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Rates of Mu transposon insertions and excisions are both high in late somatic cells of maize. In contrast, although high rates of insertions are observed in germinal cells, germinal excisions are recovered only rarely. Plants doubly homozygous for deletion alleles of rad51A1 and rad51A2 do not encode functional RAD51 protein (RAD51). Approximately 1% of the gametes from [RAD51.sup.+] plants that carry the MuDR-insertion allele al-m5216 include at least partial deletions of MuDR and the al gene. The structures of these deletions suggest they arise via the repair of MuDR-induced double-strand breaks via nonhomologous end joining. In RAD51 plants these germinal deletions are recovered at rates that are at least 40-fold higher. These rates are not substantially affected by the presence or absence of an al-containing homolog. Together, these findings indicate that in [RAD51.sup.+] gel-minal cells MuDR-induced double-strand breaks (DSBs) are efficiently repaired via RAD51-directed homologous recombination with the sister chromatid. This suggests that [RAD51.sup.-] plants may offer an efficient means to generate deletion alleles for functional genomic studies. Additionally, the high proportion of Mu-active, [RAD51.sup.-] plants that exhibit severe developmental defects suggest that RAD51 plays a critical role in the repair of MuDR-induced DSBs early in vegetative development.

As an ancient segmental tetraploid, the maize (Zea mays L.) genome contains large numbers of paralogs that are expected to have diverged by a minimum of 10% over time. Nearly/dentical paralogs (NIPs) are defined as paralogous genes that exhibit [greater than or equal to] 98% identity. Sequence analyses of the 'gene space' of the maize inbred line B73 genome, coupled with wet lab validation, have revealed that, conservatively, at least ~1% of maize genes have a NIP, a rate substantially higher than that in Arabidopsis. In most instances, both members of maize NIP pairs are expressed and are therefore at least potentially functional. Of evolutionary significance, members of many NIP families also exhibit differential expression. The finding that some families of maize NIPs are closely linked genetically while others are genetically unlinked is consistent with multiple modes of origin. NIPs provide a mechanism for the maize genome to circumvent the inherent limitation that diploid genomes can carry at most two 'alleles' per 'locus.' As such, NIPs may have played important roles during the evolution and domestication of maize and may contribute to the success of long-term selection experiments in this important crop species.

A new genetic map of maize, ISU-IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73 x Mo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations ([F.sub.2], Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.

Recent sequencing efforts have targeted the gene-rich regions of the maize (Zea mays L.) genome. We report the release of an improved assembly of maize assembled genomic islands (MAGIs). The 114,173 resulting contigs have been subjected to computational and physical quality assessments. Comparisons to the sequences of maize bacterial artificial chromosomes suggest that at least 97% (160 of 165) of MAGIs are correctly assembled. Because the rates at which junction-testing PCR primers for genomic survey sequences (90-92%) amplify genomic DNA are not significantly different from those of control primers ([approximately equal to] 91%), we conclude that a very high percentage of genic MAGIs accurately reflect the structure of the maize genome. EST alignments, ab initio gene prediction, and sequence similarity searches of the MAGIs are available at the Iowa State University MAGI web site. This assembly contains 46,688 ab initio predicted genes. The expression of almost half (628 of 1,369) of a sample of the predicted genes that lack expression evidence was validated by RT-PCR. Our analyses suggest that the maize genome contains between [approximately equal to] 33,000 and [approximately equal to] 54,000 expressed genes. Approximately 5% (32 of 628) of the maize transcripts discovered do not have detectable paralogs among maize ESTs or detectable homologs from other species in the GenBank NR nucleotide/protein database. Analyses therefore suggest that this assembly of the maize genome contains approximately 350 previously uncharacterized expressed genes. We hypothesize that these 'orphans' evolved quickly during maize evolution and/or domestication. assembly validation | gene prediction | maize genome assembly | nearly identical paralog

Root hairs are specialized epidermal cells that are thought to play an important role in plant nutrition by facilitating the absorption of water and nutrients. Three maize mutants with abnormal root hair morphologies (rth1, rth2, and ryth3) have been isolated from Mutator transposon stocks. All three root hair mutant phenotypes are controlled by single recessive alleles. The rth1 mutant initiates normal-looking root hair primordia that fail to elongate. The normal-looking root hair primordia of the rth2 mutant elongate to only approximately one-fifth to one-fourth the length of wild type root hairs. Like rth1 primordia, rth3 primordia undergo little elongation. However, unlike the relatively normal-looking rth1 primordia, rth3 primordia are distinctly abnormal when viewed through a scanning electron microscope. The rth1 mutant exhibits pleiotropic nutrient deficiencies, while the rth2 and rth3 mutants grow vigorously. This finding suggests that under some environmental conditions, root hairs are less important to plant growth than has been previously thought. The rth1, rth2, and rth3 genes have been mapped to chromosomes 1L, 5L, and 1S, respectively, via crosses with BA translocation stocks. The rth2 allele exhibits reduced transmission through the male gametophyte, but a normal rate of transmission through female gametophytes; rth1 and rth3 are transmitted at normal rates.