Annotation of the Affymetrix ® soybean GeneChip in relation to gene pathway analyses.
1. Introduction
A variety of plant parasitic nematodes (PPNs), including the soybean cyst nematode (SCN), elicit the initiation, development and maintenance of a specialized nurse cell from which they derive their nutriment (Figure 1). Remarkably, during parasitism by the PPN, the nurse cell survives the apparently significant resource drain on the root cell that would be expected to detrimentally impact normal physiological processes of the cell. This outcome indicates that the nematode has developed a well tuned apparatus to ensure that the root cell does not collapse and die during parasitism. In contrast, in the soybean-SCN pathosystem, the nurse cell and sometimes the surrounding cells are the sites of the defense response to the parasite (Ross, 1958; Endo, 1965). Therefore, plants have in place a mechanism to overcome the influence of the activities of the nematode. Identifying the factor(s) is of utmost importance in developing resistance to PPNs.
1.2. History
Documented accounts reveal that soybean has been in cultivation for thousands of years (Hymowitz et al. 1970), beginning in Asia perhaps as early as 3,500 B.C. (Liu et al. 1997). While the natural range of soybean is East Asia, after thousands of years of cultivation a true understanding of its native range is complicated at best. However, the extensive range of wild soybean and obvious differences in its growth habit indicates that while environmental cues may be responsible for changes in soybean and plant growth habit in general (Garner Allard 1930; Chapin III et al. 1985; Day et al. 1999), genetic variation that exists in wild populations is of significant benefit to agriculture for production purposes and developing resistance to its many pathogens. This assessment is particularly true for soybean and its most significant pathogen, SCN, as many ecological collections have resulted in the identification of naturally occurring resistance (Ross and Brim, 1957; Ross, 1958; Epps and Hartwig, 1972; Concibido et al. 2004; Ma et al. 2006; Li et al. 2011; Matsye et al. 2012).
While knowledge of soybean’s cultivation is long and extensive, scientific information on its dominant pathogen, the SCN, began with its description (Ichinohe, 1952). However, reports going back as early as the 1880’s (Noel 1992) and late 1930s (Ichinohe, 1961) reveal knowledge of the nematode and appreciation of its pathogenic capacity. The SCN is a devastating pathogen that causes approximately 7-10% production loss, worldwide, annually and suppresses seed yield more than any other single soybean pathogen (Wrather et al. 1995, 2001a, b, 2003, 2006; Pratt and Wrather, 1998). In contrast, in some fields, as much as a 15% loss in yield has been observed with no visible signs of disease on soybean (Wang et al. 2003). Observations such as these could complicate SCN management since the disease can occur without knowledge of it being present in a particular field.
The near perfect overlap of the agricultural range of soybean with the distribution of SCN, infection creates a scenario where there is a high probability of a widespread and significant effect on yield. Conservative reports have shown that there is approximately 1.1-1.5 billion dollars in agronomic losses, annually, worldwide (Wrather et al. 2001). The overlapping distribution of SCN with that of soybean production was not always the case. Historically, SCN was not found in the U.S., or likely even North America or the New World. That situation changed when the SCN was first identified in the U.S. in North Carolina in 1954 by Winstead et al. and published a year later (Winstead et al. 1955). Unfortunately for agriculture, SCN is readily transmissible as evidenced by its identification in localities as far away as Mississippi only a few years later by 1957 (Spears, 1957). The SCN now is a registered invasive species in the U.S. Notably, in the U.S., SCN causes more agricultural loss to soybean than the rest of its pathogens combined (Wrather et al. 2001, 2006). Making the problem worse for agriculture is the genetic diversity of the SCN (Golden et al. 1970; Riggs and Schmidt 1988; 1991; Niblack et al. 2002; Bekal et al. 2008). SCN research has determined that the nematode is a species complex originally subdivided into four races (Golden et al. 1970) which later was expanded into 16 races (Riggs and Schmidt 1988, 1991) that have been reorganized, further subdivided and reclassified into distinct populations (Niblack et al. 2002; Niblack and Riggs, 2004). The term population was designated since genetically pure clones are impossible to obtain in the sexually reproducing SCN system (Niblack et al. 2002). The classification scheme of Niblack et al. (2002) is based on the varying ability of SCN populations to infect a panel of 7 soybean genotypes that can resist infection to varying levels. It is noted that some of these designated populations are “strains” that are maintained in the greenhouse and genetically purified through hundreds of generations of single cyst descent (Niblack et al. 1993). Therefore, the genetic background in these “strains” may not resemble the original field-extracted population since allelic forms of the parasitism genes would likely be lost through this purification process.
The genetic diversity found in SCN (Golden et al. 1970; Riggs and Schmidt 1988; 1991; Niblack et al. 2002; Bekal et al. 2008) likely aids in its ability to infect and reproduce on plants other than soybean. Thus, from an ecological standpoint, SCN could pose a threat to plants that grow outside of production areas. This potential problem would be exasperated if those plant species are listed as endangered or threatened species or are a significant component of the ecological community. A number of studies have shown that the SCN reproduces on at least, but certainly is not limited to, 97 legume and 63 non-legume hosts (Epps and Chambers, 1958; Riggs and Hamblen, 1962, 1966a, b) and new SCN hosts are determined on a regular basis (Creech et al. 2006). It has been many years since species range tests have been performed for SCN so it is likely that these lists of hosts are not comprehensive. This virulence capability of SCN poses a problem in terms of its management since SCN populations could be maintained by weedy plants that grow or overwinter in fallow fields or along the boundaries of acreage that is in production (Creech et al. 2006). In addition to these problems, SCN does not even have to reproduce in the plant to still cause damage to the plant. While the genetic diversity of both soybean and SCN may appear to complicate an understanding of the process of infection and the development of resistant cultivars, the natural variation in both the germplasm of soybean (Doyle et al. 1999) and SCN (Bekal et al. 2003; 2008) presents many opportunities to understand the basic machinery of infection of the SCN and the genotype-specific nuances that regulate both susceptibility and defense. These features make the soybean-SCN pathosystem an extremely valuable experimental model (Barker et al. 1993; Opperman and Bird, 1998; Niblack et al. 2006; Klink et al. 2010a).
1.3. Methods to control SCN infection
Historically, SCN has been managed through a combination of chemical control, cropping systems, biological control and the identification and use of resistant germplasm. Chemical control for pathogens using methyl bromide first occurred in France (Schneider et al. 2003; Rosskopf et al. 2005) and had subsequently been used for decades for both pre- and post plant nematode control. However, methyl bromide is a chemical that has been phased out of use in 2005 in the U.S. (Schneider et al. 2003; Rosskopf et al. 2005) because it has been classified as a Class 1 (Group VI) stratospheric ozone depletor by the Environmental Protection Agency. Because of the loss of this major control agent for the SCN, even in developing countries by the year 2015 (Rosskopf et al. 2005), it was important to identify other strategies that could be included in the SCN management plan. Biocontrol measures that include bacteria, fungi or even their proteins are feasible (Chen and Dickson, 1996; Kim and Riggs, 1991, 1995; Liu and Chen, 2001; Meyer and Huettel, 1996; Meyer and Meyer, 1996; Timper et al., 1999). Other control methods that had already been used extensively for decades include the time honored crop rotation strategy. This strategy has reduced SCN populations below damaging levels (Francl and Dropkin, 1986; Sasser and Uzzell, 1991; Koenning et al. 1993). Rotating with nonhosts over a 2-3 year period mitigated the undesirable levels of SCN in the field (Ross, 1962; Francl and Dropkin, 1986). Other cropping systems that have had success in SCN control are the use of blending, resistant cultivars and cropping sequence, among others (Niblack and Chen, 2004). While successful, a problem with cropping strategies is that the interval is not long enough to compete with the 9 year cycle that cysts can remain viable, but dormant in production fields (Inagake and Tsutsumi, 1971). With these strategies in place it is possible to develop a tightly managed regime, incorporating some or all of these technologies and principles to mitigate SCN damage. Lastly, genetic engineering has begun to take root with potential as a method to generate resistance (Steeves et al. 2006; McLean et al. 2007; Klink et al. 2009a; Matsye et al. 2012). However, for genetic engineering to be successful, it is first required that candidate genes be identified. The identification of these genes has happened through a series of RNA gene expression studies, employing soybean germplasm that exhibits resistance to SCN.
1.3.1. Available resistant germplasm
Once SCN was identified in the U.S. (Winstead et al. 1955), a very large need existed to determine if soybean germplasm existed that could resist infection. The vast and expansive range of soybean (Morse, 1927) and visually obvious variations in growth form in its various ecological habitats provided the possibility that germplasm that was resistant to SCN existed in its wild populations. Established in 1898, the development of a substantial and publically available seed bank was initiated that is maintained by the USDA-National Plant Germplasm System (USDA-NPGS) (Morse, 1927; Bernard et al. 1987). It now contains approximately 20,000 varieties (accessions) with each accession classified as a plant introduction (PI) through a numbering system. Many of the 7,867 PIs that were already available by 1944, just 10 years before the identification of SCN in the U.S., had been collected in trips to China, Japan, India and Korea in a small window of time between 1924 and 1932 (Bernard et al. 1987). The public availability of the germplasm allowed it to be used in a series of trials to determine if any of the available accessions was resistant to SCN. A number of accessions were determined to be resistant to SCN through two large trials that studied about 5,700 accessions (Ross and Brim, 1957; Ross, 1958; Epps and Hartwig, 1972). Research on these accessions has resulted in the identification of approximately 118 sources of resistance (Concibido et al. 2004). However, only approximately seven sources are used for cultivar development in the U.S. (Shannon et al. 2004). These accessions include the
1.4. Cytological reaction during resistance
The SCN can remain viable in the soil in eggs ensheathed within the carcass of the dead mother (cyst wall) for up to 9 years (Inagake and Tsutsumi, 1971). However, the devastating interaction of the SCN with soybean begins when it burrows into the root through the epidermal and cortical cells. This has been shown both by cytological studies and gene expression studies of time points collected before the formation of syncytia (Alkharouf et al. 2006; Klink et al. 2009b). The interaction continues through the initiation and subsequent formation a multinucleate nurse cell known as a syncytium from pericycle or neighboring cells (Ross, 1958; Endo, 1964, 1992). The formation of the syncytium is likely to be a very coordinated process, occurring through the injection and subsequent activity of nematode parasitism proteins (Atkinson and Harris, 1989; Smant et al. 1999; Lambert et al. 1999; De Boer et al. 1999, 2002; Wang et al. 1999, 2001, 2003; Gao et al. 2001, 2003; Bekal et al. 2003). These substances likely orchestrate successive waves of interference of the root cell’s normal physiological processes and initiate various cell wall dissolving events (Atkinson and Harris, 1989; Smant et al. 1999; Wang et al. 1999, 2001, 2003; Lambert et al. 1999; De Boer et al. 1999, 2002; Gao et al. 2001, 2003; Bekal et al. 2003). The parasitism process merges approximately 200-250 root cells into a common cytoplasm containing as many nuclei, the definition of a syncytium (Jones and Northcote, 1972; Jones, 1981). Additional nematode activities alter the plant cell’s physiology (Klink et al. 2005, 2007a; Ithal et al. 2007). The activities benefit the nematode during the sedentary period of its life cycle as they feed and mature (Edens et al. 1995; Hermsmeier et al. 1998; Mahalingam et al. 1999; Vaghchhipawala et al. 2001; Klink et al. 2005, 2007a; Alkharouf et al. 2006; Ithal et al. 2007; Matsye et al. 2011).
Cytological studies of the SCN infection process (Figure 1) have shown that the cellular response of soybean to SCN infection can be divided into an earlier phase (phase 1) and a later phase (phase 2) (Ross, 1958; Endo, 1964, 1965, 1991; Riggs et al. 1973; Kim et al. 1987; Mahalingam and Skorpska, 1996). Phase 1 and 2 span the periods including the initiation, development and maintenance of the syncytium (Figure 1). These observations are not unique to SCN since similar observations have also been made for the cyst nematode
During phase 1, the cellular reactions leading to susceptibility or defense appear the same at the cytological level. The cellular events occurring during the earlier stages of syncytium development include hypertrophy, the dissolution of cell walls, the development of dense cytoplasm, an enlargement of nuclei and an increase in endoplasmic reticulum (ER) and ribosome content (Endo, 1964, 1965; Riggs et al. 1973; Kim et al. 1987; Kim and Riggs, 1992; Mahalingam and Skorpska, 1996). The enlargement of nuclei and increase in ER and ribosome content indicate an increase in gene expression and protein synthesis accompanies the activity of the nematode within the parasitized cells. Therefore, it is likely that the plant cell is being programmed to make specific materials to benefit the nutritional needs of the nematode. It is known that plant parasitic nematodes lack the ability to make materials such as sterols (Chitwood and Lusby, 1990). Therefore, altering the metabolism of the parasitized cell probably would involve the induction of metabolic activity that relates to these processes. Cell fate mapping experiments have demonstrated the metabolism that occurs during these stages of parasitism and some of it relates to enhanced plant sterol production (Klink et al. 2011a; Matsye et al. 2011).
After these earlier events, the cytology of susceptibility and defense become apparent and is referred to as phase 2. Phase 2 of the susceptible reaction is characterized by hypertrophy of nuclei and nucleoli. This process is accompanied by the reduction and dissolution of the vacuole. The reduction and dissolution of the vacuole suggests important events or structural features involved in membrane fusion and/or maintenance are perturbed. This topic will be described in a later section. Other cellular events that have been identified during the susceptible reaction include cell expansion as it incorporates and fuses with adjacent cells (Endo and Veech 1970; Gipson et al 1971; Jones and Northcote, 1972; Riggs et al. 1973; Jones, 1981). Additional activities include the proliferation of cytoplasmic organelles.
In contrast, the cellular aspects of the defense responses occurring during phase 2 depend on the soybean genotype being infected. Information that has been generated through a number of cytological studies have resulted in the development of a system that divides the PIs into cohorts having similar cytological reactions that is based on the cellular characteristics associated with how SCN responds during resistance (Colgrove and Niblack, 2008). Currently, the PIs have been categorized into those genotypes having the
1.5. Genomics-based studies of SCN
A number of “omics” studies in the soybean-SCN pathosystem have been performed to understand both plant and nematode gene expression at the organismal level. Many of the gene expression studies that relied on the microarray technology were modeled after earlier experiments that were performed in the model plant
The parasitism of soybean by SCN begins with and is sustained through the injection of materials that are synthesized in subventral and esophageal glands into the root cell. It is a costly life strategy since typically only about 10% of the nematodes ever make it to maturity in a fully susceptible genotype like
1.6. Reverse genetic screens to identify essential SCN genes
Unlike
The first demonstration of RNAi in SCN accomplished the experiment by taking cDNAs for the gene of interest, synthesizing double stranded RNA (dsRNA)
|
|
|
|
HgAffx.13360.1.S1_at | CB374622 | pes-9 | Yeast hypothetical 52.9 KD protein |
HgAffx.10986.1.S1_at | CA939315 | gpd-3 | NULL |
HgAffx.19591.1.S1_at | CB278666 | cpf-1 | cleavage stimulation factor like |
HgAffx.16755.1.S1_at | CA939427 | phb-1 | NULL |
HgAffx.6532.1.S1_at | CK350603 | hsp-6 | heat shock 70 protein |
HgAffx.19651.1.S1_at | CD748666 | phb-2 | Prohibitin |
HgAffx.17567.1.S1_at | CB825030 | ben-1 | tubulin |
HgAffx.20551.1.S1_at | CB281634 | E02H1.1 | rRNA methyltransferase |
HgAffx.19055.1.S1_at | CB826041 | T21B10.2 | enolase |
HgAffx.24001.2.S1_at | CK351582 | ftt-2 | 14-3-3 protein |
HgAffx.22771.2.S1_at | BI749139 | uaf-1 | NULL |
HgAffx.21332.1.S1_at | BI748882 | daf-21 | heat shock protein (HSP90) |
HgAffx.10691.1.S1_at | CD748651 | K04D7.1 | guanine nucleotide-binding protein |
HgAffx.10821.1.S1_at | CB935592 | T21B10.7 | t-complex protein 1 |
HgAffx.13633.1.S1_at | CD748017 | pyp-1 | inorganic pyrophosphatase |
HgAffx.20969.1.S1_at | CB379877 | rps-1 | Ribosomal protein S3a homolog |
HgAffx.24120.1.S1_at | CB935135 | eft-2 | Elongation factor Tu family |
HgAffx.22597.1.S1_at | CB826306 | kin-19 | casein kinase I |
HgAffx.11150.1.S1_at | CB378957 | D1005.1 | ATP citrate lyase |
HgAffx.17961.1.S1_at | CB281421 | F01G10.1 | transketolase |
HgAffx.18740.2.S1_at | CA940055 | act-4 | actin |
HgAffx.14431.1.S1_at | CB935363 | mdh-1 | malate dehydrogenase |
HgAffx.19636.2.S1_at | CA939544 | rps-4 | NULL |
HgAffx.18811.1.S1_at | CA940369 | F43G9.5 | NULL |
HgAffx.5490.1.S1_at | CD747934 | gpi-1 | glucose-6-phosphate isomerase |
HgAffx.22868.1.S1_at | BG310682 | cpl-1 | cathepsin-like protease |
HgAffx.13283.1.S1_at | CD748764 | K10D6.2 | NULL |
HgAffx.17866.1.S1_at | CB824474 | M03C11.7 | NULL |
HgAffx.20065.1.S1_at | AF318605 | hsp-1 | HSP-1 heat shock 70kd protein A |
HgAffx.15252.1.S1_at | CK348813 | rho-1 | p21 ras-related rho (RhoA) |
HgAffx.16942.1.S1_at | CK349264 | ruvb-2 | NULL |
HgAffx.23555.2.S1_at | CD748675 | Y54E10BR.6 | NULL |
The second way to perform RNAi experiments for SCN control would be to express the genes in transgenic soybean roots, allowing the nematodes to feed on the genetically engineered roots. The hypothesis is that if the SCN was able to ingest the double stranded RNA manufactured in the plant cells through its stylet in high enough concentrations and if the RNAi metabolic process occurred in SCN, there was a chance that nematode development could be controlled. Prior experiments already demonstrated that the RNAi pathway functioned in SCN (Urwin et al. 2002; Alkharouf et al. 2007). The original experiments that performed host-mediated expression of SCN genes as inverted tandemly duplicated copies for RNAi control in soybean to examine SCN biology were done by Steeves et al. (2006), examining the major sperm protein. Huang et al. (2006) demonstrated the same effect for root knot nematode in the model plant
The problem with the transgenic approach is that soybean is a difficult to genetically engineer. However, strategies whereby composite plants (Collier et al. 2005) that are chimeras having nontransformed aerial stocks having transgenic root stocks can be readily made in soybean (Klink et al. 2008, 2009a). The simplicity of the approach is evident because the transgenic plants can be made in non-axenic conditions with the use of fluorescent reporter (Collier et al. 2005) (Figure 2). The development of vectors that work in soybean (Klink et al. 2008, 2009a; Ibrahim et al. 2011; Matsye et al. 2012) have made the experiments possible. Further improvements whereby the plant expression vectors are Gateway®-compatible (Klink et al. 2009a; Ibrahim et al. 2011; Matsye et al. 2012) allows for semi-large reverse genetic screens to be performed. In such experiments, SCN homologs of the small ribosomal protein 3a (Hg-rps-3a) and Hg-rps-4, synaptobrevin (Hg-snb-1) and a spliceosomal SR protein (Hg-spk-1) were tested for functionality in host mediated expression, RNAi-based studies (Klink et al. 2009a). After 8 days of infection, the experiments demonstrated that 81–93% fewer females developed on transgenic roots containing the genes engineered as tandem inverted repeats. Those experiments resulted in lethality for SCN feeding on plants that were expressing the genes as tandemly duplicated inverted repeats (Klink et al. 2009a). The same outcome was shown for root knot nematode in soybean using the same plant expression vector system (Ibrahim et al. 2011). These observations demonstrated that broad spectrum resistance for PPNs in soybean was probable.
1.7. Proteomic studies of SCN
The prior experiments have discussed gene expression in SCN at the RNA level. These experiments are technologically simplistic to perform, because of major advances in sequencing and detection technologies. However, in these experiments using hybridization to study gene expression, little to no information is obtained as to how much protein is actually synthesized from the RNA or modifications that are known to exist on the protein molecules. Recently, the proteome of SCN was investigated (Chen et al. 2011), resulting in a reference map of protein expression. These experiments add to the already extensive gene expression databases that are available for SCN (Ithal et al. 2007; Klink et al. 2007a, 2009a; Elling et al. 2009). The advantage of the proteomic studies is that it allows for the identification of the relative amounts of the studied proteins to be known. This is in contrast to microarray-based experiments where only different levels of expression can be inferred, but their absolute amounts are not known. Chen et al. (2011) performed experiments using LC-MS/MS on pre-infective J2 SCN. The nematodes were highly pure samples since they had not yet infected soybean roots. The experiments were able to discern 803 spots on 2-D gels (Chen et al. 2011). Of those spots, 426 proteins were identified (Chen et al. 2011). Gene Ontology analyses allowed for the identification of a number of different functional groups, including secreted proteins that may act during parasitism (Chen et al. 2011). While it is likely that the protein list is not comprehensive, the work provides a solid foundation for future work to examine the proteome of SCN and compare with the gene expression studies based on the RNA.
1.8. Soybean gene expression
To understand how soybean was reacting to infection, it was going to be imperative to develop ways to monitor gene expression during infection. Unlike the model system,
To distinguish between expression of genes during the susceptible and resistant reactions, an experiment was performed whereby both susceptible and resistant reactions could be obtained in the same soybean genotype (
1.9. Improvements in annotation
The described experiments resulted in the generation of a massive amount of gene expression data and gene lists for the 38,099 genes fabricated on the Affymetrix® soybean GeneChip. Annotated gene lists for soybean genes are very useful because no information is lost from the analysis (Table 1). However, the gene lists do not provide higher order knowledge of how the many genes are functioning during a process under study. It is possible that various metabolic pathways that pertain to a specific process could be identified if the data could be organized into a higher order structure. Since the aforementioned work was done in soybean, often considered a non-model organism, it was difficult to translate the information into gene pathway analyses applications in a manner that would reveal how the gene expression is orchestrated during the process under study. However, an investigation that had been done in
1.10. Genomics of the syncytium
While strides were being made in obtaining a deep analysis of the physiological processes occurring in whole infected roots, the greater challenge would be to identify gene expression that occurred within the syncytium because it would require either drawing the cytoplasm out of the syncytium or a way to physically isolate the cells. The original studies that attempted to determine gene expression in nematode nurse cells was done by Bird et al. (1994) and Wilson et al. (1994). The hypothesis was that by extracting the cytoplasm of the cells that are specifically undergoing the parasitism, it would be possible to determine the gene expression that pertains specifically to parasitism. However, it is noted that gene expression in the cells surrounding the syncytium probably plays some role in the maintenance and development of the susceptible and resistant reactions. This approach to isolate the cytoplasm (Bird et al. 1994; Wilson et al. 1994) would be more challenging for syncytia because it is virtually impossible to determine what cells are infected by SCN. Therefore, instead of collecting the cytoplasm, the collection of the cells would have to occur and it would have to be done through their physical isolation.
The physical isolation of syncytia undergoing a susceptible reaction to the SCN was first described by Klink et al. (2005). The study collected syncytia by a procedure called laser microdissection (Isenberg et al. 1976; Meier Ruge et al. 1976; Emmert-Buck et al. 1996) (Figure 3). The experiments obtained RNA of suitable quality for making cDNA libraries, cloning and sequencing full length genes greater than 1,000 base pairs, making probes for
Genomics approaches to syncytium biology resulted in a series of investigations that have focused in on gene expression that occurs during a susceptible reaction in the syncytium (Klink et al. 2005, 2007a, 2009b, 2010b, c, 2011a; Ithal et al. 2007; Matsye et al. 2011, 2012; Kandoth et al. 2011). In these studies, a number of genes were identified. However, to understand gene expression as it specifically pertains to defense, it would be required to study the cells undergoing the defense response. The main obstacle in performing studies with this goal in mind was determining whether the cells undergoing the defense response were already dead at the time of cell collection. The prediction is that cells that were dead would have already halted their physiological processes that pertained to defense and also may not provide RNA of suitable quality for microarray studies. However, it was unlikely that the cells progressing through the earlier stages of defense were dead (Figure 1) since the EM studies revealed very specific progression of cellular architecture during the defense response, suggesting that the cells had to be alive to progress through this developmental process (Endo, 1965; Kim et al. 1987; Endo, 1991). The initial collection of syncytia undergoing the developmental process that leads to their eventual collapse and death were then performed (Klink et al. 2007a). These experiments demonstrated that the cells would be a suitable source for RNA collection and genomics-based analyses. The first set of experiments to use laser microdissected cells undergoing an incompatible reaction for genomics studies determined that the expression of lipoxygenase (LOX), arabinogalactan-protein (AGP18), annexin, a thioesterase family protein heat shock protein (HSP) 70 and superoxidase dismutase (SOD) (Klink et al. 2007a). Many of the genes have very well known roles in plant defense. Subsequent experiments examined more time points occurring during the defense response, spanning phase 1 and phase 2 (Klink et al. 2009b, 2010b, c). The experiments identified a number a genes that were very highly expressed during the resistant reaction, specifically within the syncytium. In contrast, a number of genes were very highly suppressed (>1,000 fold) during the resistant reaction (Klink et al. 2009b, 2010b, c). The experiments were repeated later by Kandoth et al. (2011) in the
|
|
|
Affymetrix® soybean GeneChip® probe sets (PS) | 38,099 | |
PS with matches to |
23,583 | 62% |
PS with enzyme commission (E.C.) numbers | 9,717 | 29% |
PS matching both |
4,156 | 11% |
PS with chromosomal coordinates | 31,188 | 82% |
1.10.1. Soybean resistance clusters
The major SCN resistance trait,
1.11. Gene expression found during defense at the rhg1 locus
Knowing how and when genes are expressed in syncytia specifically during defense would likely provide knowledge of the genes that regulate or contribute to the process. Matsye et al. (2012) demonstrated in complimentary studies, that an amino acid transporter (AAT) (Glyma18g02580) and an α soluble NSF attachment protein (α-SNAP) (Glyma18g02590) found in the
1.12. Genetic engineering as a solution for SCN
A number of approaches like conventional breeding programs have been shown for decades to generate resistance to SCN (Brim and Ross, 1966). The resistant cultivars have been shown to result in savings of hundreds of millions of dollars (Bradley and Duffy, 1982). One drawback of conventional breeding programs is that along with the resistance genes that are bred in, a number of genes are also introgressed that could have undesirable characteristics. This is especially a problem when is desirable traits are tightly linked to the undesirable traits. To circumvent this problem, it is possible to genetically engineer in genes of interest. A number of strategies that have been described in this chapter have shown promise in disrupting the soybean-SCN interaction. As noted earlier, RNAi of nematode parasitism genes has been shown in the
Another procedure to modulate gene expression in soybean to engineer resistance involves the engineering of soybean genes as overexpression constructs (Matsye et al. 2012). To do the studies, genes that are highly expressed during a resistant reaction, identified in accessions of little agronomic value can be expressed to high levels in a soybean genotype that is normally susceptible, but of great economic value. The hypothesis is that if the gene is important in the defense response, the overexpression of that gene in a genotype that is normally susceptible would result in suppressed nematode infection. Such a result was obtained by Matsye et al. (2012) with the overexpression of a naturally occurring truncated allele of an α-SNAP gene. When the α-SNAP gene that was identified in the
2. Conclusion
The soybean-SCN pathosystem has been under study for over 60 years. Through a massive amount of basic studies involving agricultural production practices, genomics and genetic engineering, solutions to the chronic and global SCN problem are emerging. The difficulty of studying the system has been met with many improvements in technology that are allowing for basic features of the pathosystem to be exploited so that agricultural practices and economic returns are improved. The basic knowledge gained in this system can now be applied as a model for understanding other recalcitrant pathogens affecting soybean, to obtain a comprehensive understanding of infection and defense.
Acknowledgments
VPK is thankful for start-up support provided by Mississippi State University and the Department of Biological Sciences; funds in the forms of a competitive Research Improvement Grant; support from the Mississippi Soybean Promotion Board. GWL is thankful to the department of Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, KSL is thankful to the Department of Entomology and Plant Pathology, Auburn University.References
- 1.
Aist JR. 1976. Papillae and related wound plugs of plant cells. Annu Rev Phytopathol 14: 145–163 - 2.
Alkharouf NW, Klink VP, Chouikha IB, Beard HS, MacDonald MH, Meyer S, Knap HT, Khan R, Matthews BF. 2006. Timecourse microarray analyses reveals global changes in gene expression of susceptible Glycine max (soybean) roots during infection byHeterodera glycines (soybean cyst nematode). Planta 224: 838-852 - 3.
Alkharouf N, Klink VP, Matthews BF. 2007. Identification of Heterodera glycines (soybean cyst nematode [SCN]) DNA sequences with high similarity to those ofCaenorhabditis elegans having lethal mutant or RNAi phenotypes.Exp Parasitol 115: 247-258 - 4.
Alvarez JP, Pekker I, Goldshmidt A, Blum E, Amsellem Z, Eshed Y. 2006. Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell 18: 1134-1151 - 5.
An Q, Ehlers K, Kogel KH, van Bel AJ, Hückelhoven R. 2006a. Multivesicular compartments proliferate in susceptible and resistant MLA12-barley leaves in response to infection by the biotrophic powdery mildew fungus. New Phytol 172: 563-57 - 6.
An Q, Hückelhoven R, Kogel KH, van Bel AJ. 2006b. Multivesicular bodies participate in a cell wall-associated defence response in barley leaves attacked by the pathogenic powdery mildew fungus. Cell Microbiol 8: 1009-1019 - 7.
Assaad FF, Qiu JL, Youngs H, Ehrhardt D, Zimmerli L, Kalde M, Wanner G, Peck SC, Edwards H, Ramonell K, Somerville CR, Thordal-Christensen H. 2004. The PEN1 syntaxin defines a novel cellular compartment upon fungal attack and is required for the timely assembly of papillae. Mol Biol Cell 15: 5118-5129 - 8.
Atkinson HJ, Harris PD. 1989. Changes in nematode antigens recognized by monoclonal antibodies during early infections of soya bean with cyst nematode Heterodera glycines. Parasitology 98: 479-487 - 9.
Bakhetia M, Urwin PE, Atkinson HJ. 2007. QPCR analysis and RNAi define pharyngeal gland cell-expressed genes of Heterodera glycines required for initial interactions with the host. Mol Plant Microbe Interact 20: 306-312 - 10.
Bakhetia M, Urwin PE, Atkinson HJ. 2008. Characterisation by RNAi of pioneer genes expressed in the dorsal pharyngeal gland cell of Heterodera glycines and the effects of combinatorial RNAi. Int J Parasitol 38: 1589-1597 - 11.
Barker KR, Koenning SR, Huber SC, Huang JS. 1993. Physiological and structural responses of plants to nematode parasitism with Glycine max-Heterodera glycines as a model system. Pp. 761-771 in DR Buxon R Shibles RA Forsberg BL Blad KH Asay GM Paulsen and RF Wilson, Eds. International Crop Science I: Madison, WI: Crop Science Society of America - 12.
Bekal S, Niblack TL, Lambert KN. 2003. A chorismate mutase from the soybean cyst nematode Heterodera glycines shows polymorphisms that correlate with virulence. Molecular Plant-Microbe Interactions 16: 439-446 - 13.
Bekal S, Craig JP, Hudson ME, Niblack TL, Domier LL, Lambert KN. 2008. Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing. Mol Genet Genomics 279:535-543 - 14.
Bennett MK, Calakos N, Scheller RH. 1992. Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257: 255-259 - 15.
Bernard RL, Juvik GA, Nelson RL. 1987. USDA Soybean Germplasm Collection Inventory, Vol. 2. INTSOY Series Number 31. IL: International Agriculture Publications, University of Illinois - 16.
Bird D McK, Wilson MA. 1994. DNA sequence and expression analysis of root-knot nematode-elicited giant cell transcripts. MPMI 7:419-424 - 17.
Bradley EB, Duffy M. 1982. The value of plant resistance to soybean cyst nematode: a case study of Forrest soybeans. National Resource Economics Staff Report No. AGES820929, USDA. Washington DC: U.S. Government Printing Office - 18.
Brucker E, Carlson S, Wright E, Niblack T, Diers B. 2005. Rhg1 alleles from soybean PI 437654 and PI 88788 respond differently to isolates of Heterodera glycines in the greenhouse. Theor Appl Genet 111: 44-49 - 19.
C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018 - 20.
Caldwell BE, Brim CA, Ross JP. 1960. Inheritance of resistance of soybeans to the soybean cyst nematode, Heterodera glycines . Agron J 52: 635-636 - 21.
Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AM, Tops BB, Silva JM, Myers MM, Hannon GJ, Plasterk RH. 2003. A micrococcal nuclease homologue inRNAi effector complexes. Nature 425: 411-414 - 22.
Chapin III FS, Shaver GR. 1985. Individualistic growth response of tundra plant species to environmental manipulations in the field. Ecology 66: 564–576 - 23.
Chen W, Chao G, Singh KB. 1996. The promoter of a H2O2-inducible, Arabidopsis glutathione S-transferase gene contains closely linked OBF- and OBP1-binding sites. Plant J 10: 955-966 - 24.
Chen SY, Dickson DW. 1996. Pathogenicity of fungi to eggs of Heterodera glycines . Journal of Nematology 28: 148-158 - 25.
Chen X, MacDonald MH. Khan F, Garrett WM, Matthews BF, Natarajan SS. 2011. Two-dimentional proteome reference maps for the soybean cyst nematode Heterodera glycines. Proteomics 11: 4742-4746 - 26.
Chitwood DG, Lusby WR: Metabolism of plant sterols by nematodes. Lipids 1990, 26: 619-627 - 27.
Clary DO, Griff IC, Rothman JE. 1990. SNAPs, a family of NSF attachment proteins involved in intracellular membrane fusion in animals and yeast. Cell 61: 709–721 - 28.
Colgrove AL, Niblack TL. 2008. Correlation of female indices from virulence assays on inbred lines and field populations of Heterodera glycines. J Nematol 40: 39–45 - 29.
Collier R, Fuchs B, Walter N, Kevin Lutke W, Taylor CG. 2005. Ex vitro composite plants: an inexpensive, rapid method for root biology. Plant J 43: 449-457 - 30.
Collins NC, Thordal-Christensen H, Lipka V, Bau S, Kombrink E, Qiu JL, Hückelhoven R, Stein M, Freialdenhoven A, Somerville SC, Schulze-Lefert P. 2003. SNARE-protein mediated disease resistance at the plant cell wall. Nature 425 : 973–977 - 31.
Concibido VC, Denny RL, Boutin SR, Hautea R, Orf JH, Young ND. 1994. DNA Marker analysis of loci underlying resistance to soybean cyst nematode ( Heterodera glycines Ichinohe). Crop Sci 34: 240–246 - 32.
Concibido VC, Diers BW, Arelli PR. 2004. A decade of QTL mapping for cyst nematode resistance in soybean. Crop Sci. 44: 1121-1131 - 33.
Creech JE, Johnson WG. 2006. Survey of broadleaf winter weeds in Indiana production fields infested with soybean cyst nematode ( Heterodera glycines ). Weed Technol. 20: 1066-1075 - 34.
Cregan PB, Mudge J, Fickus EW, Danesh D, Denny R, Young ND. 1999a. Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet 99: 811–818 - 35.
Cregan PB, Mudge J, Fickus EW, Marek LF, Danesh D, Denny R, Shoemaker RC, Matthews BF, Jarvik T, Young ND. 1999b. Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theor Appl Genet 98:919–928 - 36.
Day TA, Ruhland CT, Grobe CW, Xiong F. 1999. Growth and reproduction of Antarctic vascular plants in response to warming and UV radiation reductions in the field. Oecologia 119: 24–35 - 37.
De Boer JM, Yan Y, Wang X, Smant G, ussey RS, Davis EL. 1999. Developmentla expression of secretory beta 1, 4-endonucleases in the subventral esophageal glands of Heterodera glycines. Molecular Plant-Microbe Interactions 12: 663-669 - 38.
De Boer JM, Mc Dermott JP, Davis EL; Husses RS, Popeijus H, Smant G, Baum TJ. 2002. Cloning of a putative pectate lyase gene expressed in the subventral esophageal glands of Heterodera glycines. J. Nematology 34: 9-11 - 39.
Doyle JJ, Doyle JL, Brown AH. 1999. Origins, colonization, and lineage recombination in a widespread perennial soybean polyploid complex. Proc Natl Acad Sci 96: 10741-10745 - 40.
Edens RM, Anand SC, Bolla RI. 1995. Enzymes of the phenylpropanoid pathway in soybean infected with Meloidogyne incognita or Heterodera glycines. J Nematology. 27: 292-303 - 41.
Elling AA, Mitreva M, Gai X, Martin J, Recknor J, Davis EL, Hussey RS, Nettleton D,McCarter JP, Baum TJ. 2009. Sequence mining and transcript profiling to explore cyst nematode parasitism. BMC Genomics 10: 58 - 42.
Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA. 1996. Laser capture microdissection. Science 274: 998–1001 - 43.
Endo BY. 1964. Penetration and development of Heterodera glycines in soybean roots and related and related anatomical changes. Phytopathology 54: 79–88 - 44.
Endo BY. 1965. Histological responses of resistant and susceptible soybean varieties, and backcross progeny to entry development of Heterodera glycines . Phytopathology 55: 375–381 - 45.
Endo BY. 1991. Ultrastructure of initial responses of susceptible and resistant soybean roots to infection by Heterodera glycines . Revue Nématol 14: 73-84 - 46.
Endo BY, Veech JA. 1970. Morphology and histochemistry of soybean roots infected with Heterodera glycines . Phytopathology 60: 1493–1498 - 47.
Epps JM, Chambers AY. 1958. New host records for Heterodera glycines including one in the Labiate. Plant Disease Reporter 42: 194 - 48.
Epps JM, Hartwig EE. 1972. Reaction of soybean varieties and strains to soybean cyst nematode. J Nematol 4: 222 - 49.
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. 1998. Potent and specific genetic interference by doublestranded RNA in Caenohrabditis elegans. Nature 391:806–811 - 50.
Francl LJ, Dropkin VH. 1986. Heterodera glycines population dynamics and relation of initial population density tp soybean yield. Plant Disease: 70: 791-795 - 51.
Gao B, Allen R, Maier T, Davis EL, Baum TJ, Hussey RS. 2001. Identification of putative parasitism genes expressed in the esophageal gland cells of the soybean cyst nematode Heterodera glycines. Mol Plant Microbe Interact 2001, 14:1247-1254. - 52.
Gao B, Allen R, Maier T, Davis EL, Baum TJ, Hussey RS. 2003. The parasitome of the phytonematode Heterodera glycines. Mol Plant Microbe Interact 16: 720-726 - 53.
Garner WW, Allard HA. 1930. Photoperiodic response of soybeans in relation to temperature and other environmental factors. J. Agric. Res. 41:719-735 - 54.
Gipson I, Kim KS, Riggs RD. 1971. An ultrastructural study of syncytium development in soybean roots infected with Heterodera glycines . Phytopathology 61: 347-353 - 55.
Golden AM, Epps JM, Riggs RD, Duclos LA, Fox JA, Bernard RL. 1970. Terminology and identity of infraspecific forms of the soybean cyst nematode (Heterodera glycines). Plant Dis Rep 54: 544–546 - 56.
Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, Sato K, Kanehisa M. 1997. Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput. 1997: 175-186 - 57.
Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ. 2001. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science. 293: 1146-1150 - 58.
Hardham AR, Takemoto D, White RG. 2008. Rapid and dynamic subcellular reorganization following mechanical stimulation of Arabidopsis epidermal cells mimics responses to fungal and oomycete attack. BMC Plant Biol 8: 63 - 59.
Haseloff J, Siemering KR, Prasher DC, Hodge S. 1997. Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. Proc Natl Acad Sci U S A 94: 2122-2127 - 60.
Hermsmeier D, Mazarei M, Baum TJ. 1998. Differential display analysis of the early compatible interaction between soybean and the soybean cyst nematode. Molecular Plant-Microbe Interactions 11: 1258-1263 - 61.
Hofius D, Schultz-Larsen T, Joensen J, Tsitsigiannis DI, Petersen NH, Mattsson O, Jørgensen LB, Jones JD, Mundy J, Petersen M. 2009. Autophagic components contribute to hypersensitive cell death in Arabidopsis. Cell 137: 773-783 - 62.
Huang G, Allen R, Davis EL, Baum TJ, Hussey RS. 2006. Engineering broad root-knot resistance in transgenic plants by RNAi silencing of a conserved and essential root-knot nematode parasitism gene. Proc Natl Acad Sci USA 103: 14302-14306 - 63.
Hymowitz t. 1970. On the domestication of soybean. Economic Botany 24: 408-421 - 64.
Hyten DL, Choi IY, Song Q, Shoemaker RC, Nelson RI, Costa JM, Specht JE, Cregan PB. 2010. Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175: 1937-1944 - 65.
Ichinohe M. 1952. On the soybean nematode, Heterodera glycines n. sp., from Japan. Magazine of Applied Zoology 17: 1-4 - 66.
Ichinohe M. 1961. Studies on the soybean cyst nematode, Heterodera glycines Hakkaido National Experiment Station Report no. 56 - 67.
Inagaki H, Tsutsumi M. 1971. Survival of the soybean cyst nematode, Heterodera glycines Ichinohe (Tylenchida: Heteroderidae) under certain storage conditions. Appl Entomol Zool (Jpn) 8: 53–63 - 68.
Inoue A, Obata K, Akagawa K. 1992. Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1. J Biol Chem 267: 10613-10619 - 69.
Isenberg G, Bielser W, Meier-Ruge W, Remy E. 1976. Cell surgery by laser micro-dissection: a preparative method. J. Microsc 107: 19–24 - 70.
Ithal N, Recknor J, Nettleston D, Hearne L, Maier T, Baum TJ, Mitchum MG. 2007. Developmental transcript profiling of cyst nematode feeding cells in soybean roots. Molecular Plant-Microbe Interactions 20: 293-305 - 71.
Jones MGK. 1981. The development and function of plant cells modified by endoparasitic nematodes. Pages 255-279 in: Plant Parasitic Nematodes, Vol. III. B. M. Zuckerman and R. A. Rohde, eds. Academic Press, New York, U.S.A. - 72.
Jones MGK, Northcote DH. 1972. Nematode-induced syncytium-a multinucleate transfer cell. J Cell Sci 10: 789–809 - 73.
Kandoth PK, Ithal N, Recknor J, Maier T, Nettleton D, Baum TJ, Mitchum MG. 2011. The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells. Plant Physiol 155: 1960-1975 - 74.
Kalde M, Nühse TS, Findlay K, Peck SC. 2007. The syntaxin SYP132 contributes to plant resistance against bacteria and secretion of pathogenesis-related protein 1. Proc Natl Acad Sci U S A 104: 11850-11855 - 75.
Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, Welchman DP, Zipperlen P, Ahringer J. 2003. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421: 231–237 - 76.
Kim DG, Riggs RD. 1991. Characteristics and efficacy of a sterile hyphomycete (ARF18), a new biocontrol agent for Heterodera glycines and other nematodes. Journal of Nematology 23: 275–282 - 77.
Kim DG, Riggs RD. 1995. Efficacy of the nematophagous fungus ARF18 in alginate-clay pellet formulation against Heterodera glycines. Journal of Nematology 23:275-282 - 78.
Kim KS, Riggs RD. 1992. Cytopathological reactions of resistant soybean plants to nematode invasion. Pp. 157–168 in J. A. Wrather and R. D. Riggs, eds. Biology and Management of the Soybean Cyst Nematode. St. Paul: APS Press - 79.
Kim M, Hyten DL, Bent AF, Diers BW. 2010. Fine mapping of the SCN resistance locus rhg1-b from PI 88788. The Plant Genome 3: 81-89 - 80.
Kim YH, Riggs RD, Kim KS. 1987. Structural changes associated with resistance of soybean to Heterodera glycines . J Nematol 19: 177–187 - 81.
Klink VP, MacDonald M, Alkharouf N, Matthews BF. 2005. Laser capture microdissection (LCM) and expression analyses of Glycine max (soybean) syncytium containing root regions formed by the plant pathogenHeterodera glycines (soybean cyst nematode). Plant Mol Bio 59: 969-983 - 82.
Klink VP, Overall CC, Alkharouf N, MacDonald MH, Matthews BF. 2007a. Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean roots infected by soybean cyst nematode ( Heterodera glycines ). Planta 226: 1389-1409 - 83.
Klink VP, Overall CC, Alkharouf N, MacDonald MH, Matthews BF. 2007b. A comparative microarray analysis of an incompatible and compatible disease response by soybean (Glycine max) to soybean cyst nematode (Heterodera glycines) infection. Planta 226: 1423-1447 - 84.
Klink VP, MacDonald MH, Martins VE, Park S-C, Kim K-H, Baek S-H, Matthews BF. 2008. MiniMax, a new diminutive Glycine max variety, with a rapid life cycle, embryogenic potential and transformation capabilities. Plant Cell, Tissue and Organ Culture 92: 183-195 - 85.
Klink VP, Kim K-H, Martins VE, MacDonald MH, Beard HS, Alkharouf NW, Lee S-K, Park S-C, Matthews BF. 2009a. A correlation between host-mediated expression of parasite genes as tandem inverted repeats and abrogation of the formation of female Heterodera glycines cysts during infection of Glycine max. Planta 230: 53-71 - 86.
Klink VP, Hosseini P, Matsye P, Alkharouf N, Matthews BF. 2009b. A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection byHeterodera glycines (soybean cyst nematode) Plant Mol Bio: 71: 525-567 - 87.
Klink VP, Hosseini P, MacDonald MH, Alkharouf N, Matthews BF. 2009c. Population-specific gene expression in the plant pathogenic nematode Heterodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of the Glycine max genotype Peking. BMC-Genomics 10: 111 - 88.
Klink VP, Matsye PD, Lawrence GW. 2010a. Developmental Genomics of the Resistant Reaction of Soybean to the Soybean Cyst nematode, Pp. 249-270, In Plant Tissue Culture and Applied Biotechnology. Eds. Kumar A., Roy S. Aavishkar Publishers, Distributors, India. - 89.
Klink VP, Hosseini P, Matsye P, Alkharouf N, Matthews BF. 2010b. Syncytium gene expression in Glycine max [PI 88788] roots undergoing a resistant reaction to the parasitic nematodeHeterodera glycines Plant Physiology and Biochemistry 48: 176-193 - 90.
Klink VP, Overall CC, Alkharouf N, MacDonald MH, Matthews BF. 2010c. Microarray detection calls as a means to compare transcripts expressed within syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines). Journal of Biomedicine and Biotechnology 1-30 - 91.
Klink VP, Hosseini P, Matsye PD, Alkharouf N, Matthews BF. 2011a. Differences in gene expression amplitude overlie a conserved transcriptomic program occurring between the rapid and potent localized resistant reaction at the syncytium of the Glycine max genotype Peking (PI 548402) as compared to the prolonged and potent resistant reaction of PI 88788. Plant Mol Bio 75: 141-165 - 92.
Klink VP, Matsye PD, Lawrence GW. 2011b. Cell-specific studies of soybean resistance to its major pathogen, the soybean cyst nematode as revealed by laser capture microdissection, gene pathway analyses and functional studies. in Soybean - Molecular Aspects of Breeding pp. 397-428. Ed. Aleksandra Sudaric. Intech Publishers - 93.
Koenning SR, Schmitt DP, Barker KR. 1993. Effects of cropping systems on population density of Heterodera glycines and soybean yield. Plant Disease 77: 780-786 - 94.
Lai Z, Wang F, Zheng Z, Fan B, Chen Z. 2011. A critical role of autophagy in plant resistance to necrotrophic fungal pathogens. Plant J 66: 953-968 - 95.
Lambert KN, Allen KD, Sussex IM. 1999. Cloning and characterization of an esophageal-gland specific chorismate mutase from the phytopathogenic nematode Meloidogyne javanica. Molecular Plant-Microbe Interactions 12: 328-336 - 96.
Lenz HD, Haller E, Melzer E, Kober K, Wurster K, Stahl M, Bassham DC, Vierstra RD, Parker JE, Bautor J, Molina A, Escudero V, Shindo T, van der Hoorn RA, Gust AA, Nürnberger T. 2011. Autophagy differentially controls plant basal immunity to biotrophic and necrotrophic pathogens. Plant J 66: 818-830 - 97.
Li J, Todd TC, Oakley TR, Lee J and Trick HN. 2010. Host derived suppression of nematode reproductive and fitness genes decreases fecundity of Heterodera glycines . Planta 232: 775-785 - 98.
Li Y-H, Qi X-T, Chang R and Qiu L-J. 2011. Evaluation and Utilization of Soybean Germplasm for Resistance to Cyst Nematode in China. in Soybean - Molecular Aspects of Breeding pp. 373-396. Ed. Aleksandra Sudaric. Intech Publishers - 99.
Lipka V, Dittgen J, Bednarek P, Bhat R, Wiermer M, Stein M, Landtag J, Brandt W, Rosahl S, Scheel D, Llorente F, Molina A, Parker J, Somerville S, Schulze-Lefert P. 2005. Pre- and postinvasion defenses both contribute to nonhost resistance in Arabidopsis. Science 310: 1180-1183 - 100.
Liu X, Z, Chen SY. 2001. Screening isolates of Hirsutella species for biocontrol ofHeterodera glycines. Biocontrol Science and Technology 11:151-160 - 101.
Liu XZ, Li JQ, Zhang DS. 1997. History and status of soybean cyst nematode in China. International Journal of Nematology 7: 18-25 - 102.
Ma Y, Wang W, Liu X, Ma F, Wang P, Chang R, Qiu L. 2006. Characteristics of soybean genetic diversity and establishment of applied core collection for Chinese soybean cyst nematode resistance. Journal of Intergrative Biology 48: 722-731 - 103.
Mahalingham R, Skorupska HT. 1996. Cytological expression of early response to infection by Heterodera glycines Ichinohe in resistant PI 437654 soybean. Genome 39: 986–998 - 104.
Mahalingam R, Wang G, Knap HT. 1999. Polygalacturonidase and polygalacturonidase inhibitor protein: gene isolation and transcription in Glycine max-Heterodera glycines interactions. Molecular Plant-Microbe Interactions 12: 490-498 - 105.
Malhotra V, Orci L, Glick BS, Block MR, Rothman JE. 1988. Role of an N-ethylmaleimide-sensitive transport component in promoting fusion of transport vesicles with cisternae of the Golgi stack. Cell 54: 221–227 - 106.
Matson AL, Williams LF. 1965. Evidence of a fourth gene for resistance to the soybean cyst nematode. Crop Sci. 5: 477 - 107.
Matsye PD, Kumar R, Hosseini P, Jones CM, Alkharouf N, Matthews BF, Klink VP. 2011. Mapping cell fate decisions that occur during soybean defense responses. Plant Mol Bio 77: 513-528 - 108.
Matsye PD, Lawrence GW, Youssef RM, Kim K-H, Lawrence KS, Matthews BF, Klink VP. 2012. The expression of a naturally occurring mutant of an alpha soluble NSF attachment protein gene in Glycine max (soybean) partially suppresses infection by the plant parasitic nematodeHeterodera glycines . Plant Molecular Biology (in press) - 109.
McLean MD, Hoover GJ, Bancroft B, Makhmoudova A, Clark SM, Welacky T, Simmonds DH, Shelp BJ. 2007. Identification of the full-length Hs1pro-1 coding sequence and preliminary evaluation of soybean cyst nematode resistance in soybean transformed withHs1pro-1 cDNA. Canadian Journal of Botany 85: 437-441 - 110.
Meier-Ruge W, Bielser W, Remy E, Hillenkamp F, Nitsche R, Unsold R. 1976. The laser in the Lowry technique for microdissection of freeze-dried tissue slices. Histochem J 8: 387-401 - 111.
Meyer SLF, Huettel RN. 1996. Application of a sex pheromone, pheromone analogs, and Verticillum lecanii for management of Heterodera glycines. J. Nematology 28: 36-42 - 112.
Meyer SLF, Meyer RJ. 1996. Greenhouse studies comparing strains of the fungus Verticillium lecanii for activity against the nematodeHeterodera glycines . Fundamentals of Applied Nematology 19: 305–308 - 113.
Morse WJ. 1927. Soybeans: culture and varieties. Farmer’s bulletin NO. 1520. Washington, D.C.: U.S. Dept. of Agriculture. 38 pp - 114.
Mudge J, Cregan PB, Kenworthy JP, Kenworthy WJ, Orf JH, Young ND. 1997. Two microsatellite markers that flank the major soybean cyst nematode resistance locus. Crop Sci 37: 1611-1615 - 115.
Müssig C, Fischer S, Altmann T. 2002. Brassinosteroid-regulated gene expression. Plant Physiol 129: 1241-1251 - 116.
Niblack TL, Chen SY. 2004. Cropping systems and crop management practices. Breeding for resistance and tolerance. Pp. 181-206. in D. P. Schmitt, J. A. Wrather, and R. D. Riggs, eds. Biology and management of soybean cyst nematode, 2nd ed. Marceline, MO: Schmitt & Associates of Marceline - 117.
Niblack TL, Heinz RD, Smith GS, Donald PA (1993) Distribution, density, and diversity of Heterodera glycines in Missouri. J Nematol 25:880–886 - 118.
Niblack TL, Arelli PR, Noel GR, Opperman CH, Orf JH, Schmitt DP, Shannon JG, Tylka GL. 2002. A revised classification scheme for genetically diverse populations of Heterodera glycines . J Nematol 34: 279-288 - 119.
Niblack TL, Lambert KN, Tylka GL. 2006. A model plant pathogen from the kingdom animalia: Heterodera glycines, the Soybean Cyst Nematode. Annu Rev Phytopathol 44: 283-303 - 120.
Niblack TL, Riggs RD. 2004. Variation in virulence phenotypes. Breeding for resistance and tolerance. Pp. 57-71. in D. P. Schmitt, J. A. Wrather, and R. D. Riggs, eds. Biology and management of soybean cyst nematode, 2nd ed. Marceline, MO: Schmitt & Associates of Marceline - 121.
Noel GR. 1992. History, distribution and economics. Pp 1-13 in RD Riggs and JA Wrather, editors. Biology and Management of the soybean cyst nematode. St. Paul, MN: APS Press - 122.
Opperman CH, Bird D McK. 1998. The soybean cyst nematode, Heterodera glycines: a genetic model system for the study of plant-parasitic nematodes. Current Opinion in Plant Biology 1: 1342-1346 - 123.
Oyler GA, Higgins GA, Hart RA, Battenberg E, Billingsley M, Bloom FE, Wilson MC. 1989. The identification of a novel synaptosomal-associated protein, SNAP-25, differentially expressed by neuronal subpopulations. J Cell Biol 109: 3039-3052 - 124.
Patel S, Dinesh-Kumar SP. 2008. Arabidopsis ATG6 is required to limit the pathogen-associated cell death response. Autophagy 4: 20-27 - 125.
Piano F, Schetter AJ, Mangone M, Stein L, Kemphues KJ. 2000. RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans . Current Biology 10: 1619–1622 - 126.
Pratt PW, Wrather JA. 1998. Soybean disease loss estimates for the southern United States, 1994-1996. Plant Disease 82: 114-116 - 127.
Puthoff DP, Nettleton D, Rodermel SR, Baum TJ. 2003. Arabidopsis gene expression changes during cyst nematode parasitism revealedby statistical analyses of microarray expression profiles. Plant J 33: 911–921 - 128.
Rao-Arelli AP. 1994. Inheritance of resistance to Heterodera glycines race 3 in soybean accessions. Plant Dis. 78: 898-900. - 129.
Riggs RD, Hamblen ML. 1962. Soybean-cyst nematode host studies in the Leguminosae. Ark Agric Exp Stn Rep Series 110 Fayetteville AR 17p - 130.
Riggs RD, Hamblen ML. 1966. Additional weed hosts of Heterodera glycines . Plant Dis Rep 50: 15-16 - 131.
Riggs RD, Hamblen ML. 1966. Further studies on the host range of the soybean-cyst nematode. Ark Agric Exp Stn Bulletin 718 Fayetteville AR 19p - 132.
Riggs RD, Schmitt DP. 1988. Complete characterization of the race scheme for Heterodera glycines. J Nematol 20: 392-395 - 133.
Riggs RD, Schmitt DP. 1991. Optimization of the Heterodera glycines race test procedure. J Nematol 23: 149-154 - 134.
Riggs RD, Kim KS, Gipson I. 1973. Ultrastructural changes in Peking soybeans infected with Heterodera glycines . Phytopathology 63: 76–84 - 135.
Robinson AF, Inserra RN, Caswell-Chen EP, Vovlas N, Troccoli A. 1997. Rotylenchulus species: Identification, distribution, host ranges, and crop plant resistance. Nematropica 27: 127-180 - 136.
Ross JP, Brim CA. 1957. Resistance of soybeans to the soybean cyst nematode as determined by a double-row method. Plant Dis Rep 41: 923–924 - 137.
Ross JP. 1958. Host-Parasite relationship of the soybean cyst nematode in resistant soybean roots. Phytopathology 48: 578-579 - 138.
Ross JP. 1962. Crop rotation effects on the soybean cyst nematode population and soybean yields. Phytopathology 52: 815-818 - 139.
Brim CA, Ross JP. 1966. Registration of Pickett soybeans. Crop Science 6: 305 - 140.
Rosskopf EN, Chellemi DO, Kokalis-Burelle N, Church GT. 2005. Alternatives to Methyl Bromide: A Florida Perspective. American Phytopathological Society. APSnet feature, http://www.apsnet.org/publications/apsnetfeatures/Documents/2005/MethylBromideAlternatives.pdf - 141.
Sasser JN, Uzzell G, Jr. 1991. Control of the soybean cyst nematode by crop rotation in combination with nematicide . J. Nematology 23: 344-347 - 142.
Scheideler M, Schlaich NL, Fellenberg K, Beissbarth T, Hauser NC, Vingron M, Slusarenko AJ, Hoheisel JD. 2001. Monitoring the switch from housekeeping to pathogen defense metabolism in Arabidopsis thaliana using cDNA arrays. J Biol Chem 277: 10555–10561 - 143.
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183 - 144.
Schmelzer E. 2002. Cell polarization, a crucial process in fungal defence. Trends Plant Sci 7: 411-415 - 145.
Schneider SM, Rosskopf EN, Leesch JG, Chellemi DO, Bull CT, Mazzola M. 2003. United States Department of Agriculture-Agricultural Research Service research on alternatives to methyl bromide: pre-plant and post-harvest. Pest Manag Sci. 59: 814-826 - 146.
Shannon JG, Arelli PR, Young LD. 2004. Breeding for resistance and tolerance. Pp. 155-180. in D. P. Schmitt, J. A. Wrather, and R. D. Riggs, eds. Biology and management of soybean cyst nematode, 2nd ed. Marceline, MO: Schmitt & Associates of Marceline - 147.
Smant GA, Stokkermans JPWG, Yan Y, De Boer JM, Baum TJ, Wang X, Hussey RS, Gommers FJ, Henrissat B, Davis EL, Helder J, Schots A, Bakker J. 1998. Endogenous cellulases in animals: isolation of 1,4-endoglucanase genes from two species of plant-parasitic nematodes. PNAS USA 95: 4906-4911 - 148.
Sönnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, Röder M, Finell J, Häntsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gönczy P, Coulson A, Hyman AA, Echeverri CJ. 2005. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434: 462-429 - 149.
Spears JF. 1957. Review of soybean cyst nematode situation for presentation at public hearing on the need for Federal Domestic Plant Quarantine, July 24, 1957 - 150.
Steeves RM, Todd TC, Essig JS, Trick HN. 2006. Transgenic soybeans expressing siRNAs specific to a major sperm protein gene suppress Heterodera glycines reproduction. Funct Plant Biol 33: 991–999 - 151.
Stein M, Dittgen J, Sánchez-Rodríguez C, Hou BH, Molina A, Schulze-Lefert P, Lipka V, Somerville S. 2006. Arabidopsis PEN3/PDR8, an ATP binding cassette transporter, contributes to nonhost resistance to inappropriate pathogens that enter by direct penetration. Plant Cell 18: 731-746 - 152.
Tao Y, Xie Z, Chen W, Glazebrook J, Chang HS, Han B, Zhu T, Zou G, Katagiri F. 2003. Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae. Plant Cell 15: 317-330 - 153.
Tenllado F, Martı´nez-Garcı´a B, Vargas M, Dı´az-Ruı´z JR. 2003. Crude extracts of bacterially expressed dsRNA can be used to protect plants against virus infections. BMC Biotechnol 3:3 - 154.
Tepfer D. 1984. Transformation of several species of higher plants by Agrobacterium rhizogenes: sexual transmission of the transformed genotype and phenotype. Cell 37: 959-967 - 155.
Timmons L, Donald LC, Andrew F (2001) Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263:103–112 - 156.
Timper P, Riggs RD, Crippen DL. 1999. Parasitism of sedentary stages of Heterodera glycines by isolates of a sterile nematophagous fungus. Phytopathology 89: 1193-1199 - 157.
Urwin PE, Lilley CJ, Atkinson HJ. 2002. Ingestion of double-stranded RNA by preparasitic juvenile cyst nematodes leads to RNA interference. Mol Plant Microbe Interact 15: 747-752 - 158.
Vaghchhipawala Z, Bassuner R, Clayton K, Lewers K, Shoemaker R,m Mackenzie S. 2001. Modulations in gene expression and mapping of genes associated with cyst nematode infection of soybean. Molecular Plant-Microbe Interactions 14: 42-54 - 159.
Wang D, Stravopodis D, Teglund S, Kitazawa J, Ihle JN. 1996. Naturally occurring dominant negative variants of Stat5. Mol Cell Biol 16: 6141-6148 - 160.
Wang X, Allen R, Ding X, Goellner M, Maier T, DeBoer JM, Baum TJ, Hussey RS, Davis EL. 2001. Signal peptide-selection of cDNA cloned directly from the esophageal gland cells of the soybean cyst nematode Heterodera glycines. Molecular Plant-Microbe Interactions 14: 536-544 - 161.
Wang J, Meyers D, Yan Y, Baum T, Smant G, Hussey R. 2003. The soybean cyst nematode reduces soybean yield without causing obvious symptoms. Plant Disease 87: 623-628 - 162.
Wang X, Myers D, Yan Y, Baum T, Smant G, Hussey R, Davis E. 1999. In planta localization of a 1, 4-endoglucanase secreted by Heterodera glycines. Molecular Plant-Microbe Interactions 12: 64-67 - 163.
Weidman PJ, Melançon P, Block MR, Rothman JE. 1989. Binding of an N-ethylmaleimide-sensitive fusion protein to Golgi membranes requires both a soluble protein(s) and an integral membrane receptor. J Cell Biol 108: 1589-1596 - 164.
Wilson MA, Bird D McK van der Knaap E. 1994. A comprehensive subtractive cDNA cloning approach to identify nematode-induced transcripts in tomato. Phytopathology 84: 299-303 - 165.
Winstead NN, Skotland CB Sasser JN. 1955. Soybean cyst nematodes in North Carolina. Plant Disease Reporter 39: 9-11. - 166.
Wrather JA, Chambers AY, Fox JA, Moore WF, Sciumbato GL. 1995. Soybean disease loss estimates for the southern United States, 1974-1994. Plant Disease 79: 1076-1079 - 167.
Wrather JA, Anderson TR, Arsyad DM, Tan Y, Ploper LD, Porta-Puglia A, Ram HH, Yorinori JT. 2001a. Soybean disease loss estimates for the top ten soybean producing countries in 1998. Canadian Journal of Plant Pathology 23: 115-121 - 168.
Wrather JA, Steinstra WC, Koenning SR. 2001b. Soybean disease loss estimates for the United States from 1996-1998. Canadian Journal of Plant Pathology 23: 122-131 - 169.
Wrather JA, Koenning SR, Anderson TR. 2003. Effect of diseases on soybean yields in the United States and Ontario (1999-2002). Online. Plant Health Progress doi: 10.1094/PHP-2003-0325-01-RV, http://www.plantmanagement network.org/sub/php/review/2003/soybean/>(19 November 2003) - 170.
Wrather JA, Koenning SR. 2006. Estimates of disease effects on soybean yields in the United States 2003-2005. J Nematology 38: 173-180