Evolution of Weediness and Invasiveness: Charting the Course for Weed Genomics

Abstract

The genetic basis of weedy and invasive traits and their evolution remain poorly understood, but genomic approaches offer tremendous promise for elucidating these important features of weed biology. However, the genomic tools and resources available for weed research are currently meager compared with those available for many crops. Because genomic methodologies are becoming increasingly accessible and less expensive, the time is ripe for weed scientists to incorporate these methods into their research programs. One example is next-generation sequencing technology, which has the advantage of enhancing the sequencing output from the transcriptome of a weedy plant at a reduced cost. Successful implementation of these approaches will require collaborative efforts that focus resources on common goals and bring together expertise in weed science, molecular biology, plant physiology, and bioinformatics. We outline how these large-scale genomic programs can aid both our understanding of the biology of weedy and invasive plants and our success at managing these species in agriculture. The judicious selection of species for developing weed genomics programs is needed, and we offer up choices, but noArabidopsis-like model species exists in the world of weeds. We outline the roadmap for creating a powerful synergy of weed science and genomics, given well-placed effort and resources.

De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms

“…With few genomic resources for weeds and little expertise to utilize the available resources among the weed science community (Stewart, 2009), discovering the molecular mechanisms underlying nontarget resistance has been extremely difficult. However, now that the genomics era has found its way to weed science, we can begin to answer fundamental questions about what makes weeds so weedy and capable of adapting to control measures and, thereby, design approaches that reduce the further evolution of herbicide resistance in weeds (Basu et al, 2004;Stewart et al, 2009) and , EPSPS gene amplification (Gaines et al, 2010(Gaines et al, , 2013Jugulam et al, 2014), and vacuolar sequestration of glyphosate (Ge et al, 2010(Ge et al, , 2012(Ge et al, , 2014; however, in the last case, the genes conferring resistance have not been identified.…”

“…One critical group of plants that has been largely overlooked in the genomics revolution consists of economically significant agricultural weeds (Stewart, 2009;Stewart et al, 2009). Weeds cause about $36 billion annual damage in the United States alone (Pimentel et al, 2000).…”

“…Horseweed (Conyza canadensis), which is in the Compositae (Asteraceae) family, was the first eudicot weedy species to evolve glyphosate resistance and is also one of the most widely distributed glyphosateresistant species in the world (VanGessel, 2001;Heap, 2014). Horseweed is a true diploid (2n = 18), with a selffertilizing mating system and the smallest genome of any agricultural weed (335 Mb; Stewart et al, 2009). We sought to describe the reference genome of horseweed in order to enable genomic approaches to elucidate the mechanism of nontarget herbicide resistance and to gain a better understanding of the evolution and spread of herbicide resistance across agricultural landscapes.…”

Propagation of goldenrod (Solidago canadensis L.) from leaf and nodal explants

“…Fundamental knowledge of the genetic underpinnings of what makes a plant a weed will provide for new management strategies to mitigate the negative effects of weedy and invasive plants on food production and habitat destruction [19,20]. Therefore, establishment of a tissue culture system could allow further molecular ecology research and genetic transformation procedures that, in the future, may help us understand genetic basis of the enhanced performance of invasive plants species and the traits that have made weeds successful colonizers and troublesome pests.…”

Does an expressed sequence tag (EST) library ofSalsola iberica(tumbleweed) help to understand plant responses to environmental stresses?

“…1 There is a growing necessity of implementing genomic and transciptomic techniques to better understand the functional genomics aspect of weeds. 2 High-throughput methods, such as genomic analyses, generate large data sets, often followed by computational methods for biological interpretation. Subsequently, Larrinua and Belmar 3 have provided an in depth review on the importance that bioinformatics has on weed science research.…”