We measured sequence diversity in 21 loci distributed along chromosome 1 of maize (Zea mays ssp. mays L.). For each locus, we sequenced a common sample of 25 individuals representing 16 exotic landraces and nine U.S. inbred lines. The data indicated that maize has an average of one single nucleotide polymorphism (SNP) every 104 bp between two randomly sampled sequences, a level of diversity higher than that of either humans or Drosophila melanogaster. A comparison of genetic diversity between the landrace and inbred samples showed that inbreds retained 77% of the level of diversity of landraces, on average. In addition, Tajima's D values suggest that the frequency distribution of polymorphisms in inbreds was skewed toward fewer rare variants. Tests for selection were applied to all loci, and deviations from neutrality were detected in three loci. Sequence diversity was heterogeneous among loci, but there was no pattern of diversity along the genetic map of chromosome 1. Nonetheless, diversity was correlated (r ‫؍‬ 0.65) with sequence-based estimates of the recombination rate. Recombination in our sample was sufficient to break down linkage disequilibrium among SNPs. Intragenic linkage disequilibrium declines within 100 -200 bp on average, suggesting that genome-wide surveys for association analyses require SNPs every 100 -200 bp. Single nucleotide polymorphisms (SNPs) are valuable tools for mapping complex phenotypic traits. An SNP either can contribute directly to a phenotype or it can associate with a phenotype as a result of linkage disequilibrium (LD) (1). In either case, it is clear that successful utilization of SNPs requires detailed knowledge of patterns of genetic polymorphism throughout the genome, as well as an understanding of the evolutionary forces shaping those patterns. These forces include genomic factors, such as the distribution of recombination and mutation rates along chromosomes, and evolutionary factors, such as the history of natural selection and population demography (2).Thus far, SNPs have been surveyed extensively for evolutionary purposes in relatively few systems. The surveys have yielded four important observations about DNA sequence diversity. First, diversity varies among species; for example, Drosophila melanogaster (drosophila) is Ϸ8-to 13-fold more diverse at the DNA sequence level than humans (3). Second, the effects of natural selection and demography vary among species. Half of the loci examined in drosophila do not fit the neutral equilibrium model of evolution (4), but only 1 of 16 loci analyzed in humans deviates from the neutral model (2). Third, SNPs provide insights into population history and demography. In humans, for example, African populations contain more genetic diversity than non-African populations, and non-

The maize genome is replete with chromosomal duplications and repetitive DNA. The duplications resulted from an ancient polyploid event that occurred over 11 million years ago. Based on DNA sequence data, the polyploid event occurred after the divergence between sorghum and maize, and hence the polyploid event explains some of the difference in DNA content between these two species. Genomic rearrangement and diploidization followed the polyploid event. Most of the repetitive DNA in the maize genome is retrotransposable elements, and they comprise 50% of the genome. Retrotransposon multiplication has been relatively recent-within the last 5-6 million years-suggesting that the proliferation of retrotransposons has also contributed to differences in DNA content between sorghum and maize. There are still unanswered questions about repetitive DNA, including the distribution of repetitive DNA throughout the genome, the relative impacts of retrotransposons and chromosomal duplication in plant genome evolution, and the hypothesized correlation of duplication events with transposition. Population genetic processes also affect the evolution of genomes. We discuss how centromeric genes should, in theory, contain less genetic diversity than noncentromeric genes. In addition, studies of diversity in the wild relatives of maize indicate that different genes have different histories and also show that domestication and intensive breeding have had heterogeneous effects on genetic diversity across genes. Genomic technologies have produced a wealth of data on the organization and structure of genomes. These data range from extensive marker-based genetic maps to ''chromosome paintings'' based on fluorescent in situ hybridization to complete genomic DNA sequences. Although genomic approaches have changed the amount and type of data, the challenges of interpreting genomic data in an evolutionary context have changed little from the challenges faced by Stebbins (1) and the coauthors of the evolutionary synthesis. The challenges are to infer the mechanisms of evolution and to construct a comprehensive picture of evolutionary change.In this paper, we will focus on the processes that contribute to the evolution of plant nuclear genomes by using maize (Zea mays) as a model system. In some respects, it is premature to discuss the evolution of plant genomes, because the pending completion of the Arabidopsis (Arabidopsis thaliana) genome, with rice (Oryza sativa) following, is sure to unlock many mysteries about plant genome evolution. However, it must be remembered that Arabidopsis and rice are being sequenced, precisely because their genomes are atypically small and streamlined. Even after these genomes are sequenced, it will still be a tremendous challenge to understand the evolution of plant nuclear genomes, like the maize genome, for which entire DNA sequences will not be readily available.Maize is a member of the grass family (Poaceae). The grasses represent a range of genome size and structural complexity, with rice on one extreme. A...

AFLP) markers, to measure genetic diversity in perennial ryegrass (Huff, 1997; Roldan-Ruiz et al., 2000; An essential prerequisite to cultivar identification is to determine Sweeney and Danneberger, 1994, 1997, 2000. Both whether cultivars are differentiated genetically. We investigated genetic diversity among and within seven perennial ryegrass (Lolium RAPDs and AFLPs detect substantial genetic variation perenne L.) cultivars (Loretta, Linn, Manhattan II, Affinity, Jet, Penn-within perennial ryegrass cultivars and generally demfine, and Palmer III) using simple sequence repeat (SSR) markers, onstrate that cultivars can be discriminated on the basis with the goal of determining whether cultivars could be differentiated of genetic characteristics. However, it appears that some on the basis of genetic data. In each cultivar we genotyped 30 individuclosely related cultivars lack distinct genetic boundaries als with 22 SSR markers, 18 of which had not been reported previously. (Huff, 1997), and this can complicate cultivar identifica-Our results indicated that each of the seven cultivars contained high tion. The comingling of genetic boundaries has been but similar levels of genetic diversity. Within cultivar heterozygosity examined in detail only with RAPD data, and the extent ranged from 0.589 to 0.643. The cultivars could be distinguished by of this problem may vary among marker systems. a number of statistical criteria, including: (i) a small but significant An additional promising marker system is simple seproportion (14.6%) of among-cultivar genetic variation, based on analysis of molecular variance (AMOVA); (ii) significant between quence repeats (SSRs). SSRs are short stretches of tancultivar F ST values that ranged from 0.065 to 0.197; (iii) separation of demly repeated di-, tri-, or tetranucleotide motifs (Weindividuals in principal component analysis (PCA); and (iv) correct ber, 1990) that have become the marker of choice for identification of individuals by the genotype assignment test, which is many genetic analyses. SSRs are broadly used for four related to discriminant analysis. The genotype assignment test worked reasons. First, each SSR locus is genetically well defined particularly well; it correctly assigned all 210 individuals to their culti-

Breeding for adaptation to abiotic stress is extremely challenging due to the complexity of the target environments as well as that of the stress-adaptive mechanisms adopted by plants. While many traits have been reported in the literature, these must be considered with respect to the type of environment for which a cultivar is targeted. In theory, stress-adaptive traits can be divided into groups whose genes and/or physiological effects are likely to be relatively independent such that when parents with contrasting traits are crossed, adaptive genes will be pyramided. Currently the following groups of candidate traits are being considered for drought adaptation in wheat: traits relating to: (i) pre-anthesis growth, (ii) water extraction, (iii) water use effi ciency, (iv) photo-protection. A number of mechanisms relating to root function have potential to ameliorate drought stress. Hydraulic redistribution (HR) of water by roots of dryland shrubs enables even relatively small amounts of rainwater to be moved down into the soil profi le actively by the root system before it evaporates from the soil surface. Another example is the symbiotic relationship of plants with mycorrhizal fungi that produce a glycoprotein that has a positive effect on soil structure and moisture characteristics. From an agronomic point of view, crop water use effi ciency can be increased by exploiting the stress-adaptive mechanism whereby leaves reduce transpiration rate in response to a chemical root signal in response to drying soil. While there is limited genetic diversity for adaptation to salinity in wheat, tolerance has been found in the ancestral genomes of polyploid wheat and their relatives associated with sodium exclusion into the xylem. Wide crossing techniques such as production of synthetic hexaploids are being exploited to tap into this source of genetic diversity. Looking further into the future, progress is being made into understanding the regulatory mechanisms that are expressed under abiotic stress to maintain cellular homeostasis, as well as in the ability to genetically transform crop plants with genes from alien species.