Identification of SNP Markers Associated with Iron and Zinc Concentrations in Cicer Seeds

Nur Karaca; Duygu Ates; Seda Nemli; Esin Ozkuru; Hasan Yilmaz; Bulent Yagmur; Canan Kartal; Muzaffer Tosun; Ozgul Ozdestan; Semih Otles; Abdullah Kahriman; Peter Chang; Muhammed Bahattin Tanyolac

doi:10.2174/1389202921666200413150951

Identification of SNP Markers Associated with Iron and Zinc Concentrations in Cicer Seeds

Curr Genomics. 2020 Apr;21(3):212-223. doi: 10.2174/1389202921666200413150951.

Authors

Affiliation

¹ 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA.

Abstract

Background: Cicer reticulatum L. is the wild progenitor of chickpea Cicer arietinum L., the fourth most important pulse crop in the world. Iron (Fe) and zinc (Zn) are vital micronutrients that play crucial roles in sustaining life by acting as co-factors for various proteins.

Aims and objectives: In order to improve micronutrient-dense chickpea lines, this study aimed to investigate variability and detect DNA markers associated with Fe and Zn concentrations in the seeds of 73 cultivated (C. arietinum L.) and 107 C. reticulatum genotypes.

Methods: A set of 180 accessions was genotyped using 20,868 single nucleotide polymorphism (SNP) markers obtained from genotyping by sequencing analysis.

Results: The results revealed substantial variation in the seed Fe and Zn concentration of the surveyed population. Using STRUCTURE software, the population structure was divided into two groups according to the principal component analysis and neighbor-joining tree analysis. A total of 23 and 16 associated SNP markers related to Fe and Zn concentrations, respectively were identified in TASSEL software by the mixed linear model method. Significant SNP markers found in more than two environments were accepted as more reliable than those that only existed in a single environment.

Conclusion: The identified markers can be used in marker-assisted selection in chickpea breeding programs for the improvement of seed Fe and Zn concentrations in the chickpea.

Keywords: Association mapping studies; C. arietinum; C. reticulatum; chickpea; iron; zinc.