Molecular Ecology (1999) 8, S95 – S106 © 1999 Blackwell Science Ltd Blackwell Science, Ltd Application of genomics in assessing biodiversity in wild and cultivated barley N. MARMIROLI, E. MAESTRI, L. LIVIERO, A. MASSARI, A. MALCEVSCHI and P. MONCIARDINI Division of Genetics and Environmental Biotechnologies, Department of Environmental Sciences, University of Parma, Viale delle Scienze, 43100 Parma, Italy Abstract Biodiversity, the substrate for natural selection and adaptation to the environment, is of foremost importance in species conservation. Genomics, the study of the structure and function of complex genomes, can be applied to the assessment of the genetic component of biodiversity in animals and plants. Genomic analysis within the genus Hordeum, in cultivars of H. vulgare and in wild accessions of H. spontaneum, was performed by different types of molecular markers, such as restriction fragment length polymorphisms (RFLP) and long primer–polymerase chain reaction (LP–PCR), and simple sequence repeats (SSR). The aim of this approach was to compare the correlation existing between genotypic vari- ation at specific regions of the genome, as targeted with the different probes obtained from stress-responsive genes, and phenotypic variation, as shown by adaptation to differ- ent environments and climates. H. vulgare cultivars with contrasting growth habits (spring or winter) and H. spontaneum accessions adapted to different locations in Israel have been analysed. The results showed the existence of some tight associations between adaptive traits and markers (RFLP, LP–PCR) derived from specific genes induced in response to environmental stress. The correlation between adaptive phenotypes and genetic variation obtained with these markers was similar to that observed with SSRs. However, a consider- able amount of the global genetic variation (83% in H. vulgare and 65% in H. spontaneum) seemed to have no direct correlation with the particular genetic traits involved in differ- entiating the individuals. Molecular markers are therefore a useful tool to target genomic regions involved in adaptation to the environment. Keywords: barley, Hordeum vulgare, long primer PCR, microsatellites, restriction fragment length polymorphisms, stress-responsive genes Received 11 February 1999; revision received 2 June 1999; accepted 28 July 1999 Introduction It has been postulated that the possibilities for adaptation to the future habitats and climates produced by global change rests on the existence of genetic diversity within species (Hoffman and Parsons 1991). Loss of genetic diver- sity raises the inbreeding coefficient and leads to uniform- ity in populations, with results that are often deleterious. Moreover, in naturally inbred populations, such as in self-pollinating plant species, in which most individuals are homozygous at most loci, the disappearance of allelic variants can have harmful effects on the ability of the species to withstand any future environmental challenges. Several crop plants, including cereals, have evolved from self-pollinating wild species. Progenitors of modern cul- tivated species can still be found in the centres of origin and several efforts are concentrated on their protection and preservation in germplasm banks. Genetic information on wild species is of great import- ance for assessment and maintenance of biodiversity. This can be obtained, as pointed out by Milligan et al. (1994), through the application of simple and reproducible molecular techniques. In this way, variation at molecular marker loci could be correlated with variation influen- cing adaptive traits or to individual fitness. Recently, Pèrez Correspondence: Prof. N. Marmiroli. Fax: + 39-0521-905665; E- mail: marmirol@ipruniv.cce.unipr.it