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Understanding the evolution of the maize B chromosome requires insight into the molecular organization of a large number of B clones, which can be potentially obtained by microdissection of the chromosome. Yet, the microdissection protocols currently available are ineffective for a large-scale isolation. In an attempt to improve its efficiency, a protocol was adopted to screen a microdissected B library with probes prepared from the degenerate oligonucleotide primed-PCR product of genomic DNA. This protocol resulted in 59 new B clones, most of which were highly repetitive sequences located in various B regions but mostly in the heterochromatic blocks of the long arm. They also appeared in A chromosomes. Twenty-four of these were retrotransposons, ten knob, 18 noncoding sequences, and seven unknown sequences. The implication of the new B sequences on the B evolution is discussed

Arabidopsis histone H3 lysine 4 (H3K4) demethylases play crucial roles in several developmental processes, but their involvement in seedling establishment remain unexplored.Here, we show that Arabidopsis JUMONJI DOMAIN-CONTAINING PROTEIN17 (JMJ17), an H3K4me3 demethylase, is involved in cotyledon greening during seedling establishment. Dark-grown seedlings of jmj17 accumulated a high concentration of protochlorophyllide, an intermediate metabolite in the tetrapyrrole biosynthesis (TPB) pathway that generates chlorophyll (Chl) during photomorphogenesis. Upon light irradiation, jmj17 mutants displayed decreased cotyledon greening and reduced Chl level compared with the wild-type; overexpression of JMJ17 completely rescued the jmj17-5 phenotype.Transcriptomics analysis uncovered that several genes encoding key enzymes involved in TPB were upregulated in etiolated jmj17 seedlings. Consistently, chromatin immunoprecipitationquantitative PCR revealed elevated H3K4me3 level at the promoters of target genes. Chromatin association of JMJ17 was diminished upon light exposure. Furthermore, JMJ17 interacted with PHYTOCHROME INTERACTING FACTOR1 in the yeast two-hybrid assay.JMJ17 binds directly to gene promoters to demethylate H3K4me3 to suppress PROTOCHLOROPHYLLIDE OXIDOREDUCTASE C expression and TPB in the dark. Light results in de-repression of gene expression to modulate seedling greening during deetiolation. Our study reveals a new role for histone demethylase JMJ17 in controlling cotyledon greening in etiolated seedlings during the dark-to-light transition.

Aneuploidy features a numerical chromosome variant that the number of chromosomes in the nucleus of a cell is not an exact multiple of the haploid number, which may have an impact on morphology and gene expression. Here we report a tertiary trisomy uncovered by characterizing a T-DNA insertion mutant (aur2-1/+) in the Arabidopsis (Arabidopsis thaliana) AURORA2 locus. Whole-genome analysis with DNA tiling arrays revealed a chromosomal translocation linked to the aur2-1 allele, which collectively accounted for a tertiary trisomy 2. Morphologic, cytogenetic and genetic analyses of aur2-1 progeny showed impaired male and female gametogenesis to various degrees and a tight association of the aur2-1 allele with the tertiary trisomy that was preferentially inherited. Transcriptome analysis showed overlapping and distinct gene expression profiles between primary and tertiary trisomy 2 plants, particularly genes involved in response to stress and various types of external and internal stimuli. Additionally, transcriptome and gene ontology analyses revealed an overrepresentation of nuclear-encoded organelle-related genes functionally involved in plastids, mitochondria and peroxisomes that were differentially expressed in at least three if not all Arabidopsis trisomics. These observations support a previous hypothesis that aneuploid cells have higher energy requirement to overcome the detrimental effects of an unbalanced genome. Moreover, our findings extend the knowledge of the complex nature of the T-DNA insertion event influencing plant genomic integrity by creating high-grade trisomy. Finally, gene expression profiling results provide useful information for future research to compare primary and tertiary trisomics for the effects of aneuploidy on plant cell physiology.

The CL-repeat is a repetitive sequence that is unique to the maize B chromosome, where it resides in the centromeric knob and the first 3 distal heterochromatic regions of the long arm. Given this organization, it would be desirable to identify molecular markers that are specifically distributed in the B chromosome. In this report, the CL-repeat has been used to develop a class of molecular markers for the maize B chromosome. To this end, a modified transposon display procedure designated as CL-repeat display was used to generate and display 26 genomic fragments that are specific to the B chromosome, all of which were cloned and sequenced. The sequences of 19 fragments were highly homologous to the 5′ or 3′ terminus of the CL-repeat. Five of these fragments also contained sequences that were homologous to sequences of the B chromosome centromere. Four of the other 7 fragments shared homology with B chromosome centromere sequences, and the remaining 3 were of unidentified sequences. Using 13 B-10L translocations with various breakpoints along the B chromosome long arm, the 26 CL-repeat display markers were mapped to definite regions of the B chromosome. This strategy should be feasible for the development of molecular markers for the B chromosome in maize and in other species where B chromosome-specific repeats have been identified.