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Beránková D, Čížková J, Majzlíková G, Doležalová A, Mduma H, Brown A, Swennen R, Hřibová E. Striking variation in chromosome structure within Musa acuminata subspecies, diploid cultivars, and F1 diploid hybrids. FRONTIERS IN PLANT SCIENCE 2024; 15:1387055. [PMID: 39027673 PMCID: PMC11255410 DOI: 10.3389/fpls.2024.1387055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024]
Abstract
The majority of cultivated bananas originated from inter- and intra(sub)specific crosses between two wild diploid species, Musa acuminata and Musa balbisiana. Hybridization and polyploidization events during the evolution of bananas led to the formation of clonally propagated cultivars characterized by a high level of genome heterozygosity and reduced fertility. The combination of low fertility in edible clones and differences in the chromosome structure among M. acuminata subspecies greatly hampers the breeding of improved banana cultivars. Using comparative oligo-painting, we investigated large chromosomal rearrangements in a set of wild M. acuminata subspecies and cultivars that originated from natural and human-made crosses. Additionally, we analyzed the chromosome structure of F1 progeny that resulted from crosses between Mchare bananas and the wild M. acuminata 'Calcutta 4' genotype. Analysis of chromosome structure within M. acuminata revealed the presence of a large number of chromosomal rearrangements showing a correlation with banana speciation. Chromosome painting of F1 hybrids was complemented by Illumina resequencing to identify the contribution of parental subgenomes to the diploid hybrid clones. The balanced presence of both parental genomes was revealed in all F1 hybrids, with the exception of one clone, which contained only Mchare-specific SNPs and thus most probably originated from an unreduced diploid gamete of Mchare.
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Affiliation(s)
- Denisa Beránková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Gabriela Majzlíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Alžběta Doležalová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Hassan Mduma
- International Institute of Tropical Agriculture, Banana Breeding, Arusha, Tanzania
| | - Allan Brown
- International Institute of Tropical Agriculture, Banana Breeding, Arusha, Tanzania
| | - Rony Swennen
- International Institute of Tropical Agriculture, Kampala, Uganda
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
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Jenny C, Guignon V, Manyer I Ballester F, Ruas M, Rouard M. Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science. Database (Oxford) 2024; 2024:baae036. [PMID: 38776381 PMCID: PMC11110932 DOI: 10.1093/database/baae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/28/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
The Musa Germplasm Information System (MGIS) stands as a pivotal database for managing global banana genetic resources information. In our latest effort, we have expanded MGIS to incorporate in situ observations. We thus incorporated more than 3000 in situ observations from 133 countries primarily sourced from iNaturalist, GBIF, Flickr, Pl@ntNet, Google Street view and expert curation of the literature. This addition provides a more comprehensive and detailed view of banana diversity and its distribution. Additional graphical interfaces, supported by new Drupal modules, were developed, allowing users to compare banana accessions and explore them based on various filters including taxonomy and geographic location. The integrated maps present a unified view, showcasing both in situ observations and the collecting locations of accessions held in germplasm collections. This enhancement not only broadens the scope of MGIS but also promotes a collaborative and open approach in documenting banana diversity, to allow more effective conservation and use of banana germplasm. Furthermore, this work documents a citizen-science approach that could be relevant for other communities. Database URL: https://www.crop-diversity.org/mgis/musa-in-situ.
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Affiliation(s)
- Christophe Jenny
- CIRAD, UMR AGAP Institut, University of Montpellier, F-34398, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Valentin Guignon
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Felip Manyer I Ballester
- CIRAD, UMR AGAP Institut, University of Montpellier, F-34398, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Max Ruas
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
| | - Mathieu Rouard
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, France
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Xiao TW, Liu X, Fu N, Liu TJ, Wang ZF, Ge XJ, Huang HR. Chromosome-level genome assemblies of Musa ornata and Musa velutina provide insights into pericarp dehiscence and anthocyanin biosynthesis in banana. HORTICULTURE RESEARCH 2024; 11:uhae079. [PMID: 38766534 PMCID: PMC11101321 DOI: 10.1093/hr/uhae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/08/2024] [Indexed: 05/22/2024]
Abstract
Musa ornata and Musa velutina are members of the Musaceae family and are indigenous to the South and Southeast Asia. They are very popular in the horticultural market, but the lack of genomic sequencing data and genetic studies has hampered efforts to improve their ornamental value. In this study, we generated the first chromosome-level genome assemblies for both species by utilizing Oxford Nanopore long reads and Hi-C reads. The genomes of M. ornata and M. velutina were assembled into 11 pseudochromosomes with genome sizes of 427.85 Mb and 478.10 Mb, respectively. Repetitive sequences comprised 46.70% and 50.91% of the total genomes for M. ornata and M. velutina, respectively. Differentially expressed gene (DEG) and Gene Ontology (GO) enrichment analyses indicated that upregulated genes in the mature pericarps of M. velutina were mainly associated with the saccharide metabolic processes, particularly at the cell wall and extracellular region. Furthermore, we identified polygalacturonase (PG) genes that exhibited higher expression level in mature pericarps of M. velutina compared to other tissues, potentially being accountable for pericarp dehiscence. This study also identified genes associated with anthocyanin biosynthesis pathway. Taken together, the chromosomal-level genome assemblies of M. ornata and M. velutina provide valuable insights into the mechanism of pericarp dehiscence and anthocyanin biosynthesis in banana, which will significantly contribute to future genetic and molecular breeding efforts.
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Affiliation(s)
- Tian-Wen Xiao
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xin Liu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Fu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Zheng-Feng Wang
- South China National Botanical Garden, Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xue-Jun Ge
- South China National Botanical Garden, Guangzhou 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hui-Run Huang
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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Higgins J, Osorio-Guarín JA, Olave-Achury C, Toloza-Moreno DL, Enriquez A, Di Palma F, Yockteng R, De Vega JJ. Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages. ANNALS OF BOTANY 2024; 133:349-364. [PMID: 38097270 PMCID: PMC11005773 DOI: 10.1093/aob/mcad192] [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: 10/16/2023] [Accepted: 12/12/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. Musa acuminata, M. balbisiana and M. schizocarpa have provided the named A, B and S subgenomes that predominantly constitute these varieties. Here we aimed to characterize intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in copy-number variants (CNVs) leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterize varietal lineages better and identify sources of genetic variation. METHODS We delimited population structure and clonal lineages in a diverse panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination. RESULTS In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties. CONCLUSIONS We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on single nucleotide polymorphism (SNP) databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridization and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variations probably associated with phenotypic variation for future genetic studies.
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Affiliation(s)
- Janet Higgins
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Jaime Andrés Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
| | | | - Deisy Lisseth Toloza-Moreno
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
| | - Ayda Enriquez
- Centro de Investigación Palmira, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Palmira, Colombia
| | | | - Roxana Yockteng
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, km 14 vía Mosquera, Bogotá, Colombia
- Muséum National d’Histoire Naturelle, UMR-CNRS 7205, Paris, France
| | - Jose J De Vega
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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Peeters NGJ, Vergauwen D, De Smet I. Let's go bananas with paintings. TRENDS IN PLANT SCIENCE 2023; 28:1195-1197. [PMID: 37652757 DOI: 10.1016/j.tplants.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023]
Abstract
We tell the story of the complex history and global distribution of the very popular banana and illustrate this with amazing depictions by artists and scientists. In addition, we discuss the major changes that occurred during domestication and the risks associated with maintaining a monoculture.
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Affiliation(s)
| | - David Vergauwen
- Research and Documentation Centre (CEDOM-MADOC), B-1000 Brussels, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium.
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6
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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7
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Huang HR, Liu X, Arshad R, Wang X, Li WM, Zhou Y, Ge XJ. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. HORTICULTURE RESEARCH 2023; 10:uhad153. [PMID: 37701454 PMCID: PMC10493638 DOI: 10.1093/hr/uhad153] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/27/2023] [Indexed: 09/14/2023]
Abstract
Banana is one of the most important crops of the world. Cavendish-type bananas, which have a monospecific Musa acuminata origin (AAA), account for around half of the global banana production, thereby are of great significance for human societies. However, until now, the high-quality haplotype-resolved reference genome was still undecoded for banana cultivars. Here, we reported the telomere-to-telomere (T2T) and haplotype-resolved reference genome of 'Baxijiao' (Cavendish) consisting of three haploid assemblies. The sizes of the three haploid assemblies were estimated to be 477.16 Mb, 477.18 Mb, and 469.57 Mb, respectively. Although with monospecific origins, the three haploid assemblies showed great differences with low levels of sequence collinearity. Several large reciprocal translocations were identified among chromosomes 1, 4, and 7. An expansion of gene families that might affect fruit quality and aroma was detected, such as those belonging to sucrose/disaccharide/oligosaccharide catabolic processes, sucrose metabolic process, starch metabolic process, and aromatic compound biosynthetic process. Besides, an expansion of gene families related to anther and pollen development was observed, which could be associated with parthenocarpy and sterility of the Cavendish cultivar. Finally, much fewer resistance genes were identified in 'Baxijiao' than in M. acuminata, particularly in the gene clusters in chromosomes 3 and 10, providing potential targets to explore for molecular analysis of disease resistance in banana. This T2T haplotype-resolved reference genome will thus be a valuable genetic resource for biological studies, molecular breeding, and genetic improvement of banana.
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Affiliation(s)
- Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xin Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rida Arshad
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xu Wang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wei-Ming Li
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning 530008, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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Martin G, Baurens FC, Labadie K, Hervouet C, Salmon F, Marius F, Paulo-de-la-Reberdiere N, Van den Houwe I, Aury JM, D’Hont A, Yahiaoui N. Shared pedigree relationships and transmission of unreduced gametes in cultivated banana. ANNALS OF BOTANY 2023; 131:1149-1161. [PMID: 37267450 PMCID: PMC10457027 DOI: 10.1093/aob/mcad065] [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: 03/13/2023] [Accepted: 06/02/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND AND AIMS Cultivated bananas resulted from inter(sub)specific hybridizations involving Musa species and subspecies (M. acuminata subspecies, M. schizocarpa, M. balbisiana) and the subsequent selection, centuries ago, of hybrids with parthenocarpic, seedless fruits. Cultivars have low fertility and are vegetatively propagated, forming groups of somaclones. Relatively few of them, mainly triploids, are grown on a large scale and characterization of their parental relationships may be useful for breeding strategies. Here we investigate parental relationships and gamete-type contributions among diploid and polyploid banana cultivars. METHODS We used SNP genotyping data from whole-genome sequencing of 178 banana individuals, including 111 cultivars, 55 wild bananas and 12 synthetic F1 hybrids. We analysed the proportion of SNP sites in accordance with direct parentage with a global statistic and along chromosomes for selected individuals. KEY RESULTS We characterized parentage relationships for 7 diploid cultivars, 11 triploid cultivars and 1 tetraploid cultivar. Results showed that both diploid and triploid cultivars could have contributed gametes to other banana cultivars. Diploids may have contributed 1x or 2x gametes and triploids 1x to 3x gametes. The Mchare diploid cultivar group, nowadays only found in East Africa, was found as parent of two diploid and eight triploid cultivars. In five of its identified triploid offspring, corresponding to main export or locally popular dessert bananas, Mchare contributed a 2x gamete with full genome restitution without recombination. Analyses of remaining haplotypes in these Mchare offspring suggested ancestral pedigree relationships between different interspecific banana cultivars. CONCLUSIONS The current cultivated banana resulted from different pathways of formation, with implication of recombined or un-recombined unreduced gametes produced by diploid or triploid cultivars. Identification of dessert banana's parents and the types of gametes they contributed should support the design of breeding strategies.
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Affiliation(s)
- Guillaume Martin
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Frédéric Salmon
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
| | - Franck Marius
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, Guadeloupe, FranceFrance
| | - Nilda Paulo-de-la-Reberdiere
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, CRB-PT, F-97170 Roujol Petit-Bourg, Guadeloupe, FranceFrance
| | - Ines Van den Houwe
- Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, Montpellier F-34398, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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9
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Eyland D, Gambart C, Swennen R, Carpentier S. Unravelling the diversity in water usage among wild banana species in response to vapour pressure deficit. FRONTIERS IN PLANT SCIENCE 2023; 14:1068191. [PMID: 37670859 PMCID: PMC10475999 DOI: 10.3389/fpls.2023.1068191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/03/2023] [Indexed: 09/07/2023]
Abstract
The rise in global temperature is not only affecting plant functioning directly, but is also increasing air vapour pressure deficit (VPD). The yield of banana is heavily affected by water deficit but so far breeding programs have never addressed the issue of water deficit caused by high VPD. A reduction in transpiration at high VPD has been suggested as a key drought tolerance breeding trait to avoid excessive water loss, hydraulic failure and to increase water use efficiency. In this study, stomatal and transpiration responses under increasing VPD at the leaf and whole-plant level of 8 wild banana (sub)species were evaluated, displaying significant differences in stomatal reactivity. Three different phenotypic groups were identified under increasing VPD. While (sub)species of group III maintained high transpiration rates under increasing VPD, M. acuminata ssp. errans (group I), M. acuminata ssp. zebrina (group II) and M. balbisiana (group II) showed the highest transpiration rate limitations to increasing VPD. In contrast to group I, group II only showed strong reductions at high VPD levels, limiting the cost of reduced photosynthesis and strongly increasing their water use efficiency. M. acuminata ssp. zebrina and M. balbisiana thus show the most favourable responses. This study provides a basis for the identification of potential parent material in gene banks for breeding future-proof bananas that cope better with lack of water.
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Affiliation(s)
- David Eyland
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
| | - Clara Gambart
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
- International Institute of Tropical Agriculture, Banana Breeding, Kampala, Uganda
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Heverlee, Belgium
- Bioversity International, Biodiversity for Food and Agriculture, Leuven, Belgium
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Abstract
Plant life defines the environments to which animals adapt and provides the basis of food webs. This was equally true for hunter-gatherer economies of ancestral humans, yet through the domestication of plants and the creation of agricultural ecologies based around them, human societies transformed vegetation and transported plant taxa into new geographical regions. These human-plant interactions ultimately co-evolved, increasing human population densities, technologies of farming, and the diversification of landraces and crop complexes. Research in archaeology on preserved plant remains (archaeobotany) and on the genomes of crops, including ancient genomes, has transformed our scientific understanding of the complex relationships between humans and plants that are entailed by domestication. Key realizations of recent research include the recognition that: the co-evolution of domesticates and cultures was protracted, the adaptations of plant populations were unintended results of human economies rather than intentional breeding, domestication took place in dozens of world regions involving different crops and cultures, and convergent evolution can be recognized among cropping types - such as among seed crops, tuber crops, and fruit trees. Seven general domestication pathways can be defined for plants. Lessons for the present-day include: the importance of diversity in the past; genetic diversity within species has the potential to erode over time, but also to be rescued through processes of integration; similarly, diversification within agricultural ecosystems has undergone processes of decline, including marginalised, lost and 'forgotten' crops, as well as processes of renewal resulting from trade and human mobility that brought varied crops and varieties together.
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Affiliation(s)
- Dorian Q Fuller
- Institute of Archaeology, University College London (UCL), London, UK; School of Cultural Heritage, Northwest University, Xi'an, Shaanxi, China.
| | - Tim Denham
- School of Archaeology and Anthropology, The Australian National University, Canberra, Australia
| | - Robin Allaby
- School of Life Sciences, University of Warwick, Coventry, UK
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11
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Audi L, Shallow G, Robertson E, Bobo D, Ragone D, Gardner EM, Jhurree-Dussoruth B, Wajer J, Zerega NJC. Linking breadfruit cultivar names across the globe connects histories after 230 years of separation. Curr Biol 2023; 33:287-297.e3. [PMID: 36608689 DOI: 10.1016/j.cub.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 01/07/2023]
Abstract
Every crop has a story. The story of breadfruit (Artocarpus altilis), an increasingly valued staple crop in tropical agroforestry systems, is filled with intrigue, oppression, and remains incomplete. The Caribbean is a major producer and consumer of breadfruit, yet most breadfruit there came from a single 1793 introduction aimed at providing a cheap food source for slaves forced to work on British plantations. St. Vincent was the first significant point of Caribbean introduction and played a vital role in subsequent breadfruit distribution throughout the region. Hundreds of cultivars are documented in breadfruit's native Oceania. It remains a mystery, however, which ones were introduced to the Caribbean 230 years ago-still comprising the vast diversity found there today. Integrating local knowledge, historical documents and specimens, morphological data, and DNA, we identify eight major global breadfruit lineages-five of which are found in the Caribbean and likely represent the original 1793 introduction. Genetic data were able to match two Caribbean cultivar names confidently to their Oceania counterparts. Genetics and morphology together enabled additional possible matches. Many other named cultivars within lineages are too genetically similar to differentiate, highlighting difficulties of defining and identifying variation among clonally propagated triploid crops. Breadfruit is important in resilient agroforestry in tropical islands predicted to be especially affected by climate change. Findings reveal global links, building upon collective knowledge that can be used to inform breadfruit management. Results are also summarized in a brochure about breadfruit history and diversity in St. Vincent, and the Caribbean more broadly.
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Affiliation(s)
- Lauren Audi
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL 60022, USA; Program in Plant Biology and Conservation, Northwestern University, Evanston, IL 60201, USA; Institute for Comparative Genomics. American Museum of Natural History, New York, NY 10024, USA
| | - Gordon Shallow
- St. Vincent Botanical Garden, Kingstown 5Q8C+4W2, Saint Vincent and the Grenadines; The Ministry of Tourism, National Parks, Rivers and Beaches Authority, Kingstown 5Q6C+F6R, St. Vincent and the Grenadines
| | - Erasto Robertson
- The Ministry of Tourism, National Parks, Rivers and Beaches Authority, Kingstown 5Q6C+F6R, St. Vincent and the Grenadines
| | - Dean Bobo
- Institute for Comparative Genomics. American Museum of Natural History, New York, NY 10024, USA; The Department of Ecology Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
| | - Diane Ragone
- Breadfruit Institute, National Tropical Botanical Garden, Kalaheo, HI 96765, USA
| | - Elliot M Gardner
- International Center for Tropical Botany, Institute of Environment, Florida International University, Miami, FL 33133, USA; National Tropical Botanical Garden, Kalaheo, HI 96765, USA
| | | | - Jacek Wajer
- Natural History Museum, Cromwell Road London SW7 5BD, UK
| | - Nyree J C Zerega
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL 60022, USA; Program in Plant Biology and Conservation, Northwestern University, Evanston, IL 60201, USA.
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12
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Droc G, Martin G, Guignon V, Summo M, Sempéré G, Durant E, Soriano A, Baurens FC, Cenci A, Breton C, Shah T, Aury JM, Ge XJ, Harrison PH, Yahiaoui N, D’Hont A, Rouard M. The banana genome hub: a community database for genomics in the Musaceae. HORTICULTURE RESEARCH 2022; 9:uhac221. [PMID: 36479579 PMCID: PMC9720444 DOI: 10.1093/hr/uhac221] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.
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Affiliation(s)
| | - Guillaume Martin
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Valentin Guignon
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Marilyne Summo
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Guilhem Sempéré
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France
- INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Eloi Durant
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Syngenta Seeds SAS, Saint-Sauveur, 31790, France
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, 34830, France
| | - Alexandre Soriano
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Alberto Cenci
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Catherine Breton
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Pat Heslop Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
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