Research Note New microsatellite markers for bananas (Musa spp)

Amorim, Édson Perito; Silva, P H; Ferreira, Cláudia Fortes; V.B.O., Amorim,; Santos, Vânia Jesus dos; Vilarinhos, Alberto Duarte; Santos, Cristiane dos; Júnior, Manoel Teixeira Souza; Miller, Robert G.

doi:10.4238/2012.april.27.8

Cited by 12 publications

(11 citation statements)

References 15 publications

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“…Microsatellite (SSR) sequences have many advantages as molecular markers, due to their abundance, hypervariability, co-dominant nature, reliability, and ease of interpretation and several of groups have already identified SSR markers for Musa [37,60-63]. Type 1 SSRs (i.e.…”

Section: Resultsmentioning

confidence: 99%

“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”

et al. 2013

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BackgroundModern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been associated with improved vigour and tolerance to biotic and abiotic stresses and is thus a target for Musa breeding programs. However, while a reference M. acuminata genome has recently been released (Nature 488:213–217, 2012), little sequence data is available for the corresponding B-genome.To address these problems we carried out Next Generation gDNA sequencing of the wild diploid M. balbisiana variety ‘Pisang Klutuk Wulung’ (PKW). Our strategy was to align PKW gDNA reads against the published A-genome and to extract the mapped consensus sequences for subsequent rounds of evaluation and gene annotation.ResultsThe resulting B-genome is 79% the size of the A-genome, and contains 36,638 predicted functional gene sequences which is nearly identical to the 36,542 of the A-genome. There is substantial sequence divergence from the A-genome at a frequency of 1 homozygous SNP per 23.1 bp, and a high degree of heterozygosity corresponding to one heterozygous SNP per 55.9 bp. Using expressed small RNA data, a similar number of microRNA sequences were predicted in both A- and B-genomes, but additional novel miRNAs were detected, including some that are unique to each genome. The usefulness of this B-genome sequence was evaluated by mapping RNA-seq data from a set of triploid AAA and AAB hybrids simultaneously to both genomes. Results for the plantains demonstrated the expected 2:1 distribution of reads across the A- and B-genomes, but for the AAA genomes, results show they contain regions of significant homology to the B-genome supporting proposals that there has been a history of interspecific recombination between homeologous A and B chromosomes in Musa hybrids.ConclusionsWe have generated and annotated a draft reference Musa B-genome and demonstrate that this can be used for molecular genetic mapping of gene transcripts and small RNA expression data from several allopolyploid banana cultivars. This draft therefore represents a valuable resource to support the study of metabolism in inter- and intraspecific triploid Musa hybrids and to help direct breeding programs.

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Section: Resultsmentioning

confidence: 99%

“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”

et al. 2013

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“…Whilst the majority have been isolated from genomic libraries or BAC clones [35,63,68-71], only few gene-derived SSRs have been characterized (e.g. [72,73]).…”

Section: Resultsmentioning

confidence: 99%

Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development

et al. 2013

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BackgroundAlthough 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.ResultsThe 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.ConclusionsA 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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“…With such markers isolated from coding regions, conservation is also potentially greater, increasing transferability to related species . Amorim et al (2012) and used EST-SSR markers for banana germplasm accessions and revealed that these markers are highly informative SSR's which can be used to accelerate the banana breeding programs, improve the studies on genetic diversity and leading to the development of saturated genetic linkage maps. Passos et al (2013) tried to develop defense related gene derived SSR loci, selected on the basis of BLAST similarities and KOG (eukaryotic orthologous groups of proteins).…”

Section: Application Of Transcriptome Analysis In Banana Improvementmentioning

confidence: 99%

Sustainable Horticultural Systems

Nandwani¹

2014

Sustainable Development and Biodiversity

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This book series provides complete, comprehensive and broad subject based reviews about existing biodiversity of different habitats and conservation strategies in the framework of different technologies, ecosystem diversity, and genetic diversity. The ways by which these resources are used with sustainable management and replenishment are also dealt with. The topics of interest include but are not restricted only to sustainable development of various ecosystems and conservation of hotspots, traditional methods and role of local people, threatened and endangered species, global climate change and effect on biodiversity, invasive species, impact of various activities on biodiversity, biodiversity conservation in sustaining livelihoods and reducing poverty, and technologies available and required. The books in this series will be useful to botanists, environmentalists, marine biologists, policy makers, conservationists, and NGOs working for environment protection.More information about this series at

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Research Note New microsatellite markers for bananas (Musa spp)

Cited by 12 publications

References 15 publications

“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”

“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”

Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development

Sustainable Horticultural Systems

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