Genes, mechanisms and novel EST-SSR markers associated with metribuzin tolerance in wheat (Triticum aestivum L.): targets for improving photosynthetic capacity and yield

<title>Abstract</title> Background Weed infestation is one of the major yield-reducing factors in wheat in dry-land farming. Metribuzin is a broad-spectrum herbicide which allow effective weed management in wheat but the narrow safety margin results in crop damage decreasing grain yield. Improving our understanding of the genetic and genomic basis for metribuzin tolerance opens the potential to enhance herbicide tolerance and better productivity in wheat. The present investigation examines the genes involved in regulation of metribuzin tolerance including genetic/signalling pathways, transcription factors, phytohormones, and gene based EST-SSR markers related to photosynthesis and metabolic detoxification. Results Transcriptome sequencing of most diverse genotypes using high throughput NovaSeq 6000 RNA-Seq platform identified a total of 77,443 genes, of which 59,915 were known genes and 17,528 were novel genes. The integrative analyses of the expression profiles of genes and pathways at 0 h, 24 h and 60 h herbicide exposure indicated that modulation of reactive oxygen species (ROS) homeostasis and endogenous increase of light-harvesting chlorophyll (<italic>Lhc)</italic> a/b-binding proteins, PSII stability factor HCF136, metabolic detoxification enzymes (peroxidase, cytochrome P450, glycosyltransferase, glutathione transferase, oxidoreductase), and glucose metabolism conferred metribuzin tolerance in wheat. The validation of DEGs related to photosynthesis (<italic>Lhc a/b-</italic>binding proteins and PSII stability factor HCF136) and metabolic enzymes (cytochrome P450, peroxidase) using RT-qPCR confirmed their responsiveness to metribuzin. Over-expression of transcription factors MYB, AP2-EREBP, ABI3VP1, bHLH, and NAC played a significant roles in regulating photosynthetic and ROS scavenging activities during metribuzin stress. Transcripts with significant enrichments (q-value &lt; 0.05), related to photosynthesis and metabolic detoxification revealed 114 EST-SSRs which may be used as bio-markers. Conclusions The integrative analyses of the data suggests that high amount of sugars, modulation of ROS homeostasis and enhanced photosynthetic activity play a significant role in regulating metribuzin tolerance in wheat. Our data identified master regulators controlling metribuzin tolerance that provide promising avenues for wheat industry.