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Open Access Research article

Genetic diversity and population structure of Musa accessions in ex situ conservation

Onildo Nunes de Jesus123*, Sebastião de Oliveira e Silva3, Edson Perito Amorim3, Claudia Fortes Ferreira3, José Marcello Salabert de Campos4, Gabriela de Gaspari Silva1 and Antonio Figueira1*

Author Affiliations

1 Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil

2 Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil

3 EMBRAPA Mandioca Fruticultura, R. Embrapa s/n, Cruz das Almas, BA, 44380-000, Brazil

4 Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Martelos, Juiz de Fora, MG, 36016-900, Brazil

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BMC Plant Biology 2013, 13:41  doi:10.1186/1471-2229-13-41

Published: 12 March 2013

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.

Keywords:
Association mapping; Banana; Evolution; Flow cytometry; Internal transcribed spacer; Microsatellite; Simple sequence repeat; Structure