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Genome-wide association studies of molybdenum and selenium concentrations in C. arietinum and C. reticulatum seeds

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Abstract

Chickpea is the second most important and ancient pulse crop with its use in human diet for approximately 7500 years as one of the Neolithic founder crops. Previous studies on chickpea have predominantly focused on agronomic traits, with only limited research being dedicated to developing micronutrient-rich crops over the last half century. The objectives of this study were to identify genetic variation and population structure of Cicer reticulatum (C. reticulatum) and Cicer arietinum (C. arietinum) species and reveal marker-trait associations of seed molybdenum (Mo) and selenium (Se) concentrations in seeds by genome-wide association studies (GWAS). In this study, a population of 180 individuals including 107 wild (C. reticulatum) and 73 cultivated (C. arietinum) Cicer species was used in two different locations for 2 years, and 121,840 high-quality single nucleotide polymorphism (SNP) were identified across eight chromosomes through genotyping by sequencing (GBS) analysis. GWAS was performed for 180 individuals and alternatively two subpopulations separately, and 16 SNP markers were found significantly associated with seed Mo and Se concentrations, consistently among the four environments. The results demonstrated the high potential of GWAS mapping in revealing markers associated with Mo and Se micronutrients for wild (C. reticulatum) and cultivated (C. arietinum) species.

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Acknowledgements

We would like to thank the Aegean Agricultural Research Institute for providing the seed materials. We are also grateful to Douglas R. Cook from the Department of Plant Pathology, University of California Davis for his support.

Funding

This study was funded by The Scientific and Technological Research Council of Turkey (TUBITAK) with the project number of 214O278.

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Authors and Affiliations

  1. Department of Bioengineering, Ege University, Bornova, 35100, Izmir, Turkey

    Esin Ozkuru, Duygu Ates, Seda Nemli, Semih Erdogmus, Nur Karaca, Hasan Yilmaz & Muhammed Bahattin Tanyolac

  2. Department of Soil Science, Ege University, Bornova, 35100, Izmir, Turkey

    Bulent Yagmur

  3. Department of Food Engineering, Ege University, Bornova, 35100, Izmir, Turkey

    Canan Kartal, Ozgul Ozdestan Ocak & Semih Otles

  4. Department of Filed Crops, Ege University, Bornova, 35100, Izmir, Turkey

    Muzaffer Tosun

  5. Department of Field Crops, Harran University, 63000, S. Urfa, Turkey

    Abdullah Kahriman

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  1. Esin Ozkuru
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Correspondence to Muhammed Bahattin Tanyolac.

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Fig S1

Histograms showing distribution of seed Mo concentrations for four environments: (a) Bornova 2015, (b) Bornova 2016, (c) Sanliurfa 2015, (d) Sanliurfa 2016 for Analysis (A) and Analysis (B), consisting of C. reticulatum and C. arietinum species, respectively (PNG 222 kb)

High Resolution Image (TIF 20921 kb)

Fig S2

Histograms showing distribution of seed Se concentrations for four environments: (a) Bornova 2015, (b) Bornova 2016, (c) Sanliurfa 2015, (d) Sanliurfa 2016 for Analysis (A) and Analysis (B), consisting of C. reticulatum and C. arietinum species, respectively (PNG 150 kb)

High Resolution Image (TIF 15174 kb)

Fig S3

Distribution of SNP markers over chromosomes. (PNG 317 kb)

High Resolution Image (TIF 29327 kb)

Fig S4

Dendrogram tree analysis according to Nei’s genetic distance. (PNG 885 kb)

High Resolution Image (TIF 32153 kb)

Fig S5

The relationship between 180 individuals illustrated by 3D scatter diagram of PCA analysis. (PNG 92 kb)

High Resolution Image (TIF 4683 kb)

Fig S6

Q-Q plots of (a) Mo and (b) Se concentration for 4 environmental data sets and combined analysis. (PNG 177 kb)

High Resolution Image (TIF 8216 kb)

Table S1

List of 107 C. reticulatum and 73 C. arietinum genotypes (DOCX 14 kb)

Table S2

Summary of ANOVA for Mo and Se micronutrient concentrations in chickpea seeds. (DOCX 24 kb)

Table S3

Individuals showing minimum or maximum average concentrations for Mo and Se micronutrients among all environments. (DOCX 15 kb)

Table S4

Summary of marker distribution across 8 chromosomes and unanchored scaffold. (DOCX 21 kb)

Table S5

List of thousand seed weight analysis of 180 individuals (DOCX 17 kb)

Table S6

Number of identified SNPs among four environments and combined analysis for Analysis (A), Analysis (B) and Analysis (A+B) (with threshold of FDR < 0.05). (DOCX 27 kb)

Table S7

List of P and significance values of co-localised SNPs among Analysis (A) and Analysis (A+B) (DOCX 16 kb)

Table S8

Details of BLAST analysis for identification of putative candidate gene associations. (DOCX 16 kb)

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Ozkuru, E., Ates, D., Nemli, S. et al. Genome-wide association studies of molybdenum and selenium concentrations in C. arietinum and C. reticulatum seeds. Mol Breeding 39, 46 (2019). https://doi.org/10.1007/s11032-019-0947-x

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