Candidate Gene Markers Based Molecular Characterization for Grain Zinc Concentration in Rice

Abstract

Genetic diversity in grain zinc content was assessed among thirty-five rice genotypes presumed to be biofortified, utilising candidate gene-based primers. The research also aimed to validate the effectiveness of these markers in determining the distribution of rice genotypes based on differential grain zinc accumulation. Notably, Zinco rice and R-RGY-MH-113 exhibited the highest zinc values. Fourteen candidate gene-based markers were employed for amplification, revealing a range of 1 (OsNRAM6K) to 6 (OsYSL14K) alleles per locus. The analysis resulted in a total of 54 allelic variants with certain primers such as OsZIP3K, OsZIP7K, OsYSL2K, OsNRAMP7K and OsNACK amplifying unique alleles. OsZIP5K produced two unique alleles, averaging 4.15 alleles per locus. The polymorphic information content (PIC) values were calculated to assess primer informativeness, with OsZIP7K exhibiting the highest PIC (0.7918), followed by OsZIP3K (0.778) and OsNACK (0.7755). The amplification products were scored, and the similarity matrix for all genotypes was obtained with the Dice coefficient method using NTSYSpc-2.02j. program. The similarity coefficients ranged from 0 to 0.75. Based on these coefficient values, four main clusters were obtained, consisting of fourteen, ten, five and six genotypes respectively. Cluster I & IV predominantly included superior genotypes, cluster II comprised mainly inferior genotypes and cluster III had a dominance of moderate genotypes in terms of the differential grain zinc accumulation.