Long tomato microsatellites are predominantly associated with centromeric regions

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 536-544 ◽  
Author(s):  
Tatyana Areshchenkova ◽  
Martin W Ganal
Keyword(s):  
Molecular Structure ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Lycopersicon Esculentum ◽  
Microsatellite Markers ◽  
Genetic Map ◽  
Tomato Genome ◽  
A Genome ◽  
Tetranucleotide Microsatellites ◽  
Simple Sequence

Microsatellites as genetic markers are used in many crop plants. Major criteria for their usability as molecular markers include that they are highly polymorphic and evenly spread throughout a genome. In tomato, it has been reported that long arrays of tetranucleotide microsatellites containing the motif GATA are highly clustered around the centromeres of all chromosomes. In this study, we have isolated tomato microsatellites containing long arrays (> 20 repeats) of the dinucleotide motifs GA, GT, AT, as well as GATA, assessed their variability within Lycopersicon esculentum varieties and mapped them onto a genetic map of tomato. The investigated microsatellite markers exhibited between 1 and 5 alleles in a diverse set of L. esculentum lines. Mapping of the microsatellites onto the genetic map of tomato demonstrates that, as previously shown, GATA microsatellites are highly clustered in the regions of the tomato centromeres. Interestingly, the same centromeric location was now found for long dinucleotide microsatellite markers. Because of this uneven distribution, genetic mapping of the entire tomato genome using long dinucleotide microsatellites will be very difficult to achieve and microsatellite markers with shorter arrays of microsatellites could be more suitable for mapping experiments albeit their lower level of polymorphism. Some microsatellite markers described in this study might provide a useful tool to study the molecular structure of tomato centromeric regions and for variety identification.Key words: molecular marker, Lycopersicon esculentum, genetic variability, genetic map, simple sequence repeats.

scholarly journals 10.5937/ratpov50-4344 = Molecular evaluation of genetic variability in tomato (Lycopersicon esculentum mill.) genotypes by microsatellite markers

2013 ◽  
Vol 50 (3) ◽  
pp. 1-5
Author(s):  
Svetlana Glogovac ◽  
Adam Takac ◽  
Ljiljana Brbaklic ◽  
Dragana Trkulja ◽  
Janko Cervenski ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Lycopersicon Esculentum ◽  
Microsatellite Markers ◽  
Lycopersicon Esculentum Mill ◽  
Molecular Evaluation

scholarly journals Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1386
Author(s):  
Soyun Kim ◽  
Keunho Yun ◽  
Han Yong Park ◽  
Ju Young Ahn ◽  
Ju Yeon Yang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Raphanus Sativus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cosmetic Industry ◽  
Natural Colorants ◽  
Health Promoting ◽  
Primer Sets ◽  
Red Radish ◽  
Simple Sequence

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

scholarly journals Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

2004 ◽  
Vol 129 (2) ◽  
pp. 204-210 ◽  
Author(s):  
Riaz Ahmad ◽  
Dan Potter ◽  
Stephen M. Southwick
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sweet Cherry ◽  
Prunus Persica ◽  
Sequence Repeat ◽  
Srap Markers ◽  
Upgma Cluster Analysis ◽  
Commercially Important ◽  
Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

scholarly journals Identification of hypothetical duplicate accessions of plums (Prunus domestica L.) within the slovene plant gene bank collection using molecular markers

Agricultura ◽  
2016 ◽  
Vol 13 (1-2) ◽  
pp. 57-64 ◽  
Author(s):  
Metka Šiško
Keyword(s):  
Molecular Markers ◽  
Microsatellite Markers ◽  
Life Sciences ◽  
Genetic Distances ◽  
Gene Bank ◽  
Prunus Domestica ◽  
Dice Coefficient ◽  
Plant Materials ◽  
Plant Gene ◽  
Traditional Cultivars

Abstract The main goal of the Slovene Plant Gene Bank is preservation, maintenance and evaluation of traditional cultivars and other useful genotypes. The Faculty of Agriculture and Life Sciences houses among other plant materials also numerous accessions of plums (Prunus domestica L.). Duplicates among 15 accessions were studied using six microsatellite primer pairs. These microsatellite markers revealed an average of 7.67 alleles per locus, and a range of 4 to 10 different alleles per locus. The genetic distances between studied accessions were calculated using the Dice coefficient to form a dendrogram. The six SSRs were found to be adequate for differentiating among genotypes within the collection. Among the analysed accessions no duplicates were found.

Genetic Variability and Geographic Typicality of Italian Former Prosecco Grape Variety Using PCR-Derived Molecular Markers

2013 ◽  
Vol 56 (5) ◽  
pp. 408-420 ◽  
Author(s):  
Stefano Meneghetti ◽  
Angelo Costacurta ◽  
Luigi Bavaresco ◽  
Antonio Calo’
Keyword(s):  
Molecular Markers ◽  
Genetic Variability ◽  
Grape Variety

Linking porcine microsatellite markers to known genome regions by identifying their human orthologs

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 798-808 ◽  
Author(s):  
Zhihua Jiang ◽  
Jennifer J Michal
Keyword(s):  
Microsatellite Markers ◽  
Positional Cloning ◽  
Genome Mapping ◽  
Joint Analysis ◽  
Porcine Genome ◽  
Gene Markers ◽  
Human Orthologs ◽  
Human Genomic ◽  
Rh Panel ◽  
Simple Sequence

Microsatellites, or tandem simple sequence repeats (SSRs), have become one of the most popular molecular markers in genome mapping because of their abundance across genomes and because of their high levels of polymorphism. However, information on which genes surround or flank them has remained very limited for most SSRs, especially in livestock species. In this study, an in silico comparative mapping approach was developed to link porcine SSRs to known genome regions by identifying their human orthologs. From a total of 1321 porcine microsatellites used in this study, 228 were found to have blocks in alignment with human genomic sequences. These 228 SSRs span about 1459 cM of the porcine genome, but with uneven distributions, ranging from 2 on SSC12 to 24 on SSC14. Linking these porcine SSRs to the known genome regions in the human genome also revealed 16 new putative synteny groups between these two species. Fifteen SSRs on SSC3 with identified human orthologs were typed on a pig-hamster radiation hybrid (RH) panel and used in a joint analysis with 80 known gene markers previously mapped on SSC3 using the same panel. The analysis revealed that they were all highly linked to either one or both adjacent markers. These results indicated that assigning the porcine SSRs to known genome regions by identifying their human orthologs is a reliable approach. The process will provide a foundation for positional cloning of causative genes for economically important traits.Key words: pig, microsatellite markers, human orthologs, RH mapping.

Effects of Selection at Linked Sites on Patterns of Genetic Variability

2021 ◽  
Vol 52 (1) ◽  
pp. 177-197
Author(s):  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Frequency Distributions ◽  
A Genome ◽  
Demographic Processes ◽  
Dna Sequence Variants ◽  
Genomic Regions ◽  
Functional Components

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

scholarly journals A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita pepo L.

2018 ◽  
Vol 19 (10) ◽  
pp. 3140 ◽  
Author(s):  
Chenggang Xiang ◽  
Ying Duan ◽  
Hongbo Li ◽  
Wei Ma ◽  
Sanwen Huang ◽  
...  
Keyword(s):  
Genetic Map ◽  
Simple Sequence Repeats ◽  
Cucurbita Pepo ◽  
Economic Value ◽  
High Density ◽  
Oxidase Gene ◽  
Phenotypic Polymorphism ◽  
The Rich ◽  
Expressed Sequence ◽  
Simple Sequence

As one of the earliest domesticated species, Cucurbita pepo (including squash and pumpkin) is rich in phenotypic polymorphism and has huge economic value. In this research, using 1660 expressed sequence tags-simple sequence repeats (EST-SSRs) and 632 genomic simple sequence repeats (gSSRs), we constructed the highest-density EST-SSR-based genetic map in Cucurbita genus, which spanned 2199.1 cM in total and harbored 623 loci distributed in 20 linkage groups. Using this map as a bridge, the two previous gSSR maps were integrated by common gSSRs and the corresponding relationships around chromosomes in three sets of genomes were also collated. Meanwhile, one large segmental inversion that existed between our map and the C. pepo genome was detected. Furthermore, three Quantitative Trait Loci (QTLs) of the dwarf trait (gibberellin-sensitive dwarf type) in C. pepo were located, and the candidate region that covered the major QTL spanned 1.39 Mb, which harbored a predicted gibberellin 2-β-oxidase gene. Considering the rich phenotypic polymorphism, the important economic value in the Cucurbita genus species and several advantages of the SSR marker were identified; thus, this high-density EST-SSR-based genetic map will be useful in Pumpkin and Squash breeding work in the future.

Genetic map of eight microsatellite markers comprising two linkage groups on rat chromosome 6

1995 ◽  
Vol 68 (1-2) ◽  
pp. 107-111 ◽  
Author(s):  
Y. Du ◽  
E.F. Remmers ◽  
H. Zha ◽  
E.A. Goldmuntz ◽  
P. Mathern ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genetic Map ◽  
Chromosome 6 ◽  
Linkage Groups
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