RNA-seq and sRNA-seq analysis of maize W22 lines containing B chromosomes

The maize B chromosome is a non-essential chromosome and is not detrimental to plant development at low copy numbers. Nondisjunction of the maize B chromosome occurs at the second pollen mitosis. Maize lines containing B chromosomes are widely used in a variety of studies, such as gene dosage effect, centromere function and engineering of artificial chromosomes etc. An understanding of how the B chromosome affect gene expression is required for utilizing the B chromosome as tools for genetic studies and engineering. Therefore, we performed RNA-seq and small-RNA seq experiments on maize lines containing one through seven copies of B chromosomes to examine how gene expression responds to change of B copy numbers. Overall design: Maize lines W22 with B chromosomes were screened by Fluorescence in situ hybridization at their seedling stage for identification of B chromosomes. W22 lines with one through seven copies of B chromosomes were used as the experimental group whereas W22 lines without B chromosome were used as the control group for RNA-seq and small-RNA seq experiments. 2-4 biological replicates were used for each experimental or control conditions.