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51 results for “SNP markers”
LA1141 × OH8245 inbred backcross (IBC) single nucleotide polymorphism (SNP) markers for genetic studies
<p>The LA1141 × OH8245 157 polymorphic SNP markers from an optimized tomato panel Sim et al., 2012 were used for linkage map construction in the BC<sub>2</sub>S<sub>3</sub> IBC and composite interval mapping QTL analysis. Genetic map position and physical position corresponding to Sl4.0 (Hosmani et al., 2019), and flanking sequences are provided.</p>
Genetic diversity, population structure, and linkage disequilibrium among tropical quality protein maize (QPM) lines assessed with high-density SNP markers
<p>The study of genetic diversity (GD), population structure, and linkage disequilibrium (LD) provides a better understanding of the genetic relationships between individuals in a population which can be utilized in crop research and improvement. Genotyping-by-sequencing (GBS) was used to detect and genotype single nucleotide polymorphisms (SNPs) in a collection of 74 quality protein maize (QPM) lines and further to characterize their genetic diversity, population structure, and linkage disequilibrium. A total of 235,214 high-quality SNPs were used for different genetic analyses except for structure analysis where 11,950 SNPs were used. Analysis of molecular variance (AMOVA) based on these SNPs revealed high genetic heterozygosity among the five populations with 1% of the total genetic variation present among the subpopulations and 99% of the variation among individuals within the populations. Population structure analysis using Bayesian-based clustering revealed that the 74 lines could be clustered into four groups. However, neighbor-joining trees indicate the lines are grouped into three major clusters. Further analysis using principal component analyses (PCA) clustered the genotypes into five groups which are concordant with the groups based on pedigree information. Higher genetic diversity was detected in population 1 with a GD value of 0.484 and the lowest in population 5 (0.396) and overall, with a mean of 0.434. The LD pattern in the quality protein maize was investigated and we observed a relatively rapid LD decay of 3.53kb and 10.66kb at r<sup>2</sup> =0.2 and r<sup>2</sup>= 0.1, respectively. Our findings provide important information for future Linkage mapping studies, genome-wide association analyses, and marker-assisted selective breeding of maize as well as genomic prediction-based selection in tropical germplasm.</p>
Fig. 1 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum
Fig. 1 Measurements of branch leaf characteristics of Homalothecium spp. Leaf characters (L1-L18) are explained in Table 3
Fig. 4 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum
Fig. 4 Relationship between width and length of leaf lamina of Homalothecium leaf specimens (N = 240) collected from the allopatric populations of H. lutescens (N = 60) and H. sericeum (N = 59) and the
Fig. 6 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum
Fig. 6 The positions of putatively hybrid sporophytes from the sympatric populations of H. lutescens and H. sericeum superimposed in the PCA from Fig. 5, based on leaf morphology of the maternal gametophytes. The morphospace of leaves from allopatric populations of H. lutescens and H. sericeum are shown as encircled surfaces (blue circle = H. lutescens and yellow circle = H. sericeum). The red circle represents the morphospace of individuals from the sympatric populations. Each square represents a hybrid sporophyte specimen, collected on its
Fig. 5 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum
Fig. 5 Principal component analysis of 14 leaf characters from 240 specimens representing allopatric and sympatric populations of Homalothecium lutescens and H. sericeum. The first two axes (PC1 and PC2) representing together 36% of variation are shown. The colours and shapes of data points correspond to the population of the specimens. Leaf
Fig. 2 in Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum
Fig. 2 (a) Measurement of capsule orientation in relation to the seta in Homalothecium as the angle (in degrees) between the seta and spore capsule at the basis of the spore capsule. (b) Capsule inclinations of individuals from the allopatric populations fell into the black ranges of variation; in the sympatric populations individuals occurred with capsule inclinations ranging outside typical capsule inclinations of the pure species (red zone: 150°- 164°), indicating hybrid origin
Annotated genes harboring major effect markers (R2 ≥ 15%). Highlighted in green are genes annotated from Rhodes et al. 2014,2017, in orange genes annotated as similar to Peroxidase, in yellow new annotations from sorghum genome in Atlas. In the first three columns start and stop position on the sorghum genome and transcript name, followed by the nearest marker name and the distance of the gene from the nearest marker, then a column where are shown the GWAS methods and target traits for which the linked SNP was significant, the last column shows the category of the genes.
<p><strong>We conducted a comprehensive genomics study to map genomic loci determining the production of antioxidants in sorghum grains. Encouraging results were obtained and published in peer-reviewed article with impact factor (https://doi.org/10.1371/journal.pone.0225979). Annotated genes harboring major effect markers (R<sup>2</sup> ≥ 15%) were identified and will be of worldwide interest. </strong></p>
Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho bleekeri) using genome wide SNP markers
<p>Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in The Red List of Threatened Species compiled by the International Union for Conservation of Nature (IUCN). Specific locus amplified fragment sequencing (SLAF-seq)-based genotyping was performed for Sichuan taimen with 43 yearling individuals from 3 locations in Taibai River (a tributary of Yangtze River) that has been sequestered from its access to the ocean for more than 30 years since late 1980s. Applying the inbreeding level and genetic relatedness estimation using 15,396 genome wide SNP markers, we found that the inbreeding level of this whole isolated population was at a low level (average F=2.6×10-3±0.079), and the means of coancestry coefficients within and between the three sampling locations were all very low (close to 0), too. Genomic differentiation was negatively correlated with the geographical distances between the sampling locations (p < 0.001) and the 43 individuals could be considered as genetically independent two groups. The low levels of genomic inbreeding and relatedness indicated a relatively large number of sexually mature individuals were involved in reproduction in Taibai River. This study suggested a genomic-relatedness-guided breeding and conservation strategy for wild fish species without pedigree information records.</p>
Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers
<p>The mapping population consists of 166 recombinant inbred lines (RILs) derived from a cross between HD3086 and HI1500.</p> <p><strong>Phenotypic data</strong><br>The RILs population along with parents were evaluated under four conditions namely timely sown irrigation (TSIR) taken as control, timely sown restricted irrigation (TSRI), late sown irrigation (LSIR), and late sown restricted irrigation (LSRI) conditions at Delhi, and under restricted irrigation condition at Indore. From each plot, 20 random spikes were harvested and spikes from each plot were threshed separately. While cleaning, care was taken to prevent metal and dust contamination. The grain iron concentration (GFeC) and grain zinc concentration (GZnC) were measured using Energy Dispersive X-ray Fluorescence (ED-XRF) machine (model X-Supreme 8000 M/s Oxford Inc, USA). The thousand kernel weight (TKW) was recorded by counting 1000 grains manually and weighted with an electronic balance.</p> <p><strong>Genotypic data</strong><br>DNA was extracted from 21 days old seedlings using CTAB method (Murray and Thompson, 1980). Genomic DNA quality was determined using 0.8% agarose gel electrophoresis with λ DNA as the standard and quantified using nanodrop. The 35K SNP Axiom breeders' array was used for genotyping of parents and the RILs population.</p>
SNP markers used for QTL mapping in the inbred lines
<p><span>Young leaves of the 175 inbred lines and their seven parents were collected from seedlings grown in a greenhouse. </span><span>About 200 mg bulk leaf sample from three plants of a line was placed in 2 ml safe-lock </span><span>Eppendorf tube and stored at ‒80 </span><span>˚C for one night prior to crushing using a Mixer Mill (TissueLyser II, Qiagen, Germany). Genomic DNA was extracted using SIGMA DNA extraction kit (Sigma-Aldrich, St. Louis, MO, USA) following the manufacturer's instruction. DNA concentration and purity of the samples were assessed using a NanoDrop 2000c spectrophotometer (Thermo Scientific, Wilmington, DE, USA). The samples were processed and sequenced using tunable genotyping-by-sequencing (tGBS®) method by Data2Bio (Ames, IW, USA). Genomic DNA was digested using two restriction enzymes NSpI (5′-RCATG^Y-3′) and BfuCI/Sau3AI (5′-^GATC-3′) which created 3´and 5´overhangs, respectively. Two single-stranded oligos, one containing a sample-specific internal barcode and the other a universal oligo, were ligated to the complementary 3´ and 5´ overhangs, respectively. </span>All 175 inbred lines' and seven parents' treated DNA was pooled for construction of the tGBS library and sequencing. The raw sequence data were demultiplexed by barcode, which was subsequently removed bioinformatically from each sequence. The barcode-trimmed sequence reads of genotype were further trimmed using the trimming software, Lucy (Chou & Holmes, 2001; Li & Chou 2004) to remove low-quality reads based on Phred quality scores of Q15.</p>
Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers
<p>Dataset for the paper named "Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers"</p> <p>GBS analysis:</p> <p>- variants.vcf.gz : compressed non filtered VCF file with 208 samples and 73685 markers on 36195 loci</p> <p>- variants.filt.vcf.gz: Filtered Variant call file (compressed) - Samples with > 50% missing genotypes, and variants with genotype calls in less than 80% of samples are removed; variants with maf < 1% are removed -207 samples and 31312 markers on 19301 loci - 1 samples removed 6CL</p> <p>Microsatellites:</p> <p>TFT.fortunei_Microsatellites_FSTATFINAL_Pop.dat</p> <p>Samples file</p> <p>-Trachycarpus_Samples_sheet.xlsx : list of samples used (lab extractions) </p> <p> </p> <p> </p>
Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds
<p><span>Single-nucleotide polymorphism (SNP) analyses are a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we develop a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygotic or homozygotic for the Z-linked SNP, while females show both Z- and W-linked SNP calls. We validated the method in the Jackdaw (<em>Corvus</em> <em>monedula</em>). The reduced sexual dimorphism in this species makes it difficult to sex individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable to discriminate males and females from a sample of 927 genotyped individuals of different maturity stages with an accuracy of 99.5%. Given that SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has a great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.</span></p>
SNP markers used for QTL mapping in the inbred lines
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Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho bleekeri) using genome wide SNP markers
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Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds
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Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat (Triticum aestivum L.) using high density SNP markers
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Data from: Identifying litchi (Litchi chinensis Sonn.) cultivars and their genetic relationships using single nucleotide polymorphism (SNP) markers
Litchi is an important fruit tree in tropical and subtropical areas of the world. However, there is widespread confusion regarding litchi cultivar nomenclature and detailed information of genetic relationships among litchi germplasm is unclear. In the present study, the potential of single nucleotide polymorphism (SNP) for the identification of 96 representative litchi accessions and their genetic relationships in China was evaluated using 155 SNPs that were evenly spaced across litchi genome. Ninety SNPs with minor allele frequencies above 0.05 and a good genotyping success rate were used for further analysis. A relatively high level of genetic variation was observed among litchi accessions, as quantified by the expected heterozygosity (He = 0.305). The SNP based multilocus matching identified two synonymous groups, 'Heiye' and 'Wuye', and 'Chengtuo' and 'Baitangli 1'. A subset of 14 SNPs was sufficient to distinguish all the non-redundant litchi genotypes, and these SNPs were proven to be highly stable by repeated analyses of a selected group of cultivars. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis divided the litchi accessions analyzed into four main groups, which corresponded to the traits of extremely early-maturing, early-maturing, middle-maturing, and late-maturing, indicating that the fruit maturation period should be considered as the primary criterion for litchi taxonomy. Two subpopulations were detected among litchi accessions by STRUCTURE analysis, and accessions with extremely early- and late-maturing traits showed membership coefficients above 0.99 for Cluster 1 and Cluster 2, respectively. Accessions with early- and middle-maturing traits were identified as admixture forms with varying levels of membership shared between the two clusters, indicating their hybrid origin during litchi domestication. The results of this study will benefit litchi germplasm conservation programs and facilitate maximum genetic gains in litchi breeding programs.
Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
Construction of genetic linkage map based on SNP markers, QTL mapping and detection of candidate genes of growth-related traits in Pacific abalone using genotyping-by-sequencing
<p><a name="_Hlk72585736"><span>Pacific abalone (<i>Haliotis discus hannai</i>) is a commercially important high valued molluscan species. Its wild population has decreased in recent years. Pacific abalone is widely cultured in Korea. Traditional breeding programs have been implemented for hatchery production of abalone seeds. To obtain more genetic information for the molecular breeding program, a high-density linkage map and quantitative trait locus (QTL) for three growth-related traits was constructed for Pacific abalone. F1 cross population with two parents were sampled to construct the linkage map using genotyping by sequencing (GBS). A total of 664,630,534 clean reads and 56,686 SNPs were generated. In sum, 3,345 segregating SNPs were used to construct a consensus linkage map. The map spanned 1,747.023 cM with 18 linkage groups and an average interval of 0.55 cM. QTL analysis revealed two significant QTL in LG10 on the consensus linkage map in each growth-related trait. Both the QTLs are located in the telomere region of the chromosome. Moreover, four potential candidate genes for growth-related traits were identified in the QTL region. Expression analysis revealed that identified genes are involved in growth regulation of abalone. The newly constructed genetic linkage map, growth-related QTLs and potential candidate genes identified in the present study can be used as valuable genetic resources and will be useful for marker-assisted selection (MAS) of Pacific abalone in molecular breeding program.</span></a></p>
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