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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. Hortic Res 2023; 10:uhad153. [PMID: 37701454 PMCID: PMC10493638 DOI: 10.1093/hr/uhad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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. Ann Bot 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Martin G, Cottin A, Baurens FC, Labadie K, Hervouet C, Salmon F, Paulo-de-la-Reberdiere N, Van den Houwe I, Sardos J, Aury JM, D'Hont A, Yahiaoui N. Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea. Plant J 2023; 113:802-818. [PMID: 36575919 DOI: 10.1111/tpj.16086] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Hybridizations between Musa species and subspecies, enabled by their transport via human migration, were proposed to have played an important role in banana domestication. We exploited sequencing data of 226 Musaceae accessions, including wild and cultivated accessions, to characterize the inter(sub)specific hybridization pattern that gave rise to cultivated bananas. We identified 11 genetic pools that contributed to cultivars, including two contributors of unknown origin. Informative alleles for each of these genetic pools were pinpointed and used to obtain genome ancestry mosaics of accessions. Diploid and triploid cultivars had genome mosaics involving three up to possibly seven contributors. The simplest mosaics were found for some diploid cultivars from New Guinea, combining three contributors, i.e., banksii and zebrina representing Musa acuminata subspecies and, more unexpectedly, the New Guinean species Musa schizocarpa. Breakpoints of M. schizocarpa introgressions were found to be conserved between New Guinea cultivars and the other analyzed diploid and triploid cultivars. This suggests that plants bearing these M. schizocarpa introgressions were transported from New Guinea and gave rise to currently cultivated bananas. Many cultivars showed contrasted mosaics with predominant ancestry from their geographical origin across Southeast Asia to New Guinea. This revealed that further diversification occurred in different Southeast Asian regions through hybridization with other Musa (sub)species, including two unknown ancestors that we propose to be M. acuminata ssp. halabanensis and a yet to be characterized M. acuminata subspecies. These results highlighted a dynamic crop formation process that was initiated in New Guinea, with subsequent diversification throughout Southeast Asia.
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Affiliation(s)
- Guillaume Martin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurélien Cottin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ 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, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Frédéric Salmon
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, Guadeloupe, France
| | - Nilda Paulo-de-la-Reberdiere
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR AGAP Institut, CRB-PT, F-97170 Roujol Petit-Bourg, Guadeloupe, France
| | - Ines Van den Houwe
- Bioversity International, Willem De Croylaan 42, B-3001, Leuven, Belgium
| | - Julie Sardos
- 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, Evry, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Sardos J, Breton C, Perrier X, Van den Houwe I, Carpentier S, Paofa J, Rouard M, Roux N. Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas. Front Plant Sci 2022; 13:969220. [PMID: 36275535 PMCID: PMC9586208 DOI: 10.3389/fpls.2022.969220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/05/2022] [Indexed: 06/08/2023]
Abstract
Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.
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Affiliation(s)
- Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Catherine Breton
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Xavier Perrier
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Janet Paofa
- Papua New Guinea (PNG) National Agricultural Research Institute, Southern Regional Centre, Laloki, Port Moresby, Papua New Guinea
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
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Hinge VR, Shaikh IM, Chavhan RL, Deshmukh AS, Shelake RM, Ghuge SA, Dethe AM, Suprasanna P, Kadam US. Assessment of genetic diversity and volatile content of commercially grown banana (Musa spp.) cultivars. Sci Rep 2022; 12:7979. [PMID: 35562398 PMCID: PMC9106755 DOI: 10.1038/s41598-022-11992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/04/2022] [Indexed: 11/23/2022] Open
Abstract
Banana is an important fruit crop in the tropics and subtropics; however, limited information on biomarkers and signature volatiles is available for selecting commercial cultivars. Clonal fidelity is a major contributor to banana yield and aroma; however, there are no useful biomarkers available to validate clonal fidelity. In this study, we performed the molecular profiling of 20 banana cultivars consisting of diploid (AA or AB) and triploid (AAA or AAB or ABB) genomic groups. We screened 200 molecular markers, of which 34 markers (11 RAPD, 11 ISSR, and 12 SSR) yielded unequivocally scorable biomarker profiles. About 75, 69, and 24 allelic loci per marker were detected for RAPD, ISSR, and SSR markers, respectively. The statistical analysis of molecular variance (AMOVA) exhibited a high genetic difference of 77% with a significant FST value of 0.23 (p < 0.001). Interestingly, the UBC-858 and SSR CNMPF-13 markers were unique to Grand Nain and Ardhapuri cultivars, respectively, which could be used for clonal fidelity analysis. Furthermore, the analysis of banana fruit volatilome using headspace solid-phase microextraction-gas chromatography-tandem mass spectrometry (HS-SPME-GCMS) revealed a total of fifty-four volatile compounds in nine banana cultivars with 56% of the total volatile compounds belonging to the ester group as the significant contributor of aroma. The study assumes significance with informative biomarkers and signature volatiles which could be helpful in breeding and for the authentic identification of commercial banana cultivars.
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Affiliation(s)
- Vidya R Hinge
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Irfan M Shaikh
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Rahul L Chavhan
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Abhijit S Deshmukh
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Rahul Mahadev Shelake
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Sandip A Ghuge
- Agricultural Research Organization (ARO), The Volcani Institute, P. O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Amol M Dethe
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India
| | - Penna Suprasanna
- Homi Bhabha National Institute (HBNI) and Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Mumbai, India
| | - Ulhas Sopanrao Kadam
- Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology (Vasantrao Naik Marathwada Agricultural University, Parbhani), Latur, Maharashtra, India. .,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea.
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Kallow S, Panis B, Vu DT, Vu TD, Paofa J, Mertens A, Swennen R, Janssens SB. Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives. BMC Plant Biol 2021; 21:415. [PMID: 34503446 PMCID: PMC8431884 DOI: 10.1186/s12870-021-03142-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/06/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence ('bunch') were analysed for each population. RESULTS Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch. CONCLUSIONS We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.
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Affiliation(s)
- Simon Kallow
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.
- Royal Botanic Gardens Kew, Millennium Seed Bank, Wakehurst, Ardingly, Sussex, RH17 6TN, UK.
| | - Bart Panis
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- Bioversity International, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Dang Toan Vu
- Plant Resources Center, Ankhanh, Hoaiduc, Hà Noi, Viet Nam
| | - Tuong Dang Vu
- Plant Resources Center, Ankhanh, Hoaiduc, Hà Noi, Viet Nam
| | - Janet Paofa
- National Agricultural Research Institute, Laloki, Port Moresby, 121, Papua New Guinea
| | - Arne Mertens
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Department of Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
| | - Rony Swennen
- Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
- International Institute of Tropical Agriculture, Plot 15B Naguru East Road, Upper Naguru, 7878, Kampala, Uganda
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Department of Biology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 31, 3001, Leuven, Belgium
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Mertens A, Bawin Y, Vanden Abeele S, Kallow S, Toan Vu D, Thi Le L, Dang Vu T, Swennen R, Vandelook F, Panis B, Janssens SB. Genetic diversity and structure of Musa balbisiana populations in Vietnam and its implications for the conservation of banana crop wild relatives. PLoS One 2021; 16:e0253255. [PMID: 34161368 PMCID: PMC8221469 DOI: 10.1371/journal.pone.0253255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
Crop wild relatives (CWR) are an indispensable source of alleles to improve desired traits in related crops. While knowledge on the genetic diversity of CWR can facilitate breeding and conservation strategies, it has poorly been assessed. Cultivated bananas are a major part of the diet and income of hundreds of millions of people and can be considered as one of the most important fruits worldwide. Here, we assessed the genetic diversity and structure of Musa balbisiana, an important CWR of plantains, dessert and cooking bananas. Musa balbisiana has its origin in subtropical and tropical broadleaf forests of northern Indo-Burma. This includes a large part of northern Vietnam where until now, no populations have been sampled. We screened the genetic variation and structure present within and between 17 Vietnamese populations and six from China using 18 polymorphic SSR markers. Relatively high variation was found in populations from China and central Vietnam. Populations from northern Vietnam showed varying levels of genetic variation, with low variation in populations near the Red River. Low genetic variation was found in populations of southern Vietnam. Analyses of population structure revealed that populations of northern Vietnam formed a distinct genetic cluster from populations sampled in China. Together with populations of central Vietnam, populations from northern Vietnam could be subdivided into five clusters, likely caused by mountain ranges and connected river systems. We propose that populations sampled in central Vietnam and on the western side of the Hoang Lien Son mountain range in northern Vietnam belong to the native distribution area and should be prioritised for conservation. Southern range edge populations in central Vietnam had especially high genetic diversity, with a high number of unique alleles and might be connected with core populations in northern Laos and southwest China. Southern Vietnamese populations are considered imported and not native.
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Affiliation(s)
- Arne Mertens
- Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Yves Bawin
- Meise Botanic Garden, Meise, Belgium
- Ecology, Evolution and Biodiversity Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Simon Kallow
- Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Leuven, Belgium
- Royal Botanic Gardens Kew, Millennium Seed Bank, West Sussex, United Kingdom
| | - Dang Toan Vu
- Research Planning and International Department, Plant Resources Center, VAAS, Hanoi, Vietnam
| | - Loan Thi Le
- Department of Genebank Management, Plant Resources Center, VAAS, Hanoi, Vietnam
| | - Tuong Dang Vu
- Research Planning and International Department, Plant Resources Center, VAAS, Hanoi, Vietnam
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Department of Biosystems, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, Arusha, Tanzania
| | | | - Bart Panis
- Bioversity International, Leuven, Belgium
| | - Steven B. Janssens
- Meise Botanic Garden, Meise, Belgium
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Leuven, Belgium
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Carlier J, Bonnot F, Roussel V, Ravel S, Martinez RT, Perez-Vicente L, Abadie C, Wright S. Convergent Adaptation to Quantitative Host Resistance in a Major Plant Pathogen. mBio 2021; 12:e03129-20. [PMID: 33622734 DOI: 10.1128/mBio.03129-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance.IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
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Ponting J, Kelly TJ, Verhoef A, Watts MJ, Sizmur T. The impact of increased flooding occurrence on the mobility of potentially toxic elements in floodplain soil - A review. Sci Total Environ 2021; 754:142040. [PMID: 32916489 DOI: 10.1016/j.scitotenv.2020.142040] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
The frequency and duration of flooding events is increasing due to land-use changes increasing run-off of precipitation, and climate change causing more intense rainfall events. Floodplain soils situated downstream of urban or industrial catchments, which were traditionally considered a sink of potentially toxic elements (PTEs) arriving from the river reach, may now become a source of legacy pollution to the surrounding environment, if PTEs are mobilised by unprecedented flooding events. When a soil floods, the mobility of PTEs can increase or decrease due to the net effect of five key processes; (i) the soil redox potential decreases which can directly alter the speciation, and hence mobility, of redox sensitive PTEs (e.g. Cr, As), (ii) pH increases which usually decreases the mobility of metal cations (e.g. Cd2+, Cu2+, Ni2+, Pb2+, Zn2+), (iii) dissolved organic matter (DOM) increases, which chelates and mobilises PTEs, (iv) Fe and Mn hydroxides undergo reductive dissolution, releasing adsorbed and co-precipitated PTEs, and (v) sulphate is reduced and PTEs are immobilised due to precipitation of metal sulphides. These factors may be independent mechanisms, but they interact with one another to affect the mobility of PTEs, meaning the effect of flooding on PTE mobility is not easy to predict. Many of the processes involved in mobilising PTEs are microbially mediated, temperature dependent and the kinetics are poorly understood. Soil mineralogy and texture are properties that change spatially and will affect how the mobility of PTEs in a specific soil may be impacted by flooding. As a result, knowledge based on one river catchment may not be particularly useful for predicting the impacts of flooding at another site. This review provides a critical discussion of the mechanisms controlling the mobility of PTEs in floodplain soils. It summarises current understanding, identifies limitations to existing knowledge, and highlights requirements for further research.
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Affiliation(s)
- Jessica Ponting
- Department of Geography and Environmental Science, University of Reading, Reading RG6 6DW, UK; Inorganic Geochemistry, Centre for Environmental Geochemistry, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK
| | - Thomas J Kelly
- Department of Geography and Environmental Science, University of Reading, Reading RG6 6DW, UK; Department of Geography, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Anne Verhoef
- Department of Geography and Environmental Science, University of Reading, Reading RG6 6DW, UK
| | - Michael J Watts
- Inorganic Geochemistry, Centre for Environmental Geochemistry, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK
| | - Tom Sizmur
- Department of Geography and Environmental Science, University of Reading, Reading RG6 6DW, UK.
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Cenci A, Sardos J, Hueber Y, Martin G, Breton C, Roux N, Swennen R, Carpentier SC, Rouard M. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas. Ann Bot 2021; 127:7-20. [PMID: 32104882 DOI: 10.1093/aob/mcaa032/5760888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security. METHODS Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes. KEY RESULTS Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups. CONCLUSIONS The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploids originated, and where cultivated M. balbisiana are abundant. The result of this study clarifies the classification of ABB cultivars, possibly leading to the revision of the classification of this subgroup.
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Affiliation(s)
- Alberto Cenci
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Julie Sardos
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Yann Hueber
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Guillaume Martin
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | | | - Nicolas Roux
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Rony Swennen
- Alliance Bioversity International - CIAT, Leuven, Belgium
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, c/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | | | - Mathieu Rouard
- Alliance Bioversity International - CIAT, Montpellier, France
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Cenci A, Sardos J, Hueber Y, Martin G, Breton C, Roux N, Swennen R, Carpentier SC, Rouard M. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas. Ann Bot 2021; 127:7-20. [PMID: 32104882 PMCID: PMC7750727 DOI: 10.1093/aob/mcaa032] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security. METHODS Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes. KEY RESULTS Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups. CONCLUSIONS The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploids originated, and where cultivated M. balbisiana are abundant. The result of this study clarifies the classification of ABB cultivars, possibly leading to the revision of the classification of this subgroup.
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Affiliation(s)
- Alberto Cenci
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Julie Sardos
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Yann Hueber
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Guillaume Martin
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | | | - Nicolas Roux
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Rony Swennen
- Alliance Bioversity International - CIAT, Leuven, Belgium
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, c/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | | | - Mathieu Rouard
- Alliance Bioversity International - CIAT, Montpellier, France
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Martin G, Baurens F, Hervouet C, Salmon F, Delos J, Labadie K, Perdereau A, Mournet P, Blois L, Dupouy M, Carreel F, Ricci S, Lemainque A, Yahiaoui N, D’Hont A. Chromosome reciprocal translocations have accompanied subspecies evolution in bananas. Plant J 2020; 104:1698-1711. [PMID: 33067829 PMCID: PMC7839431 DOI: 10.1111/tpj.15031] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/02/2020] [Indexed: 05/09/2023]
Abstract
Chromosome rearrangements and the way that they impact genetic differentiation and speciation have long raised questions from evolutionary biologists. They are also a major concern for breeders because of their bearing on chromosome recombination. Banana is a major crop that derives from inter(sub)specific hybridizations between various once geographically isolated Musa species and subspecies. We sequenced 155 accessions, including banana cultivars and representatives of Musa diversity, and genotyped-by-sequencing 1059 individuals from 11 progenies. We precisely characterized six large reciprocal translocations and showed that they emerged in different (sub)species of Musa acuminata, the main contributor to currently cultivated bananas. Most diploid and triploid cultivars analyzed were structurally heterozygous for 1 to 4 M. acuminata translocations, highlighting their complex origin. We showed that all translocations induced a recombination reduction of variable intensity and extent depending on the translocations, involving only the breakpoint regions, a chromosome arm, or an entire chromosome. The translocated chromosomes were found preferentially transmitted in many cases. We explore and discuss the possible mechanisms involved in this preferential transmission and its impact on translocation colonization.
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Affiliation(s)
- Guillaume Martin
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Franc‐Christophe Baurens
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Catherine Hervouet
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Frédéric Salmon
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Jean‐Marie Delos
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Karine Labadie
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Aude Perdereau
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Pierre Mournet
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Louis Blois
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Marion Dupouy
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Françoise Carreel
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Sébastien Ricci
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
- CIRADUMR AGAPCapesterre‐Belle‐EauGuadeloupeF‐97130France
| | - Arnaud Lemainque
- GenoscopeInstitut de biologie François JacobCommissariat à l'Energie Atomique (CEA)Université Paris‐SaclayEvryFrance
| | - Nabila Yahiaoui
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
| | - Angélique D’Hont
- CIRADUMR AGAPMontpellierF‐34398France
- AGAPUniv MontpellierCIRADINRAEInstitut AgroMontpellier34060France
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Šimoníková D, Němečková A, Čížková J, Brown A, Swennen R, Doležel J, Hřibová E. Chromosome Painting in Cultivated Bananas and Their Wild Relatives ( Musa spp.) Reveals Differences in Chromosome Structure. Int J Mol Sci 2020; 21:ijms21217915. [PMID: 33114462 PMCID: PMC7672600 DOI: 10.3390/ijms21217915] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 12/17/2022] Open
Abstract
Edible banana cultivars are diploid, triploid, or tetraploid hybrids, which originated by natural cross hybridization between subspecies of diploid Musa acuminata, or between M. acuminata and diploid Musa balbisiana. The participation of two other wild diploid species Musa schizocarpa and Musa textilis was also indicated by molecular studies. The fusion of gametes with structurally different chromosome sets may give rise to progenies with structural chromosome heterozygosity and reduced fertility due to aberrant chromosome pairing and unbalanced chromosome segregation. Only a few translocations have been classified on the genomic level so far, and a comprehensive molecular cytogenetic characterization of cultivars and species of the family Musaceae is still lacking. Fluorescence in situ hybridization (FISH) with chromosome-arm-specific oligo painting probes was used for comparative karyotype analysis in a set of wild Musa species and edible banana clones. The results revealed large differences in chromosome structure, discriminating individual accessions. These results permitted the identification of putative progenitors of cultivated clones and clarified the genomic constitution and evolution of aneuploid banana clones, which seem to be common among the polyploid banana accessions. New insights into the chromosome organization and structural chromosome changes will be a valuable asset in breeding programs, particularly in the selection of appropriate parents for cross hybridization.
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Affiliation(s)
- Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (A.N.); (J.Č.); (J.D.)
| | - Alžběta Němečková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (A.N.); (J.Č.); (J.D.)
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (A.N.); (J.Č.); (J.D.)
| | - Allan Brown
- International Institute of Tropical Agriculture, Banana Breeding, PO Box 447 Arusha, Tanzania; (A.B.); (R.S.)
| | - Rony Swennen
- International Institute of Tropical Agriculture, Banana Breeding, PO Box 447 Arusha, Tanzania; (A.B.); (R.S.)
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, 3001 Leuven, Belgium
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (A.N.); (J.Č.); (J.D.)
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (A.N.); (J.Č.); (J.D.)
- Correspondence: ; Tel.: +420-585-238-713
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Fones HN, Bebber DP, Chaloner TM, Kay WT, Steinberg G, Gurr SJ. Threats to global food security from emerging fungal and oomycete crop pathogens. ACTA ACUST UNITED AC 2020; 1:332-342. [PMID: 37128085 DOI: 10.1038/s43016-020-0075-0] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/09/2020] [Indexed: 11/09/2022]
Abstract
Emerging fungal and oomycete pathogens infect staple calorie crops and economically important commodity crops, thereby posing a significant risk to global food security. Our current agricultural systems - with emphasis on intensive monoculture practices - and globalized markets drive the emergence and spread of new pathogens and problematic traits, such as fungicide resistance. Climate change further promotes the emergence of pathogens on new crops and in new places. Here we review the factors affecting the introduction and spread of pathogens and current disease control strategies, illustrating these with the historic example of the Irish potato famine and contemporary examples of soybean rust, wheat blast and blotch, banana wilt and cassava root rot. Our Review looks to the future, summarizing what we see as the main challenges and knowledge gaps, and highlighting the direction that research must take to face the challenge of emerging crop pathogens.
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Martin G, Cardi C, Sarah G, Ricci S, Jenny C, Fondi E, Perrier X, Glaszmann JC, D'Hont A, Yahiaoui N. Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana. Plant J 2020; 102:1008-1025. [PMID: 31930580 PMCID: PMC7317953 DOI: 10.1111/tpj.14683] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 12/18/2019] [Accepted: 01/02/2020] [Indexed: 05/24/2023]
Abstract
Hybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 14 M. acuminata wild accessions and 10 M. acuminata-based cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We used multivariate analysis and single nucleotide polymorphism clustering and identified five ancestral groups as contributors to these cultivars. Four of these corresponded to known M. acuminata subspecies. A fifth group, found only in cultivars, was defined based on the 'Pisang Madu' cultivar and represented two uncharacterized genetic pools. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. The commercially important triploid Cavendish banana cultivar had contributions from at least one of the uncharacterized genetic pools and three known M. acuminata subspecies. Our results highlighted that cultivated banana origins are more complex than expected - involving multiple hybridization steps - and also that major wild banana ancestors have yet to be identified. This study revealed the extent to which admixture has framed the evolution and domestication of a crop plant.
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Affiliation(s)
- Guillaume Martin
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Céline Cardi
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Gautier Sarah
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Sébastien Ricci
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CARBAP, Rue Dinde, No. 110, Bonanjo, BP 832, Douala, Cameroon
- CIRAD, UMR AGAP, F-97130, Capesterre Belle Eau, France
| | - Christophe Jenny
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Emmanuel Fondi
- CARBAP, Rue Dinde, No. 110, Bonanjo, BP 832, Douala, Cameroon
| | - Xavier Perrier
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Christophe Glaszmann
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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Dumartinet T, Abadie C, Bonnot F, Carreel F, Roussel V, Habas R, Martinez RT, Perez‐Vicente L, Carlier J. Pattern of local adaptation to quantitative host resistance in a major pathogen of a perennial crop. Evol Appl 2020; 13:824-836. [PMID: 32211070 PMCID: PMC7086059 DOI: 10.1111/eva.12904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/10/2019] [Accepted: 11/22/2019] [Indexed: 12/05/2022] Open
Abstract
Understanding the mechanisms involved in pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment, especially in perennial crops. The erosion of quantitative resistance has been recently suspected in Cuba and the Dominican Republic for a major fungal pathogen of such a crop: Pseudocercospora fijiensis, causing black leaf streak disease on banana. This study set out to test whether such erosion has resulted from an adaptation of P. fijiensis populations, and to determine whether or not the adaptation is local. Almost 600 P. fijiensis isolates from Cuba and the Dominican Republic were sampled using a paired-population sampling design on resistant and susceptible banana varieties. A low genetic structure of the P. fijiensis populations was detected in each country using 16 microsatellite markers. Cross-inoculation experiments using isolates from susceptible and resistant cultivars were carried out, measuring a quantitative trait (the diseased leaf area) related to pathogen fitness on three varieties. A further analysis based on those data suggested the existence of a local pattern of adaptation to resistant cultivars in both of the study countries, due to the existence of specific (or genotype by genotype) host-pathogen interactions. However, neither cost nor benefit effects for adapted populations were found on the widely used "Cavendish" banana group. These results highlight the need to study specific host-pathogen interactions and pathogen adaptation on a wide range of quantitative resistance phenotypes in banana, in order to develop durable strategies for resistance deployment.
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Affiliation(s)
- Thomas Dumartinet
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Catherine Abadie
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
- CIRADUMR BGPICapesterre‐Belle‐EauFrance
| | - François Bonnot
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Françoise Carreel
- UMR AGAPUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Véronique Roussel
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Rémy Habas
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | | | | | - Jean Carlier
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
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17
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Baurens FC, Martin G, Hervouet C, Salmon F, Yohomé D, Ricci S, Rouard M, Habas R, Lemainque A, Yahiaoui N, D'Hont A. Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes. Mol Biol Evol 2019; 36:97-111. [PMID: 30403808 PMCID: PMC6340459 DOI: 10.1093/molbev/msy199] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Admixture and polyploidization are major recognized eukaryotic genome evolutionary processes. Their impacts on genome dynamics vary among systems and are still partially deciphered. Many banana cultivars are triploid (sometimes diploid) interspecific hybrids between Musa acuminata (A genome) and M. balbisiana (B genome). They have no or very low fertility, are vegetatively propagated and have been classified as “AB,” “AAB,” or “ABB” based on morphological characters. We used NGS sequence data to characterize the A versus B chromosome composition of nine diploid and triploid interspecific cultivars, to compare the chromosome structures of A and B genomes and analyze A/B chromosome segregations in a polyploid context. We showed that interspecific recombination occurred frequently between A and B chromosomes. We identified two large structural variations between A and B genomes, a reciprocal translocation and an inversion that locally affected recombination and led to segregation distortion and aneuploidy in a triploid progeny. Interspecific recombination and large structural variations explained the mosaic genomes observed in edible bananas. The unprecedented resolution in deciphering their genome structure allowed us to start revisiting the origins of banana cultivars and provided new information to gain insight into the impact of interspecificity on genome evolution. It will also facilitate much more effective assessment of breeding strategies.
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Affiliation(s)
- Franc-Christophe Baurens
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frédéric Salmon
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,CIRAD, UMR AGAP, F-97130 Capesterre Belle Eau, Guadeloupe, France
| | | | - Sébastien Ricci
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,CIRAD, UMR AGAP, F-97130 Capesterre Belle Eau, Guadeloupe, France.,CARBAP, Bonanjo, Douala, Cameroon
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, Cedex 5, France
| | - Remy Habas
- CIRAD, UMR BGPI, F-34398 Montpellier, France.,BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Arnaud Lemainque
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François-Jacob, Genoscope, Evry, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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18
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Amah D, Alamu E, Adesokan M, van Biljon A, Maziya-Dixon B, Swennen R, Labuschagne M. Variability of carotenoids in a Musa germplasm collection and implications for provitamin A biofortification. Food Chem X 2019; 2:100024. [PMID: 31432011 PMCID: PMC6694864 DOI: 10.1016/j.fochx.2019.100024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/05/2019] [Accepted: 04/07/2019] [Indexed: 11/17/2022] Open
Abstract
Banana genotypes, a good source of provitamin A was screened for carotenoid content. Carotenoid in fruit pulp were quantified using high performance liquid chromatography. Total carotenoid content in the fruit varied from 1.45 to 36.21 µg/g fresh weight. 78% of carotenoids isolated were provitamin A carotenoids β-carotene and α-carotene. Data generated are useful for provitamin A biofortification strategies.
Bananas are important staples in tropical and sub-tropical regions and their potential as a source of provitamin A has recently attracted attention for biofortification. A collection of 189 banana genotypes (AAB-plantains, M. acuminata cultivars and bred hybrids) was screened to determine variability in fruit pulp provitamin A carotenoid (pVAC) content using high performance liquid chromatography. Total carotenoid content in tested genotypes varied from 1.45 µg/g for hybrid 25447-S7 R2P8 to 36.21 µg/g for M. acuminata cultivar ITC.0601 Hung Tu with a mean of 8.00 µg/g fresh weight. Predominant carotenoids identified were α-carotene (38.67%), trans-β-carotene (22.08%), lutein (22.08%), 13-cis-β-carotene (14.45%) and 9-cis-β-carotene (2.92%), indicating that about 78% of the carotenoids in bananas are pVAC. High pVAC genotypes were identified for integration into biofortification strategies to combat vitamin A deficiency in developing countries.
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Affiliation(s)
- Delphine Amah
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa.,International Institute of Tropical Agriculture, PMB 5320, Ibadan, Nigeria
| | - Emmanuel Alamu
- Food and Nutrition Sciences Laboratory, International Institute of Tropical Agriculture, Southern Africa Hub, PO Box 310142, Chelstone, Lusaka, Zambia
| | - Michael Adesokan
- International Institute of Tropical Agriculture, PMB 5320, Ibadan, Nigeria
| | - Angeline van Biljon
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa
| | | | - Rony Swennen
- International Institute of Tropical Agriculture, C/o The Nelson Mandela African Institution of Science and Technology, PO Box 344, Arusha, Tanzania.,Bioversity International, Heverlee, Belgium.,Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Maryke Labuschagne
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa
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19
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Amah D, van Biljon A, Maziya-Dixon B, Labuschagne M, Swennen R. Effects of In Vitro Polyploidization on Agronomic Characteristics and Fruit Carotenoid Content; Implications for Banana Genetic Improvement. Front Plant Sci 2019; 10:1450. [PMID: 31781149 PMCID: PMC6861373 DOI: 10.3389/fpls.2019.01450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 10/17/2019] [Indexed: 05/08/2023]
Abstract
Bananas (Musa spp.), native to South East Asia, have spread worldwide and are integrated into the diets of millions of people in tropical regions. Carotenoid content varies dramatically between different banana genotypes, providing an opportunity for vitamin A biofortification. Polyploidization is a useful tool for crop improvement with potential to generate new diversity, especially in a polyploid crop like bananas. Ten induced tetraploids generated from six diploid banana genotypes were evaluated for their agronomic attributes and fruit carotenoid content in comparison to their diploid progenitors. Tetraploids had distinct plant morphology, but generally displayed inferior vegetative and yield characteristics with 20% lower bunch weights than their original diploids. Similarly, a 50% decrease in fruit provitamin A carotenoids (α-carotene, 13-cis β-carotene, 9-cis β-carotene, trans-β-carotene) accompanied by a corresponding increase in lutein was recorded in induced tetraploids in comparison to their original diploids. Additionally, all lines were subjected to pollen viability tests to assess their fertility. Pollen viability tests indicated over 70% viability for induced tetraploids and diploid controls, suggesting their possible use in crosses. These findings provide a basis for the application of induced polyploidization in bananas to generate useful genetic material for integration in hybridization programmes aiming to produce vitamin A enriched triploids valuable to malnourished populations.
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Affiliation(s)
- Delphine Amah
- Plantain and Banana Improvement Program, International Institute of Tropical Agriculture, Ibadan, Nigeria
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa
- *Correspondence: Delphine Amah,
| | - Angeline van Biljon
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa
| | - Bussie Maziya-Dixon
- Food and Nutrition Sciences Laboratory, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Maryke Labuschagne
- Department of Plant Sciences (Plant Breeding), University of the Free State, Bloemfontein, South Africa
| | - Rony Swennen
- International Institute of Tropical Agriculture, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- Laboratory of Tropical Crop Improvement, Bioversity International, Heverlee, Belgium
- Department of Biosystems, KU Leuven, Heverlee, Belgium
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20
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Perrier X, Jenny C, Bakry F, Karamura D, Kitavi M, Dubois C, Hervouet C, Philippson G, De Langhe E. East African diploid and triploid bananas: a genetic complex transported from South-East Asia. Ann Bot 2019; 123:19-36. [PMID: 30247503 PMCID: PMC6344093 DOI: 10.1093/aob/mcy156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/27/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Besides bananas belonging to the AAA triploid Mutika subgroup, which predominates in the Great Lakes countries, other AAA triploids as well as edible AA diploids, locally of considerable cultural weight, are cultivated in East Africa and in the nearby Indian Ocean islands as far as Madagascar. All these varieties call for the genetic identification and characterization of their interrelations on account of their regional socio-economic significance and their potential for banana breeding strategies. METHODS An extensive sampling of all traditional bananas in East Africa and near Indian Ocean islands was genotyped with simple sequence repeat (SSR) markers, with particular emphasis on the diploid forms and on the bananas of the Indian Ocean islands, which remain poorly characterized. KEY RESULTS All the edible AA varieties studied here are genetically homogeneous, constituting a unique subgroup, here called 'Mchare', despite high phenotypic variation and adaptions to highly diverse ecological zones. At triploid level, and besides the well-known AAA Mutika subgroup, at least two other genetically related AAA subgroups specific to this region are identified. Neither of these East African AAA genotypes can be derived directly from the local AA Mchare diploids. However, it is demonstrated that the East African diploids and triploids together belong to the same genetic complex. The geographical distribution of their wild acuminata relatives allowed identification of the original area of this complex in a restricted part of island South-East Asia. The inferred origin leads to consideration of the history of banana introduction in Africa. Linked to biological features, documentation on the embedding of bananas in founding legends and myths and convincing linguistic elements were informative regarding the period and the peoples who introduced these Asian plants into Africa. The results point to the role of Austronesian-speaking peoples who colonized the Indian Ocean islands, particularly Madagascar, and reached the East African coasts. CONCLUSIONS Understanding of the relations between the components of this complex and identifying their Asian wild relatives and related cultivars will be a valuable asset in breeding programmes and will boost the genetic improvement of East African bananas, but also of other globally important subgroups, in particular the AAA Cavendish.
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Affiliation(s)
- Xavier Perrier
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Christophe Jenny
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frédéric Bakry
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | | | - Cécile Dubois
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Gérard Philippson
- Institut National des Langues et Civilisations Orientales, Paris, France
- Laboratoire Dynamique du Langage CNRS, Université Lyon, France
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21
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Němečková A, Christelová P, Čížková J, Nyine M, Van den houwe I, Svačina R, Uwimana B, Swennen R, Doležel J, Hřibová E. Molecular and Cytogenetic Study of East African Highland Banana. Front Plant Sci 2018; 9:1371. [PMID: 30337933 PMCID: PMC6180188 DOI: 10.3389/fpls.2018.01371] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 08/29/2018] [Indexed: 05/20/2023]
Abstract
East African highland bananas (EAHBs) are staple food crop in Uganda, Tanzania, Burundi, and other countries in the African Great Lakes region. Even though several morphologically different types exist, all EAHBs are triploid and display minimal genetic variation. To provide more insights into the genetic variation within EAHBs, genotyping using simple sequence repeat (SSR) markers, molecular analysis of ITS1-5.8S-ITS2 region of ribosomal DNA locus, and the analysis of chromosomal distribution of ribosomal DNA sequences were done. A total of 38 triploid EAHB accessions available in the Musa germplasm collection (International Transit Centre, Leuven, Belgium) were characterized. Six diploid accessions of Musa acuminata ssp. zebrina, ssp. banksii, and ssp. malaccensis representing putative parents of EAHBs were included in the study. Flow cytometric estimation of 2C nuclear DNA content revealed small differences (max ~6.5%) in genome size among the EAHB clones. While no differences in the number of 45S and 5S rDNA loci were found, genotyping using 19 SSR markers resulted in grouping the EAHB accessions into four clusters. The DNA sequence analysis of the internal transcribed spacer region indicated a relation of EAHB clones with M. acuminata and, surprisingly, also with M. schizocarpa. The results suggest that EAHB cultivars originated from a single hybrid clone with M. acuminata ssp. zebrina and ssp. banksii being its most probable parents. However, M. schizocarpa seems to have contributed to the formation of this group of banana.
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Affiliation(s)
- Alžběta Němečková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Pavla Christelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jana Čížková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Moses Nyine
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- International Institute of Tropical Agriculture, Banana Breeding, Kampala, Uganda
| | | | - Radim Svačina
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Brigitte Uwimana
- International Institute of Tropical Agriculture, Banana Breeding, Kampala, Uganda
| | - Rony Swennen
- Bioversity International, Banana Genetic Resources, Heverlee, Belgium
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, Banana Breeding, Arusha, Tanzania
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Eva Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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22
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Němečková A, Christelová P, Čížková J, Nyine M, Van den Houwe I, Svačina R, Uwimana B, Swennen R, Doležel J, Hřibová E. Molecular and Cytogenetic Study of East African Highland Banana. Front Plant Sci 2018; 9:1371. [PMID: 30337933 DOI: 10.3389/fpls.2018.01371/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 08/29/2018] [Indexed: 05/24/2023]
Abstract
East African highland bananas (EAHBs) are staple food crop in Uganda, Tanzania, Burundi, and other countries in the African Great Lakes region. Even though several morphologically different types exist, all EAHBs are triploid and display minimal genetic variation. To provide more insights into the genetic variation within EAHBs, genotyping using simple sequence repeat (SSR) markers, molecular analysis of ITS1-5.8S-ITS2 region of ribosomal DNA locus, and the analysis of chromosomal distribution of ribosomal DNA sequences were done. A total of 38 triploid EAHB accessions available in the Musa germplasm collection (International Transit Centre, Leuven, Belgium) were characterized. Six diploid accessions of Musa acuminata ssp. zebrina, ssp. banksii, and ssp. malaccensis representing putative parents of EAHBs were included in the study. Flow cytometric estimation of 2C nuclear DNA content revealed small differences (max ~6.5%) in genome size among the EAHB clones. While no differences in the number of 45S and 5S rDNA loci were found, genotyping using 19 SSR markers resulted in grouping the EAHB accessions into four clusters. The DNA sequence analysis of the internal transcribed spacer region indicated a relation of EAHB clones with M. acuminata and, surprisingly, also with M. schizocarpa. The results suggest that EAHB cultivars originated from a single hybrid clone with M. acuminata ssp. zebrina and ssp. banksii being its most probable parents. However, M. schizocarpa seems to have contributed to the formation of this group of banana.
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Affiliation(s)
- Alžběta Němečková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Pavla Christelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jana Čížková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Moses Nyine
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- International Institute of Tropical Agriculture, Banana Breeding, Kampala, Uganda
| | | | - Radim Svačina
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Brigitte Uwimana
- International Institute of Tropical Agriculture, Banana Breeding, Kampala, Uganda
| | - Rony Swennen
- Bioversity International, Banana Genetic Resources, Heverlee, Belgium
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, Banana Breeding, Arusha, Tanzania
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Eva Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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23
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Campos NA, Swennen R, Carpentier SC. The Plantain Proteome, a Focus on Allele Specific Proteins Obtained from Plantain Fruits. Proteomics 2018; 18:1700227. [PMID: 29333696 PMCID: PMC6084372 DOI: 10.1002/pmic.201700227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/31/2017] [Indexed: 01/07/2023]
Abstract
Proteomics has been applied with great potential to elucidate molecular mechanisms in plants. This is especially valid in the case of non-model crops of which their genome has not been sequenced yet, or is not well annotated. Plantains are a kind of cooking bananas that are economically very important in Africa, India, and Latin America. The aim of this work was to characterize the fruit proteome of common dessert bananas and plantains and to identify proteins that are only encoded by the plantain genome. We present the first plantain fruit proteome. All data are available via ProteomeXchange with identifier PXD005589. Using our in-house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides. Although we do not have access (yet) to whole-genome sequencing data from triploid banana cultivars, we show that proteomics is an easily accessible complementary alternative to detect different allele specific SNPs/SAAPs. These unique alleles might contribute toward the differences in the metabolism between dessert bananas and plantains. This dataset will stimulate further analysis by the scientific community, boost plantain research, and facilitate plantain breeding.
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Affiliation(s)
| | - Rony Swennen
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Department of BiosystemsKU LeuvenLeuvenBelgium
- International Institute of Tropical AgricultureArushaTanzania
- Bioversity InternationalLeuvenBelgium
| | - Sebastien C. Carpentier
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Department of BiosystemsKU LeuvenLeuvenBelgium
- Bioversity InternationalLeuvenBelgium
- SYBIOMA: Facility for SYstems BIOlogy based MAss spectrometryKU LeuvenLeuvenBelgium
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24
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Muiruri KS, Britt A, Amugune NO, Nguu E, Chan S, Tripathi L. Dominant Allele Phylogeny and Constitutive Subgenome Haplotype Inference in Bananas Using Mitochondrial and Nuclear Markers. Genome Biol Evol 2017; 9:2510-2521. [PMID: 28992303 PMCID: PMC5629815 DOI: 10.1093/gbe/evx167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2017] [Indexed: 12/22/2022] Open
Abstract
Cultivated bananas (Musa spp.) have undergone domestication patterns involving crosses of wild progenitors followed by long periods of clonal propagation. Majority of cultivated bananas are polyploids with different constitutive subgenomes and knowledge on phylogenies to their progenitors at the species and subspecies levels is essential. Here, the mitochondrial (NAD1) and nuclear (CENH3) markers were used to phylogenetically position cultivated banana genotypes to diploid progenitors. The CENH3 nuclear marker was used to identify a minimum representative haplotype number in polyploids and diploid bananas based on single nucleotide polymorphisms. The mitochondrial marker NAD1 was observed to be ideal in differentiating bananas of different genomic constitutions based on size of amplicons as well as sequence. The genotypes phylogenetically segregated based on the dominant genome; AAB genotypes grouped with AA and AAA, and the ABB together with BB. Both markers differentiated banana sections, but could not differentiate subspecies within the A genomic group. On the basis of CENH3 marker, a total of 13 haplotypes (five in both diploid and triploid, three in diploids, and rest unique to triploids) were identified from the genotypes tested. The presence of haplotypes, which were common in diploids and triploids, stipulate possibility of a shared ancestry in the genotypes involved in this study. Furthermore, the presence of multiple haplotypes in some diploid bananas indicates their being heterozygous. The haplotypes identified in this study are of importance because they can be used to check the level of homozygozity in breeding lines as well as to track segregation in progenies.
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Affiliation(s)
- Kariuki Samwel Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- School of Biological Sciences, University of Nairobi, Kenya
| | - Anne Britt
- Department of Plant Biology, University of California, Davis
| | | | - Edward Nguu
- Department of Biochemistry, University of Nairobi, Kenya
| | - Simon Chan
- Department of Plant Biology, University of California, Davis
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
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25
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Batte M, Mukiibi A, Swennen R, Uwimana B, Pocasangre L, Hovmalm HP, Geleta M, Ortiz R. Suitability of existing Musa morphological descriptors to characterize East African highland 'matooke' bananas. Genet Resour Crop Evol 2017; 65:645-657. [PMID: 33364682 PMCID: PMC7705172 DOI: 10.1007/s10722-017-0562-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 08/29/2017] [Indexed: 05/30/2023]
Abstract
Morphological traits are commonly used for characterizing plant genetic resources. Germplasm characterization should be based on distinctly identifiable, stable and heritable traits that are expressed consistently and are easy to distinguish by the human eye. Characterization and documentation of a representative sample of East African highland bananas (Lujugira-Mutika subgroup) was carried out following an internationally accepted standard protocol for bananas. Eleven cultivars were characterized using an existing set of minimum descriptors (31 qualitative and quantitative traits) with the aim of determining stable descriptors and the ability of these descriptors to distinguish among East African highland banana cultivars. There was variation in stability of these descriptors within cultivars and across the 11 cultivars. Only 10 (32%) out of 31 descriptors studied were stable in the 11 cultivars. However, they had similar scores and therefore are not suitable to distinguish between cultivars within this group. Nonetheless, these 10 descriptors may be useful for distinguishing the East African highland bananas as a group from other groups of bananas. A few descriptors were unique to the cultivar 'Tereza' and may be used to distinguish this cultivar from other 'matooke' cultivars. None of the quantitative descriptors were stable.
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Affiliation(s)
- Michael Batte
- International Institute of Tropical Agriculture (IITA), P.O. Box 7878, Kampala, Uganda
- Swedish University of Agricultural Sciences (SLU), Sundsvágen 10, Box 101, 23053 Alnarp, Sweden
| | - Alex Mukiibi
- EARTH University, San José 4442-1000, Costa Rica
| | - Rony Swennen
- International Institute of Tropical Agriculture (IITA), C/o The Nelson Mandela African Institution for Science and Technology (NM-AIST), P.O. Box 447, Arusha, Tanzania
- Laboratory of Tropical Crop Improvement, Katholieke Universiteite Leuven (KUL), Willem De Croylaan 42, Bus 2455, 3001 Leuven, Belgium
- Bioversity International, Willem De Croylaan 42, 3001 Heverlee, Belgium
| | - Brigitte Uwimana
- International Institute of Tropical Agriculture (IITA), P.O. Box 7878, Kampala, Uganda
| | | | - Helena Persson Hovmalm
- Swedish University of Agricultural Sciences (SLU), Sundsvágen 10, Box 101, 23053 Alnarp, Sweden
| | - Mulatu Geleta
- Swedish University of Agricultural Sciences (SLU), Sundsvágen 10, Box 101, 23053 Alnarp, Sweden
| | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences (SLU), Sundsvágen 10, Box 101, 23053 Alnarp, Sweden
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Nouroz F, Noreen S, Ahmad H, Heslop-Harrison JSP. The landscape and structural diversity of LTR retrotransposons in Musa genome. Mol Genet Genomics 2017; 292:1051-67. [PMID: 28601922 DOI: 10.1007/s00438-017-1333-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/07/2017] [Indexed: 10/19/2022]
Abstract
Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated, and a great number of partial copies/remnants from GenBank database. LARD-like elements were also identified with several copies dispersed among the Musa genotypes. The predominant elements were the LTR retrotransposons Copia and Gypsy, while Caulimoviridae (pararetrovirus) were rare in the Musa genome. PCR amplification of reverse transcriptase (RT) sequences revealed their abundance in almost all tested Musa accessions and their ancient nature before the divergence of Musa species. The phylogenetic analysis based on RT sequences of Musa and other retrotransposons clustered them into Gypsy, Caulimoviridae, and Copia lineages. Most of the Musa-related elements clustered in their respective groups, while some grouped with other elements indicating homologous sequences. The present work will be helpful to understand the LTR retrotransposons landscape, giving a complete picture of the nature of the elements, their structural features, annotation, and evolutionary dynamics in the Musa genome.
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Sardos J, Perrier X, Doležel J, Hřibová E, Christelová P, Van den Houwe I, Kilian A, Roux N. DArT whole genome profiling provides insights on the evolution and taxonomy of edible Banana (Musa spp.). Ann Bot 2016; 118:1269-1278. [PMID: 27590334 PMCID: PMC5155597 DOI: 10.1093/aob/mcw170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/20/2016] [Accepted: 06/17/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Dessert and cooking bananas are vegetatively propagated crops of great importance for both the subsistence and the livelihood of people in developing countries. A wide diversity of diploid and triploid cultivars including AA, AB, AS, AT, AAA, AAB, ABB, AAS and AAT genomic constitutions exists. Within each of this genome groups, cultivars are classified into subgroups that are reported to correspond to varieties clonally derived from each other after a single sexual event. The number of those founding events at the basis of the diversity of bananas is a matter of debate. METHODS We analysed a large panel of 575 accessions, 94 wild relatives and 481 cultivated accessions belonging to the section Musa with a set of 498 DArT markers previously developed. KEY RESULTS DArT appeared successful and accurate to describe Musa diversity and help in the resolution of cultivated banana genome constitution and taxonomy, and highlighted discrepancies in the acknowledged classification of some accessions. This study also argues for at least two centres of domestication corresponding to South-East Asia and New Guinea, respectively. Banana domestication in New Guinea probably followed different schemes that those previously reported where hybridization underpins the emergence of edible banana. In addition, our results suggest that not all wild ancestors of bananas are known, especially in M. acuminata subspecies. We also estimate the extent of the two consecutive bottlenecks in edible bananas by evaluating the number of sexual founding events underlying our sets of edible diploids and triploids, respectively. CONCLUSIONS The attribution of clone identity to each sample of the sets allowed the detection of subgroups represented by several sets of clones. Although morphological characterization of some of the accessions is needed to correct potentially erroneous classifications, some of the subgroups seem polyclonal.
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Affiliation(s)
- J Sardos
- Bioversity International, Parc Scientifique Agropolis II, 1990 boulevard de la Lironde, 34397 Montpellier Cedex 5, France
| | - X Perrier
- CIRAD, UMR AGAP, 34398 Montpellier, France
| | - J Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - E Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - P Christelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - I Van den Houwe
- Bioversity International, Willem De Croylaan 42, 3001 Leuven, Belgium
| | - A Kilian
- Diversity Arrays Technology Pty Ltd, Building 3, University of Canberra, Bruce, ACT 2617, Australia
| | - N Roux
- Bioversity International, Parc Scientifique Agropolis II, 1990 boulevard de la Lironde, 34397 Montpellier Cedex 5, France
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Sardos J, Rouard M, Hueber Y, Cenci A, Hyma KE, van den Houwe I, Hribova E, Courtois B, Roux N. A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop. PLoS One 2016; 11:e0154448. [PMID: 27144345 PMCID: PMC4856271 DOI: 10.1371/journal.pone.0154448] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 04/13/2016] [Indexed: 11/19/2022] Open
Abstract
Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.
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Affiliation(s)
- Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
- * E-mail:
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Katie E. Hyma
- Institute of Biotechnology, Genomic Diversity Facility, Cornell University, Ithaca, NY, 14853, United States of America
| | | | - Eva Hribova
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
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Duroy PO, Perrier X, Laboureau N, Jacquemoud-Collet JP, Iskra-Caruana ML. How endogenous plant pararetroviruses shed light on Musa evolution. Ann Bot 2016; 117:625-41. [PMID: 26971286 PMCID: PMC4817503 DOI: 10.1093/aob/mcw011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/06/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Banana genomes harbour numerous copies of viral sequences derived from banana streak viruses (BSVs) - dsDNA viruses belonging to the family Caulimoviridae.These viral integrants (eBSVs) are mostly defective, probably as a result of 'pseudogenization' driven by host genome evolution. However, some can give rise to infection by releasing a functional viral genome following abiotic stresses. These distinct infective eBSVs correspond to the three main widespread BSV species (BSOLV, BSGFV and BSIMV), fully described within the Musa balbisiana B genomes of the seedy diploid 'Pisang Klutuk Wulung' (PKW). METHODS We characterize eBSV distribution among a Musa sampling including seedy BB diploids and interspecific hybrids with Musa acuminate exhibiting different levels of ploidy for the B genome (ABB, AAB, AB). We used representative samples of the two areas of sympatry between M. acuminate and M. balbisiana species representing the native area of the most widely cultivated AAB cultivars (in India and in East Asia, ranging from the Philippines to New Guinea). Seventy-seven accessions were characterized using eBSV-related PCR markers and Southern hybridization approaches. We coded both sets of results to create a common dissimilarity matrix with which to interpret eBSV distribution. KEY RESULTS We propose a Musa phylogeny driven by the M. balbisiana genome based on a dendrogram resulting from a joint neighbour-joining analysis of the three BSV species, showing for the first time lineages between BB and ABB/AAB hybrids. eBSVs appear to be relevant phylogenetic markers that can illustrate theM. balbisiana phylogeography story. CONCLUSION The theoretical implications of this study for further elucidation of the historical and geographical process of Musa domestication are numerous. Discovery of banana plants with B genome non-infective for eBSV opens the way to the introduction of new genitors in programmes of genetic banana improvement.
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Kagy V, Wong M, Vandenbroucke H, Jenny C, Dubois C, Ollivier A, Cardi C, Mournet P, Tuia V, Roux N, Doležel J, Perrier X. Traditional Banana Diversity in Oceania: An Endangered Heritage. PLoS One 2016; 11:e0151208. [PMID: 26982801 PMCID: PMC4794170 DOI: 10.1371/journal.pone.0151208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
This study aims to understand the genetic diversity of traditional Oceanian starchy bananas in order to propose an efficient conservation strategy for these endangered varieties. SSR and DArT molecular markers are used to characterize a large sample of Pacific accessions, from New Guinea to Tahiti and Hawaii. All Pacific starchy bananas are shown of New Guinea origin, by interspecific hybridization between Musa acuminata (AA genome), more precisely its local subspecies M. acuminata ssp. banksii, and M. balbisiana (BB genome) generating triploid AAB Pacific starchy bananas. These AAB genotypes do not form a subgroup sensu stricto and genetic markers differentiate two subgroups across the three morphotypes usually identified: Iholena versus Popoulu and Maoli. The Popoulu/Maoli accessions, even if morphologically diverse throughout the Pacific, cluster in the same genetic subgroup. However, the subgroup is not strictly monophyletic and several close, but different genotypes are linked to the dominant genotype. One of the related genotypes is specific to New Caledonia (NC), with morphotypes close to Maoli, but with some primitive characters. It is concluded that the diffusion of Pacific starchy AAB bananas results from a series of introductions of triploids originating in New Guinea area from several sexual recombination events implying different genotypes of M. acuminata ssp. banksii. This scheme of multiple waves from the New Guinea zone is consistent with the archaeological data for peopling of the Pacific. The present geographic distribution suggests that a greater diversity must have existed in the past. Its erosion finds parallels with the erosion of cultural traditions, inexorably declining in most of the Polynesian or Melanesian Islands. Symmetrically, diversity hot spots appear linked to the local persistence of traditions: Maoli in New Caledonian Kanak traditions or Iholena in a few Polynesian islands. These results will contribute to optimizing the conservation strategy for the ex-situ Pacific Banana Collection supported collectively by the Pacific countries.
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Affiliation(s)
- Valérie Kagy
- Institut Agronomique néo Calédonien (IAC), Connaissance et Amélioration des Agro-Systèmes, BP 32 98880 La Foa, Nouvelle Calédonie
- * E-mail:
| | - Maurice Wong
- Service du Développement Rural (SDR), Département de la Recherche Agronomique, BP 100, 98713 Papeete—Tahiti, Polynésie française
| | - Henri Vandenbroucke
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (AGAP), Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Christophe Jenny
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (AGAP), Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Cécile Dubois
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (AGAP), Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Anthony Ollivier
- Institut Agronomique néo Calédonien (IAC), Connaissance et Amélioration des Agro-Systèmes, BP 32 98880 La Foa, Nouvelle Calédonie
| | - Céline Cardi
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (AGAP), Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Pierre Mournet
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (AGAP), Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Valérie Tuia
- Pacific Community, Land Resources Division, Centre for Pacific Crops and Trees (CePaCT), Private Mail Bag, Suva, Fiji Islands
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, F-34397 Montpellier Cedex 5, France
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Xavier Perrier
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (AGAP), Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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Kitavi M, Downing T, Lorenzen J, Karamura D, Onyango M, Nyine M, Ferguson M, Spillane C. The triploid East African Highland Banana (EAHB) genepool is genetically uniform arising from a single ancestral clone that underwent population expansion by vegetative propagation. Theor Appl Genet 2016; 129:547-61. [PMID: 26743524 DOI: 10.1007/s00122-015-2647-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/30/2015] [Indexed: 05/04/2023]
Abstract
All East African Highland Banana varieties are genetically uniform having arisen from a single clone introduced to Africa. East African Highland bananas (EAHBs) are a subgroup of triploid (AAA genome) bananas of importance to food security in the Great Lakes region of Africa. Little is known about their genetic variation, population structure and evolutionary history. Ninety phenotypically diverse EAHB cultivars were genotyped at 100 SSR microsatellite markers to investigate population genetic diversity, the correlation of genetic variability with morphological classes, and evolutionary origins since introduction to Africa. Population-level statistics were compared to those for plantain (AAB) and dessert (AAA) cultivars representing other M. acuminata subgroups. EAHBs displayed minimal genetic variation and are largely genetically uniform, irrespective of whether they were derived from the distinct Ugandan or Kenyan germplasm collections. No association was observed between EAHB genetic diversity and currently employed morphological taxonomic systems for EAHB germplasm. Population size dynamics indicated that triploid EAHBs arose as a single hybridization event, which generated a genetic bottleneck during foundation of the EAHB genepool. As EAHB triploids are sterile, subsequent asexual vegetative propagation of EAHBs allowed a recent rapid expansion in population size. This provided a basis for emergence of genetically near-isogenic somatic mutants selected across farmers and environments in East Africa over the past 2000 years since EAHBs were first introduced to the African continent.
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Affiliation(s)
- Mercy Kitavi
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, C306 Aras de Brun, National University of Ireland Galway, University Road, Galway, Ireland
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Tim Downing
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, University Road, Galway, Ireland
| | - Jim Lorenzen
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
- Bill and Melinda Gates Foundation, 500 5th Ave N, Seattle, WA, 98102, USA
| | - Deborah Karamura
- Bioversity International, PLOT 106, Katalima Road, P.O. Box 24384, Kampala, Uganda
| | - Margaret Onyango
- Kenya Agricultural Research Institute (KARI), KARI, Kisii Centre, P.O. Box 523-40200, Kisii, Kenya
| | - Moses Nyine
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Morag Ferguson
- International Institute for Tropical Agriculture (IITA), Biosciences Eastern and Central Africa (BecA-ILRI), P.O. Box 30709-00100, Nairobi, Kenya
| | - Charles Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, C306 Aras de Brun, National University of Ireland Galway, University Road, Galway, Ireland.
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Mahendhiran M, Ramirez-Prado JH, Escobedo-Gracia Medrano RM, Canto-Canché B, Tzec-Simá M, Grijalva-Arango R, James-Kay A. Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Pachuau L, Atom AD, Thangjam R. Genome classification of Musa cultivars from northeast India as revealed by ITS and IRAP markers. Appl Biochem Biotechnol 2014; 172:3939-48. [PMID: 24590891 DOI: 10.1007/s12010-014-0827-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/19/2014] [Indexed: 11/28/2022]
Abstract
Genome classification of 38 banana cultivars found in northeast India was successfully carried out using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the internal transcribed spacer (ITS) region and inter-retrotransposon amplified polymorphism (IRAP) techniques. The RsaI digestion of the ITS region revealed the composition of A genome in 32 cultivars and B genome in 29 cultivars. With the gypsy-IRAP marker, 33 cultivars were identified to be composed of B genome. The AluI digestion of the 420-bp PCR amplification product using copia-IRAP primer resulted in the identification of the ABB genome in 17 cultivars. Overall, the data obtained from 36 cultivars using the molecular markers were in accordance with the initial classification based on morphological characters except in two cultivars. The present findings provide the reliable information on the genome classification and the status of the existing banana genetic resources from the northeastern Indian region, which could be utilized in improvement and conservation programs.
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Affiliation(s)
- Lalrinfela Pachuau
- Department of Biochemistry, Government Zirtiri Residential Science College, Aizawl, 796001, India
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Iskra-Caruana ML, Chabannes M, Duroy PO, Muller E. A possible scenario for the evolution of Banana streak virus in banana. Virus Res 2014; 186:155-62. [PMID: 24457073 DOI: 10.1016/j.virusres.2014.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 12/18/2013] [Accepted: 01/10/2014] [Indexed: 01/15/2023]
Abstract
Outbreaks of Banana streak virus (BSV) have been recorded worldwide where Musa spp. is grown during the last 20 years with no convincing evidence of epidemics. Epidemics were previously reported in Uganda where BSV is currently endemic. BSV is a plant pararetrovirus of the family Caulimoviridae, genus Badnavirus it causes chlorosis leaf streak disease. The information currently available on banana streak disease makes it possible to identify a complex of distinct BSV species each causing the same disease. BSV exists in two states: one as an episomal form, infecting plant cells; the other as viral DNA integrated within the B genome of banana (endogenous BSV-eBSV) forming a viral genome for de novo viral particles. Both forms can be infectious in banana plants. The BSV phylogeny is polyphyletic with BSV distributed in two clades. Clade 1 clusters BSV species that occur worldwide and may have an eBSV counterpart, whereas Clade 3 only comprises BSV species from Uganda. Clearly, two distinct origins explain such BSV diversity. However, the epidemiology/outbreaks of BSV remains unclear and the role of eBSV needs to be clarified. In this review, the biodiversity of BSV is explained and discussed in the light of field and molecular epidemiology data. A scheme is proposed for the co-evolution of BSV and banana based on old or recent infection hypotheses related to African domestication sites and banana dissemination to explain the disease context.
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Ortiz R, Swennen R. From crossbreeding to biotechnology-facilitated improvement of banana and plantain. Biotechnol Adv 2014; 32:158-69. [DOI: 10.1016/j.biotechadv.2013.09.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 12/30/2022]
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Li LF, Wang HY, Zhang C, Wang XF, Shi FX, Chen WN, Ge XJ. Origins and domestication of cultivated banana inferred from chloroplast and nuclear genes. PLoS One 2013; 8:e80502. [PMID: 24260405 PMCID: PMC3832372 DOI: 10.1371/journal.pone.0080502] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Cultivated bananas are large, vegetatively-propagated members of the genus Musa. More than 1,000 cultivars are grown worldwide and they are major economic and food resources in numerous developing countries. It has been suggested that cultivated bananas originated from the islands of Southeast Asia (ISEA) and have been developed through complex geodomestication pathways. However, the maternal and parental donors of most cultivars are unknown, and the pattern of nucleotide diversity in domesticated banana has not been fully resolved. METHODOLOGY/PRINCIPAL FINDINGS We studied the genetics of 16 cultivated and 18 wild Musa accessions using two single-copy nuclear (granule-bound starch synthase I, GBSS I, also known as Waxy, and alcohol dehydrogenase 1, Adh1) and two chloroplast (maturase K, matK, and the trnL-F gene cluster) genes. The results of phylogenetic analyses showed that all A-genome haplotypes of cultivated bananas were grouped together with those of ISEA subspecies of M. acuminata (A-genome). Similarly, the B- and S-genome haplotypes of cultivated bananas clustered with the wild species M. balbisiana (B-genome) and M. schizocarpa (S-genome), respectively. Notably, it has been shown that distinct haplotypes of each cultivar (A-genome group) were nested together to different ISEA subspecies M. acuminata. Analyses of nucleotide polymorphism in the Waxy and Adh1 genes revealed that, in comparison to the wild relatives, cultivated banana exhibited slightly lower nucleotide diversity both across all sites and specifically at silent sites. However, dramatically reduced nucleotide diversity was found at nonsynonymous sites for cultivated bananas. CONCLUSIONS/SIGNIFICANCE Our study not only confirmed the origin of cultivated banana as arising from multiple intra- and inter-specific hybridization events, but also showed that cultivated banana may have not suffered a severe genetic bottleneck during the domestication process. Importantly, our findings suggested that multiple maternal origins and a reduction in nucleotide diversity at nonsynonymous sites are general attributes of cultivated bananas.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
| | - Hua-Ying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Cui Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Xin-Feng Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Feng-Xue Shi
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, China
| | - Wen-Na Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
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Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard JF, Lengelle J, Baurens FC, Cenci A, Pitollat B, D'Hont A, Ruiz M, Rouard M, Bocs S. The banana genome hub. Database (Oxford) 2013; 2013:bat035. [PMID: 23707967 PMCID: PMC3662865 DOI: 10.1093/database/bat035] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/
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Affiliation(s)
- Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier F-34398, France.
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de Jesus ON, Silva SDOE, Amorim EP, Ferreira CF, de Campos JMS, Silva GDG, Figueira A. Genetic diversity and population structure of Musa accessions in ex situ conservation. BMC Plant Biol 2013; 13:41. [PMID: 23497122 PMCID: PMC3636076 DOI: 10.1186/1471-2229-13-41] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/22/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Banana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa. RESULTS From the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis. CONCLUSIONS The data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the "single-step domestication" hypothesis had long predominated. These findings will have an impact in future breeding approaches. Structure analysis enabled the efficient detection of ancestry of recently developed tetraploid hybrids by breeding programs, and for some triploids. However, for the main commercial subgroups, Structure appeared to be less efficient to detect the ancestry in diploid groups, possibly due to sampling restrictions. The possibility of inferring the membership among accessions to correct the effects of genetic structure opens possibilities for its use in marker-assisted selection by association mapping.
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Affiliation(s)
- Onildo Nunes de Jesus
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
- EMBRAPA Mandioca Fruticultura, R. Embrapa s/n, Cruz das Almas, BA, 44380-000, Brazil
| | | | - Edson Perito Amorim
- EMBRAPA Mandioca Fruticultura, R. Embrapa s/n, Cruz das Almas, BA, 44380-000, Brazil
| | | | | | - Gabriela de Gaspari Silva
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil
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