by Valeryia Aleksandrovich | Maryna Siniauskaya | Aleh Liaudanski | Yahor Mishuk | Tatjana Shatarnova |
Nina Danilenko | Oleg Davydenko | Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of
Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology, NAS, Minsk, Belarus |
Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology, NAS, Minsk,
Belarus | Institute of Genetics and Cytology, NAS, Minsk, Belarus | Institute of Genetics and Cytology,
NAS, Minsk, Belarus
Motivation and Aim: The chloroplast genome of land plants is usually conservative in
structure, but variable in sequence. Today the information about the complete plastidial
sequences is growing fast. Intraspecific diversity of organelle DNA became apparent and
possibly plays an important role in successful breeding and creation of the new varieties in
plants. Here we report about the sequencing of complete plastomes of 24 early-maturing
soybean (Glycine max (L.) Merr.) cultivars. The aim of our study was to evaluate the level of
chloroplast genomes diversity in specific group of Glycine max varieties.
Methods and Algorithms: DNA was obtained from the 7-day-old seedlings by phenolchlorophorm extraction from the chloroplast fraction, isolated by differential centrifugation.
The chloroplast DNA was then sequenced on Illumina MiSeq. The NGS data processing
algorithm included reads alignment on reference G. max plastid sequence (MW357264.1)
using Burrows-Wheeler Alignment Tool followed by converting to .bam format and sorting
with Samtools. Variant calling was performed with GATK HaplotypeCaller followed by
filtering with Bcftools.
Results: Analysis of 24 complete soybean chloroplast genome sequences demonstrated the
drastically low level of genetic diversity in studied varieties. Only 3 SSRs, 1 INDEL and 5
SNP were revealed between samples. 4 SNPs were located in coding sequences of atpB,
rps4, accD and rps3 genes. All of them were synonymic. The studied chloroplast genomes
can be subdivided into 3 haplotypes based on found polymorphisms.
Conclusion: Here we report about low level of variability in chloroplast DNA of Glycine max.
Possibly it is the result of the founder effect – evidently a narrow range of ancestors was
used while this group of varieties was created.
Acknowledgements: The study was carried out as a part of the State Scientific Research
Program «Biotechnologies» 2021–2023, Subprogram 2 «Structural and functional
genomics», assignment 2.1.3