Precocious germination of grains on the spike, termed as Pre-Harvest sprouting (PHS), leads to yield loss and well as quality degradation. Various combinations of environmental and genetic factors may eliminate or reduce seed dormancy, resulting in seeds that germinate on the spike. PHS presents a considerable problem in regions where the wet season overlaps with the harvest season. Therefore, creating cultivars the optimal seed dormancy to prevent PHS while retaining the capacity for uniform germination in the field is pivotal for crop productivity.

Epigenetic control of PHS through AGO4_9 clade of Argonaute proteins (AGO802B in wheat and AGO1003 in barley) involved in the RdDM pathway has been reported previously in both barley and wheat. In wheat, a SINE (Short Interspersed Nuclear Elements) insertion in the 3’UTR of TaAGO802B was identified in some of the wheat varieties which could possibly correlate to the PHS tolerance in wheat. Our current work revealed that the majority of the PHS-resistance wheat varieties had this insertion while majority of the susceptible lines lacked this insertion and this suggests a possible role for SINE-element as a marker for screening wheat germplasm. Also, a haplotype identified in the HvAGO1003 gene in barley based on the Pan-genome database was confirmed in barley cultivar Flagship leading to changes in secondary structure. Gene expression study of TaAGO802B and HvAGO1003 showed significant differences between various wheat and barley varieties, respectively. DNA global methylation study conducted on a set of wheat varieties suggests a possible correlation between the presentation of the SINE element and the methylation levels. The knowledge gained in this study can be further explored to delineate the role of AGO1003 completely.