Genic molecular markers in plants: Development and applications

Abstract

The current advancement in plant biology research encompassing: generation of huge amount of molecular-genetic data, development of impressive methodological skills in molecular biology experimentation, and systems analyses, has set the stage to search for ways/means to utilize the available resources to strengthen interdisciplinary efforts to find solutions to the challenging goals of plant breeding efforts (such as abiotic stress tolerance) ultimately leading to gainful applications in crop improvement. A positive fall out of such a realization and efforts has been the identification/development of a new class of very useful DNA markers called genic molecular markers (GMMs) utilizing the ever-increasing archives of gene sequence information being accumulated under the EST sequencing projects on a large number of plant species in the recent years. These markers being part of the cDNA/EST-sequences, are expected to represent the functional component of the genome i.e., gene(s), in contrast to all other random DNA-based markers (RDMs) that are developed/generated from the anonymous genomic DNA sequences/domains irrespective of their genic content/information. Therefore, identifying DNA sequences that demonstrate large effects on adaptive plant behavior remains fundamental to the development of GMMs. The few recent studies have now demonstrated the utility of these markers in genetic studies, and also shown that GMMs may be superior than RDMs for use in the marker-assisted selection, comparative mapping, and exploration of the functional genetic diversity in the germplasm adapted to different environments. The only constraint of GMMs is their low level of polymorphism as compared to the RDMs expected of their origin from the relatively conserved functional portion of the genome. This chapter provides a critical review of the development and various applications of the GMMs.