Comparative Genomics in Crop Plants

Mehboob-ur-Rahman and Andrew H. Paterson

Abstract Angiosperms evolved from a common ancestral genome that incurred repeated duplications and many mutations in succeeding generations to result in the evolution of an array of plant species, setting the stage for the application of comparative genomic approaches to its descendant modern angiosperms. Presently, much genomic information including complete genome sequences from model crops is available, with partial genomic information for many other plant taxa shedding light on genome structure and gene repertoire. Comparative approaches permit inferences to be made regarding evolutionary consequences including rates of evolution of particular genes or families, differential gene loss or retention following duplications, and chromosomal rearrangements, collectively contributing to taxonomic, morphological, and physiological variation. The expanding genomic information for angiosperms may soon permit us to deduce ancestral genome karyotypes for each plant family, and perhaps even for the common ancestor of all angiosperms. Future availability of additional sequenced genomes coupled with complementary bioinformatics tools may help to redraw the plant phylogeny, identify the ancestral gene set for angiosperms and clarify the subsequent evolutionary history of these genes, and provide new insight into the causes and consequences of fluctuating genome size. Better understanding of relationships among different angiosperm genomes and their constituent genes will expedite goals ranging from isolation of genes and determination of their functions, to identifying DNA markers useful for marker-assisted breeding.

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