Bioinformatic identification and expression analysis of microRNAs involved in grain development of Iranian wheat cultivars with different bread-making quality

The bread wheat (Triticum aestivum) quality is highly dependent on the presence and composition of the gluten proteins in the grain. In this research, bread-making quality of four Iranian bread wheat cultivars (Morvarid, Sardari, Parsi, and Sepahan) was ranked from the highest to lowest based on farinographic and chemical analyses of the wheat flour and bread specific volume. To identify and compare miRNAs involved in grain development between Iranian wheat cultivars with good and poor bread-making quality, RNA-seq data of seven wheat cultivars (four cultivars with good quality and three with poor) at two grain developmental stages were downloaded and analyzed from the NCBI database. Five conserved miRNAs were selected from the identified miRNAs and their expression pattern at two grain developmental stages (10 and 20 days after anthesis) were evaluated in four Iranian wheat cultivars using Real Time PCR. The results showed that the expression pattern of miR159a, miR164a, miR172a and miR827a during grain development in all studied cultivars had an increasing trend, while the expression pattern of miR396c showed a decreasing trend. miR164a and miR396c showed the highest and lowest relative expression in Sepahan and Morvarid (with the lowest and highest 1000-grain weight), respectively, which can be due to their negative regulatory roles on grain size. Also, with increasing the baking quality of the studied cultivars, the relative expression of miR159a and miR172a involved in the synthesis of starch and grain storage proteins, respectively, reduced and the expression of miR827a involved in the remobilization of nitrogen from leaves to grains, increased indicating negative effects of miR159a and miR172a and positive effect of miR827a on the bread-making quality of wheat cultivars.