Grasses as a single genetic system: genome composition, collinearity and compatibility

Abstract

The best-known grasses are the cereals, of which three speciesrice, wheat and maizeaccount for about half of total world food production. These and other domesticated grasses (including barley, millet, oats, rye, sorghum and sugar-cane) are among the 10-11 thousand species that comprise the grass (Gramineae) family of monocotyledonous flowering plantsL Because of their unrivaled economic importance and relative ease of genetic manipulation, the cereals and forage grasses have been major targets for basic and applied plant science. Each grass species has unique agronomic properties, particularly with respect to environmental preferences and tolerances, and this variation has led to an array of independent research programs for the study and improvement of each grass. Although many individual species have been investigated intensively, the information and materials acquired have not often been used in the full range of grass species. Recent results from genome mapping and intergeneric sexual hybridization experiments suggest that we can now overcome the barriers that have traditionally isolated these systems. These studies show that the various grasses can best be viewed as different manifestations of one tractable genome, and that research priorities should be set to reflect this rich biological potential. Phylogenies based on morphology, molecular sequences and fossils argue that there is a relatively close evolutionary relationship among grass species. The first grass fossils appear in paleocene-eocene deposits some 50-60 million years old z, at a time when modem orders of mammals are known to have existed, and crops were domesticated from their wild progenitors only a few thousand years ago. Grasses are morphologically welldifferentiated from other families and have a single (monophyletic) origin3. Given the close relatedness of the grasses, it is not surprising that many cross-species sexual hybrids have been documented. Moreover, the movement of chromosome segments from one grass species to another has been a powerful tool in both basic and applied plant research. Very wide-ranging crosses between grasses have recently been made, producing transient allodiploidy or chromosomal addition line#. These interspecies and intergeneric hybrids can now be used in traditional mendelian analyses of segregants to identify the genes, mechanisms and designs that underlie the morphological and physiological differences that have evolved in the Gramineae5. Until recently the quality of genetic maps for grasses, including the cereal crops, ranged from fair to non-existent. This general deficiency was rapidly overcome with the advent of maps based on DNA markers. Now, maps have been constructed for all the major cereals, with restriction fragment length polymorphisms (RFLP) and/or randomly amplified polymorphic DNA (RAPD) probes providing anywhere from hundreds to thousands of markers. The first extensive use of DNA markers for the grasses was in studies of maize, and these programs generated large libraries of mapped probes 6-8. The fwst detailed genetic map of sorghum was generated using probes from maize9: when maize probes were hybridized to sorghum DNA, single-o,!?y sequences hybridized well (>95°/6 detected similarly low copy number bands in sorghum under standard high-stringency conditions), while most repetitive sequences hybridized poorly, or not at all. This suggests that the discrepancy in size between the maize and sorghum genomes l°.l~ (the maize genome is 3.5 times larger than that of sorghum) is due, not to differences in the number or types of genes, but rather to differences in the amount of repetitive DNA. Most interestingly,