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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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Li F, Wang K, Zhang X, Han P, Liu Y, Zhang J, Peng T, Li J, Zhao Y, Sun H, Du Y. BPB1 regulates rice ( Oryza sative L.) panicle length and panicle branch development by promoting lignin and inhibiting cellulose accumulation. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:41. [PMID: 37312745 PMCID: PMC10248638 DOI: 10.1007/s11032-023-01389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/24/2023] [Indexed: 06/15/2023]
Abstract
Panicle structure is one of the most important agronomic traits directly related to rice yield. This study identified a rice mutant basal primary branch 1 (bpb1), which exhibited a phenotype of reduced panicle length and arrested basal primary branch development. In addition, lignin content was found to be increased while cellulose content was decreased in bpb1 young panicles. Map-based cloning methods characterized the gene BPB1, which encodes a peptide transporter (PTR) family transporter. Phylogenetic tree analysis showed that the BPB1 family is highly conserved in plants, especially the PTR2 domain. It is worth noting that BPB1 is divided into two categories based on monocotyledonous and dicotyledonous plants. Transcriptome analysis showed that BPB1 mutation can promote lignin synthesis and inhibit cellulose synthesis, starch and sucrose metabolism, cell cycle, expression of various plant hormones, and some star genes, thereby inhibiting rice panicle length, resulting in basal primary branch development stagnant phenotypes. In this study, BPB1 provides new insights into the molecular mechanism of rice panicle structure regulation by BPB1 by regulating lignin and cellulose content and several transcriptional metabolic pathways. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01389-x.
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Affiliation(s)
- Fei Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ke Wang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Xiaohua Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Peijie Han
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ye Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Jing Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Ting Peng
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Junzhou Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Yafan Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046 Henan Province China
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Ookawa T, Nomura T, Kamahora E, Jiang M, Ochiai Y, Samadi AF, Yamaguchi T, Adachi S, Katsura K, Motobayashi T. Pyramiding of multiple strong-culm genes originating from indica and tropical japonica to the temperate japonica rice. Sci Rep 2022; 12:15400. [PMID: 36100633 PMCID: PMC9470567 DOI: 10.1038/s41598-022-19768-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Severe lodging has recurrently occurred at strong typhoon’s hitting in recent climate change. The identification of quantitative trait loci and their responsible genes associated with a strong culm and their pyramiding are important for developing high-yielding varieties with a superior lodging resistance. To evaluate the effects of four strong-culm genes on lodging resistance, the temperate japonica near isogenic line (NIL) with the introgressed SCM1 or SCM2 locus of the indica variety, Habataki and the other NIL with the introgeressed SCM3 or SCM4 locus of the tropical japonica variety, Chugoku 117 were developed. Then, we developed the pyramiding lines with double,triple and quadruple combinations derived from step-by-step crosses among NIL-SCM1–NIL-SCM4. Quadruple pyramiding line (NIL-SCM1 + 2 + 3 + 4) showed the largest culm diameter and the highest culm strength among the combinations and increased spikelet number due to the pleiotropic effects of these genes. Pyramiding of strong culm genes resulted in much increased culm thickness, culm strength and spikelet number due to their additive effect. SCM1 mainly contributed to enhance their pyramiding effect. These results in this study suggest the importance of identifying the combinations of superior alleles of strong culm genes among natural variation and pyramiding these genes for improving high-yielding varieties with a superior lodging resistance.
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Affiliation(s)
- Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
| | - Tomohiro Nomura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Eri Kamahora
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Mingjin Jiang
- Rice Research Institute of Guizhou Academy of Agricultural Science, Guiyang, 550006, Guizhou, China
| | - Yusuke Ochiai
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Ahmad Fahim Samadi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takuya Yamaguchi
- Toyama Prefectural Tonami Agriculture and Forestry Promotion Center, 1-7 Saiwai-cho, Tonami, Toyama, 939-1386, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Keisuke Katsura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takashi Motobayashi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
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Kato K, Hirayama Y. Development and characterization of chromosome segment substitution lines derived from backcross between japonica donor rice cultivar Yukihikari and japonica recipient cultivar Kirara397. BREEDING SCIENCE 2021; 71:283-290. [PMID: 34377077 PMCID: PMC8329885 DOI: 10.1270/jsbbs.20128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/24/2020] [Indexed: 05/27/2023]
Abstract
Grain yield-related traits and grain quality-related traits are important for rice cultivars. The quantitative trait loci (QTLs) involved in controlling the natural variation in these traits among closely related cultivars are still unclear. The present study describes the development of a novel chromosome segment substitution line (CSSL) population derived from a cross between the temperate japonica cultivars Yukihikari and Kirara397, which are grown in Hokkaido, the northernmost limit for rice cultivation. Days to heading, culm length, panicle length, panicle number, brown grain weight per plant, thousand brown grain weight, brown grain length, brown grain width, brown grain thickness, apparent amylose content, and protein content were evaluated. Panicle length, brown grain length and amylose content differed significantly in the parental cultivars. Thirty-five significant changes in the evaluated traits were identified in the CSSLs. A total of 28 QTLs were located on chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 10, 11 and 12. These findings could be useful for breeding rice cultivars in the northernmost limit for rice cultivation.
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Affiliation(s)
- Kiyoaki Kato
- Department of Agro-Environmental Science, Obihiro University of Agriculture
and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido
080-8555, Japan
| | - Yuji Hirayama
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local
Independent Administrative Agency, Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397, Japan
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Kumar A, Kumar S, Singh KB, Prasad M, Thakur JK. Designing a Mini-Core Collection Effectively Representing 3004 Diverse Rice Accessions. PLANT COMMUNICATIONS 2020; 1:100049. [PMID: 33367255 PMCID: PMC7748012 DOI: 10.1016/j.xplc.2020.100049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/13/2019] [Accepted: 04/21/2020] [Indexed: 05/14/2023]
Abstract
Genetic diversity provides the foundation for plant breeding and genetic research. Over 3000 rice genomes were recently sequenced as part of the 3K Rice Genome (3KRG) Project. We added four additional Indian rice accessions to create a panel of 3004 accessions. However, such a large collection of germplasm is difficult to preserve and evaluate. The construction of core and mini-core collections is an efficient method for the management of genetic resources. In this study, we developed a mini-core comprising 520 accessions that captured most of the SNPs and represented all of the phenotypes and geographic regions from the original panel. The mini-core was validated using different statistical analyses and contained representatives from all major rice groups, including japonica, indica, aus/boro, and aromatic/basmati. Genome-wide association analyses of the mini-core panel efficiently reproduced the marker-trait associations identified in the original panel. Haplotype analysis validated the utility of the mini-core panel. In the current era with many ongoing large-scale sequencing projects, such a strategy for mini-core design should be useful in many crops. The rice mini-core collection developed in this study would be valuable for agronomic trait evaluation and useful for rice improvement via marker-assisted molecular breeding.
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Affiliation(s)
- Angad Kumar
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shivendra Kumar
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kajol B.M. Singh
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K. Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Zhou C, Ye H, Hu J, Shi X, Hua S, Yue J, Xu Z, Yang G. Automated Counting of Rice Panicle by Applying Deep Learning Model to Images from Unmanned Aerial Vehicle Platform. SENSORS 2019; 19:s19143106. [PMID: 31337086 PMCID: PMC6679257 DOI: 10.3390/s19143106] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 12/03/2022]
Abstract
The number of panicles per unit area is a common indicator of rice yield and is of great significance to yield estimation, breeding, and phenotype analysis. Traditional counting methods have various drawbacks, such as long delay times and high subjectivity, and they are easily perturbed by noise. To improve the accuracy of rice detection and counting in the field, we developed and implemented a panicle detection and counting system that is based on improved region-based fully convolutional networks, and we use the system to automate rice-phenotype measurements. The field experiments were conducted in target areas to train and test the system and used a rotor light unmanned aerial vehicle equipped with a high-definition RGB camera to collect images. The trained model achieved a precision of 0.868 on a held-out test set, which demonstrates the feasibility of this approach. The algorithm can deal with the irregular edge of the rice panicle, the significantly different appearance between the different varieties and growing periods, the interference due to color overlapping between panicle and leaves, and the variations in illumination intensity and shading effects in the field. The result is more accurate and efficient recognition of rice-panicles, which facilitates rice breeding. Overall, the approach of training deep learning models on increasingly large and publicly available image datasets presents a clear path toward smartphone-assisted crop disease diagnosis on a global scale.
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Affiliation(s)
- Chengquan Zhou
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310000, China
| | - Hongbao Ye
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310000, China
| | - Jun Hu
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310000, China
| | - Xiaoyan Shi
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310000, China
| | - Shan Hua
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310000, China
| | - Jibo Yue
- Key Laboratory of Quantitative Remote Sensing in Agriculture of Ministry of Agriculture P. R. China, Beijing Research Center for Information Technology in Agriculture, Beijing 100089, China
- Key Laboratory of Agri-informatics, Ministry of Agriculture, Beijing 100089, China
| | - Zhifu Xu
- Institute of Agricultural Equipment, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou 310000, China.
| | - Guijun Yang
- Key Laboratory of Quantitative Remote Sensing in Agriculture of Ministry of Agriculture P. R. China, Beijing Research Center for Information Technology in Agriculture, Beijing 100089, China.
- Key Laboratory of Agri-informatics, Ministry of Agriculture, Beijing 100089, China.
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TA KN, KHONG NG, HA TL, NGUYEN DT, MAI DC, HOANG TG, PHUNG TPN, BOURRIE I, COURTOIS B, TRAN TTH, DINH BY, LA TN, DO NV, LEBRUN M, GANTET P, JOUANNIC S. A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits. BMC PLANT BIOLOGY 2018; 18:282. [PMID: 30428844 PMCID: PMC6234598 DOI: 10.1186/s12870-018-1504-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/26/2018] [Indexed: 05/20/2023]
Abstract
CONTEXT Yield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces. RESULTS Using a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits. CONCLUSIONS Our phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice.
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Affiliation(s)
- Kim Nhung TA
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- Present address: Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Ngan Giang KHONG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- Present address: Department of Molecular Biology, Palacký University, Olomouc, Czech Republic
| | - Thi Loan HA
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Dieu Thu NGUYEN
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Duc Chung MAI
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Thi Giang HOANG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Thi Phuong Nhung PHUNG
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | | | - Brigitte COURTOIS
- CIRAD, UMR AGAP, University of Montpellier, INRA, Montpellier, France
| | | | | | | | - Nang Vinh DO
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Michel LEBRUN
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR LSTM, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Pascal GANTET
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Stefan JOUANNIC
- LMI RICE, University of Montpellier, IRD, CIRAD, USTH, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
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