Review Molecular and genetic analyses of transgenic plants: Considerations and approaches S.R. Bhat *, S. Srinivasan National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India Received 4 April 2002; accepted 22 May 2002 Abstract Plant transformation has become an important experimental tool for investigations into various aspects of plant biology such as physiology, genetics, developmental biology, molecular biology etc. The precision and simplicity of the approach coupled with the power of resolution of details at the molecular level have led to its adoption to answer hitherto intractable problems. In addition, the feasibility of mobilizing and expressing foreign genes into plants has opened up whole new era of genetically engineered crop plants capable of defending against biotic and abiotic stresses and producing better quality products or novel compounds of pharmaceutical and industrial value. There are, however, aspects of plant transformation that are not well understood and cause considerable variation among independent transgenics produced under identical conditions. In this article we discuss various factors that contribute to variation among transgenics and suggest experimental approaches for genetic and molecular analyses of transgenics to derive meaningful conclusions. # 2002 Elsevier Science Ireland Ltd. All rights reserved. Keywords: Genetic analysis; Molecular analysis; Plant transformation; Somaclonal variation; Transgenics 1. Introduction Following the development of methods of plant transformation during the last two decades, transgenics are now widely used in both basic and applied studies in plant biology. Plant transformation is an important tool in the hands of molecular biologists to understand the organization and regulation of eukaryotic genes. Simi- larly, transgenics find application in almost every branch of biology such as genetics, physiology, bio- chemistry, developmental biology, virology etc. Trans- formation offers novel means to manipulate plants to withstand biotic and abiotic stress, to produce pharma- ceuticals, nutraceuticals and novel products. Transgenic crops are presently cultivated on over 52 m hectares worldwide [1]. Thus a large number of specialists in diverse fields of plant biology are engaged in production of transgenics of different plant species for a variety of purposes. Although transgenic approach appears sim- ple, straightforward and attractive, interpretation of results could be complicated due to confounding effects of various uncontrolled or uncontrollable factors. Vast differences in the level of expression of intro- duced genes have been observed among transgenic plants generated under identical conditions using the same DNA constructs. These have been generally attributed to copy number and position effect of the transgene. Further, transgenic plants may also display additional phenotypic variation not directly due to transgene effect but still showing association with the transgene. Thus generation and selection of transgenic plants suitable for detailed analysis needs careful con- sideration. In all such cases it becomes necessary to determine whether the observed variation in phenotype is solely due to introduced gene or not. Most textbooks and review articles present an oversimplified approach to the analysis of transgenic plants. The intricacies of analysis and interpretation of results, however, have not been elaborated. As more researchers from diverse disciplines adopt transgenic approach for their investi- gations, there is a need for a comprehensive article explaining critical aspects of handling and analysis of transgenic plants and their progenies, and discussing * Corresponding author. Tel.:  /91-11-5824787x204; fax:  /91-11- 5823984 E-mail address: srbhat22@rediffmail.com (S.R. Bhat). Plant Science 163 (2002) 673  /681 www.elsevier.com/locate/plantsci 0168-9452/02/$ - see front matter # 2002 Elsevier Science Ireland Ltd. All rights reserved. PII:S0168-9452(02)00152-8