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Beránková D, Čížková J, Majzlíková G, Doležalová A, Mduma H, Brown A, Swennen R, Hřibová E. Striking variation in chromosome structure within Musa acuminata subspecies, diploid cultivars, and F1 diploid hybrids. FRONTIERS IN PLANT SCIENCE 2024; 15:1387055. [PMID: 39027673 PMCID: PMC11255410 DOI: 10.3389/fpls.2024.1387055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024]
Abstract
The majority of cultivated bananas originated from inter- and intra(sub)specific crosses between two wild diploid species, Musa acuminata and Musa balbisiana. Hybridization and polyploidization events during the evolution of bananas led to the formation of clonally propagated cultivars characterized by a high level of genome heterozygosity and reduced fertility. The combination of low fertility in edible clones and differences in the chromosome structure among M. acuminata subspecies greatly hampers the breeding of improved banana cultivars. Using comparative oligo-painting, we investigated large chromosomal rearrangements in a set of wild M. acuminata subspecies and cultivars that originated from natural and human-made crosses. Additionally, we analyzed the chromosome structure of F1 progeny that resulted from crosses between Mchare bananas and the wild M. acuminata 'Calcutta 4' genotype. Analysis of chromosome structure within M. acuminata revealed the presence of a large number of chromosomal rearrangements showing a correlation with banana speciation. Chromosome painting of F1 hybrids was complemented by Illumina resequencing to identify the contribution of parental subgenomes to the diploid hybrid clones. The balanced presence of both parental genomes was revealed in all F1 hybrids, with the exception of one clone, which contained only Mchare-specific SNPs and thus most probably originated from an unreduced diploid gamete of Mchare.
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Affiliation(s)
- Denisa Beránková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Gabriela Majzlíková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Alžběta Doležalová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Hassan Mduma
- International Institute of Tropical Agriculture, Banana Breeding, Arusha, Tanzania
| | - Allan Brown
- International Institute of Tropical Agriculture, Banana Breeding, Arusha, Tanzania
| | - Rony Swennen
- International Institute of Tropical Agriculture, Kampala, Uganda
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
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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] [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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Evaluation of the Optimal Uses of Five Genotypes of Musa textilis Fiber Grown in the Tropical Region. Polymers (Basel) 2022; 14:polym14091772. [PMID: 35566940 PMCID: PMC9102293 DOI: 10.3390/polym14091772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 02/05/2023] Open
Abstract
Knowing the genotypes of Musa textilis and its fiber production properties is key for developing cultivars with homogeneous properties and focusing on specific products or market segments that generate added value to the fiber. For this reason, the objective was to determine the optimal use of five genotypes of M. textilis (MT01, MT03, MT07, MT11, and CF01) with high productivity grown in the tropical region of Costa Rica. Therefore, anatomical, physical-mechanical, chemical, and energetic analyses were carried out on these fibers to define whether any genotype has the ideal conditions for a specific use. The results showed differences between the genotypes, obtaining significant differences in physical-mechanical properties (tension, water retention, and color), chemical properties (holocellulose, lignin, extractives, and elemental values of nitrogen, carbon, and sulfur), and energetic properties (volatiles, ash, and caloric value thermogravimetric analyses), which resulted in the establishment of two groups of genotypes with a dissimilarity degree of 35%. The first group, composed of MT03 and MT01, presented characteristics suitable for paper production, biodegradable materials, and composite materials. On the other hand, the second group, made up of MT07, MT11, and CF01, showed properties suitable for textiles, heavy-duty fibers, and bioenergy.
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Dehery SK, Das AB. Genetic diversity of twelve triploid bananas and plantains under section Eumusa as evident by chromosome morphology and SSR markers. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00364-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Batte M, Nyine M, Uwimana B, Swennen R, Akech V, Brown A, Hovmalm HP, Geleta M, Ortiz R. Significant progressive heterobeltiosis in banana crossbreeding. BMC PLANT BIOLOGY 2020; 20:489. [PMID: 33109087 PMCID: PMC7590486 DOI: 10.1186/s12870-020-02667-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/23/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Heterobeltiosis is the phenomenon when the hybrid's performance is superior to its best performing parent. Banana (Musa spp. AAA) breeding is a tedious, time-consuming process, taking up to two decades to develop a consumer acceptable hybrid. Exploiting heterobeltiosis in banana breeding will help to select breeding material with high complementarity, thus increasing banana breeding efficiency. The aim of this study was therefore to determine and document the level of heterobeltiosis of bunch weight and plant stature in the East African highland bananas, in order to identify potential parents that can be used to produce offspring with desired bunch weight and stature after a few crosses. RESULTS This research found significant progressive heterobeltiosis in cross-bred 'Matooke' (highland cooking) banana hybrids, also known as NARITAs, when grown together across years with their parents and grandparents in Uganda. Most (all except 4) NARITAs exhibited positive heterobeltiosis for bunch weight, whereas slightly more than half of them had negative heterobeltiosis for stature. The secondary triploid NARITA 17 had the highest heterobeltiosis for bunch weight: 249% versus its 'Matooke' grandparent and 136% against its primary tetraploid parent. Broad sense heritability (across three cropping cycles) for yield potential and bunch weight were high (0.84 and 0.76 respectively), while that of plant stature was very low (0.0035). There was a positive significant correlation (P < 0.05) between grandparent heterobeltiosis for bunch weight and genetic distance between parents (r = 0.39, P = 0.036), bunch weight (r = 0.7, P < 0.001), plant stature (r = 0.38, P = 0.033) and yield potential (r = 0.59, P < 0.001). Grandparent heterobeltiosis for plant stature was significantly, but negatively, correlated to the genetic distance between parents (r = - 0.6, P < 0.001). CONCLUSIONS Such significant heterobeltiosis exhibited for bunch weight is to our knowledge the largest among main food crops. Since bananas are vegetatively propagated, the effect of heterobeltiosis is easily fixed in the hybrids and will not be lost over time after the release and further commercialization of these hybrids.
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Affiliation(s)
- Michael Batte
- International Institute of Tropical Agriculture (IITA), P.O. Box 7878, Kampala, Uganda.
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), P.O. Box 101, 23053, Alnarp, SE, Sweden.
| | - Moses Nyine
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Brigitte Uwimana
- International Institute of Tropical Agriculture (IITA), P.O. Box 7878, Kampala, Uganda
| | - Rony Swennen
- International Institute of Tropical Agriculture (IITA), C/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O. Box 447, Arusha, Tanzania
- Laboratory of Tropical Crop Improvement, Katholieke Universiteite Leuven (KUL), Willem De Croylaan 42, 3001, Leuven, Belgium
- Bioversity International, Willem De Croylaan 42, 3001, Heverlee, Belgium
| | - Violet Akech
- International Institute of Tropical Agriculture (IITA), P.O. Box 7878, Kampala, Uganda
| | - Allan Brown
- International Institute of Tropical Agriculture (IITA), C/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O. Box 447, Arusha, Tanzania
| | - Helena Persson Hovmalm
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), P.O. Box 101, 23053, Alnarp, SE, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), P.O. Box 101, 23053, Alnarp, SE, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), P.O. Box 101, 23053, Alnarp, SE, Sweden
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Brisibe EA, Ekanem NG. Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome). BMC Genomics 2019; 20:713. [PMID: 31521108 PMCID: PMC6744660 DOI: 10.1186/s12864-019-6083-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/06/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Inflorescence dichotomy in Musa species is a rare developmental event which leads to the production of multiple bunches on a single pseudostem at fruiting. In spite of its fascinating attraction and seductive appeal, little is known about the cytogenetic basis and molecular mechanisms that could be ascribed to this phenomenon. To bridge this gap in information, an integrative approach using cytological fingerprinting and DNA ploidy level profiling (based on chromosome counting and flow cytometry) were assayed on five inflorescence dichotomous plantain varieties and a single-bunching cultivar that served as control. This was done to assess the number and behaviour of chromosomes on the one hand and single nucleotide polymorphisms identified during analysis of nucleotide variations on the other. RESULTS Chromosomes stained with aceto-orcein were very tiny, compact, metacentric and acrocentric, and differed both in number and ploidy level between the inflorescence dichotomous and single-bunching cultivars. The dichotomous plantains were mainly diploid (2n = 2x = 22) while the single-bunching 'Agbagba' cultivar was consistently a triploid (2n = 3x = 33), as revealed by histological chromosome counting and flow cytometry, implying that there was a high incidence of genomic divergence on account of ploidy variations among the different Musa cultivars. Molecular genotyping using single nucleotide polymorphisms detected on the GTPase-protein binding gene of the leaf tissue gene complex provided further evidence indicating that differences in the number of bunches among the inflorescence dichotomous cultivars could be ascribed to nucleotide diversity that was elicited by changes in amino acid sequences in the genome of the crops. Non-synonymous nucleotide substitutions resulted mainly from transversion (from purine to pyramidine and vice versa), tacitly implying that these changes were crucial and promoted a cascade of reactions in the genome that were, probably, responsible for the non-persistence of the dichotomization event(s) or the reversals in the bunch phenotype detected among the inflorescence dichotomous cultivars. CONCLUSIONS This is the first report of cytogenetic fingerprints and nucleotide diversity detection among single- and multiple-bunching Musa cultivars. A clear distinction between the two groups was found that is indicative of variations both in ploidy level and nucleotide sequences. The pattern of single nucleotide polymorphisms provided profound clues suggesting that there was a high incidence of genomic divergence, due to random and unstable genetic events that were triggered by frequent spontaneous somatic mutations.
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Affiliation(s)
- Ebiamadon Andi Brisibe
- Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
- Bio-therapeutics/Bio-industrial and Plant Cell and Tissue Culture Research Laboratory, ACR Technologies Limited, 124 MCC Road, Calabar, Nigeria
| | - Norah Godwin Ekanem
- Department of Crop Science, Faculty of Agriculture, University of Uyo, Uyo, Nigeria
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Drapal M, de Carvalho EB, Rouard M, Amah D, Sardos J, Van den Houwe I, Brown A, Roux N, Swennen R, Fraser PD. Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and pre-flowering growth stages. Sci Rep 2019; 9:4657. [PMID: 30874619 PMCID: PMC6420674 DOI: 10.1038/s41598-019-41037-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/22/2019] [Indexed: 11/16/2022] Open
Abstract
Bananas (Musa spp.) are consumed worldwide as dessert and cooking types. Edible banana varieties are for the most part seedless and sterile and therefore vegetatively propagated. This confers difficulties for breeding approaches against pressing biotic and abiotic threats and for the nutritional enhancement of banana pulp. A panel of banana accessions, representative of the diversity of wild and cultivated bananas, was analysed to assess the range of chemotypes available globally. The focus of this assessment was banana leaves at two growth stages (juvenile and pre-flowering), to see when during the plant growth metabolic differences can be established. The metabolic data corresponded to genomic trends reported in previous studies and demonstrated a link between metabolites/pathways and the genomes of M. acuminata and M. balbisiana. Furthermore, the vigour and resistance traits of M. balbisiana was connected to the phenolic composition and showed differences with the number of B genes in the hybrid accessions. Differences in the juvenile and pre-flowering data led to low correlation between the growth stages for prediction purposes.
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Affiliation(s)
- Margit Drapal
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | | | - Mathieu Rouard
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Delphine Amah
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Julie Sardos
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | | | - Allan Brown
- International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Nicolas Roux
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Rony Swennen
- International Institute of Tropical Agriculture, Arusha, Tanzania.,Bioversity International, W. De Croylaan 42, 3001, Heverlee, Belgium.,Department of Biosystem, KU Leuven University, Oude Markt 13 - bus 5005, 3000, Leuven, Belgium
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK.
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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. ANNALS OF BOTANY 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] [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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Rouard M, Droc G, Martin G, Sardos J, Hueber Y, Guignon V, Cenci A, Geigle B, Hibbins MS, Yahiaoui N, Baurens FC, Berry V, Hahn MW, D’Hont A, Roux N. Three New Genome Assemblies Support a Rapid Radiation in Musa acuminata (Wild Banana). Genome Biol Evol 2018; 10:3129-3140. [PMID: 30321324 PMCID: PMC6282646 DOI: 10.1093/gbe/evy227] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.
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Affiliation(s)
- Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Gaetan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | - Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
| | | | - Mark S Hibbins
- Department of Biology, Indiana University
- Department of Computer Science, Indiana University
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Vincent Berry
- LIRMM, Université de Montpellier, CNRS, Montpellier, France
| | - Matthew W Hahn
- Department of Biology, Indiana University
- Department of Computer Science, Indiana University
| | - Angelique D’Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, France
| | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, France
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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. FRONTIERS IN PLANT SCIENCE 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] [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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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. FRONTIERS IN PLANT SCIENCE 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] [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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12
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Nyine M, Uwimana B, Swennen R, Batte M, Brown A, Christelová P, Hřibová E, Lorenzen J, Doležel J. Trait variation and genetic diversity in a banana genomic selection training population. PLoS One 2017; 12:e0178734. [PMID: 28586365 PMCID: PMC5460855 DOI: 10.1371/journal.pone.0178734] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 05/18/2017] [Indexed: 11/17/2022] Open
Abstract
Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31-35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.
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Affiliation(s)
- Moses Nyine
- Faculty of Science, Palacký University, Olomouc, Czech Republic
- International Institute of Tropical Agriculture, Kampala, Uganda
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Brigitte Uwimana
- International Institute of Tropical Agriculture, Kampala, Uganda
| | - Rony Swennen
- International Institute of Tropical Agriculture, Kampala, Uganda
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Katholieke Universiteit Leuven, Leuven, Belgium
- Bioversity International, Leuven, Belgium
- International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Michael Batte
- International Institute of Tropical Agriculture, Kampala, Uganda
| | - Allan Brown
- International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Pavla Christelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jim Lorenzen
- International Institute of Tropical Agriculture, Kampala, Uganda
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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13
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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.). ANNALS OF BOTANY 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] [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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14
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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] [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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15
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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. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 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] [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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16
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Čížková J, Hřibová E, Christelová P, Van den Houwe I, Häkkinen M, Roux N, Swennen R, Doležel J. Molecular and Cytogenetic Characterization of Wild Musa Species. PLoS One 2015; 10:e0134096. [PMID: 26252482 PMCID: PMC4529165 DOI: 10.1371/journal.pone.0134096] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/07/2015] [Indexed: 01/19/2023] Open
Abstract
The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region provided further information about evolutionary relationships between individual accessions and suggested that some of analyzed accessions were interspecific hybrids and/or backcross progeny.
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Affiliation(s)
- Jana Čížková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic
| | - Pavla Christelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic
| | | | - Markku Häkkinen
- Finnish Museum of Natural History, University of Helsinki, FI-00014, Helsinki, Finland
| | - Nicolas Roux
- Bioversity International, 34397 Montpellier Cedex 5, France
| | - Rony Swennen
- Bioversity International, B-3001, Leuven, Belgium
- Division of Crop Biotechnics, KU Leuven, B-3001, Leuven, Belgium
- International Institute of Tropical Agriculture, Duluti, Arusha, Tanzania
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic
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17
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Novák P, Hřibová E, Neumann P, Koblížková A, Doležel J, Macas J. Genome-wide analysis of repeat diversity across the family Musaceae. PLoS One 2014; 9:e98918. [PMID: 24932725 PMCID: PMC4059648 DOI: 10.1371/journal.pone.0098918] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/08/2014] [Indexed: 11/18/2022] Open
Abstract
Background The banana family (Musaceae) includes genetically a diverse group of species and their diploid and polyploid hybrids that are widely cultivated in the tropics. In spite of their socio-economic importance, the knowledge of Musaceae genomes is basically limited to draft genome assemblies of two species, Musa acuminata and M. balbisiana. Here we aimed to complement this information by analyzing repetitive genome fractions of six species selected to represent various phylogenetic groups within the family. Results Low-pass sequencing of M. acuminata, M. ornata, M. textilis, M. beccarii, M. balbisiana, and Ensete gilletii genomes was performed using a 454/Roche platform. Sequence reads were subjected to analysis of their overall intra- and inter-specific similarities and, all major repeat families were quantified using graph-based clustering. Maximus/SIRE and Angela lineages of Ty1/copia long terminal repeat (LTR) retrotransposons and the chromovirus lineage of Ty3/gypsy elements were found to make up most of highly repetitive DNA in all species (14–34.5% of the genome). However, there were quantitative differences and sequence variations detected for classified repeat families as well as for the bulk of total repetitive DNA. These differences were most pronounced between species from different taxonomic sections of the Musaceae family, whereas pairs of closely related species (M. acuminata/M. ornata and M. beccarii/M. textilis) shared similar populations of repetitive elements. Conclusions This study provided the first insight into the composition and sequence variation of repetitive parts of Musaceae genomes. It allowed identification of repetitive sequences specific for a single species or a group of species that can be utilized as molecular markers in breeding programs and generated computational resources that will be instrumental in repeat masking and annotation in future genome assembly projects.
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Affiliation(s)
- Petr Novák
- Biology Centre ASCR, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
- * E-mail:
| | - Eva Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Pavel Neumann
- Biology Centre ASCR, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Andrea Koblížková
- Biology Centre ASCR, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jiří Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
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18
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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: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [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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19
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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 BIOLOGY 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] [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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Passos MAN, de Cruz VO, Emediato FL, de Teixeira CC, Azevedo VCR, Brasileiro ACM, Amorim EP, Ferreira CF, Martins NF, Togawa RC, Pappas GJ, da Silva OB, Miller RNG. Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development. BMC Genomics 2013; 14:78. [PMID: 23379821 PMCID: PMC3635893 DOI: 10.1186/1471-2164-14-78] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 02/01/2013] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen conidiospores. RESULTS The study generated 846,762 high quality sequence reads, with an average length of 334 bp and totalling 283 Mbp. De novo assembly generated 36,384 and 35,269 unigene sequences for M. acuminata Calcutta 4 and Cavendish Grande Naine, respectively. A total of 64.4% of the unigenes were annotated through Basic Local Alignment Search Tool (BLAST) similarity analyses against public databases.Assembled sequences were functionally mapped to Gene Ontology (GO) terms, with unigene functions covering a diverse range of molecular functions, biological processes and cellular components. Genes from a number of defense-related pathways were observed in transcripts from each cDNA library. Over 99% of contig unigenes mapped to exon regions in the reference M. acuminata DH Pahang whole genome sequence. A total of 4068 genic-SSR loci were identified in Calcutta 4 and 4095 in Cavendish Grande Naine. A subset of 95 potential defense-related gene-derived simple sequence repeat (SSR) loci were validated for specific amplification and polymorphism across M. acuminata accessions. Fourteen loci were polymorphic, with alleles per polymorphic locus ranging from 3 to 8 and polymorphism information content ranging from 0.34 to 0.82. CONCLUSIONS A large set of unigenes were characterized in this study for both M. acuminata Calcutta 4 and Cavendish Grande Naine, increasing the number of public domain Musa ESTs. This transcriptome is an invaluable resource for furthering our understanding of biological processes elicited during biotic stresses in Musa. Gene-based markers will facilitate molecular breeding strategies, forming the basis of genetic linkage mapping and analysis of quantitative trait loci.
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Affiliation(s)
- Marco A N Passos
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, CEP 70.910-900, Brasília, D.F, Brazil
| | - Viviane Oliveira de Cruz
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, CEP 70.910-900, Brasília, D.F, Brazil
| | - Flavia L Emediato
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, CEP 70.910-900, Brasília, D.F, Brazil
| | | | - Vânia C Rennó Azevedo
- EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília, D.F, Brazil
| | - Ana C M Brasileiro
- EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília, D.F, Brazil
| | - Edson P Amorim
- EMBRAPA Mandioca e Fruticultura Tropical, Rua Embrapa, CEP 44.380-000, Cruz das Almas, BA, Brazil
| | - Claudia F Ferreira
- EMBRAPA Mandioca e Fruticultura Tropical, Rua Embrapa, CEP 44.380-000, Cruz das Almas, BA, Brazil
| | - Natalia F Martins
- EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília, D.F, Brazil
| | - Roberto C Togawa
- EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília, D.F, Brazil
| | - Georgios J Pappas
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, CEP 70.910-900, Brasília, D.F, Brazil
| | - Orzenil Bonfim da Silva
- EMBRAPA Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília, D.F, Brazil
| | - Robert NG Miller
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, CEP 70.910-900, Brasília, D.F, Brazil
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Passos MAN, de Oliveira Cruz V, Emediato FL, de Camargo Teixeira C, Souza MT, Matsumoto T, Rennó Azevedo VC, Ferreira CF, Amorim EP, de Alencar Figueiredo LF, Martins NF, de Jesus Barbosa Cavalcante M, Baurens FC, da Silva OB, Pappas GJ, Pignolet L, Abadie C, Ciampi AY, Piffanelli P, Miller RNG. Development of expressed sequence tag and expressed sequence tag-simple sequence repeat marker resources for Musa acuminata. AOB PLANTS 2012; 2012:pls030. [PMID: 23240072 PMCID: PMC3521319 DOI: 10.1093/aobpla/pls030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 09/14/2012] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Banana (Musa acuminata) is a crop contributing to global food security. Many varieties lack resistance to biotic stresses, due to sterility and narrow genetic background. The objective of this study was to develop an expressed sequence tag (EST) database of transcripts expressed during compatible and incompatible banana-Mycosphaerella fijiensis (Mf) interactions. Black leaf streak disease (BLSD), caused by Mf, is a destructive disease of banana. Microsatellite markers were developed as a resource for crop improvement. METHODOLOGY cDNA libraries were constructed from in vitro-infected leaves from BLSD-resistant M. acuminata ssp. burmaniccoides Calcutta 4 (MAC4) and susceptible M. acuminata cv. Cavendish Grande Naine (MACV). Clones were 5'-end Sanger sequenced, ESTs assembled with TGICL and unigenes annotated using BLAST, Blast2GO and InterProScan. Mreps was used to screen for simple sequence repeats (SSRs), with markers evaluated for polymorphism using 20 diploid (AA) M. acuminata accessions contrasting in resistance to Mycosphaerella leaf spot diseases. PRINCIPAL RESULTS A total of 9333 high-quality ESTs were obtained for MAC4 and 3964 for MACV, which assembled into 3995 unigenes. Of these, 2592 displayed homology to genes encoding proteins with known or putative function, and 266 to genes encoding proteins with unknown function. Gene ontology (GO) classification identified 543 GO terms, 2300 unigenes were assigned to EuKaryotic orthologous group categories and 312 mapped to Kyoto Encyclopedia of Genes and Genomes pathways. A total of 624 SSR loci were identified, with trinucleotide repeat motifs the most abundant in MAC4 (54.1 %) and MACV (57.6 %). Polymorphism across M. acuminata accessions was observed with 75 markers. Alleles per polymorphic locus ranged from 2 to 8, totalling 289. The polymorphism information content ranged from 0.08 to 0.81. CONCLUSIONS This EST collection offers a resource for studying functional genes, including transcripts expressed in banana-Mf interactions. Markers are applicable for genetic mapping, diversity characterization and marker-assisted breeding.
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Affiliation(s)
- Marco A. N. Passos
- Universidade de Brasília,
Campus Universitário Darcy Ribeiro,
Instituto de Ciências Biológicas, Asa
Norte, CEP 70910-900, Brasília, DF, Brazil
| | - Viviane de Oliveira Cruz
- Universidade de Brasília,
Campus Universitário Darcy Ribeiro,
Instituto de Ciências Biológicas, Asa
Norte, CEP 70910-900, Brasília, DF, Brazil
| | - Flavia L. Emediato
- Universidade de Brasília,
Campus Universitário Darcy Ribeiro,
Instituto de Ciências Biológicas, Asa
Norte, CEP 70910-900, Brasília, DF, Brazil
| | - Cristiane de Camargo Teixeira
- Postgraduate Program in Genomic Science and
Biotechnology, Universidade Católica de
Brasília, SGAN 916, Módulo B, CEP 70.790-160,
Brasília, DF, Brazil
| | - Manoel T. Souza
- EMBRAPA Recursos Genéticos e Biotecnologia,
Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília,
DF, Brazil
| | - Takashi Matsumoto
- National Institute of Agrobiological Resources,
Tsukuba 305-8602, Japan
| | - Vânia C. Rennó Azevedo
- EMBRAPA Recursos Genéticos e Biotecnologia,
Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília,
DF, Brazil
| | - Claudia F. Ferreira
- EMBRAPA Mandioca e Fruticultura Tropical, Rua
Embrapa, CEP 44380-000, Cruz das Almas, BA, Brazil
| | - Edson P. Amorim
- EMBRAPA Mandioca e Fruticultura Tropical, Rua
Embrapa, CEP 44380-000, Cruz das Almas, BA, Brazil
| | - Lucio Flavio de Alencar Figueiredo
- Universidade de Brasília,
Campus Universitário Darcy Ribeiro,
Instituto de Ciências Biológicas, Asa
Norte, CEP 70910-900, Brasília, DF, Brazil
| | - Natalia F. Martins
- EMBRAPA Recursos Genéticos e Biotecnologia,
Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília,
DF, Brazil
| | | | | | - Orzenil Bonfim da Silva
- EMBRAPA Recursos Genéticos e Biotecnologia,
Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília,
DF, Brazil
| | - Georgios J. Pappas
- Universidade de Brasília,
Campus Universitário Darcy Ribeiro,
Instituto de Ciências Biológicas, Asa
Norte, CEP 70910-900, Brasília, DF, Brazil
- EMBRAPA Recursos Genéticos e Biotecnologia,
Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília,
DF, Brazil
| | - Luc Pignolet
- CIRAD/UMR BGPI, TA A 54/K Campus International de
Baillarguet, 34398 Montpellier Cedex 5, France
| | - Catherine Abadie
- CIRAD/UMR BGPI, TA A 54/K Campus International de
Baillarguet, 34398 Montpellier Cedex 5, France
| | - Ana Y. Ciampi
- EMBRAPA Recursos Genéticos e Biotecnologia,
Parque Estação Biológica, CP 02372, CEP 70.770-900, Brasília,
DF, Brazil
| | - Pietro Piffanelli
- CIRAD/UMR DAP 1098, TA A 96/03 Avenue Agropolis,
34098 Montpellier Cedex 5, France
- Present address: Genomics
Platform at Parco Tecnologico Padano, Via Einstein, Località Cascina Codazza, 26900
Lodi, Italy
| | - Robert N. G. Miller
- Universidade de Brasília,
Campus Universitário Darcy Ribeiro,
Instituto de Ciências Biológicas, Asa
Norte, CEP 70910-900, Brasília, DF, Brazil
- Corresponding author's e-mail address:
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