Maize as a model for the evolution of plant nuclear genomes

Abstract

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...

Molecular Diversity, Structure and Domestication of Grasses

“…Nucleotide diversity studies have the primary advantage of being more comparable between laboratories and experimental systems. The main limitation with any type of diversity survey is that there can be a wide variance in diversity between loci, and only in maize have a large number of loci been examined thus far (Gaut et al, 2000).…”

“…mays) nucleotide diversity at silent sites averages 1n6 % for genes that appear to be behaving neutrally, while the diversity in maize's wild relative Z. mays ssp. par iglumis is roughly 2 % (Gaut et al, 2000 ;White and Doebley, 1999). At individual loci, diversity estimates have ranged from 0n2% to 5 % (White and Doebley, 1999).…”

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

“…Besides the existence of those repeated segments (for reviews see [35,36]), the major part of the sequences seems hardly distinguishable from uncorrelated or 'Markov like' short-range correlated random sequences. With the specific goal to identify periodic repetitions as well as possible hidden periodicities, Fourier and correlation function techniques have been extensively used to process eukaryotic, eubacterial and archaeal genomes [23,25,37,38,39,40].…”

Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing

“…In maize (Zea mays), retrotransposons are estimated to make up 50% to 80% of the genome (SanMiguel and Bennetzen, 1998). The repetitive sequences have little apparent sequence conservation among species (Hulbert et al, 1990; Bennetzen et al, 1994;Chen et al, 1998).Because of their widespread economic importance and genetic resources, rice and maize have been focal points for studies of genome organization and evolution in the Poaceae (Gaut et al, 2000;Isawa and Shimamoto, 1996). The small size of the rice genome makes it a particularly attractive target for large-scale sequencing projects (Goff et al, 2002;Yu et al, 2002) and physical mapping studies (http://rgp.dna.affrc.…”

“…Because of their widespread economic importance and genetic resources, rice and maize have been focal points for studies of genome organization and evolution in the Poaceae (Gaut et al, 2000;Isawa and Shimamoto, 1996). The small size of the rice genome makes it a particularly attractive target for large-scale sequencing projects (Goff et al, 2002;Yu et al, 2002) and physical mapping studies (http://rgp.dna.affrc.…”