SSR and SNP Markers for the Identification of Clones, Hybrids and Species Within the Genus Populus

Abstract Several poplar species within a section, but also between sections, are cross-compatible, thus a high number of interspecies-hybrids occur naturally or have been artificially produced during the last 100 years. Very often, systematically kept records on the production or vegetative propagation of poplar hybrids and/or clones have not been available to date. Hence the origin of the poplar plant material used for the generation of hybrids or clones is not quite clear in many cases, thus making the differentiation between the clones a difficult task. Therefore, genetic markers are needed to clearly identify and differentiate the species and hybrids in the genus Populus, including both identification of existing clones and the breeding of new ones. One aspect of this study is therefore to develop molecular markers for the identification and differentiation of species, hybrids, and clones of the genus Populus.

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Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Biology ◽

10.3390/biology10010036 ◽

2021 ◽

Vol 10 (1) ◽

pp. 36

Author(s):

Te-Hua Hsu ◽

Yu-Ting Chiu ◽

Hung-Tai Lee ◽

Hong-Yi Gong ◽

Chang-Wen Huang

Keyword(s):

Molecular Markers ◽

Expressed Sequence Tag ◽

De Novo ◽

Growth Traits ◽

Gene Diversity ◽

Snp Markers ◽

Cdna Libraries ◽

Functional Markers ◽

Genetic Management ◽

Ssr And Snp Markers

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

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Influence of cutting type and size on rooting of Lavandula dentata L

Revista Brasileira de Plantas Medicinais ◽

10.1590/s1516-05722012000100002 ◽

2012 ◽

Vol 14 (1) ◽

pp. 8-11 ◽

Cited By ~ 4

Author(s):

C.M. Bona ◽

I.R. Biasetto ◽

M. Masetto ◽

C. Deschamps ◽

L.A. Biasi

Keyword(s):

Essential Oil ◽

Vegetative Propagation ◽

Plant Material ◽

The Other ◽

Root Weight ◽

Root Number ◽

Polystyrene Foam ◽

High Quality ◽

Cutting Propagation ◽

Superior Clones

Even though the Lavandula species may be propagated by seeds, it should not be the preferred propagation method because it causes a great lack of uniformity. On the other hand, asexually propagated lavender crops would provide more homogeneous crops, and clones from high quality plant material would increase the odds for obtaining a higher quality essential oil. However, problems such as poor rooting and restrict market availability for superior clones have been a problem in vegetative propagation of the Lavandula species. The objective of this work was to define which type and size of cutting is more adequate for cutting propagation of L. dentata, a very productive Lavandula species. Cuttings with 5, 8, 10 or 13 cm and from the apical or basal parts of stems cut from L. dentata stock plants were placed in Plantmax HT® filled polystyrene foam trays and kept under intermittent mist system for two months. Averages of root number, length of the longest root, fresh and dry root weight, and percentage of rooting were evaluated. Apical cuttings combined 97.9% rooting with an average of 13.2 roots per cutting and basal cuttings 93.7% rooting with 2.98 roots per cutting. Apical cuttings with at least 10 cm in length were considered the most adequate for cutting propagation of L. dentata.

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Gintarasia and Xalocoa, two new genera to accommodate temperate to subtropical species in the predominantly tropical Graphidaceae (Ostropales, Ascomycota)

Australian Systematic Botany ◽

10.1071/sb13038 ◽

2013 ◽

Vol 26 (6) ◽

pp. 466 ◽

Cited By ~ 7

Author(s):

Ekaphan Kraichak ◽

Sittiporn Parnmen ◽

Robert Lücking ◽

H. Thorsten Lumbsch

Keyword(s):

Phylogenetic Analysis ◽

Molecular Markers ◽

Genetic Markers ◽

Phylogenetic Position ◽

New Combinations ◽

New Genera ◽

Phylogenetic Placement ◽

Complex Chemistry ◽

Subtropical Species

The phylogenetic placement of Chapsa lamellifera, C. megalophthalma and Diploschistes ocellatus was studied using a dataset of five genetic markers (mtSSU, nuLSU, RPB1, RPB2 and ITS). As extratropical species occurring in Australasia, C. lamellifera and C. megalophthalma differ from other species in that genus by having relatively large ascomata with muriform ascospores and complex chemistry of either the protocetraric or stictic acids chemosyndrome. D. ocellatus is unique within Diploschistes, in lacking lateral paraphyses and containing the norstictic acid chemosyndrome. Previous phylogenetic analysis gave inconclusive results regarding the phylogenetic position of these taxa, and hence in the present study, a larger sampling of molecular markers was employed. Our results demonstrated that the two Chapsa species and D. ocellatus are not part of their current genera. Consequently, the new genera Gintarasia Kraichak, Lücking & Lumbsch and Xalocoa Kraichak, Lücking & Lumbsch are described to accommodate these species. The new combinations Gintarasia lamellifera (Kantvilas & Vězda) Kraichak, Lücking & Lumbsch, G. lordhowensis (Mangold) Kraichak, Lücking & Lumbsch, G. megalophthalma (Müll. Arg.) Kraichak, Lücking & Lumbsch and Xalocoa ocellata (Vill.) Kraichak, Lücking & Lumbsch are also proposed.

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Genetic diversity and structure of landrace accessions, elite lineages and cultivars of common bean estimated with SSR and SNP markers

Molecular Biology Reports ◽

10.1007/s11033-020-05726-7 ◽

2020 ◽

Vol 47 (9) ◽

pp. 6705-6715

Author(s):

Marina Santos Carvalho ◽

Cintia Machado de Oliveira Moulin Carias ◽

Matheus Alves Silva ◽

Marcia Flores da Silva Ferreira ◽

Thiago Lívio Pessoa Oliveira de Souza ◽

...

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Snp Markers ◽

Genetic Diversity And Structure ◽

Ssr And Snp Markers ◽

Landrace Accessions

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Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

Plant Genetic Resources ◽

10.1017/s1479262120000143 ◽

2020 ◽

Vol 18 (3) ◽

pp. 111-119

Author(s):

Yinghu Zhang ◽

Haiye Luan ◽

Hui Zang ◽

Hongyan Yang ◽

Xiao Xu ◽

...

Keyword(s):

Molecular Markers ◽

Association Studies ◽

Starch Content ◽

Principal Component ◽

Mixed Linear Model ◽

High Linkage Disequilibrium ◽

Snp Markers ◽

Genome Wide Association Studies ◽

Hordeum Vulgare L ◽

Growing Seasons

AbstractStarch content is an important trait in barley. To evaluate the genetic diversity and identify molecular markers of starch content in barley, 40 cultivated barley genotypes collected from different regions, including genotypes whose starch content is at either the high or low end of the spectrum (15), were used in this study. All the genotypes were re-sequenced by the double-digest-restriction associated DNA sequencing method, and a total of 299,103 single-nucleotide polymorphism (SNP) markers were obtained. The genotypes were divided into four sub-populations based on FASTSTRUCTURE, principal component analysis and neighbour-joining tree analysis. All four sub-populations had a high linkage disequilibrium, especially group 3, whose members were recently bred for malting in the Jiangsu coastal area. The starch content of the barley lines was evaluated during three growing seasons (2014–2017), and the average values of starch content across the three growing seasons at the low and high ends were 51.5 and 55.0%, respectively. The starch content was affected by population structure, the barley in group 2 had a low starch content, while the barley in group 4 had a high starch content. Twenty-six SNP markers were identified as being significantly associated with starch content (P ⩽ 0.001) based on the average values across the three growing seasons using the mixed linear model method. These SNP markers were located on chromosomes 1H and 4H, and were considered loci of qSC1-1 and qSC4-1, respectively. The major identified QTLs for starch content are helpful for further research on carbohydrates and for barley breeding.

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SNP Markers as a Successful Molecular Tool for Assessing Species Identity and Geographic Origin of Trees in the Economically Important South American Legume Genus Dipteryx

Journal of Heredity ◽

10.1093/jhered/esaa011 ◽

2020 ◽

Author(s):

Eurídice N Honorio Coronado ◽

Céline Blanc-Jolivet ◽

Malte Mader ◽

Carmen R García-Dávila ◽

David Aldana Gomero ◽

...

Keyword(s):

Molecular Markers ◽

Country Of Origin ◽

Geographic Origin ◽

Snp Markers ◽

Genetic Identification ◽

Success Rates ◽

Species Identity ◽

Accurate Identification ◽

Genetic Clusters ◽

Assignment Success

Abstract Dipteryx timber has been heavily exploited in South America since 2000s due to the increasing international demand for hardwood. Developing tools for the genetic identification of Dipteryx species and their geographical origin can help to promote legal trading of timber. A collection of 800 individual trees, belonging to 6 different Dipteryx species, was genotyped based on 171 molecular markers. After the exclusion of markers out of Hardy–Weinberg equilibrium or with no polymorphism or low amplification, 83 nuclear, 29 chloroplast, 13 mitochondrial single nucleotide polymorphisms (SNPs), and 2 chloroplast and 5 mitochondrial INDELS remained. Six genetic groups were identified using Bayesian Structure analyses of the nuclear SNPs, which corresponded to the different Dipteryx species collected in the field. Seventeen highly informative markers were identified as suitable for species identification and obtained self-assignment success rates to species level of 78–96%. An additional set of 15 molecular markers was selected to determine the different genetic clusters found in Dipteryx odorata and Dipteryx ferrea, obtaining self-assignment success rates of 91–100%. The success to assign samples to the correct country of origin using all or only the informative markers improved when using the nearest neighbor approach (69–92%) compared to the Bayesian approach (33–80%). While nuclear and chloroplast SNPs were more suitable for differentiating the different Dipteryx species, mitochondrial SNPs were ideal for determining the genetic clusters of D. odorata and D. ferrea. These 32 selected SNPs will be invaluable genetic tools for the accurate identification of species and country of origin of Dipteryx timber.

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Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies

International Journal of Genomics ◽

10.1155/2017/8614160 ◽

2017 ◽

Vol 2017 ◽

pp. 1-14 ◽

Cited By ~ 4

Author(s):

Wenlan Tian ◽

Dev Paudel ◽

Wagner Vendrame ◽

Jianping Wang

Keyword(s):

De Novo ◽

Average Length ◽

Snp Markers ◽

Biodiesel Production ◽

Kegg Database ◽

Genomic Databases ◽

Important Species ◽

Biological Studies ◽

Ssr And Snp Markers ◽

De Novo Assembling

Jatropha (Jatropha curcasL.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.

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QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

Genome ◽

10.1139/g2012-001 ◽

2012 ◽

Vol 55 (2) ◽

pp. 152-163 ◽

Cited By ~ 23

Author(s):

Mirko Barbieri ◽

Thierry C. Marcel ◽

Rients E. Niks ◽

Enrico Francia ◽

Marianna Pasquariello ◽

...

Keyword(s):

Quantitative Resistance ◽

Rust Fungus ◽

Brachypodium Distachyon ◽

Transgressive Segregation ◽

Snp Markers ◽

Growth Stages ◽

Resistance Qtls ◽

Ssr And Snp Markers ◽

Model Grass ◽

Genomic Regions

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass–pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F2 population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F2, resistance was quantified in F2-derived F3 families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

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Population genetics and the conservation and management of Atlantic salmon (Salmo salar)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/d98-016 ◽

1998 ◽

Vol 55 (S1) ◽

pp. 145-152 ◽

Cited By ~ 11

Author(s):

Jennifer L Nielsen

Keyword(s):

Molecular Markers ◽

Atlantic Salmon ◽

Genetic Markers ◽

Salmo Salar ◽

Spatial Scales ◽

Rate Of Change ◽

Raw Material ◽

Gene Frequencies ◽

Atlantic Salmon Salmo Salar ◽

Major Floods

Molecular genetics provides data with temporal and spatial scales unavailable from other disciplines. Patterns of genetic diversity are influenced by adaptive, environmental, and stochastic factors. The rate of change in genetic markers allows investigations of diversity on temporal scales resulting from recent history (hundreds of years) to deep evolutionary time (millions of years). Cryptic spatial population structure is often revealed by molecular markers. Phylogeographic analysis of genes within populations can unite demographics with glaciation, uplift, climatic shifts, or major floods. Historically, the application of genetic markers has been largely limited to analyses of gene frequencies and patterns of diversity. The consequences of genetic rarity are controversial in relationship to endangerment or patterns of extinction. However, it is widely recognized that genes reflect a species' evolutionary past and represent the raw material underlying the diversity of biological expression throughout a species' range. DNA provides the architecture necessary for a species' adaptation and future survival. Conservation of this evolutionary legacy is important considering anthropomorphic manipulation of a species and the environment upon which it depends. In this paper I investigate evolution and genetic variation in Atlantic salmon (Salmo salar) based on the current literature. I further discuss conservation and restoration questions using molecular markers.

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