Connie A. Sauder

Closing the gaps: phylogenetic relationships in the Brassicaceae based on DNA sequence data of nuclear ribosomal ITS region

Sequence data from the nuclear encoded ribosomal internal transcribed spacer (ITS) region were used to determine monophyly of tribes, tribal limits, and tribal relationships of 96 so far unassigned or tentatively assigned genera (represented by 101 taxa/accessions) within the Brassicaceae. Maximum-parsimony and maximum-likelihood analyses of 185 ITS Brassicaceae sequences, which also included representatives of each of the 34 currently recognized tribes, supported the separate phylogenetic distinctness of these tribes and permitted the tribal assignment of all but 12 of the unassigned genera into tribal clades. The data support the recognition of eight new, well-resolved, uni- or oligogeneric tribes recognized herein as the Alyssopsideae [96% bootstrap support (BS); including the central and southwestern Asian Alyssopsis and Calymmatium], Asteae (100% BS; including the Mexican Asta), Eudemeae (97% BS; South American Brayopsis, Eudema, and Xerodraba), Kernereae (96% BS; European Kernera and Rhizobotrya), Notothlaspideae (100% BS; New Zealandic Notothlaspi), Oreophytoneae (100% BS; eastern African Oreophyton and southern European Murbeckiella), and Yinshanieae (100% BS; Chinese Yinshania), as well as the moderately supported Microlepidieae (75% BS; Australian Microlepidium and Carinavalva). Furthermore, the results fully support the recent findings that the tribes Schizopetaleae and Thelypodieae ought to be recognized as two distinct tribes instead of a single tribe, as well as provide some support for the re-establishment of the tribe Cremolobeae, bringing the total number to 44 tribes in the family. Nearly 92% (308) of the 336 genera in the family have been assigned to a tribe. The earlier-published Anastaticeae is taken here to replace the Malcolmieae.

Basis for Herbicide Resistance in Canadian Populations of Wild Oat (Avena fatua)

Abstract Wild oat is the second-most abundant, but most economically important, weed across the Canadian Prairies of western Canada. Despite the serious economic effects of resistance to acetyl-CoA carboxylase (ACC) or acetolactate synthase (ALS) inhibitors or both in this weed throughout the Northern Great Plains of North America, little research has examined the basis for herbicide resistance. We investigated target-site and nontarget-site mechanisms conferring ACC- and ALS-inhibitor resistance in 16 wild oat populations from across western Canada (four ACC-inhibitor resistant, four ALS-inhibitor resistant, and eight ACC- and ALS-inhibitor resistant). The ACC1 mutations were found in 8 of the 12 ACC inhibitor-resistant populations. The Ile1781Leu mutation was detected in three populations, the Trp2027Cys and Asp2078Gly mutations were in two populations each, and the Trp1999Cys, Ile2041Asn, Cys2088Arg, and Gly2096Ser substitutions were in one population each. Three populations had two ACC1 mutations. Only 2 of the 12 ALS inhibitor-resistant populations had an ALS target-site mutation—Ser653Thr and Ser653Asn substitutions. This is the first global report of ALS target-site mutations in Avena spp. and four previously undocumented ACC1 mutations in wild oat. Based on these molecular analyses, seedlings of five ACC + ALS inhibitor-resistant populations (one with an ACC1 mutation; four with no ACC or ALS mutations) were treated with malathion, a known cytochrome P450 monooxygenase inhibitor, followed by application of one of four ACC- or ALS-inhibiting herbicides. Malathion treatment often resulted in control or suppression of these populations, suggesting involvement of this enzyme system in contributing to resistance to both ACC and ALS inhibitors. Nomenclature: Wild oat, Avena fatua L. AVEFA.

PHYLOGENETIC RELATIONSHIPS IN THE TRIBES ANCHONIEAE, CHORISPOREAE, EUCLIDIEAE, AND HESPERIDEAE (BRASSICACEAE) BASED ON NUCLEAR RIBOSOMAL ITS DNA SEQUENCES

Abstract Sequence data from the nuclear ITS region of 118 species (152 accessions) were used to test the monophyletic status and interrelationships of four related tribes in the Brassicaceae: Anchonieae, Chorisporeae, Euclidieae, and Hesperideae. Both maximum parsimony and maximum likelihood analyses support the recognition of the tribes Hesperideae (unigeneric, Hesperis L.) and Chorisporeae (3 genera, including Chorispora R. Br. ex DC., Diptychocarpus Trautv., and Parrya R. Br.), whereas the Anchonieae and the Euclidieae each separate into two distinct and distant clades (designated here as Anchonieae I and II and Euclidieae I and II). The data also support the exclusion of eight genera from the latter four tribes, with appropriate tribal assignment given in parentheses: Aubrieta Adans. (Arabideae), Blennodia R. Br. (Camelineae), Erysimum L. (Camelineae), Goldbachia DC. (unresolved), Hesperidanthus (B. L. Rob.) Rydb. (Schizopetaleae), Notothlaspi Hook. f. (unresolved), Pseudocamelina (Boiss.) N. Busch (Thlaspideae), and Zuvanda (Dvorák) Askerova (unresolved). The genus Malcolmia R. Br. (ca. 35 species) was paraphyletic and divided into three tribal clades, providing support for the separate genera Malcolmia, Strigosella Boiss., and Zuvanda. The genera Anchonium DC., Desideria Pamp., Eremobium Boiss., Erysimum, Iskandera N. Busch, Matthiola R. Br., Morettia DC., Neotorularia Hedge & J. Léonard, Rhammatophyllum O. E. Schulz, Sisymbriopsis Botsch. & Tzvelev, Sterigmostemum M. Bieb., and Tetracme Bunge each fell within a single tribal clade but were not monophyletic.

Phylogenetic relationships in the tribe Alysseae (Brassicaceae) based on nuclear ribosomal ITS DNA sequences

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 85 species (131 accessions) were used to determine the tribal limits, monophyly status, and phylogenetic intra-tribal relationships of genera within the tribe Alysseae (Brassicaceae). Both maximum parsimony and maximum likelihood analyses support the recognition of the tribe Alysseae s. str. (12 genera: Alyssoides, Alyssum, Aurinia, Berteroa, Bornmuellera, Clastopus, Clypeola, Degenia, Fibigia, Galitzkya, Hormathophylla, and Physoptychis). Six well-supported clades were recognized within the Alysseae clade, including two Alyssum clades (one of which includes Clypeola), an Alyssoides and allies clade (includes Alyssoides, Bornmuellera, Clastopus, Degenia, Fibigia, Hormathophylla, and Physoptychis), a Berteroa and allies clade (includes Aurinia, Berteroa, and Galitzkya), a Bornmuellera clade, and a Hormathophylla clade. Morphological and cytological support for these clades is reviewed. The ITS data support the exclusion of...

Acetolactate Synthase Target-Site Mutations and Single Nucleotide Polymorphism Genotyping in ALS-Resistant Kochia (Kochia scoparia)

Abstract The molecular basis for acetolactate synthase (ALS)–inhibitor resistance was determined for 6 susceptible (HS) and 24 resistant (HR) kochia populations from western Canada. The latter included 3 HR populations from Alberta (AB), 3 from Manitoba (MB), and 18 from Saskatchewan (SK). HR plants survived application of the ALS-inhibitor herbicide thifensulfuron–tribenuron mixture in the greenhouse. Most of the HR populations were heterogeneous and contained both HR and HS individuals. The molecular basis for resistance was determined in 273 HR individuals by sequencing the ALS gene (2,270 base pair [bp]) or by conducting a TaqMan genotyping assay developed in this study using real-time polymerase chain reaction (PCR) for single nucleotide polymorphism (SNP) 1709, where a G to T substitution resulted in a Leu for Trp substitution at amino acid position 574 (Trp574Leu mutation). A total of 16 SNPs were identified in the ALS gene sequences (0.7% polymorphism), 5 of which resulted in amino acid changes that confer resistance to ALS-inhibiting herbicides. The SNPs correspond to three target-site mutations: Pro197 (SNPs 565 and 566), Asp376 (SNP 1116), and Trp574 (SNPs 1708 and 1709). The Trp574Leu mutation was predominant (189 HR plants). The next most common mutation was the highly variable residue Pro197 (44 HR plants) with substitution by one of nine amino acids. The least-frequent were Asp376Glu (9 plants) and Trp574Arg (3 plants) substitutions. The presence of two ALS target-site mutations was found in 30 individual kochia plants, the first report from field-selected weed populations. These include combinations Pro197 + Trp574 (23 plants) and Pro197 + Asp376 (7 plants). The detection of Pro197, Asp376, and Trp574 mutations, as well as both combinations, from geographically separate regions suggests multiple origins of these mutations. Nomenclature: Thifensulfuron; tribenuron; kochia, Kochia scoparia (L.) Schrad. KCHSC, synonym: Bassia scoparia (L.) A.J. Scott

Phylogenetic relationships in the tribes Schizopetaleae and Thelypodieae (Brassicaceae) based on nuclear ribosomal ITS region and plastid ndhF DNA sequences

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region and plastid gene ndhF of 95 species, represented by 147 accessions, were used to determine the tribal limits, monophyly status, and phylogenetic intra-tribal relationships of genera within the New World tribe Schizopetaleae (formerly Thelypodieae; Brassicaceae). Maximum parsimony, Bayesian, and maximum-likelihood analyses all support the separate recognition of three distinct and generally well-supported clades. The largest corresponds to the North–South American Thelypodieae (27 genera: Catadysia, Caulanthus, Chaunanthus, Chilocardamum, Chlorocrambe, Coelophragmus, Dictyophragmus, Dryopetalon, Englerocharis, Hesperidanthus, Mostacillastrum, Neuontobotrys, Polypsecadium, Pringlea, Pterygiosperma, Romanschulzia, Sibara, Sibaropsis, Stanleya, Streptanthella, Streptanthus, Thelypodiopsis, Thelypodium, Thysanocarpus, Warea, Weberbauera, and Werdermannia). The remaining six South American Schizopetaleae genera were divided into t...

Glyphosate- and Acetolactate Synthase Inhibitor-Resistant Kochia (Kochia scoparia) in Western Canada

Abstract In summer, 2011, we investigated suspected glyphosate-resistant (GR) kochia in three chem-fallow fields (designated F1, F2, F3, each farmed by a different grower) in southern Alberta. This study characterizes glyphosate resistance in those populations, based on data from dose–response experiments. In a greenhouse experiment, the three populations exhibited a resistance factor ranging from 4 to 6 based on shoot biomass response (GR50 ratios), or 5 to 7 based on survival response (LD50 ratios). Similar results were found in a field dose–response experiment at Lethbridge, AB, in spring 2012 using the F2 kochia population. In fall 2011, we surveyed 46 fields within a 20-km radius of the three chem-fallow fields for GR kochia. In the greenhouse, populations were screened with glyphosate at 900 g ae ha−1. Seven populations were confirmed as GR, the farthest site located about 13 km from the three originally confirmed populations. An additional GR population more than 100 km away was later confirmed. Populations were screened for acetolactate synthase (ALS)–inhibitor (thifensulfuron ∶ tribenuron) and dicamba resistance in the greenhouse, with molecular characterization of ALS-inhibitor resistance in the F1, F2, and F3 populations. All GR populations were resistant to the ALS-inhibiting herbicide, but susceptible to dicamba. ALS-inhibitor resistance in kochia was conferred by Pro197, Asp376, or Trp574 amino acid substitutions. Based upon a simple empirical model with a parameter for selection pressure, calculated from weed relative abundance and glyphosate efficacy, and a parameter for seedbank longevity, kochia, wild oat, and green foxtail were the top three weeds, respectively, predicted at risk of selection for glyphosate resistance in the semiarid Grassland region of the Canadian prairies; wild oat, green foxtail, and cleavers species were predicted at greatest risk in the subhumid Parkland region. This study confirms the first occurrence of a GR weed in western Canada. Future research on GR kochia will include monitoring, biology and ecology, fitness, mechanism of resistance, and best management practices. Nomenclature: Dicamba; glyphosate; thifensulfuron; tribenuron; cleavers: false cleavers, Galium spurium L. or catchweed bedstraw, Galium aparine L.; green foxtail, Setaria viridis (L.) Beauv.; kochia, Kochia scoparia (L.) Schrad. KCHSC, synonym: Bassia scoparia (L.) A.J. Scott.; wild oat, Avena fatua L.

Acetolactate Synthase (ALS) Target-Site Mutations in ALS Inhibitor-Resistant Russian Thistle (Salsola tragus)

Abstract ALS inhibitor-resistant biotypes are the fastest growing class of herbicide-resistant (HR) weeds. A Canadian ALS inhibitor-resistant biotype of Russian thistle was first reported in 1989. The molecular basis for ALS-inhibitor resistance is unknown for Canadian populations of this polyploid weed species, and was determined in this study for one Alberta and two Saskatchewan HR Russian thistle populations. HR plants survived spray application of the ALS-inhibitor mixture thifensulfuron  :  tribenuron in the greenhouse. All three HR Russian thistle populations were heterogeneous and contained both HR and herbicide-susceptible (HS) individuals. The molecular basis for resistance was determined by sequencing the ALS gene and/or conducting a TaqMan genotyping assay for single nucleotide polymorphism (SNP) for the Trp574Leu mutation. Two target-site mutations were observed: Trp574Leu in all three biotypes (554 individuals) and Pro197Gln in one biotype (one individual), suggesting multiple-founding events for Russian thistle HR populations in western Canada. Segregation patterns among F1 and F2 progeny arrays of HR lines sprayed under greenhouse conditions varied; some segregated (i.e., had HR and HS progeny), whereas other lines were exclusively HR. In contrast, no segregation of molecular types, i.e., Trp574, Trp/Leu574 and Leu574, as would be expected with heterozygosity at a single locus Trp/Leu574, was observed. Such lack of segregation is consistent with the polyploid genome structure of Russian thistle and the presence of two copies of the ALS gene. The presence of more than one ALS gene confounded the ability of the molecular techniques to accurately identify “true” heterozygotes in this study. Nomenclature: Thifensulfuron; tribenuron; Russian thistle, Salsola tragus L. SASKT.

Resistance in Canadian biotypes of wild mustard (Sinapis arvensis) to acetolactate synthase inhibiting herbicides

Abstract Multiple cases of ALS inhibitor-resistant weed biotypes are reported for many species, including wild mustard. The physiological extent and molecular basis of resistance to ALS inhibitors was compared in four biotypes of wild mustard from western Canada: a sulfonylurea (SU)-resistant (R) biotype from Manitoba detected in 1992; an SU (ethametsulfuron)-R biotype from Alberta detected in 1993 (metabolism-based resistance); an SU-R biotype from Manitoba detected in 2002; and a SU- and imidazolinone (IMI)-R biotype from Saskatchewan detected in 2002. Herbicide dose-response experiments confirmed that the two Manitoba biotypes were resistant to the SU herbicides ethametsulfuron and tribenuron:thifensulfuron mixture, whereas the Saskatchewan biotype was resistant to both SU herbicides and to imazethapyr, an IMI herbicide. Sequence analysis of the ALS gene detected target site mutations in three of the four R biotypes, with amino acid substitutions Pro197 (CCT) to Ser (TCT) [Domain A of the gene] in the two SU-R Manitoba biotypes and Trp574 (TGG) to Leu (TTG) [Domain B] in the Saskatchewan biotype. The Alberta SU-R biotype had the same ALS nucleotide and amino acid sequence as the susceptible population at these two positions. Two heterozygous individuals [Trp574 (Tt/gG)] were detected in the Saskatchewan biotype, and genetic segregation for nucleotide bases and resistance phenotype was consistent with single gene control. Nucleotide variation in neutral regions of the ALS gene varied with biotype, with no variation in the two Manitoba biotypes, two variants in the Saskatchewan biotype, and 16 neutral nucleotide polymorphisms (0.9%) in the Alberta biotype. The occurrence of at least three different ALS inhibitor-R biotypes in this important weed species is likely to impact negatively on the use of ALS inhibitors, such as the IMIs, and serves as a warning for strict implementation of herbicide rotations to prevent or delay the evolution and spread of such populations. Nomenclature: Ethametsulfuron; imazethapyr; thifensulfuron; tribenuron; wild mustard, Brassica kaber (DC.) L. C. Wheeler SINAR.

Occurrence and Molecular Characterization of Acetolactate Synthase (ALS) Inhibitor–Resistant Kochia (Kochia scoparia) in Western Canada

Abstract A survey of 109 fields was conducted across western Canada in spring 2007 to determine the extent of ALS-inhibitor and dicamba (synthetic auxin) resistance in kochia. Weed seedlings were collected from fields in three provinces of western Canada and transplanted into the greenhouse. Seeds were harvested from selfed plants, and the F1 progeny were screened for resistance to the ALS-inhibitor mixture thifensulfuron–tribenuron or dicamba. All kochia populations were susceptible to dicamba. ALS inhibitor–resistant kochia was found in 85% of the fields surveyed in western Canada: 80 of 95 fields in Alberta, six of seven fields in Saskatchewan, and all seven fields in Manitoba. For the 93 ALS inhibitor–resistant populations, the mean frequency (±SE) of parental plants classified as resistant was 61 ± 3%. Most of the resistant populations (87%) were heterogeneous and contained both resistant and susceptible individuals. ALS sequence data (Pro197 and Asp376 mutations) and genotyping data (Trp574 mutation) obtained for 87 kochia parental (i.e., field-collected) plants confirmed the presence of all three target-site mutations as well as two mutational combinations (Pro197 + Trp574, Asp376 + Trp574) in resistant individuals. Nomenclature: Dicamba; thifensulfuron; tribenuron; kochia, Kochia scoparia (L.) Schrad. KCHSC, synonym: Bassia scoparia (L.) A.J. Scott