Epigenetic QTL Mapping inBrassica napus

Abstract

There is increasing evidence that epigenetic marks such as DNA methylation contribute to phenotypic variation by regulating gene transcription, developmental plasticity, and interactions with the environment. However, relatively little is known about the relationship between the stability and distribution of DNA methylation within chromosomes and the ability to detect trait loci. Plant genomes have a distinct range of target sites and more extensive DNA methylation than animals. We analyzed the stability and distribution of epialleles within the complex genome of the oilseed crop plant Brassica napus. For methylation sensitive AFLP (MSAP) and retrotransposon (RT) epimarkers, we found a high degree of stability, with 90% of mapped markers retaining their allelic pattern in contrasting environments and developmental stages. Moreover, for two distinct parental lines 97% of epialleles were transmitted through five meioses and segregated in a mapping population. For the first time we have established the genetic position for 17 of the 19 centromeres within this amphidiploid species. Epiloci and genetic loci were distributed within distinct clusters, indicating differential detection of recombination events. This enabled us to identify additional significant QTL associated with seven important agronomic traits in the centromeric regions of five linkage groups.

QTL for Yield Traits and Their Association with Functional Genes in Response to Phosphorus Deficiency in Brassica napus

“…About 53 GBMs designed from 46 genes regulating P homeostasis in Arabidopsis [49] were superimposed on the framework of the existing well-defined G-map [50]. In total, the new genetic linkage map had 798 molecular markers with the average distance of 2.57 cM between adjacent markers.…”

“…In total, the new genetic linkage map had 798 molecular markers with the average distance of 2.57 cM between adjacent markers. Linkage map was constructed using JoinMap4.0 [51] and mapping was performed according to the method described by Long et al [50]. Order of markers on the new linkage map was consistent with previously published maps [25], [50].…”

In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus

“…For B. napus, many studies report QTL mapping of seed yield and related yield traits, including traits such as seed weight, pod number, seed number per pod, anthesis, and others (Basunanda et al 2010;Chen et al 2007;Fan et al 2010;Long et al 2011;Shi et al 2009;Zhang et al 2012). Due to this available body of research, it is possible to summarize and compare QTL maps for seed yield and the yield-related traits in B. napus, advancing QTL mapping research.…”

Differential DNA Methylation Patterns Are Related to Phellogen Origin and Quality of Quercus suber Cork

“…Also, MSAP markers have been mapped to protein-coding genes in sorghum [18], maize [19,20] and rice [21], and also linked with stable epigenetic quantitative trait loci (QTL epi ) of diverse agronomic traits [22]. Despite the limitations in acknowledging the exact genomic location for methylation and in whole genome coverage, MSAP still provides a significant number of anonymous loci randomly distributed throughout the genome in which the methylation state of restriction sites can be determined.…”