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Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (BETHESDA, MD.) 2023; 13:jkad174. [PMID: 37535690 PMCID: PMC10542218 DOI: 10.1093/g3journal/jkad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
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Affiliation(s)
| | | | - Philippe Cubry
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
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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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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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Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species. Sci Rep 2021; 11:18617. [PMID: 34545105 PMCID: PMC8452751 DOI: 10.1038/s41598-021-97689-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology ("DArTseq"). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies' diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks.
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Song JM, Arif M, Zi Y, Sze SH, Zhang M, Zhang HB. Molecular and genetic dissection of the USDA rice mini-core collection using high-density SNP markers. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110910. [PMID: 34034867 DOI: 10.1016/j.plantsci.2021.110910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 04/05/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Molecular tools and knowledge of crop germplasm are vital for their effective utilization. In this study, we developed 40,866 high-quality and well distributed SNPs for a rice mini-core collection (RMC) developed by the United States Department of Agriculture (USDA). The high-quality SNPs clustered the USDA-RMC into five subpopulations (Ind, indica; Aus, aus; Afr, African rice; TeJ, temperate japonica; TrJ, tropical japonica) and one admixture (Adm). This classification was further confirmed by phylogenetic and principal component analyses. The rice ARO (aromatic) subpopulation of previous studies was re-assigned with Adm and the WD (wild-type) subpopulation was re-defined to the Afr subpopulation because most of its accessions are African cultivated rice. The Aus and Ind subpopulations had a substantially wider genetic variation than the TrJ and TeJ subpopulations. The genetic diversities were much larger between the Ind or Aus subpopulation and the TrJ or TeJ subpopulation than between the Afr subpopulation and the Ind, Aus, TrJ or TeJ subpopulation. Comparative agronomic trait analysis between the subpopulations also supported the genetic structure and variation of the RMC, and suggested the existence of extensive variation in the genes controlling agronomic traits among them. Furthermore, analysis of ancestral membership of the RMC accessions revealed that reproductive barrier or wide incompatibility existed between the Indica and Japonica groups, while gene flow occurred between them. These results provide high-quality SNPs and knowledge of genetic structure and diversity of the USDA-RMC necessary for enhanced rice research and breeding.
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Affiliation(s)
- Jian-Min Song
- Crop Research Institute/National Engineering Laboratory for Wheat and Maize, Shandong Academy of Agricultural Sciences (SAAS), Jinan, 250100, PR China; Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
| | - Muhammad Arif
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA; Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
| | - Yan Zi
- Crop Research Institute/National Engineering Laboratory for Wheat and Maize, Shandong Academy of Agricultural Sciences (SAAS), Jinan, 250100, PR China
| | - Sing-Hoi Sze
- Department of Computer Science and Engineering and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
| | - Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
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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: 3] [Impact Index Per Article: 1.0] [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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Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing. Sci Rep 2020; 10:13995. [PMID: 32814806 PMCID: PMC7438528 DOI: 10.1038/s41598-020-70842-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions across 11 datasets in terms of SNP polymorphism, heterozygosity/heterogeneity, diversity indices, concordance among genetic dissimilarity matrices, population structure, and genetic differentiation; there were, however, a few discrepancies between some pairs of datasets. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.
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Pidon H, Chéron S, Ghesquière A, Albar L. Allele mining unlocks the identification of RYMV resistance genes and alleles in African cultivated rice. BMC PLANT BIOLOGY 2020; 20:222. [PMID: 32429875 PMCID: PMC7236528 DOI: 10.1186/s12870-020-02433-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/07/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Rice yellow mottle virus (RYMV) is a major rice pathogen in Africa. Three resistance genes, i.e. RYMV1, RYMV2 and RYMV3, have been previously described. RYMV1 encodes the translation initiation factor eIF(iso)4G1 and the best candidate genes for RYMV2 and RYMV3 encode a homolog of an Arabidopsis nucleoporin (CPR5) and a nucleotide-binding domain and leucine-rich repeat containing domain (NLR) protein, respectively. High resistance is very uncommon in Asian cultivated rice (Oryza sativa), with only two highly resistant accessions identified so far, but it is more frequent in African cultivated rice (Oryza glaberrima). RESULTS Here we report the findings of a resistance survey in a reference collection of 268 O. glaberrima accessions. A total of 40 resistant accessions were found, thus confirming the high frequency of resistance to RYMV in this species. We analysed the variability of resistance genes or candidate genes in this collection based on high-depth Illumina data or Sanger sequencing. Alleles previously shown to be associated with resistance were observed in 31 resistant accessions but not in any susceptible ones. Five original alleles with a frameshift or untimely stop codon in the candidate gene for RYMV2 were also identified in resistant accessions. A genetic analysis revealed that these alleles, as well as T-DNA insertions in the candidate gene, were responsible of RYMV resistance. All 40 resistant accessions were ultimately linked to a validated or candidate resistance allele at one of the three resistance genes to RYMV. CONCLUSION This study demonstrated that the RYMV2 resistance gene is homologous to the Arabidopsis CPR5 gene and revealed five new resistance alleles at this locus. It also confirmed the close association between resistance and an amino-acid substitution in the leucine-rich repeat of the NLR candidate for RYMV3. We also provide an extensive overview of the genetic diversity of resistance to RYMV in the O. glaberrima species, while underlining the contrasted pattern of diversity between O. glaberrima and O. sativa for this trait. The different resistance genes and alleles will be instrumental in breeding varieties with sustainable field resistance to RYMV.
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Affiliation(s)
- Hélène Pidon
- DIADE, Univ. Montpellier, IRD, Montpellier, France
- Present Address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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Gemenet DC, Kitavi MN, David M, Ndege D, Ssali RT, Swanckaert J, Makunde G, Yencho GC, Gruneberg W, Carey E, Mwanga RO, Andrade MI, Heck S, Campos H. Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs. PLoS One 2020; 15:e0232173. [PMID: 32330201 PMCID: PMC7182229 DOI: 10.1371/journal.pone.0232173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/08/2020] [Indexed: 11/19/2022] Open
Abstract
Quality assurance and control (QA/QC) is an essential element of a breeding program's optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)'s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping studies. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers' fields. The study also enabled evaluation of CIP's global breeding population structure and the effect of some of the most devastating stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato.
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Affiliation(s)
| | - Mercy N. Kitavi
- International Potato Center (CIP), ILRI Campus, Nairobi, Kenya
| | - Maria David
- International Potato Center (CIP), Apartado, Lima, Peru
| | - Dorcah Ndege
- International Potato Center (CIP), ILRI Campus, Nairobi, Kenya
| | | | | | | | - G. Craig Yencho
- North Carolina State University, Raleigh, North Carolina, United States of America
| | | | - Edward Carey
- International Potato Center (CIP), Kumasi, Ghana
| | | | | | - Simon Heck
- International Potato Center (CIP), ILRI Campus, Nairobi, Kenya
| | - Hugo Campos
- International Potato Center (CIP), Apartado, Lima, Peru
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Hyun DY, Sebastin R, Lee KJ, Lee GA, Shin MJ, Kim SH, Lee JR, Cho GT. Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:688. [PMID: 32625218 PMCID: PMC7311657 DOI: 10.3389/fpls.2020.00688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/30/2020] [Indexed: 05/17/2023]
Abstract
Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 species-specific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.
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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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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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Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
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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.
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Alphonse Goungoulou
- 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
| | - Dule Zhao
- 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.
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14
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Veltman MA, Flowers JM, van Andel TR, Schranz ME. Origins and geographic diversification of African rice (Oryza glaberrima). PLoS One 2019; 14:e0203508. [PMID: 30840637 PMCID: PMC6402627 DOI: 10.1371/journal.pone.0203508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/09/2019] [Indexed: 12/30/2022] Open
Abstract
Rice is a staple food for the majority of the world’s population. Whereas Asian rice (Oryza sativa) has been extensively studied, the exact origins of African rice (Oryza glaberrima) are still contested. Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice–either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest—suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.
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Affiliation(s)
- Margaretha A. Veltman
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
- * E-mail:
| | - Jonathan M. Flowers
- Center for Genomics and Systems Biology, New York University, New York City, New York, United States of America
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Tinde R. van Andel
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
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15
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Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie K, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y. The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. Curr Biol 2018; 28:2274-2282.e6. [PMID: 29983312 DOI: 10.1016/j.cub.2018.05.066] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/10/2018] [Accepted: 05/24/2018] [Indexed: 12/23/2022]
Abstract
African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10,000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2,000 years ago. During the last 5 centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. A gene, PROG1, associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, a shattering gene, SH5, showed selection signature during African rice domestication, but not during Asian rice domestication. Overall, our genomic data revealed a complex history of African rice domestication influenced by important climatic changes in the Saharan area, by the expansion of African agricultural society, and by recent replacement by another domesticated species.
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Affiliation(s)
- Philippe Cubry
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Christine Tranchant-Dubreuil
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; SouthGreen Development Platform, Agropolis Campus, Montpellier, France
| | - Anne-Céline Thuillet
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Cécile Monat
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; SouthGreen Development Platform, Agropolis Campus, Montpellier, France
| | | | - Karine Labadie
- CEA, Institut de Biologie François Jacob, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France; CNRS, UMR 8030, CP5706, Evry, France; Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Corinne Cruaud
- CEA, Institut de Biologie François Jacob, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France; CNRS, UMR 8030, CP5706, Evry, France; Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Stefan Engelen
- CEA, Institut de Biologie François Jacob, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France; CNRS, UMR 8030, CP5706, Evry, France; Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Nora Scarcelli
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Bénédicte Rhoné
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Lyon, France
| | - Concetta Burgarella
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | | | - Pierre Larmande
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; SouthGreen Development Platform, Agropolis Campus, Montpellier, France; Institut de Biologie Computationnelle (IBC), Université Montpellier 2, 860 Rue St Priest, 34095 Montpellier Cedex 5, France
| | - Patrick Wincker
- CEA, Institut de Biologie François Jacob, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France; CNRS, UMR 8030, CP5706, Evry, France; Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Olivier François
- Université Grenoble-Alpes, CNRS, UMR 5525 TIMC-IMAG, 38042 Grenoble, France
| | - François Sabot
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; SouthGreen Development Platform, Agropolis Campus, Montpellier, France; Université de Montpellier, Place Eugène Bataillon, 34000 Montpellier, France.
| | - Yves Vigouroux
- Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; Université de Montpellier, Place Eugène Bataillon, 34000 Montpellier, France.
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16
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Monat C, Pera B, Ndjiondjop MN, Sow M, Tranchant-Dubreuil C, Bastianelli L, Ghesquière A, Sabot F. De Novo Assemblies of Three Oryza glaberrima Accessions Provide First Insights about Pan-Genome of African Rices. Genome Biol Evol 2018; 9:1-6. [PMID: 28173009 PMCID: PMC5381527 DOI: 10.1093/gbe/evw253] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2016] [Indexed: 11/12/2022] Open
Abstract
Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals. The three assemblies shown large common regions, but almost 25% of the genome present collinearity breakpoints or are even individual specific.
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Affiliation(s)
- Cécile Monat
- RICE Team, DIADE UMR 232 IRD/UM, IRD France Sud, Montpellier, France
| | - Bérengère Pera
- RICE Team, DIADE UMR 232 IRD/UM, IRD France Sud, Montpellier, France.,CEA//Genoscope, Evry, France
| | | | | | | | - Leila Bastianelli
- Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Alain Ghesquière
- RICE Team, DIADE UMR 232 IRD/UM, IRD France Sud, Montpellier, France
| | - Francois Sabot
- RICE Team, DIADE UMR 232 IRD/UM, IRD France Sud, Montpellier, France
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17
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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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18
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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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19
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Mgonja EM, Park CH, Kang H, Balimponya EG, Opiyo S, Bellizzi M, Mutiga SK, Rotich F, Ganeshan VD, Mabagala R, Sneller C, Correll J, Zhou B, Talbot NJ, Mitchell TK, Wang GL. Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa. PHYTOPATHOLOGY 2017; 107:1039-1046. [PMID: 28719243 DOI: 10.1094/phyto-12-16-0421-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.
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Affiliation(s)
- Emmanuel M Mgonja
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Chan Ho Park
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Houxiang Kang
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Elias G Balimponya
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Stephen Opiyo
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Maria Bellizzi
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Samuel K Mutiga
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Felix Rotich
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Veena Devi Ganeshan
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Robert Mabagala
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Clay Sneller
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Jim Correll
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Bo Zhou
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Nicholas J Talbot
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Thomas K Mitchell
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
| | - Guo-Liang Wang
- First, second, fifth, sixth, ninth, fifteenth, and sixteenth authors: Department of Plant Pathology, The Ohio State University, Columbus; fourth and eleventh authors: Department of Horticulture and Crop science, The Ohio State University, Columbus; third author: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; tenth author: Department of Crop Science and Production, Sokoine University of Agriculture, Morogoro, Tanzania; seventh, eighth, and twelfth author: Department of Plant Pathology, University of Arkansas, Fayetteville; seventh author: Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ILRI Complex, Nairobi, Kenya; thirteenth author: International Rice Research Institute, Los Banos, Philippines; and fourteenth author, School of Biosciences, University of Exeter, UK
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20
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Pidon H, Ghesquière A, Chéron S, Issaka S, Hébrard E, Sabot F, Kolade O, Silué D, Albar L. Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:807-818. [PMID: 28144699 DOI: 10.1007/s00122-017-2853-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/04/2017] [Indexed: 05/24/2023]
Abstract
A new resistance gene against Rice yellow mottle virus was identified and mapped in a 15-kb interval. The best candidate is a CC-NBS-LRR gene. Rice yellow mottle virus (RYMV) disease is a serious constraint to the cultivation of rice in Africa and selection for resistance is considered to be the most effective management strategy. The aim of this study was to characterize the resistance of Tog5307, a highly resistant accession belonging to the African cultivated rice species (Oryza glaberrima), that has none of the previously identified resistance genes to RYMV. The specificity of Tog5307 resistance was analyzed using 18 RYMV isolates. While three of them were able to infect Tog5307 very rapidly, resistance against the others was effective despite infection events attributed to resistance-breakdown or incomplete penetrance of the resistance. Segregation of resistance in an interspecific backcross population derived from a cross between Tog5307 and the susceptible Oryza sativa variety IR64 showed that resistance is dominant and is controlled by a single gene, named RYMV3. RYMV3 was mapped in an approximately 15-kb interval in which two candidate genes, coding for a putative transmembrane protein and a CC-NBS-LRR domain-containing protein, were annotated. Sequencing revealed non-synonymous polymorphisms between Tog5307 and the O. glaberrima susceptible accession CG14 in both candidate genes. An additional resistant O. glaberrima accession, Tog5672, was found to have the Tog5307 genotype for the CC-NBS-LRR gene but not for the putative transmembrane protein gene. Analysis of the cosegregation of Tog5672 resistance with the RYMV3 locus suggests that RYMV3 is also involved in Tog5672 resistance, thereby supporting the CC-NBS-LRR gene as the best candidate for RYMV3.
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Affiliation(s)
- Hélène Pidon
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Alain Ghesquière
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Sophie Chéron
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Souley Issaka
- Africa Rice Center, Cotonou, Benin
- FSAE, Université de Tillabéri, Tillabéri, Niger
| | - Eugénie Hébrard
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement - Centre de Coopération Internationale en Recherche Agronomique pour le Développement - Université de Montpellier, Montpellier, France
| | - François Sabot
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Olufisayo Kolade
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
- Africa Rice Center, Cotonou, Benin
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Laurence Albar
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France.
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21
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Ta KN, Adam H, Staedler YM, Schönenberger J, Harrop T, Tregear J, Do NV, Gantet P, Ghesquière A, Jouannic S. Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice. EvoDevo 2017; 8:2. [PMID: 28149498 PMCID: PMC5273837 DOI: 10.1186/s13227-017-0065-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 01/14/2017] [Indexed: 11/15/2022] Open
Abstract
Background
The African rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development. Results Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development. We uncovered evidence for a wider rachis meristem in O. glaberrima than in O. barthii. At the molecular level, spatial and temporal expression profiles of orthologs of O. sativa genes related to meristem activity and meristem fate control were obtained using in situ hybridization and qRT-PCR. Despite highly conserved spatial expression patterns between O. glaberrima and O. barthii, differences in the expression levels of these early acting genes were detected. Conclusion The higher complexity of the O. glaberrima panicle compared to that of its wild relative O. barthii is associated with a wider rachis meristem and a modification of expression of branching-related genes. Our study indicates that the expression of genes in the miR156/miR529/SPL and TAW1 pathways, along with that of their target genes, is altered from the unbranched stage of development. This suggests that differences in panicle complexity between the two African rice species result from early alterations to gene expression during reproductive development. Electronic supplementary material The online version of this article (doi:10.1186/s13227-017-0065-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- K N Ta
- UMR DIADE, IRD, 911, Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.,LMI RICE, IRD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong Road, Hanoi, Vietnam
| | - H Adam
- UMR DIADE, IRD, 911, Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - Y M Staedler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - J Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - T Harrop
- UMR DIADE, IRD, 911, Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - J Tregear
- UMR DIADE, IRD, 911, Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - N V Do
- LMI RICE, IRD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong Road, Hanoi, Vietnam
| | - P Gantet
- LMI RICE, IRD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong Road, Hanoi, Vietnam.,UMR DIADE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.,Department of Biotechnology-Pharmacology, University of Science and Technology of Hanoi (USTH), 18 Hoang Quoc Viet Road, Hanoi, Vietnam
| | - A Ghesquière
- UMR DIADE, IRD, 911, Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
| | - S Jouannic
- UMR DIADE, IRD, 911, Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.,LMI RICE, IRD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong Road, Hanoi, Vietnam
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22
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Ndjiondjop MN, Semagn K, Gouda AC, Kpeki SB, Dro Tia D, Sow M, Goungoulou A, Sie M, Perrier X, Ghesquiere A, Warburton ML. Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq. FRONTIERS IN PLANT SCIENCE 2017; 8:1748. [PMID: 29093721 PMCID: PMC5651524 DOI: 10.3389/fpls.2017.01748] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/25/2017] [Indexed: 05/20/2023]
Abstract
The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.
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Affiliation(s)
- Marie-Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Bouake, Cote d'Ivoire
- *Correspondence: Marie-Noelle Ndjiondjop
| | - Kassa Semagn
- Department of Agriculture, Forestry and Nutrition Science, University of Alberta, Edmonton, Canada
| | | | | | | | - Mounirou Sow
- Africa Rice Center (AfricaRice), Ibadan, Nigeria
| | | | - Moussa Sie
- Africa Rice Center (AfricaRice), Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), Antananarivo, Madagascar
| | - Xavier Perrier
- Unité Mixte de Recherche Amélioration Génétique, CIRAD, Montpellier, France
- University of Montpellier, Montpellier, France
| | - Alain Ghesquiere
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Marilyn L. Warburton
- Corn Host Plant Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Starkville, Mississippi, United States
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Ta KN, Sabot F, Adam H, Vigouroux Y, De Mita S, Ghesquière A, Do NV, Gantet P, Jouannic S. miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species. RICE (NEW YORK, N.Y.) 2016; 9:10. [PMID: 26969003 PMCID: PMC4788661 DOI: 10.1186/s12284-016-0082-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/06/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii. RESULTS Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to miR2118-triggered phased siRNAs. A detailed expression profiling during the panicle development of O. glaberrima and O. barthii using qRT-PCRs and in situ hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators (miR2118 and MEL1 gene) in O. glaberrima compared to O. barthii. We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems. CONCLUSION Differential expression of the miR2118-triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.
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Affiliation(s)
- K. N. Ta
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
| | - F. Sabot
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - H. Adam
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - Y. Vigouroux
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - S. De Mita
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />Present address: INRA, Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, F-54280 Champenoux, France
| | - A. Ghesquière
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
| | - N. V. Do
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
| | - P. Gantet
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
- />Université de Montpellier, UMR DIADE, Place Eugène Bataillon, F-34095 Montpellier, Cedex 5 France
| | - S. Jouannic
- />IRD, UMR DIADE, 911, avenue Agropolis, BP64501, F-34394 Montpellier, Cedex 5 France
- />LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Pham Van Dong road, Hanoi, Vietnam
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24
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Hutin M, Sabot F, Ghesquière A, Koebnik R, Szurek B. A knowledge-based molecular screen uncovers a broad-spectrum OsSWEET14 resistance allele to bacterial blight from wild rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:694-703. [PMID: 26426417 DOI: 10.1111/tpj.13042] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/01/2015] [Accepted: 09/08/2015] [Indexed: 05/19/2023]
Abstract
Transcription activator-like (TAL) effectors are type III-delivered transcription factors that enhance the virulence of plant pathogenic Xanthomonas species through the activation of host susceptibility (S) genes. TAL effectors recognize their DNA target(s) via a partially degenerate code, whereby modular repeats in the TAL effector bind to nucleotide sequences in the host promoter. Although this knowledge has greatly facilitated our power to identify new S genes, it can also be easily used to screen plant genomes for variations in TAL effector target sequences and to predict for loss-of-function gene candidates in silico. In a proof-of-principle experiment, we screened a germplasm of 169 rice accessions for polymorphism in the promoter of the major bacterial blight susceptibility S gene OsSWEET14, which encodes a sugar transporter targeted by numerous strains of Xanthomonas oryzae pv. oryzae. We identified a single allele with a deletion of 18 bp overlapping with the binding sites targeted by several TAL effectors known to activate the gene. We show that this allele, which we call xa41(t), confers resistance against half of the tested Xoo strains, representative of various geographic origins and genetic lineages, highlighting the selective pressure on the pathogen to accommodate OsSWEET14 polymorphism, and reciprocally the apparent limited possibilities for the host to create variability at this particular S gene. Analysis of xa41(t) conservation across the Oryza genus enabled us to hypothesize scenarios as to its evolutionary history, prior to and during domestication. Our findings demonstrate that resistance through TAL effector-dependent loss of S-gene expression can be greatly fostered upon knowledge-based molecular screening of a large collection of host plants.
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Affiliation(s)
- Mathilde Hutin
- UMR IPME, IRD-CIRAD-Université Montpellier 2, Montpellier, France
| | - François Sabot
- UMR DIADE IRD/UM2, BP 64501, 34394, Montpellier Cedex 5, France
| | | | - Ralf Koebnik
- UMR IPME, IRD-CIRAD-Université Montpellier 2, Montpellier, France
| | - Boris Szurek
- UMR IPME, IRD-CIRAD-Université Montpellier 2, Montpellier, France
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