Transcriptomics of developing grains reveals putative candidate genes for grain zinc and iron in bread wheat cultivar Zincol-2016

A high grain zinc wheat cultivar, Zincol-2016, was released in Pakistan to mitigate mineral malnutrition. Here, we used RNAseq based approach to reveal transcriptional landscape of its developing grains, and to identify genetic variants in zinc (Zn) and iron (Fe) homeostasis genes. Differential gene expression analysis identified 8370 differentially expressed genes (DEGs) over the course of grain filling. The profiling of 265 Fe/Zn homeostasis genes revealed the homeologs of TaNAS9, TaFER1, TaNAAT2, TaDMAS, TaZIFL5-A, TaZIFL5-D, TaZIP14-B, TaNRAMP3, TaVIT1, TaPRI2-D, TabZIPF1-7B, TabZIPF1-7D, TabZIPF2-5A, and TabZIPF2-5B had increased expression in Zincol-2016 relative to other cultivars from expVIP database. The variant calling identified 358 SNPs and 34 InDels in the Fe/Zn homeostasis genes. Two of those SNPs in TaZIP14-B (TraesCS3B02G140400), and TaNAAT2-B (TraesCS1B02G300600), were associated with grain zinc and iron concentrations (GZnC and GFeC) in a diverse panel of 145 wheat cultivars. The Zincol-type alleles of both genes significantly increased GZnC and GFeC by 7.3–8.6% and 5.9–6.3%, respectively. In addition, 8 SNPs causing missense mutation and 2 InDels causing frameshift mutation were found unique to Zincol. The present study forms a basis for understanding the genetic basis of high GZnC and GFeC in Zincol-2016 and can help efforts to biofortify other wheat varieties.