Journal of Heredity Advance Access originally published online on April 13, 2005
Journal of Heredity 2005 96(4):410-416; doi:10.1093/jhered/esi065
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Amplified Fragment Length Polymorphism-Based Genetic Relationships Among Weedy Amaranthus Species
Department of Crop Sciences, University of Illinois, Urbana, IL 61801
Address correspondence to Patrick J. Tranel at the address above, or e-mail: tranel{at}uiuc.edu.
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Abstract |
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Weedy Amaranthus species frequently cause economically significant reductions in crop yields. Accurate identification of Amaranthus species is important for efficient weed control, but Amaranthus species can interbreed, which might cause difficulty when identifying hybrid-derived specimens. To determine which of several economically important weedy Amaranthus species are most genetically similar, and thus most likely to produce viable hybrids, we performed amplified fragment length polymorphism (AFLP)-based unweighted pair group method with arithmetic mean (UPGMA) analysis on 8 of these species, with 141 specimens representing 98 accessions. The analysis grouped the specimens into four principal clusters composed of Palmer amaranth (Amaranthus palmeri S. Wats.) and spiny amaranth (Amaranthus spinosus L.); Powell amaranth (Amaranthus powellii S. Wats.), redroot pigweed (Amaranthus retroflexus L.), and smooth pigweed (Amaranthus hybridus L.); waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and sandhills amaranth (Amaranthus arenicola I.M. Johnst.); and tumble pigweed (Amaranthus albus L.). The cluster analysis provided evidence suggesting hybridization among Powell amaranth, redroot pigweed, and smooth pigweed. Further investigations using molecular analysis of the ribosomal internal transcribed spacer region from atypical plants supported this notion. Three species, Palmer amaranth, sandhills amaranth, and waterhemp, are dioecious; nevertheless, the Palmer amaranth and waterhemp–sandhills amaranth clusters were distinct from each other. The Palmer amaranth–spiny amaranth cluster included a cluster of Palmer amaranth and two clusters of spiny amaranth, a monoecious species. Thus the dioecious species Palmer amaranth and waterhemp may not necessarily hybridize with each other more readily than they would to one or more of the monoecious Amaranthus species.
The genus Amaranthus L. includes many widely dispersed, economically important weed species. Correct identification of Amaranthus weed species is important for efficient weed control (Horak et al. 1994; Sweat et al. 1998). As examples, Coetzer et al. (2002) reported significantly different responses to glufosinate herbicide among waterhemp (Amaranthus tuberculatus (Moq.) Sauer and Amaranthus rudis Sauer), redroot pigweed (Amaranthus retroflexus L.), and Palmer amaranth (Amaranthus palmeri S. Wats.); and Mayo et al. (1995) reported that Palmer amaranth was more difficult to control with various herbicides than were other Amaranthus species. Correct identification of Amaranthus species is often difficult, however, and misidentification is common (Horak et al. 1994; Wax 1995). For example, Ahrens et al. (1981) found that 13 of 14 accessions that weed scientists identified as redroot pigweed were actually smooth pigweed (Amaranthus hybridus L.) or Powell amaranth (Amaranthus powellii S. Wats.). As another example, Wetzel et al. (1999a) noted, based on molecular marker analysis of ribosomal internal transcribed spacer (ITS) regions, that 12 of 92 Amaranthus accessions that had been collected and identified by weed scientists were misidentified. Although molecular marker-based identification is impractical for routine use, it could be useful for verifying the identity of troublesome biotypes with ambiguous or atypical morphology.
Identification of Amaranthus specimens could be confounded by interspecies hybridization. Murray (1940), using controlled pollinations, demonstrated that interspecies hybridization in Amaranthus is possible. Interspecies hybridization and transfer of herbicide resistance in Amaranthus has been demonstrated between two dioecious species, Palmer amaranth and waterhemp, and between waterhemp and a monoecious species, smooth pigweed (Tranel et al. 2002; Wetzel et al. 1999b). Interspecies hybridization has also been reported in wild Amaranthus populations. Grant (1959) described the karyotypes of putative interspecies Amaranthus hybrids. Hauptli and Jain (1984) described hybrids derived from cultivated amaranth (Amaranthus caudatus L.) x redroot pigweed growing wild near cultivated amaranth that had intermediate morphology and isozyme profiles similar to cultivated amaranth, but with a low frequency of redroot pigweed isozymes.
Molecular genetic cluster analysis could help define the genetic similarities among Amaranthus species and indicate which species are likely to produce fit interspecies hybrids. Previous molecular genetic analyses of Amaranthus species have been designed to determine ancestors of domestic species (Sun et al. 1999), have not included waterhemp (Chan and Sun 1997), have not included multiple samples of species (Lanoue et al. 1996), or have used single marker systems (Wetzel et al. 1999a). Using amplified fragment length polymorphism (AFLP) markers (Vos et al. 1995), we performed an unweighted pair group method with arithmetic mean analysis (UPGMA) of Amaranthus accessions representing agronomically important weedy Amaranthus species from a wide geographical area to determine genetic similarity and potential for interspecies hybridization.
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Materials and Methods |
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Plant Materials
Seeds were obtained from plants growing at sites throughout Illinois, from M. Horak (formerly of Kansas State University), who assembled a collection with cooperators across the United States and Canada, and from the USDA-ARS North Central Regional Plant Introduction Station (NCRPIS) in Ames, IA (Table 1). Seeds were stratified at approximately 5°C in damp paper towels for 2–4 weeks and planted in flats. Seedlings 10–15 cm tall were transplanted into 1.4 L pots. Plants were grown from seeds in greenhouses at Urbana, IL, with a 16-h photoperiod and supplemental sodium-vapor lighting at day and night temperatures of 28°C and 22°C, respectively.
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Morphological Identification
Plants were grown to maturity and identified based on morphology using taxonomic keys (Horak et al. 1994; Mosyakin and Robertson 1996). Following the proposal of Pratt and Clark (2001), we treated tall and common waterhemp as a single species, A. tuberculatus. Mature plants with uncertain identity were preserved by pressing to allow repeated examination by us and others for final identification. Our final identifications were revised from the collectors' field notes for nine accessions originally identified as redroot pigweed and one originally identified as Powell amaranth. These accessions were renamed (Powell 1, 2, 5, and 6; and Smooth 17, 20, 23, 24, 25, and 26) in accordance with the revised identification. There were 141 specimens representing 98 accessions and 8 species, with 1 or 2 specimens for each accession.
Molecular Methods
DNA was extracted from leaf tissue using a modification of the cetyltrimethylammonium bromide (CTAB) method of Doyle and Doyle (1990). Approximately 250–500 mg young leaf tissue was placed in a 1.5 ml microcentrifuge tube, frozen in liquid nitrogen, and ground in the tube with a micropestle. The ground tissue was suspended in 600 µl extraction buffer (100 mM Tris-Cl pH 8.0, 1.4 M NaCl, 20 mM EDTA, 2% CTAB, 20 mM ß-mercapto-ethanol) and incubated 30 min at 56°C with occasional mixing by inversion, followed by chloroform extraction. The extracted DNA was incubated 30 min at 37°C with 50 µg RNAase-A (Sigma, St. Louis, MO), followed by a second chloroform extraction and isopropanol precipitation. Dried samples were dissolved in 100 µl sterile water. The quality and concentration of the DNA was evaluated by viewing samples in agarose gels and by spectrophotometer analysis of 260 nM and 280 nM light absorption. An EcoRI test digest of each DNA sample was performed on 500 ng DNA with 5 units EcoRI (Invitrogen, Carlsbad, CA) to verify the suitability of the DNA as a substrate for enzymatic modification. (Several prostrate pigweed [Amaranthus blitoides S. Wats.] accessions were grown, but were dropped from the study because of difficulty obtaining satisfactory DNA samples from the small leaves.) AFLP (Vos et al. 1995) was performed using the Applied Biosystems kit for "regular size" plant genomes (Applied Biosystems, Foster City, CA). Template preparation was performed following the Applied Biosystems protocol, including digests with EcoRI and MseI restriction enzymes (Invitrogen) and ligation of complementary adaptors using T4 DNA ligase (New England Biolabs, Beverly, MA). The polymerase chain reactions (PCRs) were performed using a PTC100 thermal cycler (MJ Research, Waltham, MA). The PCR thermocycle profiles were the same as those for the Applied Biosystems protocol, except the denaturing time at 94°C was increased from 1 s to 5 s. The temperature ramp was 1°C/s. Selective PCR was performed with dye-labeled primers from Applied Biosystems, with the final six bases (5'–3'): CACACA, CTAACG, CTCACC, CTCACA, or CAGACA. AFLP products were separated by polyacrylamide gel electrophoresis by technicians at the University of Illinois W. M. Keck Center for Comparative and Functional Genomics using an automated sequencing gel apparatus (ABI Prism 377 DNA sequencer, Applied Biosystems), which read gels and translated them into descriptive computer files. Polymorphic AFLP markers were identified and individuals were scored for presence or absence of AFLP fragments 50–500 bp long, with a 1 bp window for each defined fragment, using the Genotyper 2.0 (Applied Biosystems) computer program.
To aid in identification of morphologically atypical accessions of redroot pigweed, smooth pigweed, and Powell amaranth, the ribosomal ITS region of selected specimens was analyzed by restriction enzyme digestion of ITS PCR products. The PCRs and restriction digests were performed as described by Wetzel et al. (1999a), with modifications. The PCRs were performed in 50 µl with 10 ng DNA, 1.25 units Taq polymerase (Invitrogen), 3 mM MgCl2, 0.3 mM each dNTP, 20 mM Tris-Cl pH 8.4, 50 mM KCl, and 0.3 µM each primer, 5'-GGAAGTAAAAGTCGTAACAAGG-3' and 5'-TCCTCCTCCGCTTATTGATATGC-3'. The PCR was performed in a PTC100 thermal cycler (MJ Research), with an initial denaturing step of 5 min at 94°C and 35 cycles of 1.5 min at 94°C, 1 min at 55°C, and 1.5 min at 72°C, ending with a final extension step of 10 min at 72°C. A 5 µl aliquot of the PCR was analyzed by gel electrophoresis in 1% agarose with 0.5 x TBE buffer to check for amplification of an approximately 750 bp fragment. After verification of amplification, 5 µl aliquots of the PCRs were digested by restriction enzyme DdeI or HaeII (New England Biolabs) in 30 µl reactions, including 3 µl of the manufacturer's 10 x reaction buffer and 5 units of restriction enzyme, with a 2 h incubation at 37°C. Products were separated by horizontal gel electrophoresis with 1% agarose and 0.5 x TBE. Classification of ITS fragments was based on Wetzel et al. (1999a), who showed that PCR amplification products of the smooth pigweed ITS are cut by DdeI and HaeII, those of Powell amaranth are cut by HaeII only, and those of redroot pigweed are cut by neither DdeI nor HaeII.
UPGMA Cluster Analysis
UPGMA analysis was performed with AFLP marker data using the PAUP* version 4.0 computer program (Sinauer Associates, Sunderland, MA; Swofford 2000). Genetic similarities among specimens were calculated from AFLP fragment presence/absence data using Nei and Li's (1979) similarity index. There were 428 polymorphic markers. To estimate the reliability of the UPGMA clusters, a bootstrap analysis was performed with 1000 replications, and a 50% majority rule consensus tree was created, with bootstrap values greater than 50% recorded.
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Results and Discussion |
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The UPGMA analysis separated the specimens into four large clusters: a Palmer amaranth–spiny amaranth cluster, aPowell amaranth–redroot pigweed–smooth pigweed cluster, a waterhemp–sandhills amaranth (Amaranthus arenicola I.M. Johnst.) cluster, and a tumble pigweed (Amaranthus albus L.) cluster (Figure 1). This generally agrees with the classification of Mosyakin and Robertson (1996), which divides Amaranthus into three subgenera: Acnida, composed only of dioecious species, including Palmer amaranth, waterhemp, and sandhills amaranth; Amaranthus, including Powell amaranth, redroot pigweed, and smooth pigweed; and Albersia, including tumble pigweed. Our UPGMA cluster analysis deviates from this classification by placing Palmer amaranth in a separate cluster from waterhemp and sandhills amaranth, and by grouping Palmer amaranth and spiny amaranth in the same cluster.
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The grouping of spiny amaranth, which has monoecious flowering, and Palmer amaranth, which has dioecious flowering, to form one of the main clusters was unexpected. Although spiny amaranth is typically monoecious, its flowers—unlike those of the other monoecious amaranths—are spatially separated (male flowers borne terminally toward the top of the plant and female flowers borne lower on the plant in leaf axils) (Murray 1940). Spiny amaranth might be in transition to developing dioecious flowering, indicating a possible genetic relationship with the dioecious Palmer amaranth (Mosyakin and Robertson 1996). Furthermore, our AFLP-based clustering of Palmer amaranth with spiny amaranth is in agreement with Franssen et al. (2001), who reported that the number and density of dimples on pollen of Palmer amaranth differed significantly from sandhills amaranth and waterhemp, but was similar to several monoecious Amaranthus species. More specifically, the density of dimples on pollen from Palmer amaranth, 25.60/µm2, was closest to that of spiny amaranth, 25.13/µm2, in a range from 18.07/µm2 for grain amaranth to 56.07/µm2 for tall waterhemp. Thus our AFLP-based clustering of spiny amaranth with Palmer amaranth has some support in morphologically based analyses by other researchers.
The Powell amaranth–redroot pigweed–smooth pigweed cluster was formed from two Powell amaranth, one redroot pigweed, and two smooth pigweed clusters. Clustering of these three species together was expected based on their very similar morphologies; they are readily distinguished only when they reach reproductive growth, and even then they are often misidentified (Ahrens et al. 1981; Horak et al. 1994). The Powell amaranth clusters included 21 specimens representing 16 accessions. Most were identified as Powell amaranth, but two accessions were identified as smooth pigweed (Smooth 23 and 20) and one as redroot pigweed (Redroot 8). Many of the accessions in the Powell amaranth clusters were morphologically atypical, and based on our morphological examinations, we revised the identities of six accessions from their original field identifications. The Powell amaranth-A cluster included Powell 2a, 2b, 5, 6, 9a, and 9b, and Smooth 20a, 20b, and 23. Except for Powell 9, the accessions had been identified as redroot pigweed when collected in the field by others. We revised the identification of the accessions based on morphology and renamed them according to our identification. Powell 2, 6, and 9, and Smooth 20 and 23 were typed for ribosomal ITS markers and had the Powell amaranth ITS marker type (Figure 2). We considered Smooth 20 a possible smooth pigweed x Powell amaranth hybrid because the sepals and other floral structures of the mature inflorescence were characteristic of smooth pigweed, but the overall inflorescence structure was most similar to Powell amaranth (data not shown), and it had the Powell amaranth ITS marker type. We also considered Smooth 23 a possible smooth pigweed x Powell amaranth hybrid because it had smooth pigweed-like morphology and the Powell amaranth ITS marker type. Powell 9 was identified by collectors in the field and by us in the laboratory as Powell amaranth, but it was heterozygous for ribosomal ITS markers, with fragments indicative of both Powell amaranth and redroot pigweed. Therefore all the members of the Powell amaranth-A cluster were in some way atypical. The Powell amaranth-B cluster included Powell 1, 3, 4, 7, 8a, 8b, 10, 11, 12a, 12b, and 13, and Redroot 8 representing nine Powell amaranth and one redroot pigweed accession. Powell 1 was identified as redroot pigweed in the field, but we found it had Powell amaranth morphology and the Powell ITS marker type, so we renamed it. Redroot 8, which we identified morphologically as redroot pigweed, had sepals that were similar to Powell amaranth. Thus many members of the Powell amaranth clusters, especially those in the cluster Powell amaranth-A, were atypical.
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The redroot pigweed cluster included nine specimens representing seven accessions (Figure 1). In contrast to the Powell amaranth cluster, identification of the members of the redroot pigweed cluster was straightforward. All were identified by collectors in the field and by us as redroot pigweed.
There were two smooth pigweed clusters, including 29 specimens representing 22 accessions. The smooth pigweed-A cluster included 10 specimens (Smooth 1, 2a, 2b, 3, 10, 11, 12, 17b, 25, and 26) representing 9 accessions, and the smooth pigweed-B cluster included 19 specimens (Smooth 4, 5a, 5b, 6a, 6b, 7a, 7b, 8, 9, 13, 14a, 14b, 15, 16a, 16b, 17a, 18, 19, 24) representing 14 accessions (Figure 1). Accessions in the smooth pigweed clusters had typical smooth pigweed morphology. Three accessions in the smooth pigweed clusters were not identified in the field as smooth pigweed: Smooth 17 was originally identified as redroot pigweed, Smooth 24 was originally identified as Powell amaranth, and Smooth 25 was originally identified as redroot pigweed. One of these, Smooth 25, was analyzed for the ITS marker and had the smooth pigweed ITS marker type (Figure 2). All three had smooth pigweed morphology, and on that basis we renamed them smooth pigweed.
The waterhemp–sandhills amaranth cluster included 39 waterhemp specimens representing 25 accessions, all of which were identified both in the field and by us as waterhemp. This cluster included a small waterhemp subcluster with Waterhemp 1a, 1b, 2, 3, 24a, and 24b, and a large waterhemp subcluster including 32 specimens representing 20 waterhemp accessions (Figure 1). Following Pratt and Clark's (2001) proposal that A. rudis and A. tuberculatus compose a single waterhemp species, we treated all the waterhemp accessions as one species, A. tuberculatus. There was a sandhills amaranth subcluster including the only two sandhills amaranth accessions, both from Kansas, plus the only waterhemp accession from outside Illinois, Waterhemp 4 from Fulton County, Ohio. Pratt and Clark (2001) noted that Ohio waterhemp accessions were much more variable than those of other states. Therefore it is not unprecedented to find an Ohio waterhemp accession diverging from the other waterhemp accessions.
Our AFLP-based UPGMA analysis, which indicated sandhills amaranth was more genetically similar to waterhemp than to Palmer amaranth, differs from the morphology-based taxonomy of Mosyakin and Robertson (1996). Within the subgenus Acnida, where they grouped all dioecious species, they placed sandhills amaranth and Palmer amaranth (along with two other species, Amaranthus watsonii and Amaranthus greggii) in the Saueranthus section of Amaranthus subgenus Acnida. However, they placed the waterhemps in another section, Acnida, indicating that, on a morphological basis, sandhills amaranth is more similar to Palmer amaranth than to waterhemp.
The tumble pigweed cluster included 17 tumble pigweed specimens representing 11 accessions, forming an independent cluster that was not joined to any other cluster, except the overall Amaranthus group.
In summary, the AFLP data were useful for grouping several weedy Amaranthus species in UPGMA analysis. The analysis indicated a genetic similarity between Palmer amaranth and spiny amaranth; among redroot pigweed, smooth pigweed, and Powell amaranth; and between waterhemp and sandhills amaranth. Tumble pigweed formed an independent cluster. Though the only dioecious species were Palmer amaranth, waterhemp, and sandhills amaranth, these were not combined in a single cluster. Many of the accessions in the Powell amaranth clusters were atypical and some were suspected hybrids, including one that was heterozygous for Powell amaranth and redroot pigweed ITS markers. This indicates some wild Powell amaranth, redroot pigweed, and smooth pigweed populations might be derived from interspecies hybrids. On the basis of these findings, and considering only genetic similarity, viable hybrids are most likely to form between Palmer amaranth and spiny amaranth; among smooth pigweed, redroot pigweed, and Powell amaranth; and between waterhemp and sandhills amaranth. Also, the dioecious species waterhemp and Palmer amaranth might be as likely to hybridize with certain monoecious Amaranthus species as with each other.
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Acknowledgments |
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We thank Ken Robertson, taxonomist with the Illinois Natural History Survey, for help with plant identification; David Brenner at North Central Regional Plant Introduction Station for advice on Amaranthus culture; Mike Horak, Aaron Hager, and others who provided seeds; and Federico Trucco for help with the ITS analysis. This material is based on work partially supported by the USDA under award no. 2001-35320-11002 and by a grant from the Illinois Soybean Program Operating Board.
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Footnotes |
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Corresponding Editor: William Tracy
Received July 23, 2004
Accepted February 15, 2005
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References |
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