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Friday, June 19, 2015

BANANA GENOMIC STUDY

  

FOR DECADES, the generation of informative banana and plantain DNA markers has been focused to catalyse progress in Musa breeding and germplasm characterisation. Important knowledge has been gained about the development of varieties resistant to various biotic and abiotic stresses, the identification of the A and B genomes, and the diagnosis of varieties and cultivars and their levels of heterozygosity. In addition, useful genes and promoters have been identified for the effective transformation of target cultivars. Despite all these achievements, intensive research has not been done on the most important fungal banana pathogens, Mycosphaerellafijiensis and M. musicola, which are still major causes of loss in banana-growing regions worldwide. The direct comparison of their population structure is expected to lead to a better understanding of the extent of their genetic diversity. Our initial efforts focused on the development of polymorphic locus-specific SSR markers for M. fijiensis and M. musicola. This technique, along with other PCR-based DNA fingerprinting techniques such as DNA Amplification Fingerprinting (DAF) and Selective Amplification of Microsatellite Polymorphic Loci (SAMPL), allowed us to carry out a comparative survey. Here we discuss the differences in genetic diversity and structure of both pathogen populations as detected by the different techniques, and the distribution of genetic diversity at regional and local levels in Central America and northern South America.


The last decade has witnessed a series of advances in banana and plantain research that are expected to catalyse progress in a major field of banana breeding: the development of Musa varieties resistant to various biotic and abiotic stresses. The contributions of molecular biologists to this advancement included the generation of informative DNA markers for the identification of the A and B genomes, the detection of genetic diversity in germplasm, the diagnosis of varieties and cultivars and levels of heterozygosity, the origin of the B genome in hybrids, the establishment of genetic maps and the construction of a bacterial artificial chromosome (BAC) library with approximately fivefold genome coverage. Useful genes and promoters have also become available for the effective transformation of target cultivars using, for example, specific Agrobacterium tumefaciens strains and optimised protocols for regeneration of embryogenic cell suspension cultures. Transgenic plants have been tested for the presence and expression of foreign genes.


Transgenic bananas expressing vaccines against human intestinal pathogens show potential [4]. Also, expression levels of a series of genes involved in the fruit-ripening process were determined. Finally, the nucleome of Musa has now been characterised in more detail, using flow cytometry and fluorescence in situ hybridisation (FISH; [6]). Telomeres of the Arabidopsis type, several gene clusters and retrotransposons have been localized, and the ploidy of any banana material can be estimated unequivocally. Notwithstanding all these (and other) achievements, a bias towards the host plant becomes obvious: a similarly intensive research activity with comparable results is lacking for the most important banana pathogens, especially the fungal pathogens. Although several laboratories are devoting their work to unravelling, for example, the infective power and potential of both pathogenic Mycosphaerellas, and though the results of this work over two decades are impressive, we lack a cooperative, dedicated, constant and engaged research effort on Mycosphaerella, especially since both ascomycetes, M. fijiensis and M. musicola,still are the major troublemakers in most banana-growing regions of the world (though Fusarium oxysporum f.sp. cubense, FOC, can also be included). Whereas the collection of isolates and their culture is routine, their genetic and pathological characterization is less common worldwide. The physiology of both fungi is more or less reduced to toxins, and the genetic make-up of Mycosphaerella is virtually unknown. For these reasons we have switched exclusively to Mycosphaerella fijiensis and M. musicola, after having isolated a series of Resistance Gene Analogues (RGAs) from banana, developed a series of informative microsatellite markers for Musa and employing them for the characterization of genetic diversity in wild and cultivated Musa.

Our initial research has focused on the development of polymorphic, locus-specific microsatellite markers for M. fijiensis and M. musicola. We have used these highly informative markers to study population structure and its dynamics in both pathogens. The comparison of the two pathogen populations is expected to lead to a better understanding of the extent of genetic diversity and genetic differentiation at local and regional levels, as well as the influence of environmental pressures on their spread to potentially new colonisation sites. Moreover, it could also predict the behaviour of new epidemic forms, thus helping breeders and farmers with basic information on genetic diversity, population structure, and fungal dynamics. To our knowledge, only one study has assessed the genetic diversity of both pathogens in parallel, but attempts to transfer molecular markers from M. fijiensis to M. musicola and vice versa were not successful. However, the polymorphic SSR markers developed for M. fijiensis and M. musicola in the course of this project, along with other PCR-based DNA fingerprinting techniques such as DNA Amplification Fingerprinting (DAF) and Selective Amplification of Microsatellite Polymorphic Loci (SAMPL), have allowed us to carry out a truly comparative survey of the genetic diversity of both pathogens. Here we report the results of such a study with populations from different Latin American countries. We discuss (a) differences in genetic diversity and structure of the two populations as detected with different techniques, (b) the distribution of genetic diversity at regional and local levels in Central America and northern South America, and (c) evidence for isolation by geographical barriers and distances. Thanks.
Source of info:  http://www.fao.org/docrep


By,
M Anem,
Senior Agronomist,
Banana Kulim Estates, Kota Tinggi,
Johor, Malaysia.
(9 Rejab 1436H)

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