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

Kirill Azarin,Maxim Makarenko,Vladimir Khachumov,Alexander Usatov,Oleg Gorbachenko,Alexey Kovalevich,Vera Gavrilova

doi:10.3844/ajbbsp.2018.39.47

Kirill Azarin, Maxim Makarenko + Show 5 more

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

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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.

Highlights

The success of a high productivity hybrids breeding with tolerant to a number of environmental factors largely depends on the genetic potential of the parental lines
About 13.2, 14.7, 9.3, 6.9 and 10.2 GB of raw DNA sequences isolated from the fertile line HA 89, CMSPET1, CMS-PET2, CMS-ANN2, CMS-MAX were obtained, respectively
The chloroplast genome consists of a circular DNA molecule, which includes a Large Single Copy region (LSC) and a small Single Copy Region (SSC) separated by two copies of Inverted Repeats (IR)

Summary

Introduction

The success of a high productivity hybrids breeding with tolerant to a number of environmental factors largely depends on the genetic potential of the parental lines. In the overwhelming majority of the analysis of genetic diversity in plants, the main emphasis is on the combination of nuclear alleles (Pervaiz et al, 2015). The potential of cytoplasmic variability and new cytoplasmic-nuclear combinations are practically not taken into account. The nuclear genome plays a significant role in the ontogenesis of plants, the effects of cytoplasmic genes has been proven both on the expression of quantitative traits so on the adaptive potential of plants to extreme environmental factors (Mashkina et al, 2010). Mitochondrial and chloroplast DNA has a much lower level of variability compared to the nuclear genome. Based on polymorphism of microsatellite loci of chloroplast genome in six Helianthus species and 46 lines of cultivated sunflower, it was demonstrated the absent cpDNA polymorphisms

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