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Zang Y, Wu K, Liu L, Ran F, Wang C, Wu S, Wang D, Guo J, Min Y. Transcriptomic study of the role of MeFtsZ2-1 in pigment accumulation in cassava leaves. BMC Genomics 2024; 25:448. [PMID: 38802758 PMCID: PMC11129481 DOI: 10.1186/s12864-024-10165-w] [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: 12/09/2023] [Accepted: 02/27/2024] [Indexed: 05/29/2024] Open
Abstract
MeFtsZ2-1 is a key gene for plant plastid division, but the mechanism by which MeFtsZ2-1 affects pigment accumulation in cassava (Manihot esculenta Crantz) through plastids remains unclear. We found that MeFtsZ2-1 overexpression in cassava (OE) exhibited darker colors of leaves, with increased levels of anthocyanins and carotenoids. Further observation via Transmission Electron Microscopy (TEM) revealed no apparent defects in chloroplast structure but an increase in the number of plastoglobule in OE leaves. RNA-seq results showed 1582 differentially expressed genes (DEGs) in leaves of OE. KEGG pathway analysis indicated that these DEGs were enriched in pathways related to flavonoid, anthocyanin, and carotenoid biosynthesis. This study reveals the role of MeFtsZ2-1 in cassava pigment accumulation from a physiological and transcriptomic perspective, providing a theoretical basis for improving cassava quality.
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Affiliation(s)
- Yuwei Zang
- Department of Biosciences, School of Life and Health, Hainan University, Haikou, Hainan, 570228, China
| | - Kunlin Wu
- Department of Biosciences, School of Life and Health, Hainan University, Haikou, Hainan, 570228, China
| | - Liangwang Liu
- Department of Biosciences, School of Life and Health, Hainan University, Haikou, Hainan, 570228, China
| | - Fangfang Ran
- Department of Biosciences, School of Life and Health, Hainan University, Haikou, Hainan, 570228, China
| | - Changyi Wang
- Department of Biosciences, School of Life and Health, Hainan University, Haikou, Hainan, 570228, China
| | - Shuwen Wu
- Department of Biosciences, School of Life and Health, Hainan University, Haikou, Hainan, 570228, China
| | - Dayong Wang
- Department of Biosciences, School of Life and Health, Hainan University, Haikou, Hainan, 570228, China.
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences and Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, Hainan University, Haikou, Hainan, 570228, China.
| | - Jianchun Guo
- Institute of Tropical Biotechnology, Sanya Institute, Chinese Academy of Tropical Agricultural Sciences, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, 572000, China.
| | - Yi Min
- Department of Biosciences, School of Life and Health, Hainan University, Haikou, Hainan, 570228, China.
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Yseki M, Pezo-Lanfranco L, Machacuay M, Novoa P, Shady R. Analysis of starch grains trapped in human dental calculus in Áspero, Peru during the Initial Formative Period (3000-1800 BCE). Sci Rep 2023; 13:14143. [PMID: 37644158 PMCID: PMC10465486 DOI: 10.1038/s41598-023-41015-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
The objective of this research is to identify the plants consumed and to determine their dietary importance in Áspero, an urban center on the coast of the Supe Valley, Peru. Consequently, starch grains trapped in the human dental calculus of nine individuals were recovered, while the results from one individual from the Sacred City of Caral, located in the interior of Supe Valley, are presented. Eight species of food plants were identified, among them C3 plants: sweet potato, squash, potato, chili pepper, algarrobo, manioc and bean and C4 plant: maize. Previous isotopic analysis indicates that C3 plants formed the foundation of the diet at Áspero and Caral. Our results indicate a high ubiquity of C3 plants like sweet potato (100%) and squash (90%) suggesting, with caution, that these taxa were an important C3 source in the menu. Maize, C4 plant, showed a similar ubiquity (100%) to sweet potato and squash, however, previous isotopic analysis indicate that maize was a marginal food in Áspero and Caral. These results support that the absence and abundance of starch grains cannot be employed to directly infer the frequency of intake of C3 and C4 plants within a small population, as suggested by previous studies.
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Affiliation(s)
- Marco Yseki
- Zona Arqueológica Caral, Unidad Ejecutora 003, Ministerio de Cultura del Perú, Lima, Peru.
| | - Luis Pezo-Lanfranco
- Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marco Machacuay
- Zona Arqueológica Caral, Unidad Ejecutora 003, Ministerio de Cultura del Perú, Lima, Peru
| | - Pedro Novoa
- Zona Arqueológica Caral, Unidad Ejecutora 003, Ministerio de Cultura del Perú, Lima, Peru
- Escuela Profesional de Arqueología, Facultad de Ciencias Sociales, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ruth Shady
- Zona Arqueológica Caral, Unidad Ejecutora 003, Ministerio de Cultura del Perú, Lima, Peru
- Escuela Profesional de Arqueología, Facultad de Ciencias Sociales, Universidad Nacional Mayor de San Marcos, Lima, Peru
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Huang H, Song J, Feng Y, Zheng L, Chen Y, Luo K. Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava. Genes (Basel) 2023; 14:genes14040870. [PMID: 37107628 PMCID: PMC10138042 DOI: 10.3390/genes14040870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.
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Affiliation(s)
- Huling Huang
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Jiming Song
- Institute of Tropical and subtropical Economic Crops, Yunnan Provincial Academy of Agricultural Sciences, Baoshan 678000, China
| | - Yating Feng
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Linling Zheng
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Kai Luo
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
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Capriles JM, García M, Valenzuela D, Domic AI, Kistler L, Rothhammer F, Santoro CM. Pre-Columbian cultivation of vegetatively propagated and fruit tree tropical crops in the Atacama Desert. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.993630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
South America is a megadiverse continent that witnessed the domestication, translocation and cultivation of various plant species from seemingly contrasting ecosystems. It was the recipient and supplier of crops brought to and from Mesoamerica (such as maize and cacao, respectively), and Polynesia to where the key staple crop sweet potato was exported. Not every instance of the trans-ecological expansion of cultivated plants (both domesticated and wild), however, resulted in successful farming. Here, we review the transregional circulation and introduction of five food tropical crops originated in the tropical and humid valleys of the eastern Andes—achira, cassava, ahipa, sweet potato, and pacay—to the hyper-arid coastal valleys of the Atacama Desert of northern Chile, where they have been found in early archeological sites. By means of an evaluation of the contexts of their deposition and supported by direct radiocarbon dating, stable isotopes analyses, and starch grain analysis, we evaluate different hypotheses for explaining their introduction and adaptation to the hyper-arid soils of northern Chile, by societal groups that after the introduction of cultigens still retained a strong dependence on marine hunting, gathering and fishing ways of life based on wide variety of marine coast resources. Many of the studied plants were part of a broader package of introduced goods and technological devices and procedures, linked to food, therapeutic medicine, social and ritual purposes that transformed previous hunter-gatherer social, economic, and ideological institutions. Based on archeological data, we discuss some of the possible socio-ecological processes involved in the development of agricultural landscapes including the adoption of tropical crops originated several hundred kilometers away from the Atacama Desert during the Late Holocene.
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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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6
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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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Hirata Sanches V, Adams C, Ferreira FF. An integrated model to study varietal diversity in traditional agroecosystems. PLoS One 2022; 17:e0263064. [PMID: 35089959 PMCID: PMC8797245 DOI: 10.1371/journal.pone.0263064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022] Open
Abstract
Agricultural diversity is one of the bases of traditional agroecosystems, having great environmental and cultural importance. The current loss of agricultural diversity is causing serious concern, mainly because of its essential role in supporting global and local food security. Stopping this loss requires a better understanding of how diversity is managed locally and what mechanisms sustain agricultural diversity. Here we propose a generalist agent-based model that couples biological, cultural, and social dynamics to obtain varietal diversity as an emergent phenomenon at the community level. With a mechanistic approach, we explore how four of the model dynamics can shape systems diversity. To validate the model, we performed a bibliographic review on Manihot esculenta and Zea mays case studies. The model yielded compatible results for manioc and maize varietal richness at both community and household levels.
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Affiliation(s)
- Vitor Hirata Sanches
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, SP, Brazil
- * E-mail:
| | - Cristina Adams
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, SP, Brazil
- Institute of Energy and Environment, University of São Paulo, São Paulo, SP, Brazil
| | - Fernando Fagundes Ferreira
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, SP, Brazil
- Department of Physics-FFCLRP, University of São Paulo, Ribeirão Preto, SP, Brazil
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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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Szyniszewska AM, Chikoti PC, Tembo M, Mulenga R, Gilligan CA, van den Bosch F, McQuaid CF. Smallholder Cassava Planting Material Movement and Grower Behavior in Zambia: Implications for the Management of Cassava Virus Diseases. PHYTOPATHOLOGY 2021; 111:1952-1962. [PMID: 33856231 DOI: 10.1094/phyto-06-20-0215-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cassava (Manihot esculenta) is an important food crop across sub-Saharan Africa, where production is severely inhibited by two viral diseases, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), both propagated by a whitefly vector and via human-mediated movement of infected cassava stems. There is limited information on growers' behavior related to movement of planting material, as well as growers' perception and awareness of cassava diseases, despite the importance of these factors for disease control. This study surveyed a total of 96 cassava subsistence growers and their fields across five provinces in Zambia between 2015 and 2017 to address these knowledge gaps. CMD symptoms were observed in 81.6% of the fields, with an average incidence of 52% across the infected fields. No CBSD symptoms were observed. Most growers used planting materials from their own (94%) or nearby (<10 km) fields of family and friends, although several large transactions over longer distances (10 to 350 km) occurred with friends (15 transactions), markets (1), middlemen (5), and nongovernmental organizations (6). Information related to cassava diseases and certified clean (disease-free) seed reached only 48% of growers. The most frequent sources of information related to cassava diseases included nearby friends, family, and neighbors, while extension workers were the most highly preferred source of information. These data provide a benchmark on which to plan management approaches to controlling CMD and CBSD, which should include clean propagation material, increasing growers' awareness of the diseases, and increasing information provided to farmers (specifically disease symptom recognition and disease management options).[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
| | - Patrick Chiza Chikoti
- Zambia Agriculture Research Institute, Plant Protection and Quarantine Division, Mt. Makulu Research Station, Chilanga, Zambia
| | - Mathias Tembo
- Zambia Agriculture Research Institute, Plant Protection and Quarantine Division, Mt. Makulu Research Station, Chilanga, Zambia
| | - Rabson Mulenga
- Zambia Agriculture Research Institute, Plant Protection and Quarantine Division, Mt. Makulu Research Station, Chilanga, Zambia
| | | | - Frank van den Bosch
- Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Bentley, Perth, WA 6102, Australia
| | - Christopher Finn McQuaid
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, WC1E 7HT London, United Kingdom
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Process-Induced Modifications on Quality Attributes of Cassava (Manihot esculenta Crantz) Flour. Processes (Basel) 2021. [DOI: 10.3390/pr9111891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cassava flour (CF) is a suitable representative and one of the easiest shelf-stable food products of the edible portion of the highly perishable cassava root (Manihot esculenta Crantz). The quality and type of CF are dependent on processing variables. Broadly categorized into fermented and unfermented CF, unfermented CF is white, odorless, and bland, while fermented CF has a sour flavor accompanied by its characteristic odor. The use of fermented CF as a composite is limited because of their off-odors. Modifications in CF processing have given rise to prefixes such as: modified, unmodified, gelatinized, fortified, native, roasted, malted, wet, and dry. Consumed alone, mostly in reconstituted dough form with soups, CF may also serve as a composite in the processing of various flour-based food products. Fermenting with microorganisms such as Rhizopus oryzae and Saccharomyces cerevisiae results in a significant increase in the protein content and a decrease in the cyanide content of CF. However, there are concerns regarding its safety for consumption. Pre-gelatinized CF has potential for the textural and structural improvement of bakery products. The average particle size of the CF also influences its functional properties and, subsequently, the quality of its products. Cassava flour is best stored at ambient temperature. Standardizing the processing of CF is a challenge because it is mostly processed in artisanal units. Furthermore, each variety of the root best suits a particular application. Therefore, understanding the influence of processing variables on the characteristics of CF may improve the utilization of CF locally and globally.
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11
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Mertens A, Bawin Y, Vanden Abeele S, Kallow S, Toan Vu D, Thi Le L, Dang Vu T, Swennen R, Vandelook F, Panis B, Janssens SB. Genetic diversity and structure of Musa balbisiana populations in Vietnam and its implications for the conservation of banana crop wild relatives. PLoS One 2021; 16:e0253255. [PMID: 34161368 PMCID: PMC8221469 DOI: 10.1371/journal.pone.0253255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
Crop wild relatives (CWR) are an indispensable source of alleles to improve desired traits in related crops. While knowledge on the genetic diversity of CWR can facilitate breeding and conservation strategies, it has poorly been assessed. Cultivated bananas are a major part of the diet and income of hundreds of millions of people and can be considered as one of the most important fruits worldwide. Here, we assessed the genetic diversity and structure of Musa balbisiana, an important CWR of plantains, dessert and cooking bananas. Musa balbisiana has its origin in subtropical and tropical broadleaf forests of northern Indo-Burma. This includes a large part of northern Vietnam where until now, no populations have been sampled. We screened the genetic variation and structure present within and between 17 Vietnamese populations and six from China using 18 polymorphic SSR markers. Relatively high variation was found in populations from China and central Vietnam. Populations from northern Vietnam showed varying levels of genetic variation, with low variation in populations near the Red River. Low genetic variation was found in populations of southern Vietnam. Analyses of population structure revealed that populations of northern Vietnam formed a distinct genetic cluster from populations sampled in China. Together with populations of central Vietnam, populations from northern Vietnam could be subdivided into five clusters, likely caused by mountain ranges and connected river systems. We propose that populations sampled in central Vietnam and on the western side of the Hoang Lien Son mountain range in northern Vietnam belong to the native distribution area and should be prioritised for conservation. Southern range edge populations in central Vietnam had especially high genetic diversity, with a high number of unique alleles and might be connected with core populations in northern Laos and southwest China. Southern Vietnamese populations are considered imported and not native.
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Affiliation(s)
- Arne Mertens
- Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Yves Bawin
- Meise Botanic Garden, Meise, Belgium
- Ecology, Evolution and Biodiversity Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Simon Kallow
- Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Leuven, Belgium
- Royal Botanic Gardens Kew, Millennium Seed Bank, West Sussex, United Kingdom
| | - Dang Toan Vu
- Research Planning and International Department, Plant Resources Center, VAAS, Hanoi, Vietnam
| | - Loan Thi Le
- Department of Genebank Management, Plant Resources Center, VAAS, Hanoi, Vietnam
| | - Tuong Dang Vu
- Research Planning and International Department, Plant Resources Center, VAAS, Hanoi, Vietnam
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, Arusha, Tanzania
| | | | - Bart Panis
- Bioversity International, Leuven, Belgium
| | - Steven B. Janssens
- Meise Botanic Garden, Meise, Belgium
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Leuven, Belgium
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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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13
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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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Mugerwa H, Colvin J, Alicai T, Omongo CA, Kabaalu R, Visendi P, Sseruwagi P, Seal SE. Genetic diversity of whitefly ( Bemisia spp.) on crop and uncultivated plants in Uganda: implications for the control of this devastating pest species complex in Africa. JOURNAL OF PEST SCIENCE 2021; 94:1307-1330. [PMID: 34720787 PMCID: PMC8550740 DOI: 10.1007/s10340-021-01355-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/09/2021] [Accepted: 02/18/2021] [Indexed: 05/12/2023]
Abstract
UNLABELLED Over the past three decades, highly increased whitefly (Bemisia tabaci) populations have been observed on the staple food crop cassava in eastern Africa and associated with ensuing viral disease pandemics and food insecurity. Increased whitefly numbers have also been observed in other key agricultural crops and weeds. Factors behind the population surges on different crops and their interrelationships are unclear, although in cassava they have been associated with specific populations within the Bemisia tabaci species complex known to infest cassava crops in Africa. This study carried out an in-depth survey to understand the distribution of B. tabaci populations infesting crops and uncultivated plant hosts in Uganda, a centre of origin for this pest complex. Whitefly samples were collected from 59 identified plant species and 25 unidentified weeds in a countrywide survey. Identities of 870 individual adult whiteflies were determined through mitochondrial cytochrome oxidase 1 sequences (651 bp) in the 3' barcode region used for B. tabaci systematics. Sixteen B. tabaci and five related whitefly putative species were identified based on > 4.0% nucleotide divergence, of which three are proposed as novel B. tabaci putative species and four as novel closely related whitefly species. The most prevalent whiteflies were classified as B. tabaci MED-ASL (30.5% of samples), sub-Saharan Africa 1 (SSA1, 22.7%) and Bemisia Uganda1 (12.1%). These species were also indicated to be the most polyphagous occurring on 33, 40 and 25 identified plant species, respectively. Multiple (≥ 3) whitefly species occurred on specific crops (bean, eggplant, pumpkin and tomato) and weeds (Sida acuta and Ocimum gratissimum). These plants may have increased potential to act as reservoirs for mixed infections of whitefly-vectored viruses. Management of whitefly pest populations in eastern Africa will require an integration of approaches that consider their degree of polyphagy and a climate that enables the continuous presence of crop and uncultivated plant hosts. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10340-021-01355-6.
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Affiliation(s)
- Habibu Mugerwa
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223 USA
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
| | - Titus Alicai
- Root Crops Programme, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Christopher A. Omongo
- Root Crops Programme, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Richard Kabaalu
- Root Crops Programme, National Crops Resources Research Institute, P. O. Box 7084, Kampala, Uganda
| | - Paul Visendi
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, 4001 Australia
| | - Peter Sseruwagi
- Biotechnology Department, Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB UK
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Lombardo U, Iriarte J, Hilbert L, Ruiz-Pérez J, Capriles JM, Veit H. Early Holocene crop cultivation and landscape modification in Amazonia. Nature 2020; 581:190-193. [PMID: 32404996 PMCID: PMC7250647 DOI: 10.1038/s41586-020-2162-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/13/2020] [Indexed: 11/21/2022]
Abstract
The beginning of plant cultivation is one of the most important cultural
transitions in human history1–4. Based on
molecular markers showing the genetic similarities between domesticated plants
and wild relatives, south-western Amazonia has been proposed as one of the early
centres of plant domestication4–6. However,
the nature of the early human occupation and the history of plant cultivation in
south-western Amazonia are still little understood. Here, we document the
cultivation of Cucurbita at ca. 10,250 cal yr BP,
Manihot at ca. 10,350 cal yr BP and Zea
mays at ca. 6,850 cal yr BP in the Llanos de Moxos. We show that,
starting ca. 10,850 cal yr BP, pre-Columbians created an anthropic landscape
made of approximately 4,700 artificial forest islands within a treeless
seasonally flooded savannah. Our results confirm the Llanos de Moxos as a
hotspot for early plant cultivation and demonstrate that ever since their
arrival, humans have caused a profound alteration of Amazonian landscapes, with
lasting repercussions for habitat heterogeneity and species conservation.
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Affiliation(s)
| | - José Iriarte
- Department of Archaeology, College of Humanities, University of Exeter, Exeter, UK
| | - Lautaro Hilbert
- Laboratório de Arqueologia dos Trópicos, Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo, Brazil
| | - Javier Ruiz-Pérez
- CaSEs - Culture and Socio-Ecological Dynamics Research Group, Pompeu Fabra University, Barcelona, Spain
| | - José M Capriles
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA.,Instituto de Investigaciones Antropológicas y Arqueológicas, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Heinz Veit
- Institute of Geography, University of Bern, Bern, Switzerland
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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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Involvement of abscisic acid-responsive element-binding factors in cassava (Manihot esculenta) dehydration stress response. Sci Rep 2019; 9:12661. [PMID: 31477771 PMCID: PMC6718394 DOI: 10.1038/s41598-019-49083-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 08/19/2019] [Indexed: 02/04/2023] Open
Abstract
Cassava (Manihot esculenta) is a major staple food, animal feed and energy crop in the tropics and subtropics. It is one of the most drought-tolerant crops, however, the mechanisms of cassava drought tolerance remain unclear. Abscisic acid (ABA)-responsive element (ABRE)-binding factors (ABFs) are transcription factors that regulate expression of target genes involved in plant tolerance to drought, high salinity, and osmotic stress by binding ABRE cis-elements in the promoter regions of these genes. However, there is little information about ABF genes in cassava. A comprehensive analysis of Manihot esculenta ABFs (MeABFs) described the phylogeny, genome location, cis-acting elements, expression profiles, and regulatory relationship between these factors and Manihot esculenta betaine aldehyde dehydrogenase genes (MeBADHs). Here we conducted genome-wide searches and subsequent molecular cloning to identify seven MeABFs that are distributed unevenly across six chromosomes in cassava. These MeABFs can be clustered into three groups according to their phylogenetic relationships to their Arabidopsis (Arabidopsis thaliana) counterparts. Analysis of the 5′-upstream region of MeABFs revealed putative cis-acting elements related to hormone signaling, stress, light, and circadian clock. MeABF expression profiles displayed clear differences among leaf, stem, root, and tuberous root tissues under non-stress and drought, osmotic, or salt stress conditions. Drought stress in cassava leaves and roots, osmotic stress in tuberous roots, and salt stress in stems induced expression of the highest number of MeABFs showing significantly elevated expression. The glycine betaine (GB) content of cassava leaves also was elevated after drought, osmotic, or salt stress treatments. BADH1 is involved in GB synthesis. We show that MeBADH1 promoter sequences contained ABREs and that MeBADH1 expression correlated with MeABF expression profiles in cassava leaves after the three stress treatments. Taken together, these results suggest that in response to various dehydration stresses, MeABFs in cassava may activate transcriptional expression of MeBADH1 by binding the MeBADH1 promoter that in turn promotes GB biosynthesis and accumulation via an increase in MeBADH1 gene expression levels and MeBADH1 enzymatic activity. These responses protect cells against dehydration stresses by preserving an osmotic balance that enhances cassava tolerance to dehydration stresses.
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18
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Zou Z, Yang J. Genomics analysis of the light-harvesting chlorophyll a/b-binding (Lhc) superfamily in cassava (Manihot esculenta Crantz). Gene 2019; 702:171-181. [DOI: 10.1016/j.gene.2019.03.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/15/2019] [Accepted: 03/30/2019] [Indexed: 12/11/2022]
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Zou Z, Yang J. Genome-wide comparison reveals divergence of cassava and rubber aquaporin family genes after the recent whole-genome duplication. BMC Genomics 2019; 20:380. [PMID: 31092186 PMCID: PMC6521647 DOI: 10.1186/s12864-019-5780-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/07/2019] [Indexed: 12/19/2022] Open
Abstract
Background Aquaporins (AQPs) are a class of integral membrane proteins that facilitate the passive transport of water and other small solutes across biological membranes. Despite their importance, little information is available in cassava (Manihot esculenta), a perennial shrub of the Euphorbiaceae family that serves the sixth major staple crop in the world. Results This study presents a genome-wide analysis of the AQP gene family in cassava. The family of 42 members in this species could be divided into five subfamilies based on phylogenetic analysis, i.e., 14 plasma membrane intrinsic proteins (PIPs), 13 tonoplast intrinsic proteins (TIPs), nine NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and two small basic intrinsic proteins (SIPs). Best-reciprocal-hit-based sequence comparison and synteny analysis revealed 34 orthologous groups (OGs) present in the Euphorbiaceae ancestor, and nearly one-to-one or two-to-one orthologous relationships were observed between cassava with rubber/physic nut, reflecting the occurrence of one so-called ρ recent whole-genome duplication (WGD) in the last common ancestor of cassava and rubber. In contrast to a predominant role of the ρ WGD on family expansion in rubber, cassava AQP duplicates were derived from the WGD as well as local duplication. Species-specific gene loss was also observed in cassava, which includes the entire NIP4 group and/or six OGs. Comparison of conserved motifs and gene expression profiles revealed divergence of paralogs in cassava as observed in rubber. Conclusions Our findings will not only improve our knowledge on family evolution in Euphorbiaceae, but also provide valuable information for further functional analysis of AQP genes in cassava and rubber. Electronic supplementary material The online version of this article (10.1186/s12864-019-5780-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhi Zou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, People's Republic of China.
| | - Jianghua Yang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, People's Republic of China
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Pérez D, Mora R, López Carrascal C. Conservación de la diversidad de yuca en los sistemas tradicionales de cultivo de la Amazonía. ACTA BIOLÓGICA COLOMBIANA 2019. [DOI: 10.15446/abc.v24n2.75428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La yuca es determinante para la seguridad alimentaria de cientos de millones de personas alrededor del mundo. A pesar de que el principal medio de propagación del cultivo es a través de semilla asexual por estacas (tallos maduros) se ha revelado una relativamente alta diversidad intraespecífica, principalmente en los sistemas de cultivo de manejo tradicional. En esta revisión se documentan algunos estudios realizados sobre la diversidad de la yuca, tanto por marcadores moleculares como morfológicos, centrándose en aquellos realizados en el Amazonas. También se exponen los principales factores que han determinado el aprovechamiento y conservación de esta diversidad, tales como la aparición espontánea de semillas de origen sexual, el sistema de chagras indígenas, la memoria biocultural y la facilidad de intercambio de semilla entre comunidades. Finalmente, se pone de manifiesto que en los sistemas de manejo tradicional la conservación y uso de la diversidad intraespecífica se constituye en un elemento prioritario que se ha perdido en los sistemas de cultivo a gran escala. En los sistemas de manejo tradicional existe un vínculo etnobotánico que pervive e invita a buscar prácticas alternativas que aseguran un mantenimiento de la diversidad, permitiendo una productividad eficiente e incluso se hace un mejor manejo para disminuir los riesgos de incidencia de algunas plagas y enfermedades.
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Lam DT, Buu BC, Lang NT, Toriyama K, Nakamura I, Ishikawa R. Genetic diversity among perennial wild rice Oryza rufipogon Griff., in the Mekong Delta. Ecol Evol 2019; 9:2964-2977. [PMID: 30891229 PMCID: PMC6405534 DOI: 10.1002/ece3.4978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/02/2022] Open
Abstract
Oryza rufipogon Griff. is a perennial species of wild rice widely distributed along the channels and rivers of the Mekong Delta, Vietnam. This study attempted to find centers of diversity among wild rice populations in this area and their inter-relationships. The highest genetic diversity was found in the Dong Thap population and the lowest in the Can Tho population. Maternal diversity evaluated using chloroplast INDELs detected ten plastid types, five of which were novel relative to other Asian countries. The mitochondrial genome suggested two unique deletions. One 699-bp deletion via short tandem repeats was accompanied by another deletion including orf153. All accessions carrying the mitochondrial type were found in a particular plastid type. This unique maternal lineage was confined to specific channels where it showed vigorous vegetative growth in comparison to upstream areas where various maternal lineages and maximum genetic diversity occurred. This area along the Mekong Delta is a center of not only nuclear but also maternal diversity.
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Affiliation(s)
- Dinh T. Lam
- United Graduate School of Agricultural ScienceIwate UniversityMoriokaJapan
- Institute of Agricultural Science for Southern VietnamHo Chi Minh CityVietnam
| | - Bui C. Buu
- Institute of Agricultural Science for Southern VietnamHo Chi Minh CityVietnam
| | - Nguyen T. Lang
- High Agricultural Technology Research Institute (HATRI)CanthoVietnam
| | - Kinya Toriyama
- Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Ikuo Nakamura
- Graduate School of HorticultureChiba UniversityMatsudoJapan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiJapan
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Wang MMH, Gardner EM, Chung RCK, Chew MY, Milan AR, Pereira JT, Zerega NJC. Origin and diversity of an underutilized fruit tree crop, cempedak (Artocarpus integer, Moraceae). AMERICAN JOURNAL OF BOTANY 2018; 105:898-914. [PMID: 29874392 DOI: 10.1002/ajb2.1094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Underutilized crops and their wild relatives are important resources for crop improvement and food security. Cempedak [Artocarpus integer (Thunb). Merr.] is a significant crop in Malaysia but underutilized elsewhere. Here we performed molecular characterization of cempedak and its putative wild relative bangkong (Artocarpus integer (Thunb). Merr. var. silvestris Corner) to address questions regarding the origin and diversity of cempedak. METHODS Using data from 12 microsatellite loci, we assessed the genetic diversity and genetic/geographic structure for 353 cempedak and 175 bangkong accessions from Malaysia and neighboring countries and employed clonal analysis to characterize cempedak cultivars. We conducted haplotype network analyses on the trnH-psbA region in a subset of these samples. We also analyzed key vegetative characters that reportedly differentiate cempedak and bangkong. KEY RESULTS We show that cempedak and bangkong are sister taxa and distinct genetically and morphologically, but the directionality of domestication origin is unclear. Genetic diversity was generally higher in bangkong than in cempedak. We found a distinct genetic cluster for cempedak from Borneo as compared to cempedak from Peninsular Malaysia. Finally, cempedak cultivars with the same names did not always share the same genetic fingerprint. CONCLUSIONS Cempedak origins are complex, with likely admixture and hybridization with bangkong, warranting further investigation. We provide a baseline of genetic diversity of cempedak and bangkong in Malaysia and found that germplasm collections in Malaysia represent diverse coverage of the four cempedak genetic clusters detected.
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Affiliation(s)
- Maria M H Wang
- Department of Plant Science, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Hogan 2-144, Evanston, IL, 60208, USA
| | - Elliot M Gardner
- Department of Plant Science, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Hogan 2-144, Evanston, IL, 60208, USA
| | - Richard C K Chung
- Forest Biodiversity Division, Forest Research Institute Malaysia, 52109, Kepong, Malaysia
| | - Ming Yee Chew
- Forest Biodiversity Division, Forest Research Institute Malaysia, 52109, Kepong, Malaysia
| | - Abd Rahman Milan
- Horticulture Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Serdang, P.O. Box 12301, 50774, Kuala Lumpur, Malaysia
| | - Joan T Pereira
- Forest Research Centre, Sabah Forestry Department, P.O. Box 1407, 90715, Sandakan, Sabah, Malaysia
| | - Nyree J C Zerega
- Department of Plant Science, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
- Plant Biology and Conservation, Northwestern University, 2205 Tech Drive, Hogan 2-144, Evanston, IL, 60208, USA
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Alves-Pereira A, Clement CR, Picanço-Rodrigues D, Veasey EA, Dequigiovanni G, Ramos SLF, Pinheiro JB, Zucchi MI. Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers. ANNALS OF BOTANY 2018; 121:625-639. [PMID: 29309531 PMCID: PMC5853005 DOI: 10.1093/aob/mcx190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/23/2017] [Indexed: 05/20/2023]
Abstract
Background and Aims Amazonia is a major world centre of plant domestication, but little is known about how the crops were dispersed across the region. Manioc (Manihot esculenta) was domesticated in the south-western Amazon basin, and is the most important staple food crop that originated in Amazonia. Current contrasting distributions may reflect distinct histories of dispersal of bitter and sweet manioc landraces. To produce new insights into the evolutionary history of the crop, we investigated the contemporary genetic diversity and structure of bitter and sweet manioc along major Amazonian rivers. Methods The patterns of genetic structure and diversity of wild and cultivated sweet and bitter manioc with four chloroplast and 14 nuclear microsatellite markers were evaluated. Results were interpreted in terms of the crop's dispersal. Key results No phylogeographic patterns among rivers were detected, and genetic structure among rivers was confounded by the bitter-sweet divergence. However, differences in the distribution of nuclear diversity and somewhat distinctive patterns of genetic structure across rivers were observed within bitter and sweet manioc. Conclusions Various pre-Columbian and post-European conquest events in the history of Amazonian occupation may explain the absence of clearer patterns of genetic structure. However, the wide distribution of the most common chloroplast haplotype agrees with an early dispersal of manioc across Brazilian Amazonia. Furthermore, differences in genetic structure and in the spatial distribution of genetic diversity suggest that bitter and sweet manioc had distinct dispersal histories. Knowledge about how prehistoric and contemporary Amazonian peoples manage their crops is valuable for the maintenance and conservation of the impressive diversity of their native crops.
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Affiliation(s)
- Alessandro Alves-Pereira
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brazil
| | | | - Elizabeth A Veasey
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Gabriel Dequigiovanni
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Santiago L F Ramos
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - José B Pinheiro
- Departamento de Genética, Escola Superior de Agricultura ‘Luiz de Queiróz’, Universidade de São Paulo (ESALQ-USP), Piracicaba, SP, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios, Pólo Centro-Sul (APTA), Piracicaba, SP, Brazil
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Expression patterns of members of the ethylene signaling-related gene families in response to dehydration stresses in cassava. PLoS One 2017; 12:e0177621. [PMID: 28542282 PMCID: PMC5441607 DOI: 10.1371/journal.pone.0177621] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 05/01/2017] [Indexed: 12/23/2022] Open
Abstract
Drought is the one of the most important environment stresses that restricts crop yield worldwide. Cassava (Manihot esculenta Crantz) is an important food and energy crop that has many desirable traits such as drought, heat and low nutrients tolerance. However, the mechanisms underlying drought tolerance in cassava are unclear. Ethylene signaling pathway, from the upstream receptors to the downstream transcription factors, plays important roles in environmental stress responses during plant growth and development. In this study, we used bioinformatics approaches to identify and characterize candidate Manihot esculenta ethylene receptor genes and transcription factor genes. Using computational methods, we localized these genes on cassava chromosomes, constructed phylogenetic trees and identified stress-responsive cis-elements within their 5’ upstream regions. Additionally, we measured the trehalose and proline contents in cassava fresh leaves after drought, osmotic, and salt stress treatments, and then it was found that the regulation patterns of contents of proline and trehalose in response to various dehydration stresses were differential, or even the opposite, which shows that plant may take different coping strategies to deal with different stresses, when stresses come. Furthermore, expression profiles of these genes in different organs and tissues under non-stress and abiotic stress were investigated through quantitative real-time PCR (qRT-PCR) analyses in cassava. Expression profiles exhibited clear differences among different tissues under non-stress and various dehydration stress conditions. We found that the leaf and tuberous root tissues had the greatest and least responses, respectively, to drought stress through the ethylene signaling pathway in cassava. Moreover, tuber and root tissues had the greatest and least reponses to osmotic and salt stresses through ethylene signaling in cassava, respectively. These results show that these plant tissues had differential expression levels of genes involved in ethylene signaling in response to the stresses tested. Moreover, after several gene duplication events, the spatiotemporally differential expression pattern of homologous genes in response to abiotic and biotic stresses may imply their functional diversity as a mechanism for adapting to the environment. Our data provide a framework for further research on the molecular mechanisms of cassava resistance to drought stress and provide a foundation for breeding drought-resistant new cultivars.
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Boczkowska M, Łapiński B, Kordulasińska I, Dostatny DF, Czembor JH. Promoting the Use of Common Oat Genetic Resources through Diversity Analysis and Core Collection Construction. PLoS One 2016; 11:e0167855. [PMID: 27959891 PMCID: PMC5154523 DOI: 10.1371/journal.pone.0167855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
Abstract
The assessment of diversity and population structure and construction of a core collection is beneficial for the efficient use and management of germplasm. A unique collection of common oat landraces, cultivated in the temperate climate of central Europe until the end of the twentieth century, is preserved in the Polish gene bank. It consists of 91 accessions that have never been used in breeding programs. In order to optimise the use of this genetic resource, we aimed to: (1) determine genetic and agro-morphological diversity, (2) identify internal genetic variation of the tested accessions, (3) form a core collection and (4) recognise the accessions useful for breeding programs or re-release for cultivation. The collection was screened using ISSR markers (1520 loci) and eight agro-morphological traits. Uniquely, we performed molecular studies based on 24 individuals of every accession instead of bulk samples. Therefore, assessment of the degree of diversity within each population and the identification of overlapping gene pools were possible. The observed internal diversity (Nei unbiased coefficient) was in the range of 0.17-0.31. Based on combined genetic and agro-morphological data, we established the core collection composed of 21 landraces. Due to valuable compositions of important traits, some accessions were also identified as useful for breeding programs. The population structure and principal coordinate analysis revealed two major clusters. Based on the previous results, the accessions classified within the smaller one were identified as obsolete varieties instead of landraces. Our results show that the oat landraces are, in general, resistant to local races of diseases, well adapted to local conditions and, in some cases, yielding at the level of modern varieties. Therefore, in situ conservation of the landraces in the near future may be satisfactory for both farmers and researchers in terms of the genetic resources preservation.
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Affiliation(s)
- Maja Boczkowska
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Bogusław Łapiński
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Izabela Kordulasińska
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Denise F. Dostatny
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
| | - Jerzy H. Czembor
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR) - National Research Institute, Radzików, Poland
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26
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Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E, Grimwood J, Schmutz J, Rabbi IY, Egesi C, Nauluvula P, Lebot V, Ndunguru J, Mkamilo G, Bart RS, Setter TL, Gleadow RM, Kulakow P, Ferguson ME, Rounsley S, Rokhsar DS. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nat Biotechnol 2016; 34:562-70. [PMID: 27088722 DOI: 10.1038/nbt.3535] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/10/2016] [Indexed: 11/09/2022]
Abstract
Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Simon E Prochnik
- United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA
| | - G Albert Wu
- United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA
| | - Cindy M Ha
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Eric Edsinger-Gonzales
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jane Grimwood
- United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Jeremy Schmutz
- United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Ismail Y Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Poasa Nauluvula
- Department of Agriculture, Ministry of Primary Industries, Koronivia Research Station, Fiji
| | - Vincent Lebot
- Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Port-Vila, Vanuatu
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute (MARI), Dar es Salaam, Tanzania
| | - Geoffrey Mkamilo
- Naliendele Agricultural Research Institute (NARI), Mtwara, Tanzania
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Tim L Setter
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Roslyn M Gleadow
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Morag E Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.,United States Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, California, USA.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
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Patel JR, Patel AA, Singh AK. Production of a protein-rich extruded snack base using tapioca starch, sorghum flour and casein. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2016; 53:71-87. [PMID: 26787933 PMCID: PMC4711443 DOI: 10.1007/s13197-015-2012-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/04/2015] [Accepted: 08/26/2015] [Indexed: 10/23/2022]
Abstract
A protein-rich puffed snack was produced using a twin screw extruder and the effects of varying levels of tapioca starch (11 to 40 parts), rennet casein (6 to 20 parts) and sorghum flour (25 to 75 parts) on physico-chemical properties and sensory attributes of the product studied. An increasing level of sorghum flour resulted in a decreasing whiteness (Hunter L* value) of the snack. Although the starch also generally tended to make the product increasingly darker, both starch and casein showed redness parameter (a* value) was not significantly influenced by the ingredients levels, the yellow hue (b* value) generally declined with the increasing sorghum level. Tapioca starch significantly increased the expansion ratio and decreased the bulk density and hardness value of the snack, whereas the opposite effects seen in case of sorghum flour. While the water solubility index was enhanced by starch, water absorption index was appreciably improved by sorghum. Incorporation of casein (up to 25 %) improved the sensory color and texture scores, and so also the overall acceptability rating of the product. Sorghum flour had an adverse impact on all the sensory attributes whereas starch only on the color score. The casein or starch level had no perceivable effect on the product's flavor score. The response surface data enabled optimization of the snack-base formulation for the desired protein level or desired sensory characteristics.
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Affiliation(s)
- Jiral R. Patel
- D.T. Division, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Ashok A. Patel
- D.T. Division, National Dairy Research Institute, Karnal, 132001 Haryana India
| | - Ashish K. Singh
- D.T. Division, National Dairy Research Institute, Karnal, 132001 Haryana India
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Renard D, Schatz B, McKey DB. Ant nest architecture and seed burial depth: Implications for seed fate and germination success in a myrmecochorous savanna shrub. ECOSCIENCE 2015. [DOI: 10.2980/17-2-3335] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Resistance gene analogs involved in tolerant cassava--geminivirus interaction that shows a recovery phenotype. Virus Genes 2015; 51:393-407. [PMID: 26370397 DOI: 10.1007/s11262-015-1246-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/02/2015] [Indexed: 10/23/2022]
Abstract
The current literature describes recovery from virus-induced symptoms as a RNA silencing defense, but immunity-related genes, including the structurally specific resistance gene analogs (RGAs) that may play a key role in tolerance and recovery is not yet reported. In this study, the transcriptome data of tolerant cassava TME3 (which exhibits a recovery phenotype) and susceptible cassava T200 infected with South African cassava mosaic virus were explored for RGAs. Putative resistance protein analogs (RPAs) with amide-like indole-3-acetic acid-Ile-Leu-Arg (IAA-ILR) and leucine-rich repeat (LRR)-kinase conserved domains were unique to TME3. Common responsive RPAs in TME3 and T200 were the dirigent-like protein, coil-coil nucleotide-binding site (NBS) and toll-interleukin-resistance, disease resistance zinc finger chromosome condensation-like protein (DZC), and NBS-apoptosis repressor with caspase recruitment (ARC)-LRR domains. Mutations in RPAs in the MHD motif of the NBS-ARC2 subdomain associated with the recovery phase in TME3 were observed. Additionally, a cohort of 25 RGAs mined solely during the recovery process in TME3 was identified. Phylogenetic and expression analyses support that diverse RGAs are differentially expressed during tolerance and recovery. This study reveals that in cassava, a perennial crop, RGAs participate in tolerance and differentially accumulate during recovery as a complementary defense mechanism to natural occurring RNA silencing to impair viral replication.
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Ceballos H, Kawuki RS, Gracen VE, Yencho GC, Hershey CH. Conventional breeding, marker-assisted selection, genomic selection and inbreeding in clonally propagated crops: a case study for cassava. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1647-67. [PMID: 26093610 PMCID: PMC4540783 DOI: 10.1007/s00122-015-2555-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 06/05/2015] [Indexed: 05/19/2023]
Abstract
Consolidates relevant molecular and phenotypic information on cassava to demonstrate relevance of heterosis, and alternatives to exploit it by integrating different tools. Ideas are useful to other asexually reproduced crops. Asexually propagated crops offer the advantage that all genetic effects can be exploited in farmers' production fields. However, non-additive effects complicate selection because, while influencing the performance of the materials under evaluation, they cannot be transmitted efficiently to the following cycle of selection. Cassava can be used as a model crop for asexually propagated crops because of its diploid nature and the absence of (known) incompatibility effects. New technologies such as genomic selection (GS), use of inbred progenitors based on doubled haploids and induction of flowering can be employed for accelerating genetic gains in cassava. Available information suggests that heterosis, non-additive genetic effects and within-family variation are relatively large for complex traits such as fresh root yield, moderate for dry matter or starch content in the roots, and low for defensive traits (pest and disease resistance) and plant architecture. The present article considers the potential impact of different technologies for maximizing gains for key traits in cassava, and highlights the advantages of integrating them. Exploiting heterosis would be optimized through the implementation of reciprocal recurrent selection. The advantages of using inbred progenitors would allow shifting the current cassava phenotypic recurrent selection method into line improvement, which in turn would allow designing outstanding hybrids rather than finding them by trial and error.
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Affiliation(s)
- Hernán Ceballos
- International Center for Tropical Agriculture (CIAT), Apartado Aéreo, 6713, Cali, Colombia,
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Cervantes-Alcayde MA, Olson ME, Olsen KM, Eguiarte LE. Apparent similarity, underlying homoplasy: Morphology and molecular phylogeny of the North American clade of Manihot. AMERICAN JOURNAL OF BOTANY 2015; 102:520-532. [PMID: 25878086 DOI: 10.3732/ajb.1500063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Morphologically diverse clades are useful for detecting adaptive morphological evolution. Each of their variants may have evolved once or several times, suggesting that their repeated appearance may be due to environmental pressures. The North American Manihot species are an excellent system to detect possible adaptations and to assess the effect of mono- or polyphyly on classification. With 20 species, this group includes growth forms from tuberous herbs to trees. The monophyly of this group and its relationship with the economically important M. esculenta were tested for the first time with complete sampling of North American species. METHODS We carried out maximum likelihood and Bayesian phylogenetic analyses on a matrix of 3662 bp from chloroplast (psbA-trnH, trnL-trnF) and nuclear loci (PEPC and two paralogous copies of G3pdh). We included all North American Manihot species, Manihotoides pauciflora, and published sequences from 34 South American species. KEY RESULTS Our results support monophyly of the North American Manihot group. Its taxonomic sections are paraphyletic, and three to four growth forms evolved repeatedly. Manihotoides pauciflora is nested within North American Manihot species. Some PEPC and G3pdh clones grouped with clones of other species and not with clones from their own species. CONCLUSIONS North and South American Manihot species are sister clades. Paraphyly of North American sections suggests that taxonomic revision is warranted. The position of Manihotoides pauciflora confirms that Manihotoides should remain subsumed within Manihot. Most growth forms likely evolved repeatedly in this group. The behavior of PEPC and G3pdhNA clones is probably due to incomplete lineage sorting.
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Affiliation(s)
- María-Angélica Cervantes-Alcayde
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria s/n, Del. Coyoacán, México D.F. 04510 Mexico
| | - Mark E Olson
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria s/n, Del. Coyoacán, México D.F. 04510 Mexico
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, Missouri 63130 USA
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria s/n, Del. Coyoacán, México D.F. 04510 Mexico
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Uchechukwu-Agua AD, Caleb OJ, Opara UL. Postharvest Handling and Storage of Fresh Cassava Root and Products: a Review. FOOD BIOPROCESS TECH 2015. [DOI: 10.1007/s11947-015-1478-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Chen X, Xia J, Xia Z, Zhang H, Zeng C, Lu C, Zhang W, Wang W. Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor. BMC PLANT BIOLOGY 2015; 15:33. [PMID: 25648603 PMCID: PMC4331152 DOI: 10.1186/s12870-014-0355-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 11/27/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are small (approximately 21 nucleotide) non-coding RNAs that are key post-transcriptional gene regulators in eukaryotic organisms. More than 100 cassava miRNAs have been identified in a conservation analysis and a repertoire of cassava miRNAs have also been characterised by next-generation sequencing (NGS) in recent studies. Here, using NGS, we profiled small non-coding RNAs and mRNA genes in two cassava cultivars and their wild progenitor to identify and characterise miRNAs that are potentially involved in plant growth and starch biosynthesis. RESULTS Six small RNA and six mRNA libraries from leaves and roots of the two cultivars, KU50 and Arg7, and their wild progenitor, W14, were subjected to NGS. Analysis of the sequencing data revealed 29 conserved miRNA families and 33 new miRNA families. Together, these miRNAs potentially targeted a total of 360 putative target genes. Whereas 16 miRNA families were highly expressed in cultivar leaves, another 13 miRNA families were highly expressed in storage roots of cultivars. Co-expression analysis revealed that the expression level of some targets had negative relationship with their corresponding miRNAs in storage roots and leaves; these targets included MYB33, ARF10, GRF1, RD19, APL2, NF-YA3 and SPL2, which are known to be involved in plant development, starch biosynthesis and response to environmental stimuli. CONCLUSION The identified miRNAs, target mRNAs and target gene ontology annotation all shed light on the possible functions of miRNAs in Manihot species. The differential expression of miRNAs between cultivars and their wild progenitor, together with our analysis of GO annotation and confirmation of miRNA: target pairs, might provide insight into know the differences between wild progenitor and cultivated cassava.
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Affiliation(s)
- Xin Chen
- The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China.
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China.
| | - Jing Xia
- Institute for Systems Biology, Jianghan University, Wuhan, 430056, China.
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, MO, 63130, USA.
| | - Zhiqiang Xia
- The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China.
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China.
| | - Hefang Zhang
- The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China.
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China.
| | - Changying Zeng
- The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China.
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China.
| | - Cheng Lu
- The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China.
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China.
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, 430056, China.
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, MO, 63130, USA.
| | - Wenquan Wang
- The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, PR China.
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, 571101, PR China.
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Ubwa ST, Otache MA, Igbum GO, Shambe T. Determination of Cyanide Content in Three Sweet Cassava Cultivars in Three Local Government Areas of Benue State, Nigeria. ACTA ACUST UNITED AC 2015. [DOI: 10.4236/fns.2015.612112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Saxena RK, von Wettberg E, Upadhyaya HD, Sanchez V, Songok S, Saxena K, Kimurto P, Varshney RK. Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs. PLoS One 2014; 9:e88568. [PMID: 24533111 PMCID: PMC3922937 DOI: 10.1371/journal.pone.0088568] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 01/07/2014] [Indexed: 11/22/2022] Open
Abstract
Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.
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Affiliation(s)
- Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Eric von Wettberg
- Department of Biological Sciences, Florida International University, Miami, Florida, United States of America
- Fairchild Tropical Botanic Garden, Kushlan Institute for Tropical Science, Miami, Florida, United States of America
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | - Vanessa Sanchez
- Florida International University, Department of Earth and Environment, Miami, Florida, United States of America
| | - Serah Songok
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
- Egerton University, Egerton, Kenya
| | - Kulbhushan Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
- * E-mail:
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Mokuwa A, Nuijten E, Okry F, Teeken B, Maat H, Richards P, Struik PC. Processes underpinning development and maintenance of diversity in rice in West Africa: evidence from combining morphological and molecular markers. PLoS One 2014; 9:e85953. [PMID: 24465809 PMCID: PMC3896413 DOI: 10.1371/journal.pone.0085953] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/19/2013] [Indexed: 02/05/2023] Open
Abstract
We assessed the interplay of artificial and natural selection in rice adaptation in low-input farming systems in West Africa. Using 20 morphological traits and 176 molecular markers, 182 farmer varieties of rice (Oryza spp.) from 6 West African countries were characterized. Principal component analysis showed that the four botanical groups (Oryza sativa ssp. indica, O. sativa ssp. japonica, O. glaberrima, and interspecific farmer hybrids) exhibited different patterns of morphological diversity. Regarding O. glaberrima, morphological and molecular data were in greater conformity than for the other botanical groups. A clear difference in morphological features was observed between O. glaberrima rices from the Togo hills and those from the Upper Guinea Coast, and among O. glaberrima rices from the Upper Guinea Coast. For the other three groups such clear patterns were not observed. We argue that this is because genetic diversity is shaped by different environmental and socio-cultural selection pressures. For O. glaberrima, recent socio-cultural selection pressures seemed to restrict genetic diversity while this was not observed for the other botanical groups. We also show that O. glaberrima still plays an important role in the selection practices of farmers and resulting variety development pathways. This is particularly apparent in the case of interspecific farmer hybrids where a relationship was found between pericarp colour, panicle attitude and genetic diversity. Farmer varieties are the product of long and complex trajectories of selection governed by local human agency. In effect, rice varieties have emerged that are adapted to West African farming conditions through genotype × environment × society interactions. The diversity farmers maintain in their rice varieties is understood to be part of a risk-spreading strategy that also facilitates successful and often serendipitous variety innovations. We advocate, therefore, that farmers and farmer varieties should be more effectively involved in crop development.
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Affiliation(s)
- Alfred Mokuwa
- Knowledge, Technology and Innovation Group (KTI), Wageningen University, Wageningen, the Netherlands
| | - Edwin Nuijten
- Knowledge, Technology and Innovation Group (KTI), Wageningen University, Wageningen, the Netherlands
- Louis Bolk Institute, Driebergen, the Netherlands
| | - Florent Okry
- Knowledge, Technology and Innovation Group (KTI), Wageningen University, Wageningen, the Netherlands
- Africa Rice Center, Cotonou, Bénin
| | - Béla Teeken
- Knowledge, Technology and Innovation Group (KTI), Wageningen University, Wageningen, the Netherlands
| | - Harro Maat
- Knowledge, Technology and Innovation Group (KTI), Wageningen University, Wageningen, the Netherlands
| | - Paul Richards
- School of Environmental Sciences, Njala University, Njala, Sierra Leone
| | - Paul C. Struik
- Centre for Crop Systems Analysis, Wageningen University, Wageningen, the Netherlands
- * E-mail:
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Alves-Pereira A, Peroni N, Abreu AG, Gribel R, Clement CR. Genetic structure of traditional varieties of bitter manioc in three soils in Central Amazonia. Genetica 2012; 139:1259-71. [PMID: 22228136 DOI: 10.1007/s10709-011-9627-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 12/23/2011] [Indexed: 11/24/2022]
Abstract
Manioc is the most important food crop that originated in Amazonia. Many studies have increased our understanding of its evolutionary dynamics under cultivation. However, most of them focused on manioc cultivation in environments with low soil fertility, generally Oxisols. Recent ethnobotanical observations showed that bitter manioc also performs well in high fertility soils, such as Amazonian dark earths (ADE) and the floodplain. We used 10 microsatellite loci to investigate the genetic diversity and structure of bitter manioc varieties grown in different soil types in communities of smallholder farmers along the middle Madeira River in Central Amazonia. The genetic diversity of some sweet varieties and seedlings was also evaluated. Adult individuals showed higher levels of genetic diversity and smaller inbreeding coefficients (A ( R ) = 5.52, H ( O ) = 0.576, f = 0.086) than seedlings (A ( R ) = 4.39, H ( O ) = 0.421, f = 0.242). Bitter manioc varieties from the floodplain showed higher levels of genetic diversity (A ( R ) = 5.19, H ( O ) = 0.606) than those from ADE (A ( R ) = 4.45, H ( O ) = 0.538) and from Oxisols (A ( R ) = 4.15, H ( O ) = 0.559). The varieties grown in the floodplain were strongly differentiated from the varieties grown in Oxisols (F ( ST ) = 0.093) and ADE (F ( ST ) = 0.108), suggesting important genetic structuring among varieties grown in the floodplain and upland soils (ADE and Oxisols). This is the first time that genetic divergence of bitter manioc varieties in cultivation in different Amazonian soils in a small geographic area is reported.
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Affiliation(s)
- Alessandro Alves-Pereira
- Instituto Nacional de Pesquisas da Amazônia, INPA, Av. André Araújo, 2936, Aleixo, Manaus, AM 69060-001, Brazil.
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Walker RS, Ribeiro LA. Bayesian phylogeography of the Arawak expansion in lowland South America. Proc Biol Sci 2011; 278:2562-7. [PMID: 21247954 DOI: 10.1098/rspb.2010.2579] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic inference based on language is a vital tool for tracing the dynamics of human population expansions. The timescale of agriculture-based expansions around the world provides an informative amount of linguistic change ideal for reconstructing phylogeographies. Here we investigate the expansion of Arawak, one of the most widely dispersed language families in the Americas, scattered from the Antilles to Argentina. It has been suggested that Northwest Amazonia is the Arawak homeland based on the large number of diverse languages in the region. We generate language trees by coding cognates of basic vocabulary words for 60 Arawak languages and dialects to estimate the phylogenetic relationships among Arawak societies, while simultaneously implementing a relaxed random walk model to infer phylogeographic history. Estimates of the Arawak homeland exclude Northwest Amazonia and are bi-modal, with one potential homeland on the Atlantic seaboard and another more likely origin in Western Amazonia. Bayesian phylogeography better supports a Western Amazonian origin, and consequent dispersal to the Caribbean and across the lowlands. Importantly, the Arawak expansion carried with it not only language but also a number of cultural traits that contrast Arawak societies with other lowland cultures.
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Affiliation(s)
- Robert S Walker
- Department of Anthropology, University of Missouri, MO, USA.
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van Etten J, Hijmans RJ. A geospatial modelling approach integrating archaeobotany and genetics to trace the origin and dispersal of domesticated plants. PLoS One 2010; 5:e12060. [PMID: 20711460 PMCID: PMC2920323 DOI: 10.1371/journal.pone.0012060] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 07/12/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The study of the prehistoric origins and dispersal routes of domesticated plants is often based on the analysis of either archaeobotanical or genetic data. As more data become available, spatially explicit models of crop dispersal can be used to combine different types of evidence. METHODOLOGY/PRINCIPAL FINDINGS We present a model in which a crop disperses through a landscape that is represented by a conductance matrix. From this matrix, we derive least-cost distances from the geographical origin of the crop and use these to predict the age of archaeological crop remains and the heterozygosity of crop populations. We use measures of the overlap and divergence of dispersal trajectories to predict genetic similarity between crop populations. The conductance matrix is constructed from environmental variables using a number of parameters. Model parameters are determined with multiple-criteria optimization, simultaneously fitting the archaeobotanical and genetic data. The consilience reached by the model is the extent to which it converges around solutions optimal for both archaeobotanical and genetic data. We apply the modelling approach to the dispersal of maize in the Americas. CONCLUSIONS/SIGNIFICANCE The approach makes possible the integrative inference of crop dispersal processes, while controlling model complexity and computational requirements.
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Affiliation(s)
- Jacob van Etten
- International Rice Research Institute, Los Baños, Philippines.
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Raji AAJ, Anderson JV, Kolade OA, Ugwu CD, Dixon AGO, Ingelbrecht IL. Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC PLANT BIOLOGY 2009; 9:118. [PMID: 19747391 PMCID: PMC2758884 DOI: 10.1186/1471-2229-9-118] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2009] [Accepted: 09/11/2009] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. RESULTS A total of 846 putative microsatellites were identified in silico from an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes. CONCLUSION A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification, taxonomic studies, and genetic mapping. The study further shows that mining ESTs is a highly efficient strategy for polymorphism detection within the cultivated cassava gene pool.
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Affiliation(s)
- Adebola AJ Raji
- International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria
| | - James V Anderson
- USDA-Agricultural Research Service, Biosciences Research Laboratory, 1605 Albrecht Blvd., Fargo, ND 58105-5674, USA
| | - Olufisayo A Kolade
- International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria
- Africa Rice Center (WARDA), 01 BP 2031, Cotonou, Benin
| | - Chike D Ugwu
- International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria
| | - Alfred GO Dixon
- International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria
| | - Ivan L Ingelbrecht
- International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria
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Pusadee T, Jamjod S, Chiang YC, Rerkasem B, Schaal BA. Genetic structure and isolation by distance in a landrace of Thai rice. Proc Natl Acad Sci U S A 2009; 106:13880-5. [PMID: 19651617 PMCID: PMC2728989 DOI: 10.1073/pnas.0906720106] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2009] [Indexed: 11/18/2022] Open
Abstract
Rice is among the 3 most important crops worldwide. While much of the world's rice harvest is based on modern high-yield varieties, traditional varieties of rice grown by indigenous groups have great importance as a resource for future crop improvement. These local landraces represent an intermediate stage of domestication between a wild ancestor and modern varieties and they serve as reservoirs of genetic variation. Such genetic variation is influenced both by natural processes such as selection and drift, and by the agriculture practices of local farmers. How these processes interact to shape and change the population genetics of landrace rice is unknown. Here, we determine the population genetic structure of a single variety of landrace rice, Bue Chomee, cultivated by Karen people of Thailand. Microsatellite markers reveal high level of genetic variation despite predominant inbreeding in the crop. Bue Chomee rice shows slight but significant genetic differentiation among Karen villages. Moreover, genetically determined traits such as flowering time can vary significantly among villages. An unanticipated result was the overall pattern of genetic differentiation across villages which conforms to an isolation by distance model of differentiation. Isolation by distance is observed in natural plant species where the likelihood of gene flow is inversely related to distance. In Karen rice, gene flow is the result of farmers' seed sharing networks. Taken together, these data suggest that landrace rice is a dynamic genetic system that responds to evolutionary forces, both natural and those imposed by humans.
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Affiliation(s)
- Tonapha Pusadee
- Department of Plant Science and Natural Resources, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sansanee Jamjod
- Department of Plant Science and Natural Resources, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Yu-Chung Chiang
- Department of Life Sciences, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Benjavan Rerkasem
- Department of Plant Science and Natural Resources, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
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Gourd and squash artifacts yield starch grains of feasting foods from preceramic Peru. Proc Natl Acad Sci U S A 2009; 106:13202-6. [PMID: 19633184 DOI: 10.1073/pnas.0903322106] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a study of residues from gourd and squash artifacts, we recovered starch grains from manioc (Manihot esculenta), potato (Solanum sp.), chili pepper (Capsicum spp.), arrowroot (Maranta arundinacea), and algarrobo (Prosopis sp.) from feasting contexts at the Buena Vista site, a central Peruvian preceramic site dating to approximately 2200 calendar years B.C. This study has implications for the study of plant food use wherever gourds or squashes are preserved, documents the earliest evidence for the consumption of algarrobo and arrowroot in Peru, and provides insights into foods consumed at feasts.
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Sardos J, McKey D, Duval MF, Malapa R, Noyer JL, Lebot V. Evolution of cassava (Manihot esculenta Crantz) after recent introduction into a South Pacific Island system: the contribution of sex to the diversification of a clonally propagated crop. Genome 2009; 51:912-21. [PMID: 18956024 DOI: 10.1139/g08-080] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cassava (Manihot esculenta Crantz) is a clonally propagated crop that was introduced into the South Pacific archipelago of Vanuatu in the 1850s. Based on a survey conducted in 10 different villages throughout the archipelago, we present here a study of its diversity. Farmers' knowledge about cultivation cycle and sexual reproduction of cassava was recorded during group interviews in each village. Using a set of 11 SSR markers, we genotyped the 104 landraces collected and 60 supplementary accessions from a within-landrace study (12 landraces x 5 plants). Out of the 104 landraces collected, we discovered 77 different multilocus genotypes and the within-landrace study identified several polyclonal landraces. Our data suggest a number of hypotheses about the dynamics of diversity of cassava in Vanuatu.
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Affiliation(s)
- J Sardos
- CIRAD, UMR DAP 1098, Montpellier, F-34398 France.
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Brown TA, Jones MK, Powell W, Allaby RG. The complex origins of domesticated crops in the Fertile Crescent. Trends Ecol Evol 2009; 24:103-9. [DOI: 10.1016/j.tree.2008.09.008] [Citation(s) in RCA: 206] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 09/12/2008] [Accepted: 09/18/2008] [Indexed: 11/26/2022]
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Rival L, McKey D. Domestication and Diversity in Manioc (Manihot esculentaCrantz ssp.esculenta, Euphorbiaceae). CURRENT ANTHROPOLOGY 2008. [DOI: 10.1086/593119] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Chapman MA, Pashley CH, Wenzler J, Hvala J, Tang S, Knapp SJ, Burke JM. A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus). THE PLANT CELL 2008; 20:2931-45. [PMID: 19017747 PMCID: PMC2613673 DOI: 10.1105/tpc.108.059808] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 10/22/2008] [Accepted: 11/04/2008] [Indexed: 05/18/2023]
Abstract
Genomic scans for selection are a useful tool for identifying genes underlying phenotypic transitions. In this article, we describe the results of a genome scan designed to identify candidates for genes targeted by selection during the evolution of cultivated sunflower. This work involved screening 492 loci derived from ESTs on a large panel of wild, primitive (i.e., landrace), and improved sunflower (Helianthus annuus) lines. This sampling strategy allowed us to identify candidates for selectively important genes and investigate the likely timing of selection. Thirty-six genes showed evidence of selection during either domestication or improvement based on multiple criteria, and a sequence-based test of selection on a subset of these loci confirmed this result. In view of what is known about the structure of linkage disequilibrium across the sunflower genome, these genes are themselves likely to have been targeted by selection, rather than being merely linked to the actual targets. While the selection candidates showed a broad range of putative functions, they were enriched for genes involved in amino acid synthesis and protein catabolism. Given that a similar pattern has been detected in maize (Zea mays), this finding suggests that selection on amino acid composition may be a general feature of the evolution of crop plants. In terms of genomic locations, the selection candidates were significantly clustered near quantitative trait loci (QTL) that contribute to phenotypic differences between wild and cultivated sunflower, and specific instances of QTL colocalization provide some clues as to the roles that these genes may have played during sunflower evolution.
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Affiliation(s)
- Mark A Chapman
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
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The genetic expectations of a protracted model for the origins of domesticated crops. Proc Natl Acad Sci U S A 2008; 105:13982-6. [PMID: 18768818 DOI: 10.1073/pnas.0803780105] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Until recently, domestication has been interpreted as a rapid process with little predomestication cultivation and a relatively rapid rise of the domestication syndrome. This interpretation has had a profound effect on the biological framework within which investigations into crop origins have been carried out. A major underlying assumption has been that artificial selection pressures were substantially stronger than natural selection pressures, resulting in genetic patterns of diversity that reflect genetic independence of geographic localities. Recent archaeobotanical evidence has overturned the notion of a rapid transition, resulting in a protracted model that undermines these assumptions. Conclusions of genome-wide multilocus studies remain problematic in their support of a rapid-transition model by indicating that domesticated crops appear to be associated by monophyly with only a single geographic locality. Simulations presented here resolve this conflict, indicating that the results observed in such studies are inevitable over time at a rate that is largely influenced by the long-term population size. Counterintuitively, multiple origin crops are shown to be more likely to produce monophyletic clades than crops of a single origin. Under the protracted transition, the importance of the rise of the domestication syndrome becomes paramount in producing the patterns of genetic diversity from which crop origins may be deduced. We identify four different interacting levels of organization that now need to be considered to track crop origins from modern genetic diversity, making crop origins a problem that could be addressed through system-based approaches.
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Genetic Variation in Triticum turgidum L. ssp. turgidum Landraces from China Assessed by EST-SSR Markers. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1671-2927(08)60143-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chacón J, Madriñán S, Debouck D, Rodriguez F, Tohme J. Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from analyses of nuclear and chloroplast DNA regions. Mol Phylogenet Evol 2008; 49:260-7. [PMID: 18706508 DOI: 10.1016/j.ympev.2008.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 07/22/2008] [Accepted: 07/23/2008] [Indexed: 10/21/2022]
Abstract
From a phylogenetic perspective, the genus Manihot can be considered as an orphan group of plants, and the scientific knowledge acquired has been mainly related to cassava, one of the most important crops in poor tropical countries. The goal of the majority of evolutionary studies in the genus has been to decipher the domestication process and identify the closest relatives of cassava. Few investigations have focused on wild Manihot species, and the phylogeny of the genus is still unclear. In this study the DNA sequence variation from two chloroplast regions, the nuclear DNA gene G3pdh and two nuclear sequences derived from the 3'-end of two cassava ESTs, were used in order to infer the phylogenetic relationships among a subset of wild Manihot species, including two species from Cnidoscolus as out-groups. Maximum parsimony and Bayesian analyses were conducted for each data set and for a combined matrix due to the low variation of each region when analyzed independently. A penalized likelihood analysis of the chloroplast region trnL-trnF, calibrated with various age estimates for genera in the Euphorbiaceae extracted from the literature was used to determine the ages of origin and diversification of the genus. The two Mesoamerican species sampled form a well-defined clade. The South American species can be grouped into clades of varying size, but the relationships amongst them cannot be established with the data available. The age of the crown node of Manihot was estimated at 6.6 million years ago. Manihot esculenta varieties do not form a monophyletic group that is consistent with the possibility of multiple introgressions of genes from other wild species. The low levels of variation observed in the DNA regions sampled suggest a recent and explosive diversification of the genus, which is confirmed by our age estimates.
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Affiliation(s)
- Juliana Chacón
- Laboratorio de Botánica y Sistemática, Universidad de los Andes, Apartado Aéreo 4976, Bogotá, D.C., Colombia
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