Tomato For Nightshades
Tomato (Solanum lycopersicum) is a member of the dicot family Solanaceae, which contains valuable vegetable species such as potato (Solanum tuberosum), tobacco (Nicotiana tabacum), eggplant (Solanum melongena), and pepper (Capsicum annuum), and important weeds such as nightshades (Solanum ssp.), horse nettle (Solanum carolinense), Jerusalem cherry (Solanum pseudocapsicum), and tropical soda apple (Solanum viarum). Despite differences in genome sizes among Solanaceae members, most species possess the same chromosome number of 12 (2n = 24).
The haploid genome size of tomato (Figure 4.1) is 953 Mb, which is among the smallest in the Solanaceae family (Arumuganathan and Earle 1991b). Tomato was considered to be an ideal model of the Solanaceae family because it has a relatively small genome, short generation time, and routine methods for Agrobacterium-mediated transformation. Also, there are ample genetic and genomic resources available including high density genetic maps (Fulton et al. 2002) and more than 200,000 expression sequence tag (EST) accessions (http://plantta.tigr. org/). Commercially available microarrays from various solanaceous species are available, and studies testing the applicability of potato microarrays to study gene expression in other solanaceous species proved successful (Rensink et al. 2005). This suggests that these tools could be used to characterize gene expression in solanaceous weeds.
Nightshades (Solanum spp.) (Figure 4.2)are annual to short-lived perennials in the Solanaceae family. Black nightshade (S. nigrum L.) is the best known noxious weed among nightshade species (Ogg et al. 1981; Defelice 2003) and is reported as a weed in more than thirty-seven crops and sixty-one countries around the world (Holm et al. 1991). Nightshades, in general, reproduce by seeds. Berries can contain fifteen to ninety- six seeds and a single plant can produce up to 30,000 seeds in a single season. Seeds remain viable after years in the soil seed bank and can germinate intermittently under favorable conditions (Defelice 2003). Nightshades also are toxic, compete with crops, impede harvest, and reduce crop quality by seed discoloration (Cooper and Johnson 1984; Lampe and McCann 1985). In addition, some nightshades have evolved resistance to photosystem II and ALS inhibitors, and bipyridiliums (Heap 2008).
Black nightshade is a hexaploid with a chromosome number of 2n = 72. Eastern black nightshade (S. ptycanthum), however, is common to the U.S. and is a diploid species with a chromosome number of 2n = 24, the same as tomato. It is possible that transformation systems developed for the various solanaceous crops could be used to transform nightshades. Also, given the sequence similarity of many genes from solanaceous crops, identifying and cloning genes of interest within the nightshades should be relatively efficient. Furthermore, most of the markers developed for mapping in tomato should be useful for mapping in the nightshade complex. Therefore, tomato resources might be of great assistance to study weedy characteristics of eastern black nightshade and other nightshade species.
Besides being an important weed with several characteristics that might make it a suitable model species, nightshades have several particularly weedy traits that could be studied using resources developed from tomato. For example, some nightshade species are annuals, while other closely related sub- species are perennials (Hobbs et al. 2000) . Some closely related nightshades also have different invasiveness characteristics (John Masiunas, personal communication). Direct comparison of related varieties of nightshade using tomato microarrays could identify the mechanisms by which the species has developed perennial growth patterns and potentially identify genes involved in different levels of invasiveness. Likewise, markers developed for tomato could allow mapping of genes and quantitative trait loci (QTL) that influence invasiveness and perennial growth.
Cultivated wheat (Triticum aestivum) (Figure 4.3) is the most widely grown crop in the world. It is an allohexaploid species with three homeologous genomes (2n = 6x = 42; AABBDD). The genome sizes of wheat are 17,000 Mb (Bennett and Smith 1976), and more than 80% of
Figure 4.1. Tomato (Solanum lycopersicum).
Figure 4.3. Cultivated wheat (Triticum aestivum).
the genome is repetitive noncoding DNA (Smith and Flavell 1975). The large genome size, combined with the high percentage of repetitive DNA, makes comprehensive sequencing of the wheat genome extremely challenging. However, there are rich genomic resources for wheat, as more than 850,000 ESTs are in dbEST (http://wheat.pw.usda.gov/genome/), which provides direct information on the mature transcripts for the coding portion of the genome. In addition, more than 20,000 EST loci have been mapped on the twenty-one chromosomes (http:/ www.ncbi.nlm.nih.gov/dbEST).
In addition to these resources, hundreds of aneuploid (one or a few chromosomes above or below the haploid number) stocks have been developed owing to the homoeology existing among the three component genomes, which allows various aneuploidy to be tolerated. Wheat aneuploid stocks include monosomic (loss of one chromosome), nullisomic (loss of a chromosome pair), trisomic (three chromosomes instead of two for a given pair), tetrasomic (four chromosomes instead of two for a given pair), and telosomic lines (half of a pair of chromosomes is missing). These lines are valuable tools for the construction of a molecular map of wheat (http://www.jic.ac.uk/GERMPLAS/prec_ce/).
In 2005, the International Wheat Genome Sequencing Consortium (IWGSC) was established to facilitate and coordinate international efforts toward obtaining the complete sequence of the common wheat genome, and the French National Institute for Agricultural Research (INRA) led the project to sequence the largest wheat chromosome (3B) based on a chromosome i specific approach (Leroy et al. 2006). Transformation protocols also exist for wheat (Jones 2005). Many of these resources can be used to study a serious weed, jointed goatgrass (Aegilops cylindrical Host).
Jointed goatgrass (Figure 4.4) is a winter annual grass; it spreads exclusively by seed. Jointed goatgrass is found in most major U.S. winter wheat (Triticum aestivum) production regions and has infested more than 5 million acres of winter wheat cropland. Total losses from jointed goatgrass infestation in the western U.S. annually exceed $145 million (Westbrooks 1998). Jointed goatgrass seeds are similar in size and shape to wheat seeds, making them difficult to separate from one another. Jointed goatgrass seeds are dormant after shattering, require after-ripening to germinate, and remain viable for three to five years in the soil seed bank (Donald and Ogg 1991i . Few, if any, herbicides can selectively control this weed in winter wheat because of species similarity (Seefeldt et al. 1998; Zemetra et al. 1998). These characteristics make crop protection extremely difficult and therefore herbicide-resistant transgenic wheat has been considered (Anderson et al. 2004 ). However, inter-specific hybridization between these species occurs and would likely result in herbicide-resistant jointed goatgrass (Seefeldt et al. 1998; Zemetra et al. 1998; Hanson et al. 2005). Jointed goatgrass is an allotetraploid and shares the D genome with winter wheat (Donald and Ogg 1991). It is thus a competitive weed that mimics the life cycle of wheat. However, this feature also allows for the utilization of wheat genomics resources for goatgrass genomics research.
Goatgrass also has some characteristics that might make it an excellent model weed. For example, goatgrass is a grassy weed that is easily propagated and manipulated in the green-
house. Because it is so similar to wheat, it could serve as the model for evolution and selection in crop mimicry. Also, since its seed dormancy is one of the characteristics that contributes to difficulty of control, resources and studies on wheat seed dormancy and pre-harvest sprouting could be directly applicable to goatgrass and vice versa.
Rice (Figure 4.5) is one of the world's most important cereal crops. It belongs to the Poaceae family which includes cereals, turf, and many serious weeds. Rice contains 389 Mb per haploid genome (IRGSP 2005), which is the smallest among all the cereal crops and only three times larger than the Arabidopsis thaliana genome. Rice can be transformed routinely using Agrobacterium. More than 400,000 rice ESTs and 32,000 full-length cDNA clones are deposited in dbEST (Vij et al. 2006). Microarray chips are commercially available (Meyers et al. 2004; Rensink and Buell 2004). These features make rice an excellent genetic model for cereal crops and grasses. The map-based, whole genome rice (Oryza sativa ssp. japonica cv. Nipponbare) sequence was reported by IRGSP in 2004 (http://rgp.dna.affrc.go. jp/IRGSP/celebrates/celebrates.html), which has had a profound impact on rice and cereal grass research.
Figure 4.5. Rice (Oryza sativa subspecies indica).
With completion of the rice genome, about 19,000 simple sequence repeat (SSR) markers have been identified and are publicly available (Vij et al. 2006), which will aid marker-assisted breeding and map -based gene cloning of related weed species. These resources ultimately allow scientists to create more desirable rice genotypes, e.g., disease- and stress-resistant, more nutritious, and varieties that are more resistant to pests. In the perspective of weed research, all these resources can be directly applied to investigate a serious annual weed, weedy rice (Oryza sativa L.).
Weedy (red) rice (Figure 4.6) is an important annual weed worldwide, especially in cultivated rice. Weedy rice could be used to investigate most of the characteristics in the above box, Characteristics Of Weeds That Might Be Considered In Selection Of A Model Experimental System. Weedy rice has been used to examine physiological, biochemical, and genetic aspects of seed germination, dormancy, and after-ripening (Leopold et al. 1988 - Footitt and Cohn 1995; Gu et al. 2004), crop interference (Diarra and Talbert 1985), allelopathy (Duke et al. 2003), gene flow between crops and weeds (Gealy et al. 2003), rhizomatousness (Hu et al. 2003), and other weedy related traits (Gu et al. 2005).
Topics of recent interest include domestication of cultivated rice (Bres-Patry et al. 2001), weedy traits such as shattering and dormancy (Cai and Morishima 2000, Gu et al. 2005 ), and gene flow from cultivated rice to weedy rice (Chen et al. 2004). One important motivation for using weedy rice as a model system is that map-based cloning of seed dormancy genes is possible because of the ample available genomic resources in cultivated rice, which is the same species as weedy rice. In fact, currently a dormancy gene, qSD7-1, has been cloned from the weedy rice based on the rice genomics information (Gu et al. 2006, 2007), providing
a good example of using the resources of a model crop in weed research. In this instance, cloning of qSD7-1, the gene encoding a transcription factor which underlies a QTL previously shown to have pleiotrophic effects on dormancy, red pericarp color, and grain weight, would have been very difficult without the assistance of rice fine maps and whole genome sequence.
Sorghum (Sorghum bicolor) is the world's fifth most important cereal crop, following wheat, rice, maize, and barley. The Sorghum genus also includes one of the world's most noxious weeds, Johnsongrass (Sorghum halepense) (Figure 4.7) . Sorghum grows well on marginal lands and can endure both drought and waterlogging (Smith and Frederiksen 2000) , both environments in which weedy species are well adapted (See the box entitled Characteristics Of Weeds That Might Be Considered In Selection Of A Model Experimental System). The sorghum genome is denoted by more than 200,000 ESTs, representing a 22,000 unigene set. In addition, many physical and genetic maps and large bacterial artificial chromosome (BAC) libraries are available (Sorghum Genomics Planning Workshop Participants 2005). The genome size of sorghum ranges from 700 Mb to 772 Mb (Arumuganathan and Earle 1991a; Peterson et al. 2002). Large-scale shotgun sequencing of sorghum was started at the end of 2005 and
completed in 2007 (http://www.phytozome.net/sorghum). These genomic resources are excellent tools to study the weedy characteristics of Johnsongrass.
Johnsongrass is a perennial, and a serious weed within the Poaceae family. Holm (1969) listed Johnsongrass as one of the ten worst weeds in the world. It is a noxious or prohibited weed in twenty-two U.S. states (http://invader.dbs.umt.edu/Noxious_Weeds/noxlist.asp last accessed September 25, 2007). Johnsongrass can interfere with the production of crops such as cotton (Gossypium spp.), corn (Zea mays), sorghum, soybean (Glycine max), and sugarcane (Saccharum officinarum) (CABI 2004a) . It reproduces through seeds and rhizomes. A single plant can produce more 28,000 seeds per year (Monaghan 1979), which remain viable and germinate intermittently for as long as six years (Leguizamon 1986). Johnsongrass can produce 8 kg fresh weight and 70 m of rhizomes, per plant, in a single growing season (Monaghan 1979), and this vigorous rhizome system can be spread effectively by tillage. Paterson et al. (1995) identified QTLs affecting rhizomatousness and tillering using progenies from the cross between S. bicolor and S. propinquum. To date, Johnsongrass has evolved resistance to several groups of herbicides: ACCase and ALS inhibitors, dinitroanilines, and others (Heap 2008). The ability to overcome herbicidal control poses a great threat to crop production. Sorghum halepense has a chromosome number of either 2n = 20 (diploid) or 2n = 40 (tetraploid). Johnsongrass, the tetra-ploid species found in the U.S., contains 1,617Mb per haploid genome (Bennett and Leitch 2003). The species likely originated from naturally occurring crosses between Sorghum bicolor (2n = 20) and Sorghum propinquum (a grassy weed, 2n = 20) (CABI 2004a). Consequently, because of its close relationship to cultivated sorghum and growth habits, Johnsongrass makes a good model weed for studying perennial growth, and vegetative reproduction in grassy weeds. Rudimentary genomics tools are available for this weed. For example, 1,200 ESTs were generated from a rhizome cDNA library of Johnsongrass (http://fungen.org/Index.htm).
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