Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 27, 2013
Publication Date: February 18, 2014
Repository URL: http://handle.nal.usda.gov/10113/61221
Citation: Lin, L., Tian, S., Kaeppler, S., Liu, Z., An, Y. 2014. Conserved transcriptional regulatory programs underlying rice and barley germination. PLoS One. 9(2):e87261.doi:10.1371/journal.pone.0087261. Interpretive Summary: Germination efficieny attracts the attention of barley researchers because of its economic importance to the malting industry and barley growers. Malting industries utilize the germination process to let the seed turn the storage proteins and starch in barley grains into amino acids and sugars for brewing. Improper germination during grain harvest and storage leads to significant economic loss for barley growers as they can no longer receive the premium price. One of the ultimate goals of barley research, centered on increasing competitiveness of US barley and the malting/brewing industry, is to develop new barley germplasm with super malting qualities and pre-harvest sprouting tolerance through engineering genetic networks that control seed germination. However, a lack of knowledge about genes important in germination is a bottleneck to achieve the objective. To effectively isolate the genes important to barley germination, we designed a computational and comparative strategy and identified 316 sets of barley genes with very similar protein sequences and germination regulated expression patterns. Gene functions are predicted from their protein sequences and expression patterns. Expression patterns and comparisons to genes from rice, a well studied crop, indicates that the 316 sets of genes play important roles in seed germination. These barley genes that have been identified will be a valuable starting point for biotechnologist/breeders to design ways to develop barley varieties with pre-harvest spouting resistance and superior malting qualities through transgenic and molecular breeding technologies.
Technical Abstract: Seed germination is accompanied with concerted transcriptional expression of many genes and biological pathways. Barley and rice germinations have been divergent from each other for 50-60 million years. However, there is little knowledge about the conservation and divergence in transcriptional regulatory programs underlying rice and barley germination. Transcriptomes of barley and rice grains representing start, middle and end points of germination were analyzed. Comparing gene sequences and expression patterns of germination regulated barley and rice genes revealed that percentage of barley and rice gene pairs (BRs) with similar expression patterns intend to correlate with their sequence homology. However, significant divergence in gene expression patterns of many BR genes with high homology was observed. Forty percentages of barley and rice genes with E-value less than -50 have low similarity or dissimilarity in their expression patterns. A total of 316 groups of conserved germination regulated barley and rice genes (cBR) with high sequence homology and strong expression pattern similarity have been identified. Their expression responsiveness to germination, expression patterns and protein sequences have been preserved after divergence from their common ancestor, strongly suggesting that the cBRs have functional significance to germination and may contribute to core biological processes shared by both barley and rice germination. The barley and rice genes in each cBR are likely to play equivalent biological functions in seed germination. The cBR genes have diverse gene expression patterns, and encode proteins involved in a variety of biological pathways such as signaling components and ubiquitin dependent degradation pathways. It was observed that early germination up-regulation of cell wall metabolic pathway and peroxidase genes and late germination up-regulation of chromatin structure and remodeling pathways are conserved in barley and rice. The studies demonstrated that significant conservation and divergence have occurred in transcriptional regulatory programs underlying barley and rice germination and also identified barley-rice gene sets and biological pathways with conserved protein sequences and conserved germination regulated expression patterns that are likely to contribute to germination characteristics shared by barley and rice.