Molecular tools for understanding distribution and spread of weed genotypes

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.

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“…, 2004). Furthermore, microsatellites can assist in tracing the movement and origin of invasive species (Baker et al. , 2007; Okada et al.…”

Section: Discussionmentioning

confidence: 99%

“…The most efficient tools to make inferences about population structure and genetic relatedness in weed species are molecular markers (Anderson, 2008; Bodo Slotta, 2008). Molecular markers can help determine the origin of invasive weed species, monitor their transport to new areas (Baker et al. , 2007; Lu et al.…”

Section: Introductionmentioning

confidence: 99%

Isolation and characterisation of the first microsatellite markers for Cyperus rotundus

Arias

Molin²,

Ray³

et al. 2011

Weed Research

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“…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 ., ).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2013

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Microsatellites were identified and characterised for a worldwide invasive weed, Ageratina adenophora, based on the Illumina sequencing technology. Using the assembled genomic sequences obtained from the Illumina GAII sequencing platform, a total of 3012 microsatellites were identified, of which mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats were 181 (6.0%), 1379 (45.8%), 1064 (35.3%), 220 (7.3%), 73 (2.4%) and 95 (3.2%) respectively. The AC/GT and GAT/ATC motifs were the most frequent motif types of di-nucleotide and tri-nucleotide repeats respectively. To validate the newly identified simple sequence repeat markers, 15 primer pairs were randomly selected to test in 24 individuals of A. adenophora, and all of these primer sets could amplify PCR products of expected size. Of them, eight loci displayed polymorphism with the number of alleles per locus ranging from two to four and values for observed and expected heterozygosities ranging from 0.042 to 1 and from 0.082 to 0.551, with the averages of 0.578 and 0.371 respectively. These novel microsatellites should be useful for investigation of the genetic structure and genetic diversity between the invasive and native populations of this species.

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“…At the same time, it also indicates that more durable species are rapidly spreading. It has been emphasized in various previous studies that resistance to herbicides among populations with high genetic similarities can spread by gene transfer (Rutledge et al, 2000;Stankiewicz et al, 2001;Tsuji et al, 2003;Merotto et al, 2010;Claerhout et al, 2015;Karn and Jasieniuk, 2017), and that gene transfer takes place more often through spreading of seeds rather than through pollens, taking into account the self-pollinating properties of E. oryzoides (Baker et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

Determination of Morphological and Genetic Diversity of ALS (Acetolactate Synthase)- Herbicide-Resistant Echinochloa oryzoides Biotypes in Rice

Altop¹

2018

IJAB

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This work aimed to evaluate the genetic and morphological diversity of 62 biotypes of Echinochloa oryzoides (Ard.) Fritsch.(early watergrass) that are resistant to ALS-inhibitor herbicides (bispyribac-sodium and penoxsulam), using the single sequence repeat (SSR) marker system. To determine the morphological diversity, the weed was grown (five seeds from each population) under screenhouse conditions and morphological characteristics were recorded. Parameter values subjected to a hierarchical clustering analysis showed significant variation among the populations. The genetic variation among populations was determined using the 5′-SSR primer. Populations were classified into two main groups according to the results obtained from the SSR alleles. The allele numbers ranged between 2-6 per locus, the diversity values ranged between 0.27-0.99. The morphological and molecular analyses revealed differences in terms of several quantitative characteristics among the populations examined. Similarities were also found among different E. oryzoides populations grown in different regions in terms of their morphological characteristics, the genetic diversity was found to be higher. There is a potential for the spread of resistance through gene flow owing to high genetic diversity and low differentiation among population of E. oryzoides. Under such situations to prevent further resistance spread, early watergrass management in this area should focus both on reducing seed movement among rice fields and the field management practices such as implementation of crop rotation, use of herbicides with new mode of actions or cultural methods.

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Molecular tools for understanding distribution and spread of weed genotypes

Cited by 11 publications

References 27 publications

Isolation and characterisation of the first microsatellite markers for Cyperus rotundus

Isolation and characterisation of the first microsatellite markers for Cyperus rotundus

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

Determination of Morphological and Genetic Diversity of ALS (Acetolactate Synthase)- Herbicide-Resistant Echinochloa oryzoides Biotypes in Rice

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