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Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas

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Abstract

Bananas in Thailand have been surveyed by our team to be at least 140 cultivars in the plantations, 10 wild species and, 4 introduced species. To characterize the genetic relationship of species and cultivars, a set of novel SSR markers was developed. Totaling 53 clones containing SSR motifs were isolated from SSR-enriched library of wild Musa balbisiana Colla ‘Tani’ (BB). Selected positive clones were used to design 28 primer pairs for amplification of 12 wild and 82 cultivar accessions with genome designations AA, AB, AAA, AAB, ABB, and BBB. These SSR markers loci were homology searched to the banana genomes to map their locations. The seven-sets multiplex PCR approach using four fluorescent-labeled universal primers were utilized for cost effectiveness. Capillary fragment analysis yielded the accurate size of amplicons for evaluation of particular patterns for each cultivar. Phylogram and Structure analysis presented the specific genotype of genome groups (A and B genotypes, polyploid hybrid genomes) and cultivar groups. By A:B specific alleles ratio, accurate genome designations of hybrids can be determined. Additionally, a marker, characterized to be partial plastid ycf2 gene, indicated the maternal identification of hybrid cultivars. One SSR marker was also preliminary tested with some wild species and advised to be the candidate fingerprinting marker for species identification. In conclusion, SSR marker sets developed here proved their exploitation in detailed identity and relationship of cultivated bananas, which would be useful for genetic conservation and ongoing breeding programs in Thailand and other areas.

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Acknowledgments

This research was financially supported by the Thailand Research Fund in collaboration with the Commission on Higher Education of Thailand to JS (MRG5380133) and to SCS (MRG5280100) and Plant Genetic Conservation Project, under the Royal Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn to PPC. Research Assistant Supporting Grant was provided by Faculty of Science, Mahidol University to TR. The authors are grateful for banana samples and knowledge from all institutes and collectors including Pra Sobhon Khanaporn and Mr. Samadchai Chattrakhom.

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Authors and Affiliations

  1. Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand

    Tiwa Rotchanapreeda & Jamorn Somana

  2. Central Instrument Facility, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand

    Sirapope Wongniam

  3. Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand

    Tiwa Rotchanapreeda & Sasivimon C. Swangpol

  4. Plant Genetic Conservation Project under the Royal Initiative of Her Royal Highness Princess Maha Chakri Sirindhorn, Bangkok, 10303, Thailand

    Piyarat P. Chareonsap

  5. Art Education Section, Faculty of Anthropology and Social Science, Muban Chombueng Rajabhat University, Ratchaburi, 70150, Thailand

    Narongsak Sukkaewmanee

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  1. Tiwa Rotchanapreeda
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Handling editor: Eric Schranz.

Below is the link to the electronic supplementary material.

606_2015_1274_MOESM1_ESM.doc

Online Resource 1 Banana samples, 12 wild and 82 cultivar accessions from the collections in Thailand, with their source locations (DOC 166 kb)

Online Resource 2 Supplementary materials and methods (DOC 35 kb)

Online Resource 3 List of banana cultivars in Thailand with previous and suggested genome designations (DOC 45 kb)

606_2015_1274_MOESM4_ESM.doc

Online Resource 4 SSR loci information and position on designated chromosomes of AA genome: Musa acuminata accession ‘Pahang’ (DOC 246 kb)

606_2015_1274_MOESM5_ESM.doc

Online Resource 5 SSR loci information and position on designated chromosomes of BB genome: Musa balbisiana accession ‘Pisung Klutuk Wulung’ (DOC 237 kb)

Online Resource 6 Microsatellite profiling of A- and B-genome specific alleles in 17 SSR markers (DOC 47 kb)

Online Resource 7 Estimation of optimal K evaluated by Structure Harvester program (DOC 199 kb)

Information on Electronic Supplementary Material

Information on Electronic Supplementary Material

Online Resource 1. Banana samples, 12 wild and 82 cultivar accessions from the collections in Thailand, with their source locations.

Online Resource 2. Supplementary materials and methods.

Online Resource 3. List of banana cultivars in Thailand with previous and suggested genome designations.

Online Resource 4. SSR loci information and position on designated chromosomes of AA genome: Musa acuminata accession ‘Pahang’.

Online Resource 5. SSR loci information and position on designated chromosomes of BB genome: Musa balbisiana accession ‘Pisung Klutuk Wulung’.

Online Resource 6. Microsatellite profiling of A- and B-genome specific alleles in 17 SSR markers.

Online Resource 7. Estimation of optimal K evaluated by Structure Harvester program.

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Rotchanapreeda, T., Wongniam, S., Swangpol, S.C. et al. Development of SSR markers from Musa balbisiana for genetic diversity analysis among Thai bananas. Plant Syst Evol 302, 739–761 (2016). https://doi.org/10.1007/s00606-015-1274-2

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