Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.).

Allele-specific expression (ASE) can lead to phenotypic diversity and evolution. However, the mechanisms regulating ASE are not well understood, particularly in woody perennial plants. In this study, we investigated ASE genes in the apple cultivar 'Royal Gala' (RG).

microRNA172 targets APETALA2 to regulate flavonoid biosynthesis in apple (Malus domestica).

MicroRNA172 (miR172) plays a role in regulating a diverse range of plant developmental processes, including flowering, fruit development and nodulation. However, its role in regulating flavonoid biosynthesis is unclear. In this study, we show that transgenic apple plants over-expressing miR172 show a reduction in red coloration and anthocyanin accumulation in various tissue types.

Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages.

Background: MicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple ( Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes.

Genomic analyses provide insights into peach local adaptation and responses to climate change.

The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach adaptation to diverse climates.

Identification of gene co-expression networks and key genes regulating flavonoid accumulation in apple (Malus × domestica) fruit skin.

Anthocyanin provides a red color for apple and health benefit for human. To better understand the molecular mechanisms of regulating apple color formation, we analyzed 27 transcriptomes of fruit skin from three cultivars 'Huashuo' (red-skinned), 'Hongcuibao' (red-skinned), and 'Golden Delicious' (yellow-skinned) at 0, 2, and 6 days after bag removal. Using pairwise comparisons and weighted gene co-expression network analyses (WGCNA), we constructed 17 co-expression modules.

Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history.

Background: Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important traits, but genetic bases underlying these changes and the effects of artificial selection on genomic diversity are not well understood.

Results: Here, we report a comprehensive analysis of peach evolution based on genome sequences of 480 wild and cultivated accessions.

Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach ().

Fruit shape is an important external characteristic that consumers use to select preferred fruit cultivars. In peach, the flat fruit cultivars have become more and more popular worldwide. Genetic markers closely linking to the flat fruit trait have been identified and are useful for marker-assisted breeding.

Transcriptome analysis reveals novel genes involved in anthocyanin biosynthesis in the flesh of peach.

Peach is an important deciduous fruit tree species. Anthocyanins play an important role in fruit color formation and, through linkage analysis, previous studies have identified and mapped the key genes regulating anthocyanins' accumulation to chromosomes 3 and 5 in two different germplasms. To understand the overall regulatory network of anthocyanins biosynthesis, genes co-expressed with these key genes were identified in the red-fleshed 'Tianjin Shui Mi' and white-fleshed 'Hakuho' germplasms.