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51 results for “Genome wide association mapping”
Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
<p>A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French <em>Arabidopsis thaliana</em> population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.</p>
Identification of novel genes involved in phosphate accumulation in Lotus japonicus through Genome Wide Association mapping of root system architecture and anion content
<p>130 Lotus japonicus accessions were used. The names and accession numbers are<br> listed in S6 Table. Seeds were scarified with sandpaper and then sterilized 14 minutes in 0.05%<br> sodium hypochlorite. Subsequently, seeds were rinsed and washed 5 times in sterile distilled<br> water. For the germination, seeds were positioned in imbibed filter paper, in sterile Petri dishes,<br> and wrapped in aluminium foil. After 3 days at 21°C, young seedling were transferred to square<br> plates (12 x 12 cm) containing growth medium. Both media used in this<br> study were based on Long-Ashton solution (with two levels of phosphate concentration -20 or<br> 750 μM, LP or HP, respectively) with 0.8% MES buffer (Duchefa Biochemie,<br> Haarlem, The Netherlands), 0.8% agarose (to minimize phosphate contamination), and adjusted<br> to pH 5.7 with 1M KOH. After adding the medium, plates were dried, closed, overnight in a<br> sterile laminar flow hood. Two accessions, with four replicates per each accession, were placed<br> on each plate. Each plate was replicated, with mirrored position of each accession to minimize<br> any positional growth effects. Plates were placed vertically, and plants grown under long-day<br> conditions (21°C, 16 h light/8 h dark cycle) with white light bulbs emitting 50 μmol/m 2 /s and<br> roots were exposed to light. Every day at the same time, the racks were transported to the image<br> acquisition room where images of each plate were acquired with eight Epson V600 CCD flatbed<br> color image scanners (Seiko Epson) and then immediately returned to the growth chamber.</p>
Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
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Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice
<p>To investigate the genetic architecture underlying cold tolerance during germination in rice (<i>Oryza sativa</i>), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch's Lab at Cornell University and consists of 7,098 SNPs (Morales et al. 2020, under review). After genotyping 257 rice accessions with the 7K array (C7AIR), poor-performing SNP markers (SNPs of call rate <90%; minor allele frequency <5%; or heterozygosity >20%) were removed from the dataset. For our study, a subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis. The dataset representing the genotype data of 5,185 SNP markers by 257 rice accessions is presented here.</p>
Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice
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Supplemental material for: Genome-wide association study and fine-mapping using imputed sequences to prioritize candidate genes for 30 complex traits in 50,309 Holstein bulls
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Data from: Genome-wide SNP identification and association mapping for seed mineral concentration in Mung bean (Vigna radiata L.)
<p><span><span>Mung bean (<i>Vigna radiata</i> L.) quality is dependent on seed chemical composition, which in turn determines the benefits of mung bean consumption for human health. While rich in a range of nutritional components, such as protein, macro- and micro- nutrients, carbohydrates and vitamins, mung bean remains less well studied than other legume crops. Mung bean genomics and genetic resources are relatively sparse. To further improve nutritional levels of mung bean grain requires genome-wide marker system tools. The objectives of this research were to develop these tools and conduct nutrient analysis in order to 1) identify single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS) and to 2) perform genome-wide association studies (GWAS) for levels of calcium, iron, potassium, manganese, phosphorous, sulfur, and zinc in mung bean grain produced over two years of field experiment. A total of 112 GWAS models were explored using 6,486 high quality SNPs discovered in 92 cultivated mung bean accessions chosen from USDA core collection that represented 13 countries. The data obtained allowed for the identification of 43 associated SNPs and 20 main genomic regions that explained on average 22 % of the overall variation in seed macro- and micro- nutrients concentration on the basis of a multiple-year analysis. Most of the regions discovered in this study provide valuable candidate gene to use in future breeding of new varieties of mung bean with novel nutritional properties. Identification of the <a>underlying genes</a> will help to reveal the genetic control of mung bean seed nutritional property. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) in the species <i>V</i>. <i>radiata</i>, including wide and narrow crosses with / between cultivated and wild mung bean.</span></span></p>
Data from: Genome-wide association mapping of resistance to Septoria nodorum leaf blotch in a Nordic spring wheat collection
Parastagonospora nodorum is the causal agent of septoria nodorum blotch (SNB) in wheat. It is the most important leaf blotch pathogen in Norwegian spring wheat. Several quantitative trait loci (QTL) for SNB susceptibility have been identified. Some of these QTL are the result of underlying gene-for-gene interactions involving necrotrophic effectors (NEs) and corresponding sensitivity (Snn) genes. A collection of diverse spring wheat lines was evaluated for SNB resistance/susceptibility over seven growing seasons in the field. In addition, wheat seedlings were inoculated and infiltrated with culture filtrates (CFs) from four single spore isolates and infiltrated with semi-purified NEs (SnToxA, SnTox1 and SnTox3) under greenhouse conditions. In adult plants, the most stable SNB resistance QTL were located on 2B, 2D, 4A, 4B, 5A, 6B, 7A and 7B. The QTL on 2D was effective most years in the field. At the seedling stage, the most significant QTL after inoculation were located on 1A, 1B, 3A, 4B, 5B, 6B, 7A and 7B. The QTL on 3A and 6B were significant both after inoculation and CF infiltration, indicating the presence of novel NE-Snn interactions. The QTL on 4B and 7A were significant in both seedlings and adult plants. Correlations between SnToxA sensitivity and disease severity in the field were significant. To our knowledge, this is the first genome wide association mapping study (GWAS) to investigate SNB resistance at the adult plant stage under field conditions.
Data from: Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae
The genetic architecture of adaptive traits can reflect the evolutionary history of populations and also shape divergence among populations. Despite this central role in evolution, relatively little is known regarding the genetic architecture of adaptive traits in nature, particularly for traits subject to known selection intensities. Here we quantitatively describe the genetic architecture of traits that are subject to known intensities of differential selection between host plant species in Timema cristinae stick insects. Specifically, we used phenotypic measurements of 10 traits and 211,004 single-nucleotide polymorphisms (SNPs) to conduct multilocus genome-wide association mapping. We identified a modest number of SNPs that were associated with traits and sometimes explained a large proportion of trait variation. These SNPs varied in their strength of association with traits, and both major and minor effect loci were discovered. However, we found no relationship between variation in levels of divergence among traits in nature and variation in parameters describing the genetic architecture of those same traits. Our results provide a first step toward identifying loci underlying adaptation in T. cristinae. Future studies will examine the genomic location, population differentiation, and response to selection of the trait-associated SNPs described here.
Data from: Genome wide association mapping of floral traits in cultivated sunflower (Helianthus annuus)
Floral morphology and pigmentation are both charismatic and economically relevant traits associated with cultivated sunflower (Helianthus annuus L.). Recent work has linked floral morphology and pigmentation to pollinator efficiency and seed yield. Understanding the genetic architecture of such traits is essential for crop improvement, and gives insight into the role of genetic constraints in shaping floral diversity. A diversity panel of 288 sunflower genotypes was phenotyped for a variety of morphological, phenological, and color traits in both a greenhouse and a field setting. Association mapping was performed using 5788 SNP markers using a mixed linear model approach. Several dozen markers across ten linkage groups were significantly associated with variation in morphological and color trait variation. Substantial trait plasticity was observed between greenhouse and field phenotyping, and associations differed between environments. Color traits mapped more strongly than morphology in both settings, with markers together explaining 16% of petal carotenoid content in the greenhouse, and 17% and 24% of variation in disc anthocyanin presence in the field and greenhouse, respectively. Morphological traits like disc size mapped more strongly in the field, with markers together explaining up to 19% of disc size variation. Loci identified here through association mapping within cultivated germplasm differ from those identified through biparental crosses between modern cultivated sunflower and either its wild progenitor or domesticated landraces. Several loci lie within genomic regions involved in domestication. Differences between phenotype expression under greenhouse and field conditions highlight the importance of plasticity in determining floral morphology and pigmentation.
Genome-wide association mapping for component traits of drought and heat tolerance in wheat
<p>The study material in GWAS panel with 282 advanced breeding line of bread wheat genotypes from IARI stress breeding program was selected to map the genomic regions responsible for Drought and heat tolerance component traits.</p> <p>Phenotypic data:</p> <p>The GWAS panel was evaluated at multiple locations namely, IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m), ARI, Pune - PUNE (18.5204° N, 73.8567° E, MSL 560m), IIWBR, Karnal - IIWBR (29.6857° N, 76.9905°E, MSL 243m), IARI, Jharkhand - JR (24.1929° N, 85.3756° E, MSL 580m) and IARI RS, Indore - IND (22.7196° N, 75.8577° E, MSL 553 m) with augmented RCBD design. Three tratments viz, IR (Irrigated), RI (Restricted irrigated) and LS (Late sown) were imposed for control, drought and heat stress, respectively. Data was collected on traits like Days to heading (DH), Days to maturity (DM), Normalized Difference Vegetation Index (NDVI) at anthesis and grain filling stage, chlorophyll content (SPAD) of flag leaf at post anthesis stage, Plant height (PH), Canopy temperature (CT), Grain weight per spike (GWPS), Thousand Grain weight (TGW), Plot Yield (PLTY) and Biomass.</p> <p>Genotypic data:</p> <p>Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder's Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >20%, and heterozygote frequency >25% were removed from the analysis. The remaining set of 10546 high-quality SNPs was used in GWAS analysis.</p> <p>The detailed information of the methods and software used, data analysis and GWAS is provided at doi: 10.3389/fpls.2022.943033</p>
Data from: Genome-wide association mapping of date palm fruit traits
Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial crop species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform GWAS mapping of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor (VIRESCENS) gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crop species, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.
Data from: Genome wide association mapping of floral traits in cultivated sunflower (Helianthus annuus)
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Data from: Genome-wide association mapping of resistance to Septoria nodorum leaf blotch in a Nordic spring wheat collection
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Data from: Genome-wide association mapping of date palm fruit traits
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Data from: Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs
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Data from: Use of a natural hybrid zone for genome-wide association mapping of craniofacial traits in the house mouse
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Data from: Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae
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Data from: Genome-wide SNP identification and association mapping for seed mineral concentration in Mung bean (Vigna radiata L.)
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Genome-wide association mapping for component traits of drought and heat tolerance in wheat
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