2,301 research outputs found
SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"
No full textThe 318 sampled wild barley accensions, known as the Wild Barley Diversity Collection (WBDC), were genotyped using the Illumina Golden Gate Genotyping Assay with two Barley Oligo Pool assay chips (BOPA1 and BOPA2). The genotype calls were based on machine-scored data using the program ALCHEMY and the SNPs were annotated using the program SNPMeta. The BOPA1 & 2 files contains the output of the ALCHEMY program.
Finally the original individual SSR for barley are publicly available at the website called GrainGenes and the sample used in this dataset are included as a txt file. All three files (tsv and txt) can be opened by text editors.Two Barley Oligo Pool Assay chips (BOPA 1 and 2) were genotyped from the Wild Barley Diversity Collection. Due to its broad geographic distribution and ecological adaptation, this collection is a valuable source of potentially useful genes.USDA NIFA 2011-68002-30029University of Minnesota Doctoral Dissertation FellowshipLieberman-Okinow Endowment at the University of MinnesotaUSAID-funded Cereals Comparative Genomics InitiativeFang, Zhou; Gonzales, Ana M; Clegg, Michael T; Smith, Kevin P; Muehlbauer, Gary J; Steffenson, Brian J; Morrell, Peter L. (2016). SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley". Retrieved from the University Digital Conservancy, http://doi.org/10.13020/D6B59N
CASA as an aid to selecting sperm suspensions for artificial insemination in Callithrix jacchus
No full textD-0201: 81 North 500 West, Logan, Utah, Heber G. Morrell Jr./Wanda M. and Louis J. Thornley residence. Lot 5-6 Block 9 Plat A
No full textD-0201: 81 North 500 West, Logan, Utah, Heber G. Morrell Jr./Wanda M. and Louis J. Thornley residence. Lot 5-6 Block 9 Plat
Identification of genetic variation associated with high-temperature tolerance in cowpea
No full text1. File List
A. Filename: Cowpea_enviormental_ancest_822
Short description: Dataset related to environmental ancestry analysis in cowpea lines.
B. Filename: Partner_Favorites.vcf.gz
Short description: VCF file of variants from selected partner-preferred cowpea lines.
C. Filename: README.md
Short description: Markdown-formatted readme containing project metadata and notes.
D. Filename: README_WIP_Roland_Cowpea.txt
Short description: In-progress readme draft with additional annotation and format testing notes.
E. Filename: Readme_published_V5.txt
Short description: Final published version of the project readme with all required metadata.
F. Filename: VIGNA_rate6_ANCEST.bed
Short description: Ancestral state inference output using rate6 model in BED format.
G. Filename: VIGNA_rate6_ANCEST_ESTSFS.bed
Short description: BED file with ancestral states inferred using EST-SFS for comparison.
H. Filename: all_hits_MAF 3.bed.numbers
Short description: BED file annotated with allele frequency hit counts.
I. Filename: cowpea_490_stats_AA_rename.vcf.gz
Short description: VCF file with ancestral allele statistics for 490 cowpea samples.
J. Filename: cowpea_490_stats_AA_rename.vcf.gz.csi
Short description: Index file for the cowpea_490_stats_AA_rename VCF.
K. Filename: iSelect_ancestral.bed
Short description: Ancestral state calls for iSelect SNP array loci in BED format.This dataset includes filtered and unfiltered variant call files (VCFs), structural variant data (BEDPE), callable and uncallable region masks (BED), and phenotype data collected from mutagenized barley lines and control hybrids. It incorporates sequencing results from 10x Genomics, Oxford Nanopore, PacBio, and Illumina platforms.This study was funded by the Foundation for Food & Agriculture Research (Award# ICRC20-0000000032) to EFR, KJB, MA-M, OB, and PLM. The authors thank Tchamba Marimagne (IITA Genebank, Nigeria) for his valuable input during passport data curation, and Fiona Todd (University of Minnesota, USA) for the curation of materials associated with the manuscript. This research was carried out with software and hardware support provided by the Minnesota Supercomputing Institute (MSI) at the University of Minnesota. This research benefited from the advice and guidance of Timothy J. Close (U. of California Riverside, USA).Akakpo, Roland; Morrell, Peter; Lee, Elaine; Pacheco, Jacob; Rios, Esteban; Kantar, Michael; Boukar, Ousmane; Volz, Kevin; Akinmade, Habib; Alonso, Luis; Boote, Kenneth; Muñoz-Amatriaín, María. (2025). Identification of genetic variation associated with high-temperature tolerance in cowpea. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/XXPS-Q694
Variants from "The role of deleterious substitutions in crop genomes"
No full textThere are two gzipped VCF (variant call format) files with variant calls for barley and soybean. A total of 652,797 SNPs were identified in the barley lines, which consisted of 13 cultivars and 2 wild accessions. For soybean, 7 cultivars and 1 wild accession were used, and 586,102 SNPs were called. Whether a variant is deleterious or not was determined using SIFT (http://sift.jcvi.org/), PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/), and a likelihood ratio test of sequence conservation. Raw reads are available through the SRA accession numbers in Table S1 of Kono et al. 2016. The code used for this research, BAD_Mutations, is open source and freely available at https://github.com/MorrellLAB/BAD_Mutations.SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.USDA NIFA National Needs Fellowship (Appropriation No. 5430-21000-006-00D)MnDrive 2014 Food Security FellowshipMinnesota Agricultural Experiment Station Variety Development fundUnited Soybean BoardU.S. NSF Plant Genome Program (BDI-1339393)Kono, Thomas J Y; Fu, Fengli; Mohammadi, Mohsen; Hoffman, Paul J; Liu, Chaochih; Stupar, Robert M; Smith, Kevin P; Tiffin, Peter; Fay, Justin C; Morrell, Peter L. (2016). Variants from "The role of deleterious substitutions in crop genomes". Retrieved from the University Digital Conservancy, http://doi.org/10.13020/D65C7D
Influence of semen collection method on ejaculate characteristics in the common marmoset, Callithrix jacchus
No full textA source of normal spermatozoa (sperm) is required for many andrological and reproductive studies. Ideally the method used for semen collection should be repeatable and reliable but should not influence sperm characteristics or sperm function. Two methods of semen collection from marmosets, vaginal washing after copulation and electroejaculation, were compared in terms of the success rate in obtaining samples and the characteristics of the sperm suspensions. Vaginal washing was shown to be a reliable, repeatable, and apparently non-stressful method of obtaining ejaculates, with 8 out of 10 males ejaculating on at least four of the five attempts. The semen was of good quality as assessed by conventional means, and the sperm were highly fertile when used for artificial insemination (Al; 100% conception rate). In contrast, fewer ejaculates were obtained from the same males by electroejaculation (success rate 30%), sperm survival in vitro was reduced compared to sperm collected by vaginal washing (0.93 +/- 0.15 days for electroejaculated sperm compared to 1.98 +/- 0.3 days for sperm from vaginal washing), and the number of animals giving birth after Al was smaller (0 vs. 6; P < 0.05). The proportions of motile (74.8 vs. 70.7%), live (84.7 vs. 81%), and morphologically normal (91.9 vs. 87.6%) sperm in the ejaculates were not affected by the semen collection method, but velocity parameters, such as curvilinear velocity, straight line velocity, and average path velocity, as assessed by computerized motility analysis, were significantly lower in vaginal washings than in electroejaculates (P < 0.023, 0.008, and 0.008, respectively). Mean angular deviation and beat cross frequency were greater in vaginal washings than in electroejaculates (P < 0.016 and 0.008, respectively). Therefore the effect of semen collection method on sperm function should always be considered when designing reproductive studies
Influence of semen collection method on ejaculate characteristics in the common marmoset, Callithrix jacchus
No full textA source of normal spermatozoa (sperm) is required for many andrological and reproductive studies. Ideally the method used for semen collection should be repeatable and reliable but should not influence sperm characteristics or sperm function. Two methods of semen collection from marmosets, vaginal washing after copulation and electroejaculation, were compared in terms of the success rate in obtaining samples and the characteristics of the sperm suspensions. Vaginal washing was shown to be a reliable, repeatable, and apparently non-stressful method of obtaining ejaculates, with 8 out of 10 males ejaculating on at least four of the five attempts. The semen was of good quality as assessed by conventional means, and the sperm were highly fertile when used for artificial insemination (Al; 100% conception rate). In contrast, fewer ejaculates were obtained from the same males by electroejaculation (success rate 30%), sperm survival in vitro was reduced compared to sperm collected by vaginal washing (0.93 +/- 0.15 days for electroejaculated sperm compared to 1.98 +/- 0.3 days for sperm from vaginal washing), and the number of animals giving birth after Al was smaller (0 vs. 6; P < 0.05). The proportions of motile (74.8 vs. 70.7%), live (84.7 vs. 81%), and morphologically normal (91.9 vs. 87.6%) sperm in the ejaculates were not affected by the semen collection method, but velocity parameters, such as curvilinear velocity, straight line velocity, and average path velocity, as assessed by computerized motility analysis, were significantly lower in vaginal washings than in electroejaculates (P < 0.023, 0.008, and 0.008, respectively). Mean angular deviation and beat cross frequency were greater in vaginal washings than in electroejaculates (P < 0.016 and 0.008, respectively). Therefore the effect of semen collection method on sperm function should always be considered when designing reproductive studies
Retrospective observation of the effect of accidental exposure to organophosphates on the success of embryo transfer in mice
No full textRetrospective observation of the effect of accidental exposure to organophosphates on the success of embryo transfer in mice
No full textBirth of offspring following artificial insemination in the common marmoset,Callithrix jacchus
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