DNA Methylation Alterations at 5'-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus

Functional Identification of EjGIF1 in Arabidopsis and Preliminary Analysis of Its Regulatory Mechanisms in the Formation of Triploid Loquat Leaf Heterosis

Although several results have been obtained in triploid loquat heterosis (i.e., leaf size of triploid loquat) studies in the past years, the underlying mechanisms of the heterosis are still largely unknown, especially the regulation effects of one specific gene on the corresponding morphology heterosis. In this study, we sought to further illustrate the regulatory mechanisms of one specific gene on the leaf size heterosis of triploid loquats. A leaf size development-related gene (EjGIF1) and its promoter were successfully cloned. Ectopic expression of EjGIF1 in Arabidopsis showed that the leaf size of transgenic plantlets was larger than that of WTs, and the transgenic plantlets had more leaves than WTs. Quantitative Reverse Transcription PCR (qRT-PCR) showed that the expression level of EjGIF1 showed an AHP expression pattern in most of the hybrids, and this was consistent with our previous phenotype observations. Structure analysis of EjGIF1 promoter showed that there were significantly more light-responsive elements than other elements. To further ascertain the regulatory mechanisms of EjGIF1 on triploid loquat heterosis, the methylation levels of EjGIF1 promoter in different ploidy loquats were analyzed by using bisulfite sequencing. Surprisingly, the total methylation levels of EjGIF1 promoter in triploid showed a decreasing trend compared with the mid-parent value (MPV), and this was also consistent with the qRT-PCR results of EjGIF1. Taken together, our results suggested that EjGIF1 played an important role in promoting leaf size development of loquat, and demethylation of EjGIF1 promoter in triploid loquats caused EjGIF1 to exhibit over-dominance expression pattern and then further to promote leaf heterosis formation. In conclusion, EjGIF1 played an important role in the formation of triploid loquat leaf size heterosis.

Extensive genetic and DNA methylation variation contribute to heterosis in triploid loquat hybrids

We aim to overcome the unclear origin of the loquat and elucidate the heterosis mechanism of the triploid loquat. Here we investigated the genetic and epigenetic variations between the triploid plant and its parental lines using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified fragment length polymorphism (MSAP) analyses. We show that in addition to genetic variations, extensive DNA methylation variation occurred during the formation process of triploid loquat, with the triploid hybrid having increased DNA methylation compared to the parents. Furthermore, a correlation existed between genetic variation and DNA methylation remodeling, suggesting that genome instability may lead to DNA methylation variation or vice versa. Sequence analysis of the MSAP bands revealed that over 53% of them overlap with protein-coding genes, which may indicate a functional role of the differential DNA methylation in gene regulation and hence heterosis phenotypes. Consistent with this, the genetic and epigenetic alterations were associated closely to the heterosis phenotypes of triploid loquat, and this association varied for different traits. Our results suggested that the formation of triploid is accompanied by extensive genetic and DNA methylation variation, and these changes contribute to the heterosis phenotypes of the triploid loquats from the two cross lines.

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data

Genotyping-by-sequencing (GBS) or restriction-site associated DNA marker sequencing (RAD-seq) is a practical and cost-effective method for analysing large genomes from high diversity species. This method of sequencing, coupled with methylation-sensitive enzymes (often referred to as methylation-sensitive restriction enzyme sequencing or MRE-seq), is an effective tool to study DNA methylation in parts of the genome that are inaccessible in other sequencing techniques or are not annotated in microarray technologies. Current software tools do not fulfil all methylation-sensitive restriction sequencing assays for determining differences in DNA methylation between samples. To fill this computational need, we present msgbsR, an R package that contains tools for the analysis of methylation-sensitive restriction enzyme sequencing experiments. msgbsR can be used to identify and quantify read counts at methylated sites directly from alignment files (BAM files) and enables verification of restriction enzyme cut sites with the correct recognition sequence of the individual enzyme. In addition, msgbsR assesses DNA methylation based on read coverage, similar to RNA sequencing experiments, rather than methylation proportion and is a useful tool in analysing differential methylation on large populations. The package is fully documented and available freely online as a Bioconductor package (https://bioconductor.org/packages/release/bioc/html/msgbsR.html).

A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes

Resistance to common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli, in Phaseolus vulgaris is conditioned by several loci on different chromosomes. Previous studies with OAC-Rex, a CBB-resistant, white bean variety of Mesoamerican origin, identified two resistance loci associated with the molecular markers Pv-CTT001 and SU91, on chromosome 4 and 8, respectively. Resistance to CBB is assumed to be derived from an interspecific cross with Phaseolus acutifolius in the pedigree of OAC-Rex. Our current whole genome sequencing effort with OAC-Rex provided the opportunity to compare its genome in the regions associated with CBB resistance with the v1.0 release of the P. vulgaris line G19833, which is a large seeded bean of Andean origin, and (assumed to be) CBB susceptible. In addition, the genomic regions containing SAP6, a marker associated with P. vulgaris-derived CBB-resistance on chromosome 10, were compared. These analyses indicated that gene content was highly conserved between G19833 and OAC-Rex across the regions examined (>80%). However, fifty-nine genes unique to OAC Rex were identified, with resistance gene homologues making up the largest category (10 genes identified). Two unique genes in OAC-Rex located within the SU91 resistance QTL have homology to P. acutifolius ESTs and may be potential sources of CBB resistance. As the genomic sequence assembly of OAC-Rex is completed, we expect that further comparisons between it and the G19833 genome will lead to a greater understanding of CBB resistance in bean.