Genomic Regions, Molecular Markers, and Flanking Genes of Metribuzin Tolerance in Wheat (Triticum aestivum L.)

Abstract

Understanding the genetics of metribuzin (a group C herbicide) tolerance in wheat is vital in developing tolerant cultivars to improve wheat productivity in dryland farming systems. This study investigated metribuzin tolerance in wheat by conducting a Genome-wide Association Studies (GWAS) with a panel of 150 wheat genotypes of diverse genetic backgrounds and genotyped them with the wheat 90 K SNP genotyping assay. The phenotyping was conducted in a temperature-controlled glasshouse at the University of Western Australia (UWA). Genotypes were sprayed with a metribuzin dose of 400 grams of active ingredient (g. a.i.) ha−1 as pre-emergent in a specialized spraying cabinet and transferred to the glasshouse where the tolerance level of the genotypes was assessed by measuring the relative reduction in chlorophyll content of the leaves. The decrease in chlorophyll content of the treated plants compared to the control was regarded as the phytotoxic effects of metribuzin. GWAS analysis following a mixed linear model revealed 19 genomic regions with significant marker-trait associations (MTAs), including ten on chromosome 6A, three on chromosome 2B, and one on chromosomes 3A, 5B, 6B 6D, 7A, and 7B, respectively. Sequences of the significant markers were blasted against the wheat genome, IWGSC RefSeq V1.0, and candidate genes having annotations related to herbicide tolerance in wheat, especially in pathways reported to be involved in metribuzin tolerance, such as cytochrome P450 pathways and ATP Binding Cassette (ABC) superfamilies, were identified in these genomic regions. These included TraesCS6A01G028800, TraesCS6A02G353700, TraesCS6A01G326200, TraesCS7A02G331000, and TraesCS2B01G465200. These genomic regions were validated on 30 top tolerant and 30 most susceptible genotypes using the five closest SSR makers to the flanked SNPs. Sufficient polymorphism was detected on two markers (wms193 and barc1036) that were found to differentiate between the susceptible and tolerant alleles and a t-test analysis of the phenotypic data shows a significant (value of p < 0.001) difference suggesting that these markers can be used for marker-assisted selection (MAS) in metribuzin studies and wheat breeding programs.

Genome-wide association study of drought tolerance in wheat (Triticum aestivum L.) identifies SNP markers and candidate genes

“…4 ). A similar LD pattern for the whole genome, sub-genomes A, B, and D has been reported for the same population in a previous study (Kurya et al 2022 ). A faster LD decay in the D genome, comparable to A and B genomes was also observed in wheat pre-breeding lines (Ledesma-Ramírez et al 2019 ).…”

“…The faster LD decay suggests high levels of genetic diversity in the mapping population used in this study, which consists of lines selected from a wide range of genetic backgrounds. The high diversity of this panel has also been observed in previous studies (Kurya et al 2022 ; Liu et al 2022 ).…”

“…Navigating the trade-off between sensitivity and specificity, we selected a less strict threshold to enhance sensitivity while mitigating the risk of false negatives. This choice aligns with practices in comparable studies and is further supported by the consideration of biological plausibility (Kurya et al 2022 ; Liu et al 2022 ). Associations identified using less stringent thresholds are considered preliminary, so we recommend rigorous follow-up analyses and validation steps, including assessments in independent datasets and functional studies, to ensure a comprehensive validation process for the identified candidate markers.…”

Identification of novel genes associated with herbicide tolerance in Lentil (Lens culinaris ssp. culinaris Medik.).

“…Furthermore, Van Eerd, Hoagland, Zablotowicz, & Hall, (2003) acknowledged that this enzyme is typically associated with herbicide metabolism and plant detoxi cation. Moreover, genes encoding for ABC transporters proteins were also detected in wheat (Triticum aestivum L.) 55,56 , Arabidopsis thaliana 57 , and soybean 58 , and performed the function of detoxi cation of plants from imazethapyr and metribuzin. In this study, the HDS discerned the recovery of some accessions from phytotoxicity symptoms after imazethapyr or metribuzin treatments which might be due to the role of detoxi cation executed by ABC transporters.…”