1. 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
- Author
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Minxiao Liu, Song Laiqing, Yanbo Wang, Daliang Liu, Zhang Xueyong, Jiang Zhongwu, Liu Xueqing, Xiaoyun Du, Sun Yanxia, Zhao Lingling, and Tang Yan
- Subjects
0106 biological sciences ,0301 basic medicine ,Mutant ,Fruit Crops ,Artificial Gene Amplification and Extension ,medicine.disease_cause ,Biochemistry ,01 natural sciences ,Epigenesis, Genetic ,Genetics ,Mutation ,DNA methylation ,Multidisciplinary ,Nucleotides ,Organic Compounds ,Agriculture ,Methylation ,Chromatin ,Nucleic acids ,Chemistry ,Amplified Fragment Length Polymorphism ,Malus ,Physical Sciences ,Medicine ,Epigenetics ,DNA modification ,Chromatin modification ,Research Article ,Chromosome biology ,Cell biology ,DNA, Plant ,Science ,Crops ,Biology ,Research and Analysis Methods ,Cytosine ,03 medical and health sciences ,Genetic variation ,medicine ,Molecular Biology Techniques ,Molecular Biology ,Evolutionary Biology ,Genetic diversity ,Biology and life sciences ,Population Biology ,Organic Chemistry ,Chemical Compounds ,DNA ,genomic DNA ,Pyrimidines ,030104 developmental biology ,Genetic Loci ,Genetic Polymorphism ,Gene expression ,Population Genetics ,Crop Science ,010606 plant biology & botany - 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.
- Published
- 2020