Dataset Information

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing.

ABSTRACT: To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions across 11 datasets in terms of SNP polymorphism, heterozygosity/heterogeneity, diversity indices, concordance among genetic dissimilarity matrices, population structure, and genetic differentiation; there were, however, a few discrepancies between some pairs of datasets. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.

SUBMITTER: Gouda AC

PROVIDER: S-EPMC7438528 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing.

Gouda Arnaud Comlan AC Ndjiondjop Marie Noelle MN Djedatin Gustave L GL Warburton Marilyn L ML Goungoulou Alphonse A Kpeki Sèdjro Bienvenu SB N'Diaye Amidou A Semagn Kassa K

Scientific reports 20200819 1

To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties ...[more]

PMID: 32814806

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Project description:BackgroundComparisons across studies of generalized joint hypermobility are often difficult since there are several classification methods and methodological differences in the performance exist. The Beighton score is most commonly used and has been tested for inter- and intra-rater reliability. The Contompasis score and the Hospital del Mar criteria have not yet been evaluated for reliability. The aim of this study was to investigate the inter- and intra-rater reliability for measurements of range of motion in joints included in these three hypermobility assessment methods using a structured protocol.MethodsThe study was planned in accordance with guidelines for reporting reliability studies. Healthy adults were consecutively recruited (49 for inter- and 29 for intra-rater assessments). Intra-class correlations, two-way random effects model, (ICC 2.1) with 95% confidence intervals, standard error of measurement, percentage of agreement, Cohen's Kappa (κ) and prevalence-adjusted bias-adjusted kappa were calculated for single-joint measured in degrees and for total scores.ResultsThe inter- and intra-rater reliability in total scores were ICC 2.1: 0.72-0.82 and 0.76-0.86 and for single-joint measurements in degrees 0.44-0.91 and 0.44-0.90, respectively. The difference between ratings was within 5 degrees in all but one joint. Standard error of measurement ranged from 1.0 to 6.9 degrees. The inter- and intra-rater reliability for prevalence of positive hypermobility findings the Cohen's κ for total scores were 0.54-0.78 and 0.27-0.78 and in single joints 0.21-1.00 and 0.19-1.00, respectively. The prevalence- and bias adjusted Cohen's κ, increased all but two values.ConclusionsFollowing a structured protocol, the inter- and intra-rater reliability was good-to-excellent for total scores and in all but two single joints, measured in degrees. The inter- and intra-rater reliability for prevalence of positive hypermobility findings was fair-to-almost perfect for total scores and slight-to-almost-perfect in single joints. By using a structured protocol, we attempted to standardize the assessment of range of motion in clinical and in research settings. This standardization could be helpful in the first part of the process of standardizing the tests thus avoiding that assessment of GJH is based on chance.

Project description:BackgroundMeasuring the physical condition of long-lasting insecticidal nets (LLINs) under field conditions is of great importance for malaria control programmes to guide decisions on how frequently to replace LLINs. Current guidelines by the World Health Organization Pesticide Evaluation Scheme (WHOPES) propose a proportionate hole index (pHI) for assessing LLIN condition by counting the number of holes the size of a thumb, fist, head, and larger than a head. However, this method does not account for irregular hole shapes or exact hole sizes which could result in inaccurate decisions about when to replace LLINs.MethodsLLINs were collected during a 2013 health facility-based malaria case control study in Machinga District, Malawi. To evaluate the accuracy of the pHI, the physical condition of 277 LLINs was estimated by the WHOPES method and then compared with two more thorough measurement methods: image analysis of digital photographs of each LLIN side; and for 10 nets, ruler measurements of the length, width, and location of each hole. Total hole counts and areas per net were estimated by each method, and detailed results of hole shapes and composite pictures of hole locations were generated using image analysis.ResultsThe WHOPES method and image analysis resulted in similar estimates of total hole counts, each with a median of 10 (inter-quartile range (IQR) 4-24 and 4-23, respectively; p = 0.004); however, estimated hole areas were significantly larger using the WHOPES method (median 162 cm2, IQR 28-793) than image analysis (median 13 cm2, IQR 3-101; p < 0.0001). The WHOPES method classified fewer LLINs in 'good condition' compared to image analysis (42% vs 74%). The ruler method detected significantly more holes than image analysis did (p = 0.002) in 10 LLINs; however, total hole area was not significantly different (p = 0.16). Most holes were not circular but roughly 2-5 times longer in one direction. The lower quarter of LLIN sides was found to have the most holes.ConclusionsThe WHOPES method overestimated total hole area, likely because holes are elongated rather than circular, suggesting further adjustments to the pHI formula may be warranted when considering LLIN replacement strategies.

Dataset Information

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing.

Publications

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing.

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