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Development of Dof (DNA binding with one finger) transcription factor gene-specific primers through data mining as a functional marker and their use for genetic diversity study in barley (Hordeum vulgare L.) germplasm

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Abstract

The genetic diversity among Hordeum vulgare L. species were assessed based on PCR amplification pattern derived from 75 set of Dof domain and Dof genes specific primers. Multiple bands showing variability in terms of both number and sizes of bands ranging from 0.1 to 3.0 kbp were observed. Out of a total of 2449 bands, 2328 polymorphic and 121 monomorphic bands were obtained and the percentage of polymorphism ranged from 70.27 to 100%. A very high degree of polymorphism was observed with all the primers except HvDof3, HvDof4, HvDof10, HvDof16, HvDof18, HvDof18, HvDof24, Dof4, Dof11, Dof13, Dof15, Dof16, Dof19, Dof20, Dof21, Dof22, Dof23, Dof28, dof38, sbDof23 and sbDof24 primers. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard’s similarity coefficient matrix. According to results, the genetic resources and diversity in barley germplasm of H. vulgare were rich. The number of polymorphic fragments per primer detected ranged from 11 to 56 bands with an average of 32.65 bands. Average polymorphic information content (PIC) was 0.81 in overall Dof domain and gene specific primers. HvDof 39 showed the highest PIC (0.99) which can be a good candidate primer to verify genetic diversity in H. vulgare. The unweighted pair-group method of the arithmetic average and principal coordinate analysis showed a clear distinction among the genotypes and the genotypes divided into three clusters in the dendrogram results. A model-based structure analysis revealed the presence of three groups. The study showed that genetic variation and population structure are determined among the species of H. vulgare collected from different geographical origins.

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Abbreviations

Dof:

DNA-binding with one zinc finger

TFs:

Transcription factors

PIC:

Polymorphism information content

HS:

Within accession diversity

HT:

Total gene diversity

UPGMA:

Unweighted pair group method with arithmetic average

Na:

Observed alleles

Ne:

Effective alleles

SI:

Shannon’s information index

D:

Genetic distance

I:

Genetic identity

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Acknowledgements

The authors wish to acknowledge Shahid Chamran University of Ahvaz, Iran for providing financial support for research and development in faculty of Agriculture (Grant No. SHU/FAG/1394). We thank the Institut für Pflanzengenetik und ulturpflanzenforschung (IPK) OT Gatersleben Corrensstraße 3 06466 Stadt Seeland (http://www.ipk-gatersleben.de), Germany; for providing Hordeum vulgare species. We also thank the two anonymous reviewers for their constructive suggestions that greatly helped to improve the manuscript.

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  1. Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box. 61355/144, Ahvaz, Iran

    Sahar Rouhian, Daryoush Nabati Ahmadi & Karim Sorkheh

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Sahar Rouhian, Daryoush Nabati Ahmadi, and Karim Sorkheh have contributed equally to this work.

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Rouhian, S., Ahmadi, D.N. & Sorkheh, K. Development of Dof (DNA binding with one finger) transcription factor gene-specific primers through data mining as a functional marker and their use for genetic diversity study in barley (Hordeum vulgare L.) germplasm. Genes Genom 39, 567–579 (2017). https://doi.org/10.1007/s13258-016-0510-7

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