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In-depth genome diversity, population structure and linkage disequilibrium analysis of worldwide diverse safflower (Carthamus tinctorius L.) accessions using NGS data generated by DArTseq technology

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Abstract

Safflower (Carthamus tinctorius L.) is one of the most important oilseed crops for its seed oil rich in unsaturated fatty acids. Precise utilization of diverse genetic resources is fundamental in breeding programs to improve high yield genotypes with desirable traits. In this study, for the first time we report successful application of DArTseq technology; an efficient genotyping-by-sequencing (NGS); to analysis genetic diversity and population structure of 89 safflower accessions from worldwide origins. Totally, 19,639 DArTseq markers (10,130 SilicoDArTs and 9509 SNPs) generated through DArTseq genotyping. After filtering the data, 3431 polymorphic DArTseq markers (1136 SilicoDArTs and 2295 SNPs) used for genetic diversity, population structure and linkage disequilibrium analysis in safflower genotypes. All the SilicoDArT and SNP markers showed high reproducibility and call rate. Polymorphism information content (PIC) values ranged from 0.1 to 0.5, while ≥ 0.50% of SilicoDArTs and ≥ 0.64% SNPs showed PIC values more than median. Genotypes grouping using DArTseq markers resulted in three distinct clusters. Results showed weak correlation between safflower diversity pattern and origins. Analysis of molecular variance revealed that the majority of genetic variation was attributed to the differences among varieties within cluster populations and there was no significant molecular variance between origins. However, safflower of accessions belonged to Iran, Turkey, Pakistan and India indeed appear to be genetically similar and grouped close in referred cluster, while the accessions from Near East (Afghanistan, China) being distinct. Our results were in agreement with hypothesis that safflower domesticated in somewhere west of Fertile Crescent and then expanded through Africa and Europe. Present study using a panel of globally diverse safflower accessions and large number of DArTseq markers set the stage for future analysis of safflower domestication using large germplasm from proposed domestication centers. Also, studied germplasm in this study can be used as a valuable source for future genomic studies in safflower for mapping desirable traits through genome-wide association mapping studies.

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Abbreviations

NGS:

Next generation sequencing

DArT:

Diversity array technology

SNP:

Single nucleotide polymorphism

DAPC:

Discriminant analysis of principal component

LD:

Linkage disequilibrium

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Acknowledgements

This study was supported by the Islamic Azad University, Sanandaj Branch, Iran and Sararood Dryland Agricultural Research Institute, Kermanshah, Iran.

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The author(s) received no financial support for the research, authorship, and/or publication of this article.

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Authors and Affiliations

  1. Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran

    Seyed Mohammad Reza Hassani, Reza Talebi & Farzad Fayaz

  2. Dryland Agricultural Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Kermanshah, 1164-67145, Iran

    Sayyed Saeid Pourdad

  3. Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahed University, Tehran, Iran

    Amir Mohammad Naji

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  1. Seyed Mohammad Reza Hassani
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  2. Reza Talebi
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Correspondence to Reza Talebi.

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Supplementary file1 List of SilicoDArT and SNP marker used in this study (XLSX 498 kb)

11033_2020_5312_MOESM2_ESM.xlsx

Supplementary file2 Kinship matrix for pairs of genotypes based on SilicoDArT and SNP marker calculated in TASSEL (XLSX 233 kb)

Supplementary file3 Genetic distance of genotypes based on SilicoDArT and SNP marker calculated in TASSEL (XLSX 162 kb)

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Hassani, S.M.R., Talebi, R., Pourdad, S.S. et al. In-depth genome diversity, population structure and linkage disequilibrium analysis of worldwide diverse safflower (Carthamus tinctorius L.) accessions using NGS data generated by DArTseq technology. Mol Biol Rep 47, 2123–2135 (2020). https://doi.org/10.1007/s11033-020-05312-x

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