Research Article Open Access

Comparative Analysis of the Complete Chloroplast Genome of the Alloplasmic Sunflower (Helianthus L.) Lines with Various CMS Types

Kirill Azarin1, Maxim Makarenko1, Alexander Usatov1, Vladimir Khachumov1, Alexey Kovalevich1, Oleg Gorbachenko2 and Vera Gavrilova3
  • 1 Southern Federal University, Russia
  • 2 All Russia Research Institute of Oil Crops, Russia
  • 3 N. I. Vavilov Institute of Plant Genetic Resources, Russia

Abstract

The complete chloroplast genomes of sunflower fertile line HA89 and isonuclear CMS lines with four different cytoplasmic backgrounds (PET1, PET2, ANN2 and MAX) were sequenced. A total of 451 polymorphic sites, with including 58 SSRs, 317 SNPs and 76 microindels were revealed between the fertile and CMS cytotypes. Among the alloplasmic male-sterile lines, cpDNA of CMS-MAX had the largest number of polymorphisms. The lowest number of polymorphic sites was revealed in CMS-PET1. Like as CMS-PET1, CMS-PET2 was obtained as a result of interspecific crossing between H. petiolaris and cultivated sunflower H. annuus. Nevertheless, the number of INDELs and SNPs in CMS-PET2 chloroplast genome was more than 4-fold and 6.5-fold higher than that in cpDNA of CMS-PET1. The average frequency of SNPs and INDELs in the non-genic regions and genic regions were 0.0062 and 0.0046, respectively. Increased mutation rates were found in the psbM-rpoB, rps16 intron, atpA-psbD, rps4-ndhJ and ndhc-atpE non-coding regions, as well as in the rpoC2, atpA, rbcL, ndhF and ycf1 genes. In addition to short insertions and deletions ranging from 1 to 5 bp, the relatively long INDELs (14-24 bp) unique for each CMS line were found. These insertions and deletions may be of use for PCR differentiation of the CMS lines due to differences in the amplicons length.

American Journal of Biochemistry and Biotechnology
Volume 14 No. 1, 2018, 39-47

DOI: https://doi.org/10.3844/ajbbsp.2018.39.47

Submitted On: 22 December 2017 Published On: 2 March 2018

How to Cite: Azarin, K., Makarenko, M., Usatov, A., Khachumov, V., Kovalevich, A., Gorbachenko, O. & Gavrilova, V. (2018). Comparative Analysis of the Complete Chloroplast Genome of the Alloplasmic Sunflower (Helianthus L.) Lines with Various CMS Types. American Journal of Biochemistry and Biotechnology, 14(1), 39-47. https://doi.org/10.3844/ajbbsp.2018.39.47

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Keywords

  • Complete Chloroplast Genome
  • Alloplasmic Lines
  • CMS
  • Sunflower