Academic journal article Genetics

Structure and Evolution of the R/b Chromosomal Regions in Rice, Maize and Sorghum

Academic journal article Genetics

Structure and Evolution of the R/b Chromosomal Regions in Rice, Maize and Sorghum

Article excerpt

ABSTRACT

The r1 and b1 genes of maize, each derived from the chromosomes of two progenitors that hybridized >4.8 million years ago (MYA), have been a rich source for studying transposition, recombination, genomic imprinting, and paramutation. To provide a phylogenetic context to the genetic studies, we sequenced orthologous regions from maize and sorghum (>600 kb) surrounding these genes and compared them with the rice genome. This comparison showed that the homeologous regions underwent complete or partial gene deletions, selective retention of orthologous genes, and insertion of nonorthologous genes. Phylogenetic analyses of the r/b genes revealed that the ancestral gene was amplified independently in different grass lineages, that rice experienced an intragenomic gene movement and parallel duplication, that the maize r1 and b1 genes are descendants of two divergent progenitors, and that the two paralogous r genes of sorghum are almost as old as the sorghum lineage. Such sequence mobility also extends to linked genes. The cisZOG genes are characterized by gene amplification in an ancestral grass, parallel duplications and deletions in different grass lineages, and movement to a nonorthologous position in maize. In addition to gene mobility, both maize and rice regions experienced recent transposition (<3 MYA).

THE grass family (Poaceae) is well known for the economic importance of its members, such as rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), oats (Avena sativa), sorghum (Sorghum spp.), wheat (Triticum spp.), and rye (secale céréale). Even though nuclear DNA content among members of the family varies extensively, >400 -fold (BENNETT and SMITH 1976; BENNETT et al. 2000), comparative mapping studies (HULBERT et al. 1990; AHN and TANKSLEY 1993; MOORE et al. 1995; GALE and DEVOS 1998; FEUILLET and KELLER 2002) have demonstrated that significant portions of the genomes are conserved (collinear) and that, aside from polyploidization, the large size of a genome is mostly due to a high content of repetitive elements (SANMiGUEL and BENNETZEN 1998; MEYERS et al. 2001). Large-scale studies using genetic maps based on DNA markers are limited to the detection of large-scale chromosomal rearrangements, such as translocations, intrachromosomal inversions, genome replication, chromosomal fusion, and rearrangements that characterize spécifie clades. For instance, three translocations marked the ancestral lineage of Panicoideae (GALE and DEVOS 1998) and genome replication, chromosomal fusion, and rearrangements occurred on the Brassica lineage after its divergence from the Arabidopsis thaliana lineage (LAGERCRANTZ 1998). However, evolutionary forces that lead to speciation of closely related species work locally within the genomes. Recently, to uncover characteristics of local evolution of plant genomes, several researchers compared the genomic content and organization of orthologous regions at the sequence level across various grass species. Regions analyzed to date are the sh2/al region (CnEN et al 1997, 1998), the Lrk region (FEUILLET and KELLER 1999), the adhl/2 region (TiKHONOV et al 1999; ILIC et al 2003), the 22-kD Zein cluster region (SoNGeiaZ. 2002), the Vrn 1 region (RAMAKRISHNA et al. 2002a), the RpI region (RAMAKRISHNA et al 2002b), the Rph7 region (BRUNNER et al 2003), and the 1rs/Igregion (LANGHAM et al. 2004). Although these studies generally confirmed gene conservation (microcollinearity) among orthologous segments of various grass taxa, they also reported small-scale genie rearrangements, such as gene insertions, deletions, amplifications, inversions, and translocations.

These studies are too few in number to produce a general picture of genome evolution. Only a few of them compare sequences from more than two species and very few studied duplicated (homeologous) regions of polyploid species. Furthermore, evolutionary analytical methods accompanied only a small number of them. …

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