Identification and Validation of EST-Derived Molecular Markers, TRAP and VNTRs, for Banana Research

The advent of high-throughput sequencing technology has generated abundant information on DNA sequences for the genomes of many plant species. Expressed Sequence Tags (ESTs), which are unique DNA sequences derived from a cDNA library and therefore representing genes transcribed in specific tissues or at some stage of development, are one type of DNA sequences highly available today for many important crop species. Molecular markers are used for bridging DNA sequence information with particular phenotypes and are useful tools for genotyping germplasm collections and also for tagging genes involved in desirable agronomic traits. In this sense, there is always a strong demand for suitable marker techniques to better utilise existing sequence information. A transcriptome database from banana (Musa spp.), DATAMusa, containing 42,724 ESTs from 11 different cDNA libraries and encompassing approximately 24 Mb of DNA sequence, was used in this study for the design of primers to PCR-amplify two types of EST-derived molecular markers, Variable Nucleotide Tandem Repeat (VNTR) and Target Region Amplification Polymorphism (TRAP). These primers were then validated against a panel of 14 diploid Musa genotypes and produced 32 (VNTR) and 119 (TRAP) alleles. Used separately or together, both types of markers were able to discriminate Musa genotypes from different genome background (A or B genomes). The TRAP alleles identified were derived from only one EST, while the VNTR alleles were derived from 12 unigenes. Based on the results of this study, EST-derived markers can be an important source of polymorphism to be used in genetic diversity and gene discovery studies in banan

Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp)

ABSTRACT. We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas (Musa spp). Recently, the entire genome sequence of M. fijiensis became available. We screened this database for VNTR markers. Forty-two primer pairs were selected for validation, based on repeat type and length and the number of repeat units. Five VNTR markers showing multiple alleles were validated with a reference set of isolates from different parts of the world and a population from a banana plantation in Costa Rica. Polymorphism information content values varied from 0.6414 to 0.7544 for the reference set and from 0.0400 and 0.7373 for the population set. Eighty percent of the polymorphism information content values were above 0.60, indicating that the markers are highly informative. These markers allowed robust scoring of agarose gels and proved to be useful for variability and population genetics studies. In conclusion, the strategy we developed to identify and validate VNTR markers is an efficient means to incorporate markers that can be used for fungicide resistance management and to develop breeding strategies to control banana black leaf streak disease. This is the first report of VNTR-minisatellites from the M. fijiensis genome sequence. Key words: Molecular markers; VNTRs; Genetic diversity; Population genetics; Black Sigatok

Arbuscular mycorrhizal networks: process and functions. A review

International audienceAn unprecedented, rapid change in environmental conditions is being observed, which invariably overrules the adaptive capacity of land plants. These environmental changes mainly originate from anthropogenic activities, which have aggravated air and soil pollution, acid precipitation, soil degradation, salinity, contamination of natural and agro-ecosystems with heavy metals such as cadmium (Cd), lead (Pb), mercury (Hg), arsenic (As), global climate change, etc. The restoration of degraded natural habitats using sustainable, low-input cropping systems with the aim of maximizing yields of crop plants is the need of the hour. Thus, incorporation of the natural roles of beneficial microorganisms in maintaining soil fertility and plant productivity is gaining importance and may be an important approach. Symbiotic association of the majority of crop plants with arbuscular mycorrhizal (AM) fungi plays a central role in many microbiological and ecological processes. In mycorrhizal associations, the fungal partner assists its plant host in phosphorus (P) and nitrogen (N) uptake and also some of the relatively immobile trace elements such as zinc (Zn), copper (Cu) and iron (Fe). AM fungi also benefit plants by increasing water uptake, plant resistance and biocontrol of phytopathogens, adaptation to a variety of environmental stresses such as drought, heat, salinity, heavy metal contamination, production of growth hormones and certain enzymes, and even in the uptake of radioactive elements. The establishment of symbiotic association usually involves mutual recognition and a high degree of coordination at the morphological and physiological level, which requires a continuous cellular and molecular dialogue between both the partners. This has led to the identification of the genes, signal transduction pathways and the chemical structures of components relevant to symbiosis; however, scientific knowledge on the physiology and function of these fungi is still limited. This review unfolds our current knowledge on signals and mechanisms in the development of AM symbiosis; the molecular basis of nutrient exchange between AM fungi and host plants; and the role of AM fungi in water uptake, disease protection, alleviation of various abiotic soil stresses and increasing grain production