Isolation and characterisation of the first microsatellite markers for Cyperus rotundus

Abstract

SummaryThis is the first report of microsatellite markers for Cyperus rotundus. A total of 191 sequence-specific microsatellite markers were isolated and used to screen 12 accessions of C. rotundus and one accession of Cyperus esculentus collected from 10 different countries. Polymorphisms were observed in 49% of the markers tested, 22% of the markers were monomorphic and 29% had weak or no amplification. The best 57 markers are reported, and cluster analysis was used to analyse their resolving power. BLASTx screening of the contig sequences was also performed. Multiallelic loci over all samples ranged from 24% to 60%. The maximum number of alleles detected by the markers suggests a polyploidy nature of all C. rotundus accessions tested, except for the sample N25-Brazil. Chromosome number was determined for N12-Taiwan and used as an internal flow cytometry standard to estimate the amount of DNA within haploid nuclei of the remaining material. Chromosome numbers estimated for C. rotundus were 16 and 24. The markers identified in this study can be used for the identification of biotypes and detection of potential crosses of C. rotundus, to implement management practices for the effective control of this weed.

Variation in 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) Coding Sequences and Glyphosate Response among <i>Cyperus rotundus</i> L. Populations

“…For this to occur, there had to have been conditions supporting greater incidence of mutation and selection in that region of the world. These results are consistent with the findings determined by RAPD and morphological trait analysis [6] [7] [9] [10] [11]. Mutations conferring resistance to glyphosate had not occurred.…”

“…Four accessions were from the USA and 8 were from outside of the USA. Yellow nutsedge was clearly separated from the purple nutsedge accessions and the purple nutsedge was divided into 3 clusters [11]. In this study, Brazil was grouped with Indonesia, Sudan was with Greece, and Taiwan China, Thailand Australia and El Salvador were grouped with the USA accessions.…”

“…Variations among purple nutsedge populations and clonal relationships have been derived from cluster analyses of morphological traits, chemical analysis of sesquiterpenes and random amplified polymorphic DNA (RAPD) patterns with decamer primers and microsatellite DNA markers [6] [7] [9] [10] [11]. Traditional morphological taxonomy recognized eight varieties and four subspecies based on morphology [12].…”

Large‐scale identification of microsatellites for a major invasive weed, Ageratina adenophora, using the Illumina sequencing technology

“…Molecular markers are one of most important and efficient tools for invasive biological and weedy studies, which helps to determine the origin of invasive weed species, monitor their invasion route, trace source populations, and compare genetic structure and genetic drift between native and invasive populations (Baker et al ., ; Anderson, ). However, the development of molecular markers in weed species has lagged far behind other model plants, and only a few weed species have been investigated for the microsatellite loci (Arias et al ., ). To the best of our knowledge, no large‐scale identification and development of SSR markers has been performed in A. adenophora using the NGS technology, limiting the molecular ecological and genetic research of this invasive weed.…”

Microsatellite variability of sulfonylurea‐resistant and susceptible populations of Schoenoplectus juncoides (Cyperaceae) in Kinki, Japan

“…In this study, we assessed the genetic diversity within and among local populations of S. juncoides in Kinki, Japan that exhibit various degrees of resistance to SU. The knowledge of genetic variation of herbicide‐resistant populations helps to develop weed control practices (Arias et al ., ).…”