Validating DNA Polymorphisms Using KASP Assay in Prairie Cordgrass (Spartina pectinata Link) Populations in the U.S.

Single nucleotide polymorphisms (SNPs) are one of the most abundant DNA variants found in plant genomes and are highly efficient when comparing genome and transcriptome sequences. SNP marker analysis can be used to analyze genetic diversity, create genetic maps, and utilize marker-assisted selection breeding in many crop species. In order to utilize these technologies, one must first identify and validate putative SNPs. In this study, 121 putative SNPs, developed from a nuclear transcriptome of prairie cordgrass (Spartina pectinata Link), were analyzed using KASP technology in order to validate the SNPs. Fifty-nine SNPs were validated using a core collection of 38 natural populations and a phylogenetic tree was created with one main clade. Samples from the same population tended to cluster in the same location on the tree. Polymorphisms were identified within 52.6% of the populations, split evenly between the tetraploid and octoploid cytotypes. Twelve selected SNP markers were used to assess the fidelity of tetraploid crosses of prairie cordgrass and their resulting F2population. These markers were able to distinguish true crosses and selfs. This study provides insight into the genomic structure of prairie cordgrass, but further analysis must be done on other cytotypes to fully understand the structure of this species. This study validates putative SNPs and confirms the potential usefulness of SNP marker technology in future breeding programs of this species.

Localization of repetitive DNA sequences on in vitro Xenopus laevis chromosomes by primed in situ labeling (PRINS).

Xenopus laevis is an important reference model organism used in many vertebrate studies. Gene mapping in X. laevis, in comparison to other reference organisms, is in its early stages. Few studies have been conducted to localize DNA sequences on X. laevis chromosomes. Primed in situ labeling (PRINS) is a recently developed innovative tool that has been used to locate specific DNA sequences in various organisms. PRINS has been reported to have increased sensitivity compared to other in situ hybridization techniques. In the present study, PRINS was first used to label the location of telomeres at the ends of in vitro X. laevis chromosomes. The terminal location was as expected from in vivo reports, however, the overall amount seemed to decrease in the in vitro chromosomes. Once the PRINS technique was optimized, this technique was used to determine the chromosomal location of the satellite 1 repetitive sequence, which is an important sequence in X. laevis development. The sequence was observed on the interstitial regions of the majority of the chromosomes similar to the in vivo locations reported. In contrast to the telomeric sequence, the amount of sequence appeared to increase in the satellite 1 sequence. PRINS was found to be useful in the localization of repetitive DNA sequences in the X. laevis genome.

Fertility, segregation at a herbicide-resistance locus, and genome structure in BC hybrids from two important weedy Amaranthus species.

Field studies have established high potential for hybridization between two important and often coexisting weedy species, Amaranthus hybridus and Amaranthus tuberculatus. Prezygotic reproductive barriers between these species are believed to be limited to pollen competition and availability. A greenhouse study showed that a herbicide-resistance gene (ALS) from A. hybridus could be introgressed into an advanced A. tuberculatus background (BC2). However, evidence is lacking in support of such transfer in nature. Postzygotic reproductive barriers may minimize, if not preclude, natural introgression. Indeed, A. hybridus xA. tuberculatus hybrids are characterized by reduced fertility and even floral neuterism. The purpose of this study was to assess hybrid fertility in the BC1 generation and its relationship with genome structure and segregation at ALS. Fertility was assessed by measuring seed output and by pollen evaluation, and segregation at ALS was determined via a molecular marker system. The two parental species have the same ploidy (2n = 32) but differ in DNA content (2C) values, with A. tuberculatus chromosomes being on average 29% greater than those of A. hybridus. Given that most (98%) BC(1)s were homoploid, 2C values were used as indicators of relative genomic constitution. Fertility in the BC1 generation was greater than that of F1s, and 3% of BC1s had seed output similar to that of the parental species. Fertility in the BC1 did not correlate (in a strict way) with reconstitution of parental genomes. Hybrid sterility appeared to be controlled by relatively few loci. Heterozygosity at ALS was negatively correlated with fertility. Also, the A. tuberculatus ALS allele was not observed in the A. hybridus sexual condition, monoecism. Linkage of ALS to a locus associated (directly or via epistasis) with hybrid sterility may explain the fertility penalty observed with ALS introgression. Moreover, this linkage might explain why sequenced herbicide-resistance ALS alleles from sympatric A. tuberculatus and A. hybridus populations show independent evolution.

Amaranthus hybridus can be pollinated frequently by A. tuberculatus under field conditions.

Recent studies have confirmed that weedy Amaranthus species are capable of interspecific hybridization, and such hybridization may foster the evolution of herbicide resistance. However, the extent to which hybridization among these species occurs in nature is unknown. The purpose of this study was to determine the frequency under field conditions at which A. hybridus, a monoecious and predominantly self-pollinated species, would be pollinated by A. tuberculatus, a dioecious species. To do this, parents carrying different alleles at the ALS locus, which encodes a herbicide target site, were used. Male A. tuberculatus parents were homozygous for a dominant herbicide-insensitive allele, while A. hybridus parents were homozygous for a sensitive form. Hybrid progeny therefore could be detected via herbicide selection. Mean hybridization frequencies between 0.4 and 2.3% were obtained, depending on the proximity between parents (P=0.02). The robustness of the hybrid selection assay was verified using a molecular marker and DNA content analyses. Using these techniques, more than 99% of the progeny that survived the herbicide were confirmed to be hybrids. Frequencies obtained in this study were many times higher than the generally expected rate of mutation. Therefore, even minimal fertility in hybrid progeny would support the view that hybridization could play a role in adaptive evolution of weedy Amaranthus species.

In vivo genotoxicity of atrazine to anuran larvae.

Atrazine has been an environmental contaminant for more than two decades. While there can be little dispute as to the presence of atrazine in non-target watersheds, the debate has centered on the consequences of this contamination. The purpose of this study was to determine if atrazine is genotoxic to developing anurans. Anurans are one of the groups that have the highest potential for being affected by watershed contamination. In initial studies, larvae from two anuran species were exposed to known genotoxic agents. Upon flow cytometric analysis, those organisms exposed to the genotoxic agents resulted in a statistically significant increase in nuclear heterogeneity. Having demonstrated that flow cytometric analysis could be used to detect genotoxicity in anuran larvae, the larvae of the two species were exposed to different levels of atrazine for various durations. The concentrations and lengths of exposure were consistent (albeit on the higher side) with conditions found in the Midwestern US. In neither species was an increase in nuclear heterogeneity observed. Thus, atrazine at levels and time of exposure representing conditions found contaminating Midwestern watersheds does not appear to be genotoxic to developing anurans.

Comparing the clastogenic potential of atrazine with caffeine using Chinese hamster ovary (CHO) cells.

The agronomically important herbicide atrazine has been reported to cause damage to animal chromosomes at levels of atrazine found contaminating drinking water supplies. While documenting potential chromosome damage is important it is equally important to compare the damage with the potential consequences of compounds readily found in our food and water supply. In this study atrazine and caffeine, a ubiquitous food additive, were compared at equal levels and at real exposure levels for their ability to damage animals chromosomes in cell culture. Nuclei and chromosomes from treated and control cells were analyzed by flow cytometry. At extremely low levels, atrazine was found to be a more potent clastogen. Caffeine had no effect on the chromosomes at the lower levels. Both chemicals were genotoxic at the potential exposure levels with caffeine being more disruptive than atrazine. Atrazine appears to be a more potent damaging agent than caffeine at similar levels of exposure; however, the levels of caffeine one is exposed to during everyday life appears to be more damaging on the endpoints analyzed in this study than the levels of atrazine found contaminating water supplies. The advantages and limitations of whole cell clasotgenicity are also presented in light of these results.

Use of fluorescence genomic in situ hybridization (GISH) to detect the presence of alien chromatin in wheat lines differing in nuclear DNA content.

BACKGROUND: Many times small differences in genome size are reported between or within plant species in which no cytologic confirmation is made. Attempts to repeat these studies have met with limited success. The controversy then becomes whether or not these small differences that were not confirmed cytologically are real. The present study was undertaken to determine if the approximately 1% nuclear variation seen by flow cytometry among wheat lines selected for aluminum response was due to actual chromatin differences. METHODS: The three parental wheat cultivars used in the aluminum selection along with the isolines resulting from the selection were analyzed. One parental line had previously been reported to have alien chromatin substituted for the corresponding wheat homologous chromatin. Genomic in situ hybridization was used to determine the presence or absence of rye chromatin in three cultivars and six near-isolines of wheat. RESULTS: Upon observing metaphase chromosomes of the Century parent and its isolines, two of the chromosomes were observed to be one-half yellow-orange, indicating rye chromatin with the remaining portion of the chromosomes and the other 40 wheat chromosomes having no label indicating wheat chromatin. In the Chisholm parent and its isolines, none of the chromosomes were labeled, indicating the absence of rye chromatin. In addition, none of the third parents' chromosomes had the rye yellow-orange signal. CONCLUSIONS: The wheat lines with the larger DNA contents were observed to have alien DNA present. DNA differences between the normal wheat chromosomes and the substituting alien chromatin were calculated based on total chromosome length. The increase in genome size of the wheat lines containing the alien chromatin appears to be the result of the alien chromatin having approximately 43% more DNA than the wheat chromatin it is replacing. Thus, the small DNA difference previously reported by flow cytometry was demonstrated to be a real DNA variation due to the presence of small fragments of alien chromosomes added to the wheat genome.

Antimutagenic activity of chemical fractions isolated from a commercial soybean processing by-product.

Commercial products of agronomic crop plants may become a reliable and inexpensive source of phytonutrients, such as antimutagenic food supplements. We previously demonstrated that PCC, an ethanol extract of a commercial soybean processing by-product, was able to repress induced genomic DNA damage, whole cell clastogenicity, and point mutation in mammalian cells. In this paper we separated PCC into a series of chemically defined fractions and determined their ability to repress induced mutagenic damage in Chinese hamster lung cells, Chinese hamster ovary cells and human lymphocytes. Fraction PCC70 (PCC 70% methanol eluate) contained the flavonoids from PCC and daidzin and genistin repressed 2-acetoxyacetylaminofluorene (2AAAF)-induced DNA damage measured with single cell gel electrophoresis. Genistein, however, enhanced the genotoxic impact of 2AAAF. Fraction PCC100 (PCC 100% methanol eluate) had the greatest level of antigenotoxic activity against 2AAAF in CHO cells and repressed the genotoxic capacity of the dietary carcinogen 2-amino-3-methylimidazo-(4,5-f)quinoline (IQ) in human lymphocytes. These data indicate that commercial soybean products and by-products may be a source of chemoprotective food additives.

Reference standards for determination of DNA content of plant nuclei.

Flow cytometry was used to compare 14 potential reference standards for plant DNA content determination. Both chicken and plant internal standards were used, as were propidium iodide (PI) and 4'-6-diamidino-2-phenylindole (DAPI) as fluorochromes. Means and standard errors of the means are presented for the 14 potential reference standards, and the means are compared to those obtained by Feulgen densitometry. Five species are recommended as an initial set of international standards for future plant DNA content determinations: Sorghum bicolor cv. Pioneer 8695 (2C = 1.74 pg), Pisum sativum cv. Minerva Maple (2C = 9.56 pg), Hordeum vulgare cv. Sultan (2C = 11.12 pg), Vicia faba (2C = 26.66 pg), and Allium cepa cv. Ailsa Craig (2C = 33.55 pg). It is recommended that the reference standard of choice be one with 2C and 4C nuclear DNA content peaks similar to, but not overlapping, the 2C and 4C peaks of the target species. We recommend PI as the fluorochrome of choice for flow cytometric determination of plant DNA content. DAPI should be used only if the estimated DNA value is corroborated by using a second stain that has no bias for AT- or GC-rich sequences within genomes.

The use of single cell gel electrophoresis and flow cytometry to identify antimutagens from commercial soybean by-products.

Single cell gel electrophoresis (alkaline Comet assay) and flow cytometric methods were combined into an assay that enables the analysis of direct DNA damage and longer-term whole cell clastogenicity in mammalian cells. We employed these techniques to analyze the antimutagenic activity of by-products of commercial soybean processing. At a concentration of 1 mg/ml, the soybean molasses by-product was found to repress 66% of the mutagenic capacity of the direct-acting mutagen 2-acetoxyacetylaminofluorene (2AAAF) in Chinese hamster lung (CHL) cells. At a concentration of 50 microg/ml, fraction PCC (an ethanol extract of soybean molasses) repressed 70% of the genotoxic potency of 500 nM 2AAAF as measured by the Comet assay. Fraction PCC was also effective in protecting CHL cells from 2AAAF-induced clastogenic damage. Using a forward mutation assay in Chinese hamster ovary cells (line AS52), PCC protected the cells against 2AAAF-induced cytotoxicity and point mutation at a specific gene target. These data indicate that agronomic crops such as soybean may yield a wealth of commercially available antimutagenic agents that may be suitable as chemoprotective food supplements.

The clastogenic potential of triazine herbicide combinations found in potable water supplies.

Pesticide contamination of drinking water supplies has increased over the past decade. A major concern is how exposure to combinations of low levels of pesticides, especially herbicides, could affect public health. Flow cytometric analysis was performed to determine the clastogenic potential of herbicide interaction on Chinese hamster ovary (CHO) cells. The cells were exposed to atrazine, simazine, cyanazine, and all possible combinations of these chemicals for 48 hr. Two concentrations were used for each sample: the U.S. EPA maximum contamination level (MCL) and the highest contamination level found in Illinois water supplies. Nuclei were isolated from the cells and analyzed by flow cytometry. The effects of clastogenicity were measured by the coefficient of variation (CV) of the G1 peak of whole cells and the change in CV of the largest chromosome in the flow karyotype. At both levels tested, atrazine caused chromosomal damage to the CHO cells. Simazine was observed to induce whole-cell clastogenicity but not flow karyotype damage. Cyanazine did not induce any measurable chromosomal damage in either analysis. Each of the herbicides, although all three were triazines, had different effects with respect to chromosome damage as measured by flow cytometry. CHO cells treated with a combination of atrazine and simazine, or atrazine and cyanazine, were observed to have whole-cell and flow karyotype damage. This damage was, however, equal to or less severe than the damage caused by either atrazine or simazine alone. No synergy was observed. When all three herbicides were combined, three of the four possible combinations gave no observable clastogenic response.

Calibration of the single cell gel electrophoresis assay, flow cytometry analysis and forward mutation in Chinese hamster ovary cells.

The induction kinetics of genetic damage were measured in one clone of a mammalian cell line (CHO AS52) with three genotoxicity assays, the single cell gel electrophoresis (Comet) assay, laser beam flow cytometry and forward mutation. The first two assays allow for the rapid analysis of genotoxic damage in individual nuclei. The alkaline Comet assay detects DNA strand breaks, alkali-labile sites and incomplete excision repair sites. Flow cytometry measures chromosome damage that results in an unequal distribution of nuclear DNA in daughter cells. We calibrated these assays to compare acute DNA damage and longer term clastogenicity with forward mutation at the gpt locus using ethyl methanesulfonate (EMS). The EMS treatments were conducted in F12 medium for 2 h. AS52 cells carry a single functional gpt gene which provides for quantitation of gpt mutants by selecting for 6-thioguanine resistance. EMS induced a concentration-dependent response with median Comet tail moment values of 1.06 microns for the negative control and 64.6 microns with 20 mM. The coefficient of variation (CV) of the negative-control with flow cytometry was 2.33; the CV value increased to 4.87 in cells treated with 20 mM EMS, EMS (8 mM) induced a mutant frequency of 779.8 x 10(-6) at a relative survival of 64.4%. Genetic response factors were calculated and the data demonstrate that the induction kinetics of genetic damage as measured by the Comet assay (15.6) and flow cytometry (14.2) were more closely related than that determined for mutation induction (7.9). These three assays measure a wide spectrum of genetic events at the level of DNA, the gene and the chromosome and demonstrate the usefulness of the Comet assay and flow cytometry as two relatively rapid procedures to detect genotoxic damage in mammalian cells.

Analysis of mutagens with single cell gel electrophoresis, flow cytometry, and forward mutation assays in an isolated clone of Chinese hamster ovary cells.

We investigated the induction of DNA strand breaks in the single cell gel electrophoresis (SCGE or comet) assay with whole cell clastogenicity measured with flow cytometric analysis in cells from an isolated clone of the Chinese hamster ovary (CHO) AS52 cell line. Under identical treatment conditions the responses were compared with forward mutation at gpt using 2-acetoxyacetylaminofluorene (2AAAF), ultraviolet radiation (UV) and ethyl methanesulfonate (EMS). Cytotoxicity for each agent was evaluated in the SCGE and forward mutation assays. Forward mutation was 4-10-fold more sensitive than DNA strand breaks detected in the SCGE assay. For 2AAAF and EMS, the kinetics of the induction of genetic damage were similar for the three assays, although there were differences in sensitivity. With UV, the induction kinetics of gpt mutation differed from that expressed by SCGE and flow cytometric analysis. With the chemical mutagens 2AAAF and EMS, there was a high correlation between the SCGE assay and forward mutation and also between the SCGE assay and flow cytometry. There was no significant correlation between flow cytometry and forward mutation. With UV, only the SCGE assay and flow cytometry were correlated. Agent-specific variations in the intragenomic distribution of DNA damage for each mutagen was measured in the SCGE assay.

Flow cytogenetic analysis of whole cell clastogenicity of herbicides found in groundwater.

Agronomic practices followed in recent years have caused the agrarian sector to depend heavily on agri-chemicals such as herbicides, but herbicides have negative environmental consequences. Their usage has resulted in chemicals being introduced into the groundwater. Although the contaminants are in trace amounts, little is known about their potential clastogenic effects at low concentrations. In the present study, the potential of flow cytometric analysis to detect the whole cell clastogenic properties of low level chemical exposure is examined. Chinese Hamster Ovary (CHO) cells were exposed to three herbicides (atrazine, bentazon and simazine) and two known clastogens (adriamycin and ara-C) at low concentrations for 48 h. Nuclei were isolated from control as well as treatments and analyzed by flow cytometry. The clastogenic property was assessed by measuring the coefficient of variation (CV) of G1 peaks in different treatments. Exposure to known clastogens resulted in increasing CVs with increasing concentrations. Flow cytometry was a very accurate and sensitive technique for the whole cell clastogenic assay. The results indicated that atrazine has the potential to cause whole cell clastogenicity, even at a very low concentration. Bentazon showed indications of clastogenic potential but the increases in CVs observed with this herbicide were not statistically significant. The CVs are unaffected by simazine exposure, thus indicating that simazine does not cause whole cell clastogenesis under short term exposure. Flow cytometry proved to be an excellent tool for assaying the clastogenic potential of agri-chemicals.

Identification of the 1RS rye chromosomal segment in wheat by RAPD analysis.

The introgression of rye DNA into the wheat genome was studied using random decamer and specific primers with the polymerase chain reaction (PCR). DNA from paired near-isolines in Chisholm and Arkan backgrounds differing with respect to the presence of a 1 RS.1 BL translocation was amplified with 120 arbitrary sequence primers. Two of the primers (OPR 19 and OPJ07) amplified rye-specific DNA fragments. The OPR19 primer amplified a 1.35-kb fragment that appeared to be specific to the 1 RS.1 BL translocation, based on its presence only in lines carrying the 1 RS. 1 BL translocation. A fragment of the same size was also amplified in 1 RS.1 AL translocation lines. This 1 RS. 1 BL marker locus was designated Ximc 1. The other primer, OPJ07, amplified a 1.2-kb DNA sequence, that was designated Ximc 2, specific to the wheat-rye translocation in various wheat backgrounds. The sequences of the two marker loci were found to be different from each other. The Ximc 1 locus was a low-copy sequence which was also present in Balboa rye genomic DNA. Through the use of specific primers, the presence of the rye-specific marker was confirmed in hexaploid as well as in tetraploid wheat backgrounds. The use of RAPDs for the study of smaller alien introgressions into wheat is discussed.

Relationship between genome size and maturity group in soybean.

Previous studies have reported a correlation between genome size and relative maturity among plant species. The objective of this study was to determine whether such a relationship exists in soybean. Twenty cultivars, representing maturity groups ranging from 000 to IX, were analyzed using flow cytometric procedures. A 15% difference in genome size was observed ranging from 'BSR 201' at 2.88 pg to 'Maple Presto' at 2.51 pg. A highly significant correlation (r = 0.55) was observed between maturity and the genome size of the 20 cultivars.

Nuclear DNA amount, growth, and yield parameters in maize.

Extensive nuclear DNA content variation has been observed inZea mays. Of particular interest is the effect of this variation on the agronomic potential of maize. In the present study, yield and growth data were collected on 12 southwestern US maize open-pollinated populations. These populations, originally cultivated by the Indians of the southwestern US for both human and animal consumption and adapted to various altitudes, were grown in replicated plots at the University of Illinois Agronomy-Plant Pathology South Farm. All growth and yield parameters were found to be negatively correlated with nuclear DNA amount. The negative correlations of nuclear DNA amount and growth parameters were more pronounced at 60 days after planting (DAP) than 30 DAP. Agronomically-important yield parameters, such as ear or seed weight and seed number per plant, also exhibited a significant negative correlations with nuclear DNA amount. These correlations demonstrate how the nucleotype may exhibit a high degree of influence on the agronomic phenotype. Although the results presented here represent only three replications at one location in 1 year, the observations noted suggest that nucleotype plays an integral role in determining the agronomic performance of maize. Further studies are needed to fully document this role.

Flow cytometric DNA analysis of wheat-rye addition lines.

The nuclear DNA content of the 7 wheat-rye chromosome addition lines were determined by flow cytometry. The nuclear DNA content of each line was compared to the original wheat parental line. From this information, the amount of DNA per rye chromosome was calculated. The DNA per chromosome ranged from 0.8 picograms (pg) in chromosome 3R to 1.4 pg in chromosome 7R. Flow cytometry was proven to be a rapid and reliable technique for the evaluation of aneuploid plant populations. Flow cytometry has the potential to allow for more rapid screening of aneuploid and euploid cytological stocks than conventional cytogenetic techniques.