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Kehinde BO, Xie L, Song BK, Zheng X, Fan L. African Cultivated, Wild and Weedy Rice ( Oryza spp.): Anticipating Further Genomic Studies. BIOLOGY 2024; 13:697. [PMID: 39336124 PMCID: PMC11428565 DOI: 10.3390/biology13090697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024]
Abstract
Rice is a staple crop in sub-Saharan Africa, and it is mostly produced by Asian cultivars of Oryza sativa that were introduced to the continent around the fifteenth or sixteenth century. O. glaberrima, the native African rice, has also been planted due to its valuable traits of insect and drought tolerance. Due to competition and resistance evolution, weedy rice has evolved from O. sativa and O. glaberrima, posing an increasing threat to rice production. This paper provides an overview of current knowledge on the introduction and domestication history of cultivated rice in Africa, as well as the genetic properties of African weedy rice that invades paddy fields. Recent developments in genome sequencing have made it possible to uncover findings about O. glaberrima's population structure, stress resilience genes, and domestication bottleneck. Future rice genomic research in Africa should prioritize producing more high-quality reference genomes, quantifying the impact of crop-wild hybridization, elucidating weed adaptation mechanisms through resequencing, and establishing a connection between genomic variation and stress tolerance phenotypes to accelerate breeding efforts.
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Affiliation(s)
- Babatunde O Kehinde
- Institute of Crop Science, Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
- Department of Zoology, University of Lagos, Akoka-Yaba, Lagos 101245, Nigeria
| | - Lingjuan Xie
- Institute of Crop Science, Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, Bandar Sunway 46150, Selangor, Malaysia
| | - Xiaoming Zheng
- Yazhouwan National Laboratory, Yazhou District, Sanya 572024, China
| | - Longjiang Fan
- Institute of Crop Science, Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
- Yazhouwan National Laboratory, Yazhou District, Sanya 572024, China
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Qi Z, Meng X, Xu M, Du Y, Yu J, Song T, Pan X, Zhang R, Cao H, Yu M, Telebanco-Yanoria MJ, Lu G, Zhou B, Liu Y. A novel Pik allele confers extended resistance to rice blast. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39087779 DOI: 10.1111/pce.15072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
In the ongoing arms race between rice and Magnaporthe oryzae, the pathogen employs effectors to evade the immune response, while the host develops resistance genes to recognise these effectors and confer resistance. In this study, we identified a novel Pik allele, Pik-W25, from wild rice WR25 through bulked-segregant analysis, creating the Pik-W25 NIL (Near-isogenic Lines) named G9. Pik-W25 conferred resistance to isolates expressing AvrPik-C/D/E alleles. CRISPR-Cas9 editing was used to generate transgenic lines with a loss of function in Pik-W25-1 and Pik-W25-2, resulting in loss of resistance in G9 to isolates expressing the three alleles, confirming that Pik-W25-induced immunity required both Pik-W25-1 and Pik-W25-2. Yeast two-hybrid (Y2H) and split luciferase complementation assays showed interactions between Pik-W25-1 and the three alleles, while Pik-W25-2 could not interact with AvrPik-C, -D, and -E alleles with Y2H assay, indicating Pik-W25-1 acts as an adaptor and Pik-W25-2 transduces the signal to trigger resistance. The Pik-W25 NIL exhibited enhanced field resistance to leaf and panicle blast without significant changes in morphology or development compared to the parent variety CO39, suggesting its potential for resistance breeding. These findings advance our knowledge of rice blast resistance mechanisms and offer valuable resources for effective and sustainable control strategies.
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Affiliation(s)
- Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
- IRRI-JAAS Joint Laboratory, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Xiuli Meng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Genetics and Biotechnology Division, International Rice Research Institute, College, Los Banos, Laguna, Philippines
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Ming Xu
- High-throughput Genotyping Shared Laboratory, Seed Administration Department of Jiangsu Province, Nanjing, China
| | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Tianqiao Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Rongsheng Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | - Mina Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
| | | | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Bo Zhou
- IRRI-JAAS Joint Laboratory, Jiangsu Academy of Agricultural Science, Nanjing, China
- Genetics and Biotechnology Division, International Rice Research Institute, College, Los Banos, Laguna, Philippines
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing, China
- IRRI-JAAS Joint Laboratory, Jiangsu Academy of Agricultural Science, Nanjing, China
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Adegbaju MS, Ajose T, Adegbaju IE, Omosebi T, Ajenifujah-Solebo SO, Falana OY, Shittu OB, Adetunji CO, Akinbo O. Genetic engineering and genome editing technologies as catalyst for Africa's food security: the case of plant biotechnology in Nigeria. Front Genome Ed 2024; 6:1398813. [PMID: 39045572 PMCID: PMC11263695 DOI: 10.3389/fgeed.2024.1398813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/15/2024] [Indexed: 07/25/2024] Open
Abstract
Many African countries are unable to meet the food demands of their growing population and the situation is worsened by climate change and disease outbreaks. This issue of food insecurity may lead to a crisis of epic proportion if effective measures are not in place to make more food available. Thus, deploying biotechnology towards the improvement of existing crop varieties for tolerance or resistance to both biotic and abiotic stresses is crucial to increasing crop production. In order to optimize crop production, several African countries have implemented strategies to make the most of this innovative technology. For example, Nigerian government has implemented the National Biotechnology Policy to facilitate capacity building, research, bioresource development and commercialization of biotechnology products for over two decades. Several government ministries, research centers, universities, and agencies have worked together to implement the policy, resulting in the release of some genetically modified crops to farmers for cultivation and Commercialization, which is a significant accomplishment. However, the transgenic crops were only brought to Nigeria for confined field trials; the manufacturing of the transgenic crops took place outside the country. This may have contributed to the suspicion of pressure groups and embolden proponents of biotechnology as an alien technology. Likewise, this may also be the underlying issue preventing the adoption of biotechnology products in other African countries. It is therefore necessary that African universities develop capacity in various aspects of biotechnology, to continuously train indigenous scientists who can generate innovative ideas tailored towards solving problems that are peculiar to respective country. Therefore, this study intends to establish the role of genetic engineering and genome editing towards the achievement of food security in Africa while using Nigeria as a case study. In our opinion, biotechnology approaches will not only complement conventional breeding methods in the pursuit of crop improvements, but it remains a viable and sustainable means of tackling specific issues hindering optimal crop production. Furthermore, we suggest that financial institutions should offer low-interest loans to new businesses. In order to promote the growth of biotechnology products, especially through the creation of jobs and revenues through molecular farming.
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Affiliation(s)
- Muyiwa Seyi Adegbaju
- Department of Crop, Soil and Pest Management, Federal University of Technology Akure, Akure, Ondo, Nigeria
| | - Titilayo Ajose
- Fruits and Spices Department, National Horticultural Institute, Ibadan, Oyo, Nigeria
| | | | - Temitayo Omosebi
- Department of Agricultural Technology, Federal College of Forestry, Jos, Nigeria
| | | | - Olaitan Yetunde Falana
- Department of Genetics, Genomic and Bioinformatics, National Biotechnology Research and Development Agency, Abuja, Nigeria
| | - Olufunke Bolatito Shittu
- Department of Microbiology, College of Biosciences, Federal University of Agriculture, Abeokuta, Nigeria
| | | | - Olalekan Akinbo
- African Union Development Agency-NEPAD, Office of Science, Technology and Innovation, Midrand, South Africa
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Labroo MR, Clark LV, Zhang S, Hu F, Tao D, Hamilton RS, Sacks EJ. Solving the mystery of Obake rice in Africa: population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1278196. [PMID: 38034553 PMCID: PMC10684938 DOI: 10.3389/fpls.2023.1278196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
The undomesticated rice relative Oryza longistaminata is a valuable genetic resource for the improvement of the domesticated Asian rice, Oryza sativa. To facilitate the conservation, management, and use of O. longistaminata germplasm, we sought to quantify the population structure and diversity of this species across its geographic range, which includes most of sub-Saharan Africa, and to determine phylogenetic relationships to other AA-genome species of rice present in Africa, including the prevalence of interspecific hybridization between O. longistaminata and O. sativa. Though past plant breeding efforts to introgress genes from O. longistaminata have improved biotic stress resistance, ratooning ability, and yield in O. sativa, progress has been limited by substantial breeding barriers. Nevertheless, despite the strong breeding barriers observed by plant breeders who have attempted this interspecific cross, there have been multiple reports of spontaneous hybrids of O. sativa and O. longistaminata (aka "Obake") obtained from natural populations in Africa. However, the frequency and extent of such natural introgressions and their effect on the evolution of O. longistaminata had not been previously investigated. We studied 190 O. longistaminata accessions, primarily from the International Rice Research Institute genebank collection, along with 309 O. sativa, 25 Oryza barthii, and 83 Oryza glaberrima control outgroups, and 17 control interspecific O. sativa/O. longistaminata hybrids. We analyzed the materials using 178,651 single-nucleotide polymorphisms (SNPs) and seven plastid microsatellite markers. This study identified three genetic subpopulations of O. longistaminata, which correspond geographically to Northwestern Africa, Pan-Africa, and Southern Africa. We confirmed that O. longistaminata is, perhaps counterintuitively, more closely related to the Asian species, O. sativa, than the African species O. barthii and O. glaberrima. We identified 19 recent spontaneous interspecific hybrid individuals between O. sativa and O. longistaminata in the germplasm sampled. Notably, the recent introgression between O. sativa and O. longistaminata has been bidirectional. Moreover, low levels of O. sativa alleles admixed in many predominantly O. longistaminata accessions suggest that introgression also occurred in the distant past, but only in Southern Africa.
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Affiliation(s)
- Marlee R. Labroo
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Lindsay V. Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Shilai Zhang
- School of Agriculture, Research Center for Perennial Rice Engineering and Technology in Yunnan, Yunnan University, Kunming, China
| | - Fengyi Hu
- School of Agriculture, Research Center for Perennial Rice Engineering and Technology in Yunnan, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Seed Laboratory & Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Ruaraidh Sackville Hamilton
- T.T. Chang Genetic Resources Center, International Rice Research Institute (IRRI), Los Baños, Philippines
- CGIAR Genebank Initiative, Salisbury, United Kingdom
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Zhou J, Yang Y, Lv Y, Pu Q, Li J, Zhang Y, Deng X, Wang M, Wang J, Tao D. Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L. FRONTIERS IN PLANT SCIENCE 2022; 13:932737. [PMID: 35845644 PMCID: PMC9280345 DOI: 10.3389/fpls.2022.932737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.
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Affiliation(s)
- Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ying Yang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yonggang Lv
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiuhong Pu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jing Li
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yu Zhang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianneng Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Min Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Jie Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Wambugu PW, Henry R. Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies. Mol Ecol 2022; 31:2207-2222. [PMID: 35170117 PMCID: PMC9303585 DOI: 10.1111/mec.16402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/27/2022]
Abstract
The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.
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Affiliation(s)
- Peterson W Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, 00100, Nairobi, Kenya
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, 4072, Australia
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Chang L, Hu M, Ning J, He W, Gao J, Ndjiondjop MN, Fu Y, Liu F, Sun H, Gu P, Sun C, Zhu Z. The genetic control of glabrous glume during African rice domestication. J Genet Genomics 2022; 49:427-436. [DOI: 10.1016/j.jgg.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/27/2022]
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Mutiga SK, Rotich F, Were VM, Kimani JM, Mwongera DT, Mgonja E, Onaga G, Konaté K, Razanaboahirana C, Bigirimana J, Ndayiragije A, Gichuhi E, Yanoria MJ, Otipa M, Wasilwa L, Ouedraogo I, Mitchell T, Wang GL, Correll JC, Talbot NJ. Integrated Strategies for Durable Rice Blast Resistance in Sub-Saharan Africa. PLANT DISEASE 2021; 105:2749-2770. [PMID: 34253045 DOI: 10.1094/pdis-03-21-0593-fe] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally based blast resistance breeding programs. To develop blast-resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.
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Affiliation(s)
- Samuel K Mutiga
- Biosciences eastern and central Africa - International Livestock Research Institute (BecA-ILRI), Nairobi, Kenya
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Felix Rotich
- Department of Agricultural Resource Management, University of Embu, Embu, Kenya
| | - Vincent M Were
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, U.K
| | - John M Kimani
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi, Kenya
| | - David T Mwongera
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi, Kenya
| | | | - Geoffrey Onaga
- National Agricultural Research Organization, Kampala, Uganda
| | - Kadougoudiou Konaté
- Institute of Environment and Agricultural Research, Bobo-Dioulasso, Burkina Faso
| | | | | | | | - Emily Gichuhi
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi, Kenya
| | | | - Miriam Otipa
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi, Kenya
| | - Lusike Wasilwa
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi, Kenya
| | - Ibrahima Ouedraogo
- Institute of Environment and Agricultural Research, Bobo-Dioulasso, Burkina Faso
| | - Thomas Mitchell
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
| | - James C Correll
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, U.K
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Xie J, Wang X, Xu J, Xie H, Cai Y, Liu Y, Ding X. Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata). RICE (NEW YORK, N.Y.) 2021; 14:79. [PMID: 34495440 PMCID: PMC8426455 DOI: 10.1186/s12284-021-00522-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress. RESULTS We find that the response of the wild rice microbiome to drought was divided into aboveground-underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased 'dispersal limitation', and enhanced 'drift'. CONCLUSIONS Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.
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Affiliation(s)
- Jian Xie
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Xiaoqing Wang
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Jiawang Xu
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, Jiangxi, China
| | - Yizheng Liu
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Xia Ding
- School of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China.
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Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021; 14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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Affiliation(s)
- Peterson W. Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, Nairobi, 00100 Kenya
| | - Marie-Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551 Bouaké 01, Côte d’Ivoire
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
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Thein HW, Yamagata Y, Van Mai T, Yasui H. Four resistance alleles derived from Oryza longistaminata (A. Chev. & Roehrich) against green rice leafhopper, Nephotettix cincticeps (Uhler) identified using novel introgression lines. BREEDING SCIENCE 2019; 69:573-584. [PMID: 31988621 PMCID: PMC6977446 DOI: 10.1270/jsbbs.19060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/30/2019] [Indexed: 05/19/2023]
Abstract
The green rice leafhopper (GRH, Nephotettix cincticeps Uhler) is a serious insect pest of rice (Oryza sativa L.) in temperate regions of Asia. Wild Oryza species are the main source of resistance to insects. The W1413 accession of African wild rice (O. longistaminata A. Chev. & Roehrich) is resistant to GRH. To analyze its resistance, we developed 28 BC3F3 introgression lines carrying W1413 segments in the genetic background of Nipponbare, a susceptible rice cultivar, and evaluated their GRH resistance. Five BC3F3 populations were used for quantitative trait locus (QTL) analysis and seven BC3F4 populations for QTL validation. Four significant QTLs on the long arm of chromosome 2 (qGRH2), short arm of chromosome 4 (qGRH4), short arm of chromosome 5 (qGRH5), and long arm of chromosome 11 (qGRH11) were identified. The contribution of the W1413 allele at qGRH11 was the largest among the four QTLs; the other QTLs also contributed to GRH resistance. Chromosomal locations suggested that qGRH11 corresponds to the previously reported GRH resistance gene Grh2, qGRH4 to Grh6, and qGRH5 to Grh1. qGRH2 is a novel QTL for resistance to GRH. Thus, resistance of O. longistaminata to GRH can be explained by at least four QTLs.
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Affiliation(s)
- Hnin Wah Thein
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University,
744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
| | - Yoshiyuki Yamagata
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University,
744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
| | - Tan Van Mai
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University,
744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University,
744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
- Corresponding author (e-mail: )
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12
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Advances in Molecular Genetics and Genomics of African Rice ( Oryza glaberrima Steud). PLANTS 2019; 8:plants8100376. [PMID: 31561516 PMCID: PMC6843444 DOI: 10.3390/plants8100376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023]
Abstract
African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.
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An asymmetric allelic interaction drives allele transmission bias in interspecific rice hybrids. Nat Commun 2019; 10:2501. [PMID: 31175302 PMCID: PMC6555797 DOI: 10.1038/s41467-019-10488-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/15/2019] [Indexed: 12/30/2022] Open
Abstract
Hybrid sterility (HS) between Oryza sativa (Asian rice) and O. glaberrima (African rice) is mainly controlled by the S1 locus. However, our limited understanding of the HS mechanism hampers utilization of the strong interspecific heterosis. Here, we show that three closely linked genes (S1A4, S1TPR, and S1A6) in the African S1 allele (S1-g) constitute a killer-protector system that eliminates gametes carrying the Asian allele (S1-s). In Asian–African rice hybrids (S1-gS1-s), the S1TPR-S1A4-S1A6 interaction in sporophytic tissues generates an abortion signal to male and female gametes. However, S1TPR can rescue S1-g gametes, while the S1-s gametes selectively abort for lacking S1TPR. Knockout of any of the S1-g genes eliminates the HS. Evolutionary analysis suggests that S1 may have arisen from newly evolved genes, multi-step recombination, and nucleotide variations. Our findings will help to overcome the interspecific reproductive barrier and use Asian–African hybrids for increasing rice production. Our limited understanding of the hybrid sterility (HS) mechanism in Asian–African rice hybrids hampers utilization of the interspecific heterosis for rice production. Here, the authors identify S1-mediated HS-related tripartite gamete killer-protector system, and explore their evolutionary relationship.
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Wambugu PW, Ndjiondjop MN, Henry RJ. Role of genomics in promoting the utilization of plant genetic resources in genebanks. Brief Funct Genomics 2019; 17:198-206. [PMID: 29688255 PMCID: PMC5967547 DOI: 10.1093/bfgp/ely014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and the user community is also recommended.
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Affiliation(s)
- Peterson W Wambugu
- Corresponding author: Robert Henry, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia. Tel.: ±61733460551; Fax: ±61733460555; E-mail:
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Chen E, Huang X, Tian Z, Wing RA, Han B. The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:639-665. [PMID: 31035826 DOI: 10.1146/annurev-arplant-050718-100320] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice (Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.
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Affiliation(s)
- Erwang Chen
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;
| | - Bin Han
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
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Ndjiondjop MN, Semagn K, Zhang J, Gouda AC, Kpeki SB, Goungoulou A, Wambugu P, Dramé KN, Bimpong IK, Zhao D. Development of species diagnostic SNP markers for quality control genotyping in four rice ( Oryza L.) species. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:131. [PMID: 30416368 PMCID: PMC6208651 DOI: 10.1007/s11032-018-0885-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/17/2018] [Indexed: 05/04/2023]
Abstract
Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Kassa Semagn
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6G 2P5 Canada
| | - Jianwei Zhang
- Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Thomas W. Keating Bioresearch Bldg., 1657 E. Helen Street, Tucson, AZ 85721 USA
| | - Arnaud Comlan Gouda
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Sèdjro Bienvenu Kpeki
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Alphonse Goungoulou
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Peterson Wambugu
- Kenya Agricultural and Livestock Research Organization (KALRO), Genetic Resources Research Institute, Nairobi, Kenya
| | | | - Isaac Kofi Bimpong
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Dule Zhao
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
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Wambugu P, Ndjiondjop M, Furtado A, Henry R. Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:100-110. [PMID: 28499072 PMCID: PMC5785344 DOI: 10.1111/pbi.12752] [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: 03/09/2017] [Revised: 04/25/2017] [Accepted: 05/01/2017] [Indexed: 05/03/2023]
Abstract
Amylose content (AC) is a key quality trait in rice. A cross between Oryza glaberrima (African rice) and Oryza sativa (Asian rice) segregating for AC was analysed by sequencing bulks of individuals with high and low AC. SNP associated with the granule bound starch synthase (GBSS1) locus on chromosome 6 were polymorphic between the bulks. In particular, a G/A SNP that would result in an Asp to Asn mutation was identified. This amino acid substitution may be responsible for differences in GBSS activity as it is adjacent to a disulphide linkage conserved in all grass GBSS proteins. Other polymorphisms in genomic regions closely surrounding this variation may be the result of linkage drag. In addition to the variant in the starch biosynthesis gene, SNP on chromosomes 1 and 11 linked to AC was also identified. SNP was found in the genes encoding the NAC and CCAAT-HAP5 transcription factors that have previously been linked to starch biosynthesis. This study has demonstrated that the approach of sequencing bulks was able to identify genes on different chromosomes associated with this complex trait.
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Affiliation(s)
- Peterson Wambugu
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
- Present address:
Kenya Agricultural and Livestock Research Organization (KALRO)Genetic Resources Research InstituteNairobiKenya
| | | | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQldAustralia
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Brozynska M, Copetti D, Furtado A, Wing RA, Crayn D, Fox G, Ishikawa R, Henry RJ. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:765-774. [PMID: 27889940 PMCID: PMC5425390 DOI: 10.1111/pbi.12674] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/10/2016] [Accepted: 11/23/2016] [Indexed: 05/04/2023]
Abstract
The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Dario Copetti
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityCairnsQLDAustralia
| | - Glen Fox
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandToowoombaQLDAustralia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
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Brozynska M, Furtado A, Henry RJ. Genomics of crop wild relatives: expanding the gene pool for crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1070-85. [PMID: 26311018 DOI: 10.1111/pbi.12454] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 05/20/2023]
Abstract
Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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Henry RJ, Rangan P, Furtado A. Functional cereals for production in new and variable climates. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:11-18. [PMID: 26828379 DOI: 10.1016/j.pbi.2015.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/14/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
Adaptation of cereal crops to variable or changing climates requires that essential quality attributes are maintained to deliver food that will be acceptable to human consumers. Advances in cereal genomics are delivering insights into the molecular basis of nutritional and functional quality traits in cereals and defining new genetic resources. Understanding the influence of the environment on expression of these traits will support the retention of these essential functional properties during climate adaptation. New cereals for use as whole grain or ground to flour for other food products may be based upon the traditional species such as rice and wheat currently used in these food applications but may also include new options exploiting genomics tools to allow accelerated domestication of new species.
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Affiliation(s)
- Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Parimalan Rangan
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
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Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Sci Rep 2015; 5:13957. [PMID: 26355750 PMCID: PMC4564799 DOI: 10.1038/srep13957] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 08/13/2015] [Indexed: 01/21/2023] Open
Abstract
Rice is the most important crop in the world, acting as the staple food for over half of the world’s population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.
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The biosynthesis, structure and gelatinization properties of starches from wild and cultivated African rice species (Oryza barthii and Oryza glaberrima). Carbohydr Polym 2015; 129:92-100. [PMID: 26050893 DOI: 10.1016/j.carbpol.2015.04.035] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 12/12/2022]
Abstract
The molecular structure and gelatinization properties of starches from domesticated African rice (Oryza glaberrima) and its wild progenitor (Oryza barthii) are determined and comparison made with Asian domesticated rice (Oryza sativa), the commonest commercial rice. This suggests possible enzymatic processes contributing to the unique traits of the African varieties. These have similar starch structures, including smaller amylose molecules, but larger amounts of amylose chains across the whole amylose chain-length distribution, and higher amylose contents, than O. sativa. They also show a higher proportion of two- and three-lamellae spanning amylopectin branch chains (degree of polymerization 34-100) than O. sativa, which contributes to their higher gelatinization temperatures. Fitting amylopectin chain-length distribution with a biosynthesis-based mathematical model suggests that the reason for this difference might be because O. glaberrima and O. barthii have more active SSIIIa and/or less active SBEIIb enzymes.
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Henry RJ. Genomics strategies for germplasm characterization and the development of climate resilient crops. FRONTIERS IN PLANT SCIENCE 2014; 5:68. [PMID: 24616732 PMCID: PMC3934019 DOI: 10.3389/fpls.2014.00068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 02/10/2014] [Indexed: 05/05/2023]
Abstract
Food security requires the development and deployment of crop varieties resilient to climate variation and change. The study of variations in the genome of wild plant populations can be used to guide crop improvement. Genome variation found in wild crop relatives may be directly relevant to the breeding of environmentally adapted and climate resilient crops. Analysis of the genomes of populations growing in contrasting environments will reveal the genes subject to natural selection in adaptation to climate variations. Whole genome sequencing of these populations should define the numbers and types of genes associated with climate adaptation. This strategy is facilitated by recent advances in sequencing technologies. Wild relatives of rice and barley have been used to assess these approaches. This strategy is most easily applied to species for which a high quality reference genome sequence is available and where populations of wild relatives can be found growing in diverse environments or across environmental gradients.
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Affiliation(s)
- Robert J. Henry
- *Correspondence: Robert J. Henry, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia e-mail:
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