Utilizing Short Interspersed Nuclear Element as a Genetic Marker for Pre-Harvest Sprouting in Wheat.

Pre-harvest sprouting (PHS) is a complex abiotic stress caused by multiple exogenous and endogenous variables that results in random but significant quality and yield loss at the terminal crop stage in more than half of the wheat-producing areas of the world. Systematic research over more than five decades suggests that addressing this challenge requires tools beyond the traditional genetic manipulation approach. Previous molecular studies indicate a possible role of epigenetics in the regulation of seed dormancy and PHS in crops, especially through RNA-directed DNA methylation (RdDM) pathways mediated by Argonaute (AGO) proteins. In this study, we explore the role of the gene associated with PHS resistance in wheat, through the presence of a SINE retrotransposon insertion. The current study found the SINE insertion at 3'UTR of the present in 73.2% of 41 cultivars analyzed and in 92.6% of the resistant cultivar subset. The average expression of in cultivars with the SINE insertion was 73.3% lower than in cultivars without insertion. This study also indicated a significant positive correlation between the PHS score and methylation levels in the cultivars. The resistant cultivars with the SINE insertion recorded 54.7% lower methylation levels than susceptible cultivars. Further analysis of a DH population (Sadash × P2711) reveals that SINE insertion co-segregates with PHS resistance. This sets forth the SINE insertion in as a genetic marker for screening wheat germplasm and as an efficient tool for breeding PHS-resistant wheat cultivars.