Information Criterion (AIC). The three-factor loadings from the FA3 model explained, on average across the 27 environments, 53.5% [FA (1)], 14.0% [FA (2)], and 11.5% [FA (3)] of the genetic effect, and altogether accounted for 79.0% of total genetic variability. The association of factor loadings with weather covariates using partial least squares regression (PLSR) revealed that minimum temperature, precipitation and relative humidity are weather conditions influencing the genotypic response across the testing environments in the southern region and maximum temperature, wind speed, and temperature range for those in the northern region of Nigeria. We conclude that the FA3 model identified the common latent factors to dissect and account for complex interaction in multi-environment field trials, and the PLSR is an effective approach for describing GEI variability in the context of multi-environment trials where external environmental covariables are included in modeling.
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Affiliation(s)
- Moshood A. Bakare
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Cynthia I. Aghogho
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - Marnin D. Wolfe
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- Department of Crop, Soil and Environmental Sciences, College of Agriculture, Auburn University, Auburn, AL, United States
| | | | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute (NRCRI), Umudike, Umuahia, Nigeria
| | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
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Wang Z, Cai Q, Xia H, Han B, Li M, Wang Y, Zhu M, Jiao C, Wang D, Zhu J, Yuan W, Zhu D, Xu C, Wang H, Zhou M, Zhang X, Shi J, Chen J. Genome-Wide Identification and Comparative Analysis of WOX Genes in Four Euphorbiaceae Species and Their Expression Patterns in Jatropha curcas. Front Genet 2022; 13:878554. [PMID: 35846114 PMCID: PMC9280045 DOI: 10.3389/fgene.2022.878554] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
The WUSCHEL-related homeobox (WOX) proteins are widely distributed in plants and play important regulatory roles in growth and development processes such as embryonic development and organ development. Here, series of bioinformatics methods were utilized to unravel the structural basis and genetic hierarchy of WOX genes, followed by regulation of the WOX genes in four Euphorbiaceae species. A genome-wide survey identified 59 WOX genes in Hevea brasiliensis (H. brasiliensis: 20 genes), Jatropha curcas (J. curcas: 10 genes), Manihot esculenta (M. esculenta: 18 genes), and Ricinus communis (R. communis: 11 genes). The phylogenetic analysis revealed that these WOX members could be clustered into three close proximal clades, such as namely ancient, intermediate and modern/WUS clades. In addition, gene structures and conserved motif analyses further validated that the WOX genes were conserved within each phylogenetic clade. These results suggested the relationships among WOX members in the four Euphorbiaceae species. We found that WOX genes in H. brasiliensis and M. esculenta exhibit close genetic relationship with J. curcas and R. communis. Additionally, the presence of various cis-acting regulatory elements in the promoter of J. curcas WOX genes (JcWOXs) reflected distinct functions. These speculations were further validated with the differential expression profiles of various JcWOXs in seeds, reflecting the importance of two JcWOX genes (JcWOX6 and JcWOX13) during plant growth and development. Our quantitative real-time PCR (qRT-PCR) analysis demonstrated that the JcWOX11 gene plays an indispensable role in regulating plant callus. Taken together, the present study reports the comprehensive characteristics and relationships of WOX genes in four Euphorbiaceae species, providing new insights into their characterization.
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Affiliation(s)
- Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Qianwen Cai
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Haimeng Xia
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Bingqing Han
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minhui Li
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Yue Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minhui Zhu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Chunyan Jiao
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Dandan Wang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Junjie Zhu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenya Yuan
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Di Zhu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Congcong Xu
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Hongyan Wang
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Minghui Zhou
- College of Life Sciences, Hefei Normal University, Hefei, China
| | - Xie Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jinhui Chen,
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19
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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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20
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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
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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21
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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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22
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High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids. Sci Rep 2022; 12:3346. [PMID: 35228611 PMCID: PMC8885740 DOI: 10.1038/s41598-022-07318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/11/2022] [Indexed: 11/26/2022] Open
Abstract
Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.
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23
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Alves-Pereira A, Zucchi MI, Clement CR, Viana JPG, Pinheiro JB, Veasey EA, de Souza AP. Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties. Sci Rep 2022; 12:1268. [PMID: 35075210 PMCID: PMC8786832 DOI: 10.1038/s41598-022-05160-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/05/2022] [Indexed: 11/09/2022] Open
Abstract
Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia Dos Agronegócios (APTA), Pólo Centro-Sul. Rodovia SP 127, km 30, Piracicaba, SP, 13400-970, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM, 69067-375, Brazil
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign (UIUC), AW-101 Turner Hall, 1102 South Goodwin Avenue, Urbana, IL, 61801-4798, USA
| | - José Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiróz", Universidade de São Paulo (ESALQ/USP), Av. Pádua Dias, 11, Piracicaba, SP, 13400-970, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil. .,Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Av. Cândido Rondon, 400, Cidade Universitária, CP: 6010, Campinas, SP, 13083-875, Brazil.
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24
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Jaramillo AM, Sierra S, Chavarriaga-Aguirre P, Castillo DK, Gkanogiannis A, López-Lavalle LAB, Arciniegas JP, Sun T, Li L, Welsch R, Boy E, Álvarez D. Characterization of cassava ORANGE proteins and their capability to increase provitamin A carotenoids accumulation. PLoS One 2022; 17:e0262412. [PMID: 34995328 PMCID: PMC8741059 DOI: 10.1371/journal.pone.0262412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 12/23/2021] [Indexed: 11/19/2022] Open
Abstract
Cassava (Manihot esculenta Crantz) biofortification with provitamin A carotenoids is an ongoing process that aims to alleviate vitamin A deficiency. The moderate content of provitamin A carotenoids achieved so far limits the contribution to providing adequate dietary vitamin A levels. Strategies to increase carotenoid content focused on genes from the carotenoids biosynthesis pathway. In recent years, special emphasis was given to ORANGE protein (OR), which promotes the accumulation of carotenoids and their stability in several plants. The aim of this work was to identify, characterize and investigate the role of OR in the biosynthesis and stabilization of carotenoids in cassava and its relationship with phytoene synthase (PSY), the rate-limiting enzyme of the carotenoids biosynthesis pathway. Gene and protein characterization of OR, expression levels, protein amounts and carotenoids levels were evaluated in roots of one white (60444) and two yellow cassava cultivars (GM5309-57 and GM3736-37). Four OR variants were found in yellow cassava roots. Although comparable expression was found for three variants, significantly higher OR protein amounts were observed in the yellow varieties. In contrast, cassava PSY1 expression was significantly higher in the yellow cultivars, but PSY protein amount did not vary. Furthermore, we evaluated whether expression of one of the variants, MeOR_X1, affected carotenoid accumulation in cassava Friable Embryogenic Callus (FEC). Overexpression of maize PSY1 alone resulted in carotenoids accumulation and induced crystal formation. Co-expression with MeOR_X1 led to greatly increase of carotenoids although PSY1 expression was high in the co-expressed FEC. Our data suggest that posttranslational mechanisms controlling OR and PSY protein stability contribute to higher carotenoid levels in yellow cassava. Moreover, we showed that cassava FEC can be used to study the efficiency of single and combinatorial gene expression in increasing the carotenoid content prior to its application for the generation of biofortified cassava with enhanced carotenoids levels.
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Affiliation(s)
- Angélica M. Jaramillo
- HarvestPlus, c/o The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Santiago Sierra
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Paul Chavarriaga-Aguirre
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Diana Katherine Castillo
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Anestis Gkanogiannis
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Juan Pablo Arciniegas
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, New York, United States of America
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, New York, United States of America
| | - Ralf Welsch
- Faculty of Biology II, University of Freiburg, Freiburg, Germany
| | - Erick Boy
- HarvestPlus, International Food Policy Research Institute, Washington, DC, United States of America
| | - Daniel Álvarez
- HarvestPlus, c/o The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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25
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Tello-Ruiz MK, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol 2022; 2443:101-131. [PMID: 35037202 DOI: 10.1007/978-1-0716-2067-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end-users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.
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Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, USA.
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26
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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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Torres LG, de Oliveira EJ, Ogbonna AC, Bauchet GJ, Mueller LA, Azevedo CF, Fonseca e Silva F, Simiqueli GF, de Resende MDV. Can Cross-Country Genomic Predictions Be a Reasonable Strategy to Support Germplasm Exchange? - A Case Study With Hydrogen Cyanide in Cassava. FRONTIERS IN PLANT SCIENCE 2021; 12:742638. [PMID: 34956254 PMCID: PMC8692580 DOI: 10.3389/fpls.2021.742638] [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: 07/16/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Genomic prediction (GP) offers great opportunities for accelerated genetic gains by optimizing the breeding pipeline. One of the key factors to be considered is how the training populations (TP) are composed in terms of genetic improvement, kinship/origin, and their impacts on GP. Hydrogen cyanide content (HCN) is a determinant trait to guide cassava's products usage and processing. This work aimed to achieve the following objectives: (i) evaluate the feasibility of using cross-country (CC) GP between germplasm's of Embrapa Mandioca e Fruticultura (Embrapa, Brazil) and The International Institute of Tropical Agriculture (IITA, Nigeria) for HCN; (ii) provide an assessment of population structure for the joint dataset; (iii) estimate the genetic parameters based on single nucleotide polymorphisms (SNPs) and a haplotype-approach. Datasets of HCN from Embrapa and IITA breeding programs were analyzed, separately and jointly, with 1,230, 590, and 1,820 clones, respectively. After quality control, ∼14K SNPs were used for GP. The genomic estimated breeding values (GEBVs) were predicted based on SNP effects from analyses with TP composed of the following: (i) Embrapa genotypic and phenotypic data, (ii) IITA genotypic and phenotypic data, and (iii) the joint datasets. Comparisons on GEBVs' estimation were made considering the hypothetical situation of not having the phenotypic characterization for a set of clones for a certain research institute/country and might need to use the markers' effects that were trained with data from other research institutes/country's germplasm to estimate their clones' GEBV. Fixation index (FST) among the genetic groups identified within the joint dataset ranged from 0.002 to 0.091. The joint dataset provided an improved accuracy (0.8-0.85) compared to the prediction accuracy of either germplasm's sources individually (0.51-0.67). CC GP proved to have potential use under the present study's scenario, the correlation between GEBVs predicted with TP from Embrapa and IITA was 0.55 for Embrapa's germplasm, whereas for IITA's it was 0.1. This seems to be among the first attempts to evaluate the CC GP in plants. As such, a lot of useful new information was provided on the subject, which can guide new research on this very important and emerging field.
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Affiliation(s)
- Lívia Gomes Torres
- Department of Plant Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Alex C. Ogbonna
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- Boyce Thompson Institute, Ithaca, NY, United States
| | | | - Lukas A. Mueller
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- Boyce Thompson Institute, Ithaca, NY, United States
| | | | | | | | - Marcos Deon Vilela de Resende
- Department of Forestry Engineering, Universidade Federal de Viçosa, Viçosa, Brazil
- Embrapa Café, Universidade Federal de Viçosa, Viçosa, Brazil
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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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Joo KA, Muszynski MG, Kantar MB, Wang ML, He X, Del Valle Echevarria AR. Utilizing CRISPR-Cas in Tropical Crop Improvement: A Decision Process for Fitting Genome Engineering to Your Species. Front Genet 2021; 12:786140. [PMID: 34868276 PMCID: PMC8633396 DOI: 10.3389/fgene.2021.786140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.
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Affiliation(s)
- Kathleen A Joo
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael G Muszynski
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael B Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Waipahu, HI, United States
| | - Xiaoling He
- Hawaii Agriculture Research Center, Waipahu, HI, United States
| | - Angel R Del Valle Echevarria
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States.,Hawaii Agriculture Research Center, Waipahu, HI, United States
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Mansfeld BN, Boyher A, Berry JC, Wilson M, Ou S, Polydore S, Michael TP, Fahlgren N, Bart RS. Large structural variations in the haplotype-resolved African cassava genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1830-1848. [PMID: 34661327 PMCID: PMC9299708 DOI: 10.1111/tpj.15543] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 05/12/2023]
Abstract
Cassava (Manihot esculenta Crantz, 2n = 36) is a global food security crop. It has a highly heterozygous genome, high genetic load, and genotype-dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi-C to resolve each haplotype of the genome of a farmer-preferred cassava line, TME7 (Oko-iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON-Phase and Hi-C read data. The ultralong-range information from Hi-C sequencing was also used for scaffolding. Comparison of the two phases revealed >5000 large haplotype-specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele-specific expression was further explored. RNA-sequencing data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy-to-use web-based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype-specific structural variation, gene hemizygosity, and allele-specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava.
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Affiliation(s)
| | - Adam Boyher
- Donald Danforth Plant Science CenterSt. LouisMO63132USA
| | | | - Mark Wilson
- Donald Danforth Plant Science CenterSt. LouisMO63132USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Seth Polydore
- Donald Danforth Plant Science CenterSt. LouisMO63132USA
| | - Todd P. Michael
- The Molecular and Cellular Biology LaboratoryThe Salk Institute for Biological StudiesLa JollaCA92037USA
| | - Noah Fahlgren
- Donald Danforth Plant Science CenterSt. LouisMO63132USA
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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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32
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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: 2] [Impact Index Per Article: 0.7] [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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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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34
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Amelework AB, Bairu MW, Maema O, Venter SL, Laing M. Adoption and Promotion of Resilient Crops for Climate Risk Mitigation and Import Substitution: A Case Analysis of Cassava for South African Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.617783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cassava is an important starchy root crop grown globally in tropical and subtropical regions. The ability of cassava to withstand difficult growing conditions and long-term storability underground makes it a resilient crop, contributing to food security. Historically, small-scale farmers have grown cassava as a minor crop in the far north-eastern part of the country. However, there is an initiative to scale up cassava production, with two discrete areas of interest: large-scale production for industrial starch, and expanding its footprint as a food security crop for small-scale farmers, especially in the context of climate change. In this scoping study, production, processing and marketing data for cassava were accessed from the FAO and US Commercial trade databases. Other domestic market and demand analysis case studies were also explored. There is no cassava data available for South Africa. The study indicated that South Africa imports more than 66,000 tons of starch annually, of which 33% is cassava starch, showing the availability of a local market. The potential of cassava for the South African economy is discussed. Significant industrial opportunities exist for the production and use of cassava in South Africa. However, the realization of these opportunities will depend on the reliable supply of good quality cassava roots. However, the lack of a well-established cassava research program, and a lack of an existing value chain for the industrial scale cassava production and processing are barriers to the development of cassava industry in South Africa. As the initial step to the development of a successful cassava industry, high potential germplasm is imported, characterized and bred for local conditions to ensure the sustainable primary production of cassava. Subsequently, industrial value chains will need to be developed as the optimization of the breeding and agronomy of the crop are completed, and yield potentials are quantified in the different regions of the country.
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Bester R, Cook G, Maree HJ. Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing. Viruses 2021; 13:168. [PMID: 33498597 PMCID: PMC7910887 DOI: 10.3390/v13020168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.
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Affiliation(s)
- Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa;
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Citrus Research International, Stellenbosch, P.O. Box 2201, Matieland 7602, South Africa
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36
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Chatukuta P, Rey MEC. A cassava protoplast system for screening genes associated with the response to South African cassava mosaic virus. Virol J 2020; 17:184. [PMID: 33228712 PMCID: PMC7685591 DOI: 10.1186/s12985-020-01453-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
Background The study of transient gene expression in cassava plants during virus infection using existing protocols is laborious and may take approximately fifteen weeks due to cassava’s recalcitrance to transformation. The combination of a protoplast system with CRISPR-mediated gene editing promises to shorten the turnaround time from plant tissue culture to high-throughput gene expression screening for candidate genes. Here, we detail a protocol for screening genes associated with the response to South African cassava mosaic virus (SACMV) in cassava protoplasts, with reference to the ubiquitin E3 ligase gene, MeE3L.
Methods Cassava protoplasts of model, and SACMV-susceptible and -tolerant genotypes, were transformed with SACMV infectious clones and/or a CRISPR-editing construct targeting the MeE3L using PEG4000-mediated transfection. DNA and RNA were extracted from transformed protoplasts at 24 h post-transfection. Relative SACMV DNA accumulation was determined via qPCR using DpnI-digested total DNA, MeE3L relative expression was determined via reverse transcriptase qPCR, and results were analysed using one-way ANOVA, Tukey’s HSD test and the 2−ΔΔCTstatistical method. The MeE3L exonic region was sequenced on the ABI 3500XL Genetic Analyzer platform; and sequences were analysed for mutations using MAFTT and MEGA-X software. Construction of a phylogenetic tree was done using the Maximum Likelihood method and Jones-Taylor-Thornton (JTT) matrix-based model. Results The differential expression of unedited and mutant MeE3L during SACMV infection of model, susceptible and tolerant cassava protoplasts was determined within 7 weeks after commencement of tissue culture. The study also revealed that SACMV DNA accumulation in cassava protoplasts is genotype-dependent and induces multiple mutations in the tolerant landrace MeE3L homolog. Notably, the susceptible cassava landrace encodes a RINGless MeE3Lwhich is silenced by SACMV-induced mutations. SACMV also induces mutations which silence the MeE3L RING domain in protoplasts from and tolerant cassava landraces. Conclusions This protocol presented here halves the turnaround time for high-throughput screening of genes associated with the host response to SACMV. It provides evidence that a cassava E3 ligase is associated with the response to SACMV and forms a basis for validation of these findings by in planta functional and interaction studies.
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Affiliation(s)
- Patience Chatukuta
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Marie Emma Christine Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
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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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Zhou W, Zhao S, He S, Ma Q, Lu X, Hao X, Wang H, Yang J, Zhang P. Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:832-846. [PMID: 31180179 DOI: 10.1111/jipb.12848] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/30/2019] [Indexed: 06/09/2023]
Abstract
High amylose starch can be produced by plants deficient in the function of branching enzymes (BEs). Here we report the production of transgenic cassava (Manihot esculenta Crantz) with starches containing up to 50% amylose due to the constitutive expression of hair-pin dsRNAs targeting the BE1 or BE2 genes. All BE1-RNAi plant lines (BE1i) and BE2-RNAi plant lines (BE2i) were grown up in the field, but with reduced total biomass production. Considerably high amylose content in the storage roots of BE2i plant lines was achieved. Storage starch granules of BE1i and BE2i plants had similar morphology as wild type (WT), however, the size of BE1i starch granules were bigger than that of WT. Comparisons of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i starches. Glucan chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i lines. Furthermore, BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT starches. Therefore, cassava BE1 and BE2 function differently in storage root starch biosynthesis.
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Affiliation(s)
- Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shanshan Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Shutao He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaomeng Hao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongxia Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Chen JD, Zheng C, Ma JQ, Jiang CK, Ercisli S, Yao MZ, Chen L. The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant. HORTICULTURE RESEARCH 2020; 7:63. [PMID: 32377354 PMCID: PMC7192901 DOI: 10.1038/s41438-020-0288-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/02/2020] [Accepted: 03/08/2020] [Indexed: 05/07/2023]
Abstract
Tea is one of the most popular nonalcoholic beverages due to its characteristic secondary metabolites with numerous health benefits. Although two draft genomes of tea plant (Camellia sinensis) have been published recently, the lack of chromosome-scale assembly hampers the understanding of the fundamental genomic architecture of tea plant and potential improvement. Here, we performed a genome-wide chromosome conformation capture technique (Hi-C) to obtain a chromosome-scale assembly based on the draft genome of C. sinensis var. sinensis and successfully ordered 2984.7 Mb (94.7%) scaffolds into 15 chromosomes. The scaffold N50 of the improved genome was 218.1 Mb, ~157-fold higher than that of the draft genome. Collinearity comparison of genome sequences and two genetic maps validated the high contiguity and accuracy of the chromosome-scale assembly. We clarified that only one Camellia recent tetraploidization event (CRT, 58.9-61.7 million years ago (Mya)) occurred after the core-eudicot common hexaploidization event (146.6-152.7 Mya). Meanwhile, 9243 genes (28.6%) occurred in tandem duplication, and most of these expanded after the CRT event. These gene duplicates increased functionally divergent genes that play important roles in tea-specific biosynthesis or stress response. Sixty-four catechin- and caffeine-related quantitative trait loci (QTLs) were anchored to chromosome assembly. Of these, two catechin-related QTL hotspots were derived from the CRT event, which illustrated that polyploidy has played a dramatic role in the diversification of tea germplasms. The availability of a chromosome-scale genome of tea plant holds great promise for the understanding of genome evolution and the discovery of novel genes contributing to agronomically beneficial traits in future breeding programs.
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Affiliation(s)
- Jie-Dan Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Chao Zheng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Chen-Kai Jiang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Ming-Zhe Yao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Science, Hangzhou, 310008 China
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Malik AI, Kongsil P, Nguyễn VA, Ou W, Sholihin, Srean P, Sheela MN, Becerra López-Lavalle LA, Utsumi Y, Lu C, Kittipadakul P, Nguyễn HH, Ceballos H, Nguyễn TH, Selvaraj Gomez M, Aiemnaka P, Labarta R, Chen S, Amawan S, Sok S, Youabee L, Seki M, Tokunaga H, Wang W, Li K, Nguyễn HA, Nguyễn VĐ, Hàm LH, Ishitani M. Cassava breeding and agronomy in Asia: 50 years of history and future directions. BREEDING SCIENCE 2020; 70:145-166. [PMID: 32523397 PMCID: PMC7272245 DOI: 10.1270/jsbbs.18180] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 09/29/2019] [Indexed: 09/29/2023]
Abstract
In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha-1 in 1996 to 21.3 t ha-1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.
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Affiliation(s)
- Al Imran Malik
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Pasajee Kongsil
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Vũ Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Wenjun Ou
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Sholihin
- Indonesian Legume and Tuber Crops Research Institute, Kendalpayak Km 8, PO BOX 66, Malang 65101, Indonesia
| | - Pao Srean
- Faculty of Agriculture & Food Processing, University of Battambang, Battambang, Cambodia
| | - MN Sheela
- Central Tuber Crops Research Institute Sreekariyam, Thiruvananthapuram-605 017, Kerala, India
| | | | - Yoshinori Utsumi
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Cheng Lu
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Piya Kittipadakul
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Hữu Hỷ Nguyễn
- Hung Loc Agricultural Research Center, Institute for Agriculture in Southern Vietnam, 121 Nguyen Binh Khiem, District 1, HCM City, Vietnam
| | - Hernan Ceballos
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Trọng Hiển Nguyễn
- Root and Tuber Crop Research and Development Center, Food and Field Crop Research Institute, Vinh Quynh, Thanh Tri, Hanoi, Vietnam
| | - Michael Selvaraj Gomez
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Pornsak Aiemnaka
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, 50 Ngam Wong Wan Rd, Chatuchak Bangkok 10900, Thailand
| | - Ricardo Labarta
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
| | - Songbi Chen
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Suwaluk Amawan
- Rayong Field Crops Research Center, Sukumvit Rd, Huaypong, Meang, Rayong 21150, Thailand
| | - Sophearith Sok
- International Center for Tropical Agriculture (CIAT-Asia), Phnom Penh, Cambodia
| | - Laothao Youabee
- International Center for Tropical Agriculture (CIAT-Laos), Lao PDR Office, Dong Dok, Ban Nongviengkham, Vientiane, Lao PDR
| | - Motoaki Seki
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Tokunaga
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Wenquan Wang
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Kaimian Li
- Chinese Academy of Tropical Agricultural Sciences (CATAS), 571737, Hainan Province, the People’s Republic of China
| | - Hai Anh Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Văn Đồng Nguyễn
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Lê Huy Hàm
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
| | - Manabu Ishitani
- International Laboratory for Cassava Molecular Breeding, National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Pham Van Dong Rd, Bac Tu Liem District, Hanoi, Vietnam
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira Apartado Aéreo 6713, Cali, Colombia
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Alves‐Pereira A, Clement CR, Picanço‐Rodrigues D, Veasey EA, Dequigiovanni G, Ramos SLF, Pinheiro JB, de Souza AP, Zucchi MI. A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. Evol Appl 2020; 13:342-361. [PMID: 31993081 PMCID: PMC6976959 DOI: 10.1111/eva.12873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/14/2019] [Indexed: 12/19/2022] Open
Abstract
Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.
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Affiliation(s)
- Alessandro Alves‐Pereira
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
| | | | | | - Elizabeth Ann Veasey
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Gabriel Dequigiovanni
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Santiago Linorio Ferreyra Ramos
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - José Baldin Pinheiro
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Anete Pereira de Souza
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
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Li J, Gao X, Sang S, Liu C. Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae. BMC Genomics 2019; 20:912. [PMID: 31874634 PMCID: PMC6929338 DOI: 10.1186/s12864-019-6319-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/21/2019] [Indexed: 01/19/2023] Open
Abstract
Background Euphorbiaceae is one of the largest families of flowering plants. Due to its exceptional growth form diversity and near-cosmopolitan distribution, it has attracted much interest since ancient times. SBP-box (SBP) genes encode plant-specific transcription factors that play critical roles in numerous biological processes, especially flower development. We performed genome-wide identification and characterization of SBP genes from four economically important Euphorbiaceae species. Results In total, 77 SBP genes were identified in four Euphorbiaceae genomes. The SBP proteins were divided into three length ranges and 10 groups. Group-6 was absent in Arabidopsis thaliana but conserved in Euphorbiaceae. Segmental duplication played the most important role in the expansion processes of Euphorbiaceae SBP genes, and all the duplicated genes were subjected to purify selection. In addition, about two-thirds of the Euphorbiaceae SBP genes are potential targets of miR156, and some miR-regulated SBP genes exhibited high intensity expression and differential expression in different tissues. The expression profiles related to different stress treatments demonstrated broad involvement of Euphorbiaceae SBP genes in response to various abiotic factors and hormonal treatments. Conclusions In this study, 77 SBP genes were identified in four Euphorbiaceae species, and their phylogenetic relationships, protein physicochemical characteristics, duplication, tissue and stress response expression, and potential roles in Euphorbiaceae development were studied. This study lays a foundation for further studies of Euphorbiaceae SBP genes, providing valuable information for future functional exploration of Euphorbiaceae SBP genes.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyang Gao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shiye Sang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China. .,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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Wolfe MD, Bauchet GJ, Chan AW, Lozano R, Ramu P, Egesi C, Kawuki R, Kulakow P, Rabbi I, Jannink JL. Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection. Genetics 2019; 213:1237-1253. [PMID: 31624088 PMCID: PMC6893375 DOI: 10.1534/genetics.119.302757] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Introgression of alleles from wild relatives has often been adaptive in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally propagated root and tuber crops in the developing world, and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed Manihot glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of a 1930s era breeding to combat disease epidemics. African landraces and improved varieties were, on average, 3.8% (max 13.6%) introgressed. Introgressions accounted for a significant (mean 20%, max 56%) portion of the heritability of tested traits. M. glaziovii alleles on the distal 10 Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressions in a 20 Mb region improved harvest index and brown streak disease tolerance. We observed the introgression frequency on chr. 1 double over three cycles of selection, and that later stage trials selectively excluded homozygotes from consideration as varieties. This indicates a heterozygous advantage of introgressions. However, we also found that maintaining large recombination-suppressed introgressions in the heterozygous state allowed the accumulation of deleterious mutations. We conclude that targeted recombination of introgressions would increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.
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Affiliation(s)
- Marnin D Wolfe
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | | | - Ariel W Chan
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | - Roberto Lozano
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | - Punna Ramu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850
| | - Chiedozie Egesi
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14850
- National Root Crops Research Institute (NRCRI), Umudike, Umuahia, 440221, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Robert Kawuki
- National Root Crops Resources Research Institute, Namulonge, Uganda
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
- United States Department of Agriculture - Agriculture Research Service, Ithaca, New York 14850
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Vilperte V, Lucaciu CR, Halbwirth H, Boehm R, Rattei T, Debener T. Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts. BMC Genomics 2019; 20:900. [PMID: 31775622 PMCID: PMC6882326 DOI: 10.1186/s12864-019-6247-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/30/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Poinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of knowledge about the genetics and molecular biology of poinsettia, especially on the mechanisms of color formation. We performed an RNA-Seq analysis in order to shed light on the transcriptome of poinsettia bracts. Moreover, we analyzed the transcriptome differences of red- and white-bracted poinsettia varieties during bract development and coloration. For the assembly of a bract transcriptome, two paired-end cDNA libraries from a red and white poinsettia pair were sequenced with the Illumina technology, and one library from a red-bracted variety was used for PacBio sequencing. Both short and long reads were assembled using a hybrid de novo strategy. Samples of red- and white-bracted poinsettias were sequenced and comparatively analyzed in three color developmental stages in order to understand the mechanisms of color formation and accumulation in the species. RESULTS The final transcriptome contains 288,524 contigs, with 33% showing confident protein annotation against the TAIR10 database. The BUSCO pipeline, which is based on near-universal orthologous gene groups, was applied to assess the transcriptome completeness. From a total of 1440 BUSCO groups searched, 77% were categorized as complete (41% as single-copy and 36% as duplicated), 10% as fragmented and 13% as missing BUSCOs. The gene expression comparison between red and white varieties of poinsettia showed a differential regulation of the flavonoid biosynthesis pathway only at particular stages of bract development. An initial impairment of the flavonoid pathway early in the color accumulation process for the white poinsettia variety was observed, but these differences were no longer present in the subsequent stages of bract development. Nonetheless, GSTF11 and UGT79B10 showed a lower expression in the last stage of bract development for the white variety and, therefore, are potential candidates for further studies on poinsettia coloration. CONCLUSIONS In summary, this transcriptome analysis provides a valuable foundation for further studies on poinsettia, such as plant breeding and genetics, and highlights crucial information on the molecular mechanism of color formation.
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Affiliation(s)
- Vinicius Vilperte
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.,Klemm + Sohn GmbH & Co., 70379, Stuttgart, KG, Germany
| | - Calin Rares Lucaciu
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria
| | - Heidi Halbwirth
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, 1060, Vienna, Austria
| | - Robert Boehm
- Klemm + Sohn GmbH & Co., 70379, Stuttgart, KG, Germany
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria.
| | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.
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Chen Q, Liang X, Wu C, Gao J, Chen Q, Zhang Z. Density threshold-based acaricide application for the two-spotted spider mite Tetranychus urticae on cassava: from laboratory to the field. PEST MANAGEMENT SCIENCE 2019; 75:2634-2641. [PMID: 30706630 DOI: 10.1002/ps.5366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUD The red spider mite Tetranychus urticae is known as a worldwide pest in cassava production which can caused serious economic losses. Because no threshold levels are established for T. urticae in cassava cropping, many growers in China are applying excessive chemical applications per cassava cropping period. This is not only expensive, but also results in lower yields because of severe leaf damage and development of resistance. This study aims to develop an immediate threshold level for T. urticae control which could be determined in the laboratory and fit the field application requirements. RESULTS The mite density of 25 mites/leaf was the threshold which caused significant decrease of photosynthetic pigment contents and protective enzyme activities in cassava leaves in the laboratory. Moreover, 25 mites/leaf was also the threshold density which resulted in significantly lower leaf damage and higher yield levels compared with a higher level of mites/leaf where calendar sprays were used. CONCLUSION The mite density threshold that brought about significant physiological and biochemical changes in the laboratory basically coincided with the threshold that resulted in significant yield loss in the field. It is therefore concluded that the optimum threshold acaricide spray for T. urticae on cassava is 25 mites/leaf. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Qing Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Haikou, Hainan, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Hainan Engineering Research Center for Biological Control of Tropical Crops Diseases and Insect Pests, Haikou, Hainan, China
| | - Xiao Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Haikou, Hainan, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Hainan Engineering Research Center for Biological Control of Tropical Crops Diseases and Insect Pests, Haikou, Hainan, China
| | - Chunling Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Haikou, Hainan, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Hainan Engineering Research Center for Biological Control of Tropical Crops Diseases and Insect Pests, Haikou, Hainan, China
| | - Jintao Gao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Haikou, Hainan, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Hainan Engineering Research Center for Biological Control of Tropical Crops Diseases and Insect Pests, Haikou, Hainan, China
| | - Qian Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Haikou, Hainan, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Hainan Engineering Research Center for Biological Control of Tropical Crops Diseases and Insect Pests, Haikou, Hainan, China
| | - Zhe Zhang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Haikou, Hainan, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Hainan Engineering Research Center for Biological Control of Tropical Crops Diseases and Insect Pests, Haikou, Hainan, China
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Maniglia BC, Lima DC, Matta Junior MD, Le-Bail P, Le-Bail A, Augusto PE. Hydrogels based on ozonated cassava starch: Effect of ozone processing and gelatinization conditions on enhancing 3D-printing applications. Int J Biol Macromol 2019; 138:1087-1097. [DOI: 10.1016/j.ijbiomac.2019.07.124] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/20/2019] [Accepted: 07/20/2019] [Indexed: 01/27/2023]
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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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48
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Genomic selection for productive traits in biparental cassava breeding populations. PLoS One 2019; 14:e0220245. [PMID: 31344109 PMCID: PMC6658084 DOI: 10.1371/journal.pone.0220245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/11/2019] [Indexed: 11/19/2022] Open
Abstract
Cassava improvement using traditional breeding strategies is slow due to the species’ long breeding cycle. However, the use of genomic selection can lead to a shorter breeding cycle. This study aimed to estimate genetic parameters for productive traits based on pedigree (pedigree and phenotypic information) and genomic (markers and phenotypic information) analyses using biparental crosses at different stages of selection. A total of 290 clones were genotyped and phenotyped for fresh root yield (FRY), dry matter content (DMC), dry yield (DY), fresh shoot yield (FSY) and harvest index (HI). The clones were evaluated in clonal evaluation trials (CET), preliminary yield trials (PYT), advanced yield trials (AYT) and uniform yield trials (UYT), from 2013 to 2018 in ten locations. The breeding stages were analyzed as follows: one stage (CET), two stages (CET and PYT), three stages (CET, PYT and AYT) and four stages (CET, PYT, AYT and UYT). The genomic predictions were analyzed via k-fold cross-validation based on the genomic best linear unbiased prediction (GBLUP) considering a model with genetic additive effects and genotype × location interactions. Genomic and pedigree accuracies were moderate to high (0.56–0.72 and 0.62–0.78, respectively) for important starch-related traits such as DY and FRY; when considering one breeding stage (CET) with the aim of early selection, the genomic accuracies ranged from 0.60 (DMC) to 0.71 (HI). Moreover, the correlations between the genomic estimation breeding values of one-stage genomic analysis and the estimated breeding values of the four-stage (full data set) pedigree analysis were high for all traits as well as for a selection index including all traits. The results indicate great possibilities for genomic selection in cassava, especially for selection early in the breeding cycle (saving time and effort).
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Ramos Abril LN, Pineda LM, Wasek I, Wedzony M, Ceballos H. Reproductive biology in cassava: stigma receptivity and pollen tube growth. Commun Integr Biol 2019; 12:96-111. [PMID: 31308874 PMCID: PMC6615524 DOI: 10.1080/19420889.2019.1631110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 11/18/2022] Open
Abstract
Knowledge on the reproductive biology of cassava, relevant to breeders and molecular geneticists, is still limited. Therefore, different studies were carried out to determine the duration of stigma receptivity and the rate of pollen tube growth. Inflorescences were covered for up to 3 days after the first opening of the bracts (e.g. anthesis day) to prevent open pollination. Results indicate that fruit and seed set are drastically reduced when flowers were covered for 2 or 3 days. However, fruits and seeds were obtained even from flowers that had been covered for 3 days after anthesis, although at low frequency. The rate of pollen tube growth was assessed in many combinations of female and male progenitors crossed through controlled pollinations and collecting the pistils at varying hours after pollination (HAP). Pollen tube growth is fast during the first 6 HAP reaching the tip of the nucellar beak. The growth slows down thereafter, taking 10 additional hours to reach the end of the beak. The growth of pollen tubes slows down even further until they enter the embryo sac. Only 10% of samples showed pollen tubes entering the embryo sac between 48 and 66 HAP. Although several tubes may reach the nucellar beak, only one was observed entering the embryo sac. Results, across the different experiments, were highly variable suggesting that the timeline of fertilization is influenced both by genotypic and environmental factors as well as the manual manipulation of inflorescences and cyathia.
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Affiliation(s)
- L N Ramos Abril
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia.,Universidad Nacional de Colombia, Palmira, Colombia
| | - L M Pineda
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - I Wasek
- Pedagogical University, Cracow, Poland
| | - M Wedzony
- Pedagogical University, Cracow, Poland
| | - H Ceballos
- Cassava Program, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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50
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Piližota I, Train CM, Altenhoff A, Redestig H, Dessimoz C. Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome. Bioinformatics 2019; 35:1159-1166. [PMID: 30184069 PMCID: PMC6449756 DOI: 10.1093/bioinformatics/bty772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 07/30/2018] [Accepted: 08/31/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION As the time and cost of sequencing decrease, the number of available genomes and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene annotations varies considerably and often remains poor, affecting downstream analyses. This is particularly true when fragments of the same gene are annotated as distinct genes, which may cause them to be mistaken as paralogs. RESULTS In this study, we introduce two novel phylogenetic tests to infer non-overlapping or partially overlapping genes that are in fact parts of the same gene. One approach collapses branches with low bootstrap support and the other computes a likelihood ratio test. We extensively validated these methods by (i) introducing and recovering fragmentation on the bread wheat, Triticum aestivum cv. Chinese Spring, chromosome 3B; (ii) by applying the methods to the low-quality 3B assembly and validating predictions against the high-quality 3B assembly; and (iii) by comparing the performance of the proposed methods to the performance of existing methods, namely Ensembl Compara and ESPRIT. Application of this combination to a draft shotgun assembly of the entire bread wheat genome revealed 1221 pairs of genes that are highly likely to be fragments of the same gene. Our approach demonstrates the power of fine-grained evolutionary inferences across multiple species to improving genome assemblies and annotations. AVAILABILITY AND IMPLEMENTATION An open source software tool is available at https://github.com/DessimozLab/esprit2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ivana Piližota
- Department of Genetics Evolution & Environment, University College London, UK.,Department of Computer Science, University College London, UK
| | - Clément-Marie Train
- Department of Computational Biology, Lausanne, Switzerland.,Center for Integrative Genomics University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Biophore Building, Lausanne, Switzerland
| | - Adrian Altenhoff
- Swiss Institute of Bioinformatics, Biophore Building, Lausanne, Switzerland
| | | | - Christophe Dessimoz
- Department of Genetics Evolution & Environment, University College London, UK.,Department of Computer Science, University College London, UK.,Department of Computational Biology, Lausanne, Switzerland.,Center for Integrative Genomics University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Biophore Building, Lausanne, Switzerland
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