Development of highly informative microsatellite markers for the genetic analysis of sunflower
Abstract
Background. The existing microsatellite loci markers, used for studying and identifying sunflower genetic diversity, have certain limitations. There is a need for new markers that will meet the following criteria: three or more nucleotides in the microsatellite motif, specificity to the target locus, and high discriminatory power.
Materials and methods. Microsatellite loci were mined using the GMATA software based on the reference genome assembly of sunflower HanXRQr2.0-SUNRISE. Loci with flanking regions were screened for the presence of copies on other chromosomes using Nucleotide BLAST, and primer pairs were designed using Primer-BLAST (NCBI). The expected polymorphism of each microsatellite locus was evaluated by aligning the predicted PCR product to other sunflower genome assemblies from the GenBank database using Nucleotide BLAST. The performance of the developed markers was tested by PCR and separation of amplification products by capillary electrophoresis under denaturing conditions.
Results. A total of 186 markers were developed. Of these, 16 were characterized by nonspecific amplification, 31 showed complete absence of amplification, 26 revealed SSR-specific artifacts, and 19 were monomorphic. The remaining 94 markers were informative and detected from 2 to 6 alleles. Among the selected sequences, simple microsatellites with trinucleotide motifs were the most prevalent. The number of markers per chromosome ranged from 2 to 19. The size range of the amplified DNA fragments was from 125 to 469 bp. A statistically significant correlation was found between the number of repeats in the microsatellite locus and the number of detected alleles.
Conclusion. The obtained data make it possible to select the most informative markers for the development of multiplex SSR assays and the establishment of an effective genotyping system for sunflower.
About the Authors
S. Z. GuchetlRussian Federation
Saida Z. Guchetl, Cand. Sci. (Biology), Head of a Laboratory
17 Filatova St., Krasnodar 350038, Russia
A. V. Golovatskaya
Russian Federation
Anna V. Golovatskaya, Associate Researcher
17 Filatova St., Krasnodar 350038, Russia
D. L. Savichenko
Russian Federation
Dmitrii L. Savichenko, Researcher
17 Filatova St., Krasnodar 350038, Russia
E. D. Loginova
Russian Federation
Elizaveta D. Loginova, Associate Researcher
17 Filatova St., Krasnodar 350038, Russia
E. I. Zhudina
Russian Federation
Elvina I. Zhudina, Analyst
17 Filatova St., Krasnodar 350038, Russia
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For citations:
Guchetl S.Z., Golovatskaya A.V., Savichenko D.L., Loginova E.D., Zhudina E.I. Development of highly informative microsatellite markers for the genetic analysis of sunflower. Proceedings on applied botany, genetics and breeding.
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