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Sequence analysis of recombination break points has defined a 377-bp recombination hot spot within the anthocyanin 1 (a1) gene. One-fifth of all recombination events that occurred within the 140-kb a1-shrunken 2 interval resolved within this 377-bp hot spot. In yeast, meiotic double-strand breaks in chromosomal DNA are thought to initiate recombination and are generally located 5' of coding regions, near transcription promoter sequences. Because the a1 recombination hot spot is located within the 5' transcribed region of the a1 gene, the sites at which recombination events initiate and resolve appear to be different, but both appear to be regulated in relation to transcribed sequences. Although transposon insertions are known to suppress recombination and alter the ratio of crossovers to apparent gene conversions, the Mutator 1 transposon insertion in the a1-mum2 allele does not alter the sites at which recombination events resolve.

Picky is an efficient oligo microarray design tool for large genomes. Picky integrates novel computer science techniques and the best known nearest-neighbor parameters to quickly identify sequence similarities and estimate their hybridization properties. Oligos designed by Picky are computationally optimized to guarantee the best specificity, sensitivity and uniformity under the given design constrains. Picky can be used to design arrays for whole genomes, or for only a subset of genes. The latter can still be screened against a whole genome to attain the same quality as a whole genome array, thereby permitting low budget, pathway-specific experiments to be conducted with large genomes. Picky is the fastest oligo array design tool currently available to the public, requiring only a few hours to process large gene sets from rice, maize or human.

The Maize Genome Sequencing Consortium has deposited into GenBank more than 850,000 maize (Zea mays) genome survey sequences (GSSs) generated via two gene enrichment strategies, methylation filtration and high-C 0 t (HC) fractionation. These GSSs are a valuable resource for generating genome assemblies and the discovery of single nucleotide polymorphisms and nearly identical paralogs. Based on the rate of mismatches between 183 GSSs (105 methylation filtration 1 78 HC) and 10 control genes, the rate of sequencing errors in these GSSs is 2.3 3 10 23 . As expected many of these errors were derived from insufficient vector trimming and base-calling errors. Surprisingly, however, some errors were due to cloning artifacts. These G d C to A d T transitions are restricted to HC clones; over 40% of HC clones contain at least one such artifact. Because it is not possible to distinguish the cloning artifacts from biologically relevant polymorphisms, HC sequences should be used with caution for the discovery of single nucleotide polymorphisms or paramorphisms. The average rate of sequencing errors was reduced 6-fold (to 3.6 3 10 24 ) by applying more stringent trimming parameters. This trimming resulted in the loss of only 11% of the bases (15,469/144,968). Due to redundancy among GSSs this more stringent trimming reduced coverage of promoters, exons, and introns by only 0%, 1%, and 4%, respectively. Hence, at the cost of a very modest loss of gene coverage, the quality of these maize GSSs can approach Bermuda standards, even prior to assembly.

SummaryEtched1 (et1) is a pleiotropic, recessive mutation of maize that causes ®ssured and cracked mature kernels and virescent seedlings. Microscopic examinations of the et1 phenotype revealed an aberrant plastid development in mutant kernels and mutant leaves. Here, we report on the cloning of the et1 gene by transposon tagging, the localization of the gene product in chloroplasts, and its putative function in the plastid transcriptional apparatus. Several alleles of Mutator (Mu)-induced et1 mutants, the et1-reference (et1-R) mutant, and Et1 wild-type were cloned and analyzed at the molecular level. Northern analyses with wildtype plants revealed that Et1 transcripts are present in kernels, leaves, and other types of tissue, and no Et1 expression could be detected in the et1 mutants analyzed. The ET1 protein is imported by chloroplasts and has been immunologically detected in transcriptionally active chromosome (TAC) fractions derived from chloroplasts. Accordingly, the relative transcriptional activity of TAC fractions was signi®cantly reduced in chloroplasts of et1-R plants. ET1 is the ®rst zinc ribbon (ZR) protein shown to be targeted to plastids. With regard to its localization and its striking structural similarity to the eukaryotic transcription elongation factor TFIIS, it is feasible that ET1 functions in plastid transcription elongation by reactivation of arrested RNA polymerases.Keywords: etched1, plastid nucleoids, transcriptional active chromosome, transposon tagging, plastid transcription, TFIIS. IntroductionThe analysis of genes involved in the development of the maize endosperm is of particular interest in order to understand the structural and regulatory features of seed growth. In maize, many mutants and a number of genes affecting tissue and organ development have been isolated. Numerous mutants have been described, which exhibit abnormal endosperm development (for review: Coe et al., 1988). Among these, a few are pleiotropic and thus of particular interest because they affect the development of different tissue types. Etched1 (et1) is one such mutation, which affects the development of kernels as well as of seedlings.Etched1 is a recessive mutation that was ®rst identi®ed and described by Stadler (1940). The mutant reference allele (et1-reference (et1-R)) was isolated from the progeny of a population of maize plants pollinated with X-ray irradiated pollen. Kernels homozygous for the et1-R allele are ®ssured because of depressions and crevices on the endosperm surface (Figure 1a±c). Prior biochemical and structural analyses of the et1-R kernels revealed that starch synthesis is reduced and starchless endosperm cells are present around the cracks and scars in the kernels (Figure 1; Sangeetha and Reddy, 1991). The et1 kernel phenotype becomes visible approximately 15 days after pollination (DAP). The degree of etching differs among the kernels on an ear and can vary from a weak to a very severe phenotype. This phenotypic variation is apparently not correlated with any speci®c genetic background ...