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Deciphering the level of genetic diversity in some aegilops species using CAAT box-derived polymorphism (CBDP) and start codon target polymorphism (SCoT) markers

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Abstract

Background

Maintaining genetic diversity is of the most essential principle for a long-term conservation of plant genetic resources and could play a crucial role in their management. The genus Aegilops is one important member of wheat germplasm, and there are evidences that novel genes of this genus’ species can be studied/utilized as ideal sources for the wheat cultivar improvement. The objective of this study was to dissect the genetic diversity and population structure among a set of Iranian Aegilops using two gene-based molecular markers.

Methods and results

This study investigated the level of genetic diversity among 157 Aegilops accessions consisting of Ae. tauschii Coss. (DD genome), Ae. crassa Boiss. (DDMM genome), and Ae. cylindrica Host. (CCDD genome) belonging to NPGBI using two sets of CBDP and SCoT markers. The SCoT and CBDP primers yielded 171 and 174 fragments, out of which 145 (90.23%) and 167 (97.66%) fragments were polymorphic, respectively. The average of polymorphism information content (PIC)/ marker index (MI)/resolving power (Rp) for SCoT and CBDP markers were 0.32/3.59/16.03 and 0.29/3.01/16.26, respectively. Results of AMOVA revealed the genetic variability within species was greater than the variation observed among them (SCoT: 88% vs. 12%; CBDP: 72% vs. 28%; SCoT + CBDP: 80% vs. 20%). Based on the information obtained from both markers, the higher level of genetic diversity was found in Ae. tauschii as compared to other species. The grouping patterns obtained by Neighbor-joining algorithms, principal coordinate analysis (PCoA), and Bayesian-model-based structure were consistent with each other and resulted in grouping all studied accessions according to their genomic constitutions.

Conclusion

The results of this study revealed a high level of genetic diversity among Iranian Aegilops germplasm. Moreover, SCoT and CBDP marker systems were efficient in deciphering DNA polymorphism and classification of Aegilops germplasm.

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Data availability

The data in this manuscript are available from the corresponding author upon reasonable request.

Abbreviations

CBDP:

CAAT box-derived polymorphism

SCoT:

Start codon target polymorphism

NAF:

The number of amplified fragments

NPF:

The number of polymorphic fragments

PIC:

Polymorphism information content

Rp:

Resolving power

MI:

Marker index

PCR:

Polymerase chain reaction

PPL:

Percentage polymorphic loci

Na:

The numbers of observed alleles

Ne:

The numbers of effective alleles

I:

Shannon’s information content

He:

Nei’s gene diversity

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Authors and Affiliations

  1. Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran

    Ali Sajjad Bokaei, Omid Sofalian & Ali Asghari

  2. Seed and Plant Improvement Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran

    Behzad Sorkhilalehloo & Alireza Pour-Aboughadareh

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  1. Ali Sajjad Bokaei
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Correspondence to Alireza Pour-Aboughadareh.

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Bokaei, A.S., Sofalian, O., Sorkhilalehloo, B. et al. Deciphering the level of genetic diversity in some aegilops species using CAAT box-derived polymorphism (CBDP) and start codon target polymorphism (SCoT) markers. Mol Biol Rep 50, 5791–5806 (2023). https://doi.org/10.1007/s11033-023-08488-0

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