The assessment of epigenetic diversity, differentiation, and structure in the ‘Fuji’ mutation line implicates roles of epigenetic modification in the occurrence of different mutant groups as well as spontaneous mutants

Abstract

The 'Fuji' line includes many varieties with a similar genetic background and consistent inducement factors with epigenetic occurrence, thus it may be considered an ideal candidate for epigenetic research. In this study, 91 bud mutations of 'Fuji' apple were used as the test materials. Using the genetic variation within 'Fuji' as the control, the characteristics of epigenetic variation at different levels in both varieties and mutant groups were examined. The results showed that: (1) the global genomic DNA methylation level of the 91 bud mutants of 'Fuji' ranged from 29.120%-45.084%, with an average of 35.910%. Internal cytosine methylation was the main DNA methylation pattern. Regarding the variation of methylation patterns of 'Fuji' mutants, the vast majority of loci maintained the original methylation pattern existed in 'Fuji'. CHG methylation variation was the main type of variation; (2) the variation in methylation patterns between the mutant groups was greater than that of methylation levels. Among these patterns, the variation in CHG methylation patterns (including CHG hypermethylation and CHG demethylation) was expected to be dominant. The observed variation in methylation levels was more important in the Color mutant group; however, the variation in methylation patterns was more obvious in both the early maturation and Spur mutant groups. Moreover, the range of variation in the Early-maturation group was much wider than that in the Spur mutant group; (3) epigenetic diversity and genetic diversity were both low between the mutant groups. In the 'Fuji' mutant groups, there was few correlation between genetic and epigenetic variation, and epigenetic differentiation resulted in more loci with moderate or greater differentiation; (4) the purifying selection seemed to play a major role in the differentiation of different groups of 'Fuji' mutants (65.618%), but epigenetic diversity selection still occurred at nearly 35% of loci. Sixteen epigenetic outlier loci were detected.

Insight Into the Multiple Branches Traits of a Mutant in Larix olgensis by Morphological, Cytological, and Transcriptional Analyses

“…Bud mutation preserves the desirable parent plant qualities and provides valuable new characteristics (Foster and Aranzana, 2018). Therefore, as a source of plant variation, bud mutation not only selects new varieties directly, but also provides new germplasm for hybrid breeding, and thereby making it a simple and effective method for breeding new varieties (Wang et al, 2017;Du et al, 2020).…”

Field study of the fire‐blight‐resistant cisgenic apple line C44.4.146

“…Somaclonal variation could have affected the expression of the flavonoid pathway (e.g. the genes MdMyb1 / MdMyb10 ), which influences skin color in apple sports (Du et al., 2020; El‐Sharkawy et al., 2015; Qian et al., 2014; Zhang et al., 2019). Most of the deeper red‐skinned ‘Gala’ mutants were described to be L2‐derived periclinal chimera (Dickinson & White, 1986), which could also be true for ‘Gala Galaxy’.…”

Effect of Paper-Bagging on Apple Skin Patterning Associated with MdMYB10 Promoter Methylation

“…When the bag was removed, hypomethylation is detected especially in the CHG pattern. Although there is a dramatically lower CHH cytosine methylation in other red fruits [ 20 , 24 ], the importance of the CHG cytosine methylation in fruit coloration has been emphasized in ‘Fuji’ apples [ 23 , 38 ]. Since methylation in the M7 region is located upstream than the M2 region, the recovery of methylation would be correlated positively with MdMYB10 expression and anthocyanin accumulation.…”