Variation in different characters of living organisms is the link between DNA and phenotype, providing for selection to act to improve fitness in a particular environment (whether natural or agricultural), and lying at the heart of both the Darwinian


Plant Genomics and Mol Breeding Labs, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan

Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, 30602, USA e-mail: [email protected]

S.M. Jain and D.S. Brar (eds.), Molecular Techniques in Crop Improvement, DOI 10.1007/978-90-481-2967-6_2, © Springer Science+Business Media B.V. 2010

evolutionary principles and the Mendelian genetic principles. Comparison of traits between two organisms, especially within a plant species, started with the proposition of Vavilov's law of homologous series in variation. In the last two decades, especially with the availability of genetic maps and genome sequence information, the concept was broadened to include comparisons of genomes structure and function that are now referred to as comparative genomics.

Key to plant comparative genomic studies is that the locations of some genes has remained stable across long evolutionary times, providing a framework useful for inferring correspondence among even distantly-related genomes, and among genes that have diverged beyond recognition or been relocated (Tang et al. 2008a). However, the degree to which the genes remain on corresponding chromosomes (synteny) and in corresponding orders (collinearity) over time differs markedly among taxa (Coghlan et al. 2005), with angiosperms incurring differential retention of genes and or gene families following repeated genome duplications and mobility of DNA sequences (Bowers et al. 2005; Tang et al. 2008a). Determining the extent of col-linearity between model plant species and related crops is valuable for applying genomic information to crop improvement.

Much progress has been made in linking plant genomes through comparative genetic/physical maps, especially for species belonging to the same family. For example, close relationships have been revealed among the genomes of many members of the grass family, among the Solanaceae (nightshade) crops, among the Brassicaceae (cole) crops, and among several legume crops (Paterson et al. 2000; Wu et al. 2006), facilitating reconstruction of ancestral genomes (Blanchette et al. 2004), phylogenetic studies (Rokas et al. 2003), deciphering of patterns of natural selection on coding regions (Bustamante et al. 2005), transferring predictions of common gene function between the species (Eisen 1998; Doganlar et al. 2002b) etc., and other applications. Integration of sequencing and detailed functional analysis of sexually incompatible species is advantageous to both the geneticist and breeder for better understanding and improving many understudied crops (Gale and Devos 1998) which was practically demonstrated on 22 genotypes representing eight different genera of the Poaceae family (Feltus et al. 2006). Comparative alignment of chromosomes across the species has shown that quantitative trait loci (QTLs) and major genes often occur in corresponding locations (Lin et al. 1995; Paterson et al. 1995; Pereira and Lee 1995), perhaps helping in isolating candidate genes for corresponding QTLs in different species (Lagercrantz et al. 1996).

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