Journal
BMC PLANT BIOLOGY
Volume 16, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12870-016-0775-7
Keywords
Maize; B chromosome; RNA-seq; Transcription; Evolution
Categories
Funding
- National Natural Science Foundation of China [31171563, 31421005]
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Background: The dispensable maize (Zea mays L.) B chromosome is highly heterochromatic and widely believed to be devoid of functional genes. Although low-copy B chromosome causes no obvious phenotype variation, its existence might influence A genome gene expression. Previous studies suggested that B chromosomes are evolved from standard chromosomes; therefore, they might contain genic regions showing homology with A chromosome sequences. Results: Our data suggested that maize B chromosome influences the A-genome transcription with stronger effect associated with an increase in copy number of B chromosome. In total 130 differently expressed genes were detected in comparison between with and without B chromosome lines. These differentially expressed genes are mainly involved in cell metabolism and nucleotide binding. Using Starter + B, we amplified ten B chromosome loci with high sequence similarity to A-genome genes. Fluorescence in situ hybridization (FISH) confirmed that at least four similar to 5 kb-sized genes are located on the B chromosome. In addition, through de novo assembly of the reads not unmapped to maize B73 reference genome together with PCR validation, we found three B-located LTR; in particular, one of them, the 3.2 kb comp75688, is expressed in a B-dosage dependent manner. Conclusion: We found that in the presence of maize B chromosome, the transcription of A genome genes was altered, with more impact by the increase of the B chromosome number. The B-located transcriptionally active genes showed high similarity to their A-genome homologues, and retrotransposons on B chromosome also have partial homologous to A genome sequences. Our data shed more lights on the genome structure and evolution of the maize B chromosome.
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