Analysis of Gene Expression in Resynthesized Brassica napus Allopolyploids Using Arabidopsis 70mer Oligo Microarrays

Background Studies in resynthesized Brassica napus allopolyploids indicate that homoeologous chromosome exchanges in advanced generations (S5:6) alter gene expression through the loss and doubling of homoeologous genes within the rearrangements. Rearrangements may also indirectly affect global gene expression if homoeologous copies of gene regulators within rearrangements have differential affects on the transcription of genes in networks. Methodology/Principal Findings We utilized Arabidopsis 70mer oligonucleotide microarrays for exploring gene expression in three resynthesized B. napus lineages at the S0:1 and S5:6 generations as well as their diploid progenitors B. rapa and B. oleracea. Differential gene expression between the progenitors and additive (midparent) expression in the allopolyploids were tested. The S5:6 lines differed in the number of genetic rearrangements, allowing us to test if the number of genes displaying nonadditive expression was related to the number of rearrangements. Estimates using per-gene and common variance ANOVA models indicated that 6–15% of 26,107 genes were differentially expressed between the progenitors. Individual allopolyploids showed nonadditive expression for 1.6–32% of all genes. Less than 0.3% of genes displayed nonadditive expression in all S0:1lines and 0.1–0.2% were nonadditive among all S5:6 lines. Differentially expressed genes in the polyploids were over-represented by genes differential between the progenitors. The total number of differentially expressed genes was correlated with the number of genetic changes in S5:6 lines under the common variance model; however, there was no relationship using a per-gene variance model, and many genes showed nonadditive expression in S0:1 lines. Conclusions/Significance Few genes reproducibly demonstrated nonadditive expression among lineages, suggesting few changes resulted from a general response to polyploidization. Furthermore, our microarray analysis did not provide strong evidence that homoeologous rearrangements were a determinant of genome-wide nonadditive gene expression. In light of the inherent limitations of the Arabidopsis microarray to measure gene expression in polyploid Brassicas, further studies are warranted

Salt Stress Induced Variation in DNA Methylation Pattern and Its Influence on Gene Expression in Contrasting Rice Genotypes

BACKGROUND: Salinity is a major environmental factor limiting productivity of crop plants including rice in which wide range of natural variability exists. Although recent evidences implicate epigenetic mechanisms for modulating the gene expression in plants under environmental stresses, epigenetic changes and their functional consequences under salinity stress in rice are underexplored. DNA methylation is one of the epigenetic mechanisms regulating gene expression in plant's responses to environmental stresses. Better understanding of epigenetic regulation of plant growth and response to environmental stresses may create novel heritable variation for crop improvement. METHODOLOGY/PRINCIPAL FINDINGS: Methylation sensitive amplification polymorphism (MSAP) technique was used to assess the effect of salt stress on extent and patterns of DNA methylation in four genotypes of rice differing in the degree of salinity tolerance. Overall, the amount of DNA methylation was more in shoot compared to root and the contribution of fully methylated loci was always more than hemi-methylated loci. Sequencing of ten randomly selected MSAP fragments indicated gene-body specific DNA methylation of retrotransposons, stress responsive genes, and chromatin modification genes, distributed on different rice chromosomes. Bisulphite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied with genotypes and tissue types irrespective of the level of salinity tolerance of rice genotypes. CONCLUSIONS/SIGNIFICANCE: The gene body methylation may have an important role in regulating gene expression in organ and genotype specific manner under salinity stress. Association between salt tolerance and methylation changes observed in some cases suggested that many methylation changes are not "directed". The natural genetic variation for salt tolerance observed in rice germplasm may be independent of the extent and pattern of DNA methylation which may have been induced by abiotic stress followed by accumulation through the natural selection process

DNA methylation in diploid inbred lines of potatoes and its possible role in the regulation of heterosis

Self-incompatible diploid potatoes were altered to self-compatible ones by a function of S-locus inhibitor gene and continued selfing generated highly homozygous inbreds. In this study, this process was investigated for the status of DNA methylation by a simple method using genomic DNA digested by methylation-sensitive restriction enzymes prior to RAPD analysis. We detected 31 methylation-sensitive RAPD bands, of which 11 were newly appeared in the selfed progenies, and 6 of them stably inherited to subsequent generations. Aberrant segregations and paternal- or atavism-like transmission were also found. Segregating methylation-sensitive bands in initial populations became fixed in the advanced selfed progenies by 75.0–93.8%, of which 41.7% were fixed to all present and 58.3% to all absent. Because DNA methylation is generally recognized to suppress gene expression as regulatory factors, homozygosity/heterozygosity of methylated DNA may be involved in inbreeding depression/heterosis

Heritable Epigenetic Variation among Maize Inbreds

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation was profiled using immunoprecipitation of methylated DNA followed by hybridization to a high-density tiling microarray. The comparison of the DNA methylation levels in the two genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions (DMRs). Several of these DMRs occur in genomic regions that are apparently identical by descent in B73 and Mo17 suggesting that they may be examples of pure epigenetic variation. The methylation levels of the DMRs were further studied in a panel of near-isogenic lines to evaluate the stable inheritance of the methylation levels and to assess the contribution of cis- and trans- acting information to natural epigenetic variation. The majority of DMRs that occur in genomic regions without genetic variation are controlled by cis-acting differences and exhibit relatively stable inheritance. This study provides evidence for naturally occurring epigenetic variation in maize, including examples of pure epigenetic variation that is not conditioned by genetic differences. The epigenetic differences are variable within maize populations and exhibit relatively stable trans-generational inheritance. The detected examples of epigenetic variation, including some without tightly linked genetic variation, may contribute to complex trait variation

Methods for predicting superior genotypes under multiple environments based on QTL effects

Methods were developed for predicting two kinds of superior genotypes (superior line and superior hybrid) based on quantative trait locus (QTL) effects including epistatic and QTL × environment interaction effects. Formulae were derived for predicting the total genetic effect of any individual with known QTLs genotype derived from the mapping population in a specific environment. Two algorithms, enumeration algorithm and stepwise tuning algorithm, were used to select the best multi-locus combination of all the putative QTLs. Grain weight per plant (GW) in rice was analyzed as a working example to demonstrate the proposed methods. Results showed that the predicted superior lines and superior hybrids had great superiorities over the F hybrid, indicating large breeding potential remained for further improvement on GW. Results also showed that epistatic effects and their interaction with environments largely contributed to the superiorities of the predicted superior lines and superior hybrids. User-friendly software, QTLNetwork, version 1.0, was developed based on the methods in the present paper