Characterization of imprinted genes in rice reveals regulation and imprinting conservation at some loci in plant species

Genomic imprinting is an epigenetic phenomenon by which certain genes display differential expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which contrasts with findings from Arabidopsis. Generally, imprinting in rice is conserved within species, but intraspecific variation was detected as well. Overall design: To explore imprinted genes in rice, we used three-line hybrid rice strains to construct reciprocal crosses. A cytoplasmic male sterile (CMS) line carries a sterility gene encoded in the cytoplasmic genome, such that the pollen produced is sterile. A “maintainer” line shares the same nuclear genome as its corresponding CMS line but has a distinct cytoplasmic genome. Due to the absence of the cytoplasmic sterility gene, the maintainer line is fertile. Using rice CMS and maintainer lines for crossing greatly increases the efficiency of hybridization and enables us to rigorously control the timing of fertilization and to avoid false hybridization events. Here, we used the japonica CMS lines (Liuqianxin-A and Yu6-A) and their maintainer lines (Liuqianxin-B and Yu6-B), and the indica CMS lines (Rongfeng-A and Wufeng-A) with their corresponding maintainer lines (Rongfeng-B and Wufeng-B) to make two distinct reciprocal-cross sets, which we refer to as Liuqianxin-A/Rongfeng-B (LR), Rongfeng-A/Liuqianxin-B (RL), Yu6-A/Wufeng-B (YW), and Wufeng-A/Yu6-B (WY). The LR and RL reciprocal crosses, and YW and WY reciprocal crosses are indicated as LR-RL and YW-WY hereafter for convenience. Meanwhile, we made crosses of Wufeng-A/Wufeng-B (WW), Rongfeng-A/Rongfeng-B (RR), Liuqianxin-A/Liuqianxin-B (LL), and Yu6-A/Yu6-B (YY), which resembled selfing inbred lines as controls to validate imprinting. The following crosses are represented in this Series: liuqianxinA-liuqianxinB, liuqianxinA-rongfengB, rongfengA-liuqianxinB, rongfengA-rongfengB, wufengAyu6B, yu6A-wufengB

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Chen C, Li T, Zhu S, Liu Z, Shi Z, Zheng X, Chen R, Huang J, Shen Y, Luo S, Wang L, Liu QQ, E Z