Variability of organelle genomes in a collection of early maturing soybean varieties

Variability of the genomes of cellular organelles (chloroplast and mitochondria) is an important component of the overall variability of the plant genome. A large amount of data has already been obtained on the comparative characteristics of the organization of organelle DNA sequences for different groups of plants. This paper presents new original data on the variability of mitochondrial and chloroplast genomes in soybean (Glycine max (L.) Merr.), a crop of great economic importance widely cultivated in Central Europe, including the Republic of Belarus. Initially, we supposed that the peculiarities of soybean organelle DNA sequence or organization promote certain soybean cultivars to be the best maternal and others, alternatively, the best paternal forms. As a result of the study, new complete nucleotide sequences of chloroplast and mitochondrial genomes of 46 soybean samples were obtained by the next generation sequencing method (NGS) on the Illumina platform. A comprehensive bioinformatic comparative study of intraspecific organelle genome variability in 46 soybean varieties of diverse geographical origin was conducted. Polymorphic loci of genomes were discovered. Data on DNA variability were verified by Sanger sequencing. The spectrum of organelle DNA variability of cultivated soybean was represented by three chloroplast DNA haplotypes (C1–C3) and five mitochondrial DNA haplotypes (M1–M5). A comparatively low level of intraspecific variability of organelle genomes in G. max was revealed. The soybean chloroplast genome had a lower level of sequence variability than the mitochondrial genome. A set of DNA markers for polymorphic loci of organelle genomes was developed, allowing the differentiation of varieties of the studied group into plasmatypes. Additionally, 90 soybean samples from the collection were studied using PCR followed by Sanger sequencing. The low level of intraspecific variability of organelle genomes in G. max was confirmed on the extended group of samples. The majority of cultivars were represented by three plasmatypes – C1/M1, C2/M2 and C1/M3. 46 complete chloroplast DNA sequences have been deposited in NCBI GenBank. The hypothesis that organelle DNA influences the combining ability of different varieties has not yet been confirmed. A more detailed study of the mechanisms of nuclear-cytoplasmic interaction is required, as well as a search for nuclear markers that affect the expression of organelle genes.

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