Parental CG and CHG methylation variation is associated with allelic-specific expression in elite hybrid rice

ABSTRACTHeterosis refers to the superior performance of the hybrid over the inbred parental lines. Besides genetic variation, epigenetic difference between the parental lines has been suggested to be involved in heterosis. However, precise nature and extent of parental epigenome difference and reprograming in hybrids governing heterotic gene expression remain unclear. In this work, we analyzed DNA methylomes and transcriptomes of the widely cultivated and genetically studied elite hybrid rice SY63, the reciprocal hybrid, and the parental varieties ZS97 and MH63, of which the high-quality reference genomic sequences are available. We show that the parental varieties display important variation in genic methylation at CG and CHG (H=A, C, or T) sequences. Compared with the parents the hybrids display dynamic methylation variation during development. However, many parental differentially methylated regions (DMR) at CG and CHG sites are maintained in the hybrid. Only a small fraction of the DMRs display non-additive DNA methylation variation which, however, shows no overall correlation with gene expression variation. By contrast, most of the allelic-specific expression (ASE) genes in the hybrid are associated with DNA methylation and the ASE negatively correlates with allelic-specific methylation (ASM) at CHG but positively at CG sites. The results reveal a specific DNA methylation reprogramming pattern in the hybrid rice and point to a role of parental CG and CHG methylation divergence in allelic specific expression that has been associated with phenotype variation and hybrid vigor in several plant species.One sentence summaryParental CG and CHG methylation divergence is maintained in hybrid and is related to allelic specific expression associated with phenotype variation and hybrid vigor.

Silver nanoparticles induce genetic, biochemical, and phenotype variation in chrysanthemum

Despite the tremendous progress in breeding, novel and user-friendly techniques of plant improvement are desirable. The study aimed to analyze the usefulness of silver nanoparticles (AgNPs) in the breeding of chrysanthemum: one of the top ornamental plant species. In vitro regeneration of adventitious shoots from internodes of chrysanthemum ‘Lilac Wonder’ was induced on the modified Murashige and Skoog (MS) medium supplemented with 0.6 mg L−1 6-benzylaminopurine (BAP), 2 mg L−1 indole-3-acetic acid (IAA) and AgNPs at 0, 5, 10 and 20 ppm concentration. The efficiency of callogenesis and caulogenesis were analyzed after 10 weeks of culture. The concentration of chlorophylls, carotenoids, and phenolic compounds in shoots and calli were estimated. Plants obtained from 20 ppm AgNPs treatment were additionally analyzed on the genetic level using randomly amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers. In vitro rooted shoots were acclimatized in the glasshouse and subjected to biochemical and phenotype stability evaluation. AgNPs at the highest concentration (20 ppm) suppressed both callogenesis and caulogenesis in vitro. The concentration of metabolites in callus was stable, regardless of AgNPs treatment, except for carotenoids which production was enhanced by 20 ppm AgNPs. In contrast, the content of chlorophyll a and b in shoots varied depending on AgNPs treatment. Polymorphic loci were detected in 12 and 9 AgNPs-treated-plants by RAPD and ISSR markers, respectively (one of which was common to both marker systems). Rooting and acclimatization were fully successful in all experimental combinations. Phenotype alternations were detected in six plants; one from 10 ppm AgNPs treatment and five from 20 ppm treatment. They included variation in pigment content (anthocyanins and carotenoids) and/or inflorescence shape. Interestingly, only two plants revealed both genetic and phenotype polymorphisms. No genetic or phenotype variation was detected in the control plants. In conclusion, AgNPs can be used in chrysanthemum breeding.