Microarray expression analysis of the main inflorescence in B. napus

The effect of the number of pods on the main inflorescence (NPMIs) on seed yield in Brassica napus plants grown at high density is a topic of great economic and scientific interest. We sought to identify patterns of gene expression that are associated with inflorescence and PMI differentiation and development in Brassica napus. In this study, we monitored the gene expression profiles in the main inflorescence of two B. napus F6 RIL pools, each composed of nine extremely low- or high-PMI lines, and their elite parental lines Zhongshuang 11 (ZS11) and 73290, which exhibit striking differences in NPMIs at the pistil-stamen differentiation stage, using a Brassica 90K elements oligonucleotide array. We found that 4,805 of the 85,307 probes present in the array were differentially expressed, with a fold-change of at least 1.5, between the low- and high-NPMI samples. About 92.8% of the DEGs mapped to chromosomes that originated from B. rapa and B. oleracea, and 1.6% of the DEGs co-localized with two QTL intervals (PMI10 and PMI11) known to be associated with the NPMI.