Table 1.
Ability of individual primer combinations to generate polymorphic products that distinguish the original cultivar from the in vitro generated somaclone.
Table 2.
Schema of the sample preparation for deep amplicon sequencing.
Fig 1.
Whole experimental pipeline of newly introduced approach combining MSAP and NGS techniques
Fig 2.
Pipeline for management of contigs to identify repeated polymorphic amplicons across the standard cultivars and their derived somaclones.
Fig 3.
Example of MSAP spectra showing polymorphism between standard cultivar and derived somaclonal individuals.
Top window shows MSAP spectra obtained by analysis of four different individuals of LX987 standard cultivar by using HpaII/MspI-GCAT + EcoRI-AGG (FAM) adaptors. Second window shows MSAP spectra obtained by analysis of four different individuals of AS208 “bread quality” somaclones by using identical adaptors as for the samples in top window. Third window shows MSAP spectra obtained by analysis of four different individuals of YM66 standard cultivar by using identical adaptors as for the samples in top window. Fourth window shows MSAP spectra obtained by analysis of four different individuals of AS34 dwarfing somaclones by using identical adaptors as for the samples in top window.
Fig 4.
Dendrogram showing similarity of DNA methylation landscapes between samples
Fig 5.
Extraction of contigs representing amplicons differentially appeared across the standard cultivars and their derived somaclones repeatedly for both pairs.
Table 3.
Characteristics of the repeatedly polymorphic contigs across somaclone and standard cultivar pairs.
Fig 6.
Character and frequency of repeatedly polymorphic contigs with identified role/function.