Omics in Weed Science: A Perspective from Genomics, Transcriptomics, and Metabolomics Approaches

Abstract

Modern high-throughput molecular and analytical tools offer exciting opportunities to gain a mechanistic understanding of unique traits of weeds. During the past decade, tremendous progress has been made within the weed science discipline using genomic techniques to gain deeper insights into weedy traits such as invasiveness, hybridization, and herbicide resistance. Though the adoption of newer “omics” techniques such as proteomics, metabolomics, and physionomics has been slow, applications of these omics platforms to study plants, especially agriculturally important crops and weeds, have been increasing over the years. In weed science, these platforms are now used more frequently to understand mechanisms of herbicide resistance, weed resistance evolution, and crop–weed interactions. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding weedy traits. Although these techniques can provide robust insights about the molecular functioning of plants, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. Therefore, it is desirable to integrate the different omics technologies to give a better understanding of molecular functioning of biological systems. This multidimensional integrated approach can therefore offer new avenues for better understanding of questions of interest to weed scientists. This review offers a retrospective and prospective examination of omics platforms employed to investigate weed physiology and novel approaches and new technologies that can provide holistic and knowledge-based weed management strategies for future.

Applications of Biotechnology for Characterization of Plants and Pests as the Key Components of Plant Protection and Production Strategies: A Review

“…These include (i) OMICS in general, (ii) Genomics (iii) Transcriptomics (iv) Proteomics, (v) Metabolomics, (vi) Metagenomics, (vii) Phenomics, (viii) Bioinformatics. Van Emon, 2015;Mosa et al, 2017) increased resistance of plants to pathogens (Gomez-Casati et al, 2016), biological control of pathogens (Massart et al, 2015), Insect biology (Boerjan et al, 2012); plant defense against insects (Barah and Bones, 2015) weed science (Maroli et al, 2018) Genomics Genetic diversity (Beyrouthy et al, 2014;Doležel et al, 2014;Mosa et al, 2017), effects of climate change (Kole et al, 2015;Chown et al, 2014) Management of diseases (Klosterman et al, 2016;Tiwari et al, 2017); Plantmicrobe interactions (Imam et al, 2016) Trends in entomology Roy 2013; insect-pest management (Haymer, 2015) Weed science (Horvath, 2010), Weediness and Invasiveness (Stewart et al, 2009):…”

Omics Potential in Herbicide-Resistant Weed Management

“…Potential applications of genomics for improving applied weed control have been reviewed [5,6,27,28,83]. A striking example of technology that could advance weed management is the gene drive system [84].…”

“…Within weed science, genomics and transcriptomics have been the most utilized of the various omics techniques and are the focus of this review. Proteomics and metabolomics are also emerging as potential areas of research for herbicide resistance [2][3][4]; however, the full potential of omics techniques has not yet been realized [5].…”

The power and potential of genomics in weed biology and management

“…Later, at the WSSA meeting in 2007, an Emerging Technologies Symposium considered how advances in genomics, transcriptomics, proteomics and bioinformatics might be applied to studies of weed biology. This was followed by another WSSA symposium in 2015 on the integration of ‘omics’ approaches in weed science . Many other researchers have considered the potential of weed molecular biology and weed genomics to contribute to advances in basic and applied weed science and have called for the pooling of resources towards a community effort to generate genomic data and resources for major weed species .…”

“…This was followed by another WSSA symposium in 2015 on the integration of 'omics' approaches in weed science. 11 Many other researchers have considered the potential of weed molecular biology 12 and weed genomics [13][14][15] to contribute to advances in basic and applied weed science and have called for the pooling of resources towards a community effort to generate genomic data and resources for major weed species. 16 Detractors of weed genomics argue that existing plant model genomes should be sufficient, but this view is incorrect because there is a great diversity of weedy traits and variation in the evolutionary strategies of weeds that is not represented in wild and domesticated model plants such as Arabidopsis and rice.…”