Curation of wheat maps to improve map accuracy and QTL detection

Three Australian doubled haploid populations were used to illustrate the importance of map curation in order to improve the quality of linkage maps and quantative trait locus (QTL) detection. The maps were refined and improved by re-examining the order of markers, inspection of the genetic maps in relation to a consensus map, editing the marker data for double crossovers, and determining estimated recombination fractions for all pairs of markers. The re-ordering of markers and replacing genotypes at double crossovers with missing values resulted in an overall decrease in the length of the maps. Fewer apparent genotyping errors, associated with the presence of double recombinants, were identified with restriction fragment length polymorphisms (RFLPs) than with other types of markers used in this study. The complications that translocations may cause in the ordering of markers and subsequent QTL analysis were investigated. QTL analysis using both the original and revised maps indicated that QTL peaks were more sharply located or had improved log-likelihood (LOD) scores in the revised maps. An accurate indication of the QTL peak and a significant LOD score are both essential for the identification of markers suitable for marker-assisted selection. Recommendations are provided for the improvement of the quality of linkage maps.

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Comprehensive survey among statistical members of medical ethics committees in Germany on their personal impression of completeness and correctness of biostatistical aspects of submitted study protocols

BMJ Open ◽

10.1136/bmjopen-2019-032864 ◽

2020 ◽

Vol 10 (2) ◽

pp. e032864

Author(s):

Geraldine Rauch ◽

Lorena Hafermann ◽

Ulrich Mansmann ◽

Iris Pigeot

Keyword(s):

Medical Ethics ◽

Missing Values ◽

Sample Size Calculation ◽

Ethics Committees ◽

Secondary Outcome ◽

Study Protocols ◽

Individual Assessment ◽

Statistical Problems ◽

Multiple Comparison Procedures

ObjectivesTo assess biostatistical quality of study protocols submitted to German medical ethics committees according to personal appraisal of their statistical members.DesignWe conducted a web-based survey among biostatisticians who have been active as members in German medical ethics committees during the past 3 years.SettingThe study population was identified by a comprehensive web search on websites of German medical ethics committees.ParticipantsThe final list comprised 86 eligible persons. In total, 57 (66%) completed the survey.QuestionnaireThe first item checked whether the inclusion criterion was met. The last item assessed satisfaction with the survey. Four items aimed to characterise the medical ethics committee in terms of type and location, one item asked for the urgency of biostatistical training addressed to the medical investigators. The main 2×12 items reported an individual assessment of the quality of biostatistical aspects in the submitted study protocols, while distinguishing studies according to the German Medicines Act (AMG)/German Act on Medical Devices (MPG) and studies non-regulated by these laws.Primary and secondary outcome measuresThe individual assessment of the quality of biostatistical aspects corresponds to the primary objective. Thus, participants were asked to complete the sentence ‘In x% of the submitted study protocols, the following problem occurs’, where 12 different statistical problems were formulated. All other items assess secondary endpoints.ResultsFor all biostatistical aspects, 45 of 49 (91.8%) participants judged the quality of AMG/MPG study protocols much better than that of ‘non-regulated’ studies. The latter are in median affected 20%–60% more often by statistical problems. The highest need for training was reported for sample size calculation, missing values and multiple comparison procedures.ConclusionsBiostatisticians being active in German medical ethics committees classify the biostatistical quality of study protocols as low for ‘non-regulated’ studies, whereas quality is much better for AMG/MPG studies.

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VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽

10.1093/aobpla/plaa064 ◽

2020 ◽

Vol 12 (6) ◽

Author(s):

Morad M Mokhtar ◽

Ebtissam H A Hussein ◽

Salah El-Din S El-Assal ◽

Mohamed A M Atia

Keyword(s):

Vicia Faba ◽

Faba Bean ◽

Expressed Sequence Tags ◽

Genetic Linkage ◽

Genetic Maps ◽

Linkage Maps ◽

Microrna Target ◽

Genetic Linkage Maps ◽

Expressed Sequence ◽

Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

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A Consensus Map for Loblolly Pine (Pinus taeda L.). I. Construction and Integration of Individual Linkage Maps From Two Outbred Three-Generation Pedigrees

Genetics ◽

10.1093/genetics/151.1.321 ◽

1999 ◽

Vol 151 (1) ◽

pp. 321-330 ◽

Cited By ~ 4

Author(s):

Mitchell M Sewell ◽

Bradley K Sherman ◽

David B Neale

Keyword(s):

Pinus Taeda ◽

Loblolly Pine ◽

Fragment Length Polymorphism ◽

Random Amplified Polymorphic Dna ◽

Mapping Function ◽

Genetic Maps ◽

Linkage Data ◽

Linkage Maps ◽

Consensus Map ◽

Pinus Taeda L

Abstract A consensus map for loblolly pine (Pinus taeda L.) was constructed from the integration of linkage data from two unrelated three-generation outbred pedigrees. The progeny segregation data from restriction fragment length polymorphism, random amplified polymorphic DNA, and isozyme genetic markers from each pedigree were recoded to reflect the two independent populations of parental meioses, and genetic maps were constructed to represent each parent. The rate of meiotic recombination was significantly greater for males than females, as was the average estimate of genome length for males {1983.7 cM [Kosambi mapping function (K)]} and females [1339.5 cM(K)]. The integration of individual maps allows for the synthesis of genetic information from independent sources onto a single consensus map and facilitates the consolidation of linkage groups to represent the chromosomes (n = 12) of loblolly pine. The resulting consensus map consists of 357 unique molecular markers and covers ∼1300 cM(K).

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A genetic linkage map for the domesticated silkworm, Bombyx mori, based on restriction fragment length polymorphisms

Genetics Research ◽

10.1017/s0016672300034467 ◽

1995 ◽

Vol 66 (2) ◽

pp. 109-126 ◽

Cited By ~ 48

Author(s):

Jinrui Shi ◽

David G. Heckel ◽

Marian R. Goldsmith

Keyword(s):

Linkage Map ◽

Bombyx Mori ◽

Restriction Fragment ◽

Fragment Length ◽

Restriction Fragment Length Polymorphisms ◽

Genetic Maps ◽

Crossing Over ◽

Linkage Groups ◽

Length Polymorphisms ◽

Restriction Fragment Length

SummaryWe present data for the initial construction of a molecular linkage map for the domesticated silkworm, Bombyx mori, based on 52 progeny from an F2 cross from a pair mating of inbred strains p50 and C108, using restriction fragment length polymorphisms (RFLPs). The map contains 15 characterized single copy sequences, 36 anonymous sequences derived from a follicular cDNA library, and 10 loci corresponding to a low copy number retrotransposon, mag. The 15 linkage groups and 8 ungrouped loci account for 23 of the 28 chromosomes and span a total recombination length of 413 cM; 10 linkage groups were correlated with established classic genetic maps. Scoring data from Southern blots were analysed using two Pascal programs written specifically to analyse linkage data in Lepidoptera, where females are the heterogametic sex and have achiasmatic meiosis (no crossing-over). These first examine evidence for linkage by calculating the maximum lod score under the hypothesis that the two loci are linked over the likelihood under the hypothesis that the two loci assort independently, and then determine multilocus linkage maps for groups of putatively syntenic loci by calculating the maximum likelihood estimate of the recombination fractions and the log likelihood using the EM algorithm for a specified order of loci along the chromosome. In addition, the possibility of spurious linkage was exhaustively tested by searching for genotypes forbidden by the absence of crossing-over in one sex.

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QTL analysis of self-selected macronutrient diet intake: fat, carbohydrate, and total kilocalories

Physiological Genomics ◽

10.1152/physiolgenomics.00037.2002 ◽

2002 ◽

Vol 11 (3) ◽

pp. 205-217 ◽

Cited By ~ 47

Author(s):

Brenda K. Smith Richards ◽

Brenda N. Belton ◽

Angela C. Poole ◽

James J. Mancuso ◽

Gary A. Churchill ◽

...

Keyword(s):

Body Weight ◽

Qtl Analysis ◽

Genetic Basis ◽

Body Weight Gain ◽

Macronutrient Intake ◽

Naturally Occurring ◽

Trait Locus ◽

Diet Intake ◽

Insight Into ◽

Protein Quantitative Trait Locus

The present study investigated the inheritance of dietary fat, carbohydrate, and kilocalorie intake traits in an F2 population derived from an intercross between C57BL/6J (fat-preferring) and CAST/EiJ (carbohydrate-preferring) mice. Mice were phenotyped for self-selected food intake in a paradigm which provided for 10 days a choice between two macronutrient diets containing 78/22% of energy as a composite of either fat/protein or carbohydrate/protein. Quantitative trait locus (QTL) analysis identified six significant loci for macronutrient intake: three for fat intake on chromosomes (Chrs) 8 ( Mnif1), 18 ( Mnif2), and X ( Mnif3), and three for carbohydrate intake on Chrs 17 ( Mnic1), 6 ( Mnic2), and X ( Mnic3). An absence of interactions among these QTL suggests the existence of separate mechanisms controlling the intake of fat and carbohydrate. Two significant QTL for cumulative kilocalorie intake, adjusted for baseline body weight, were found on Chrs 17 ( Kcal1) and 18 ( Kcal2). Without body weight adjustment, another significant kcal locus appeared on distal Chr 2 ( Kcal3). These macronutrient and kilocalorie QTL, with the exception of loci on Chrs 8 and X, encompassed chromosomal regions influencing body weight gain and adiposity in this F2 population. These results provide new insight into the genetic basis of naturally occurring variation in nutrient intake phenotypes.

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Quantitative trait locus (QTL) analysis of wood quality traits in Eucalyptus nitens

Tree Genetics & Genomes ◽

10.1007/s11295-009-0250-9 ◽

2009 ◽

Vol 6 (2) ◽

pp. 305-317 ◽

Cited By ~ 63

Author(s):

Bala R. Thumma ◽

Simon G. Southerton ◽

John C. Bell ◽

John V. Owen ◽

Martin L. Henery ◽

...

Keyword(s):

Quantitative Trait Locus ◽

Qtl Analysis ◽

Quantitative Trait ◽

Wood Quality ◽

Quality Traits ◽

Eucalyptus Nitens ◽

Trait Locus

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Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.

Genetics ◽

10.1093/genetics/121.1.185 ◽

1989 ◽

Vol 121 (1) ◽

pp. 185-199 ◽

Cited By ~ 119

Author(s):

E S Lander ◽

D Botstein

Keyword(s):

Dna Markers ◽

Quantitative Trait ◽

Quantitative Traits ◽

Human Genetics ◽

Substantial Reduction ◽

Interval Mapping ◽

Genetic Dissection ◽

Linkage Maps ◽

Phenotypic Effect ◽

Length Polymorphisms

Abstract The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic dissection of discrete Mendelian factors underlying quantitative traits in experimental organisms. We describe here a set of analytical methods that modify and extend the classical theory for mapping such quantitative trait loci (QTLs). These include: (i) a method of identifying promising crosses for QTL mapping by exploiting a classical formula of SEWALL WRIGHT; (ii) a method (interval mapping) for exploiting the full power of RFLP linkage maps by adapting the approach of LOD score analysis used in human genetics, to obtain accurate estimates of the genetic location and phenotypic effect of QTLs; and (iii) a method (selective genotyping) that allows a substantial reduction in the number of progeny that need to be scored with the DNA markers. In addition to the exposition of the methods, explicit graphs are provided that allow experimental geneticists to estimate, in any particular case, the number of progeny required to map QTLs underlying a quantitative trait.

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fullsibQTL: an R package for QTL mapping in biparental populations of outcrossing species

10.1101/2020.12.04.412262 ◽

2020 ◽

Author(s):

Rodrigo Gazaffi ◽

Rodrigo R. Amadeu ◽

Marcelo Mollinari ◽

João R. B. F. Rosa ◽

Cristiane H. Taniguti ◽

...

Keyword(s):

Qtl Mapping ◽

Open Source ◽

Qtl Analysis ◽

Source Code ◽

R Package ◽

Genetic Maps ◽

Linkage Phase ◽

Position Effects ◽

Genetic Features ◽

Outcrossing Species

ABSTRACTAccurate QTL mapping in outcrossing species requires software programs which consider genetic features of these populations, such as markers with different segregation patterns and different level of information. Although the available mapping procedures to date allow inferring QTL position and effects, they are mostly not based on multilocus genetic maps. Having a QTL analysis based in such maps is crucial since they allow informative markers to propagate their information to less informative intervals of the map. We developed fullsibQTL, a novel and freely available R package to perform composite interval QTL mapping considering outcrossing populations and markers with different segregation patterns. It allows to estimate QTL position, effects, segregation patterns, and linkage phase with flanking markers. Additionally, several statistical and graphical tools are implemented, for straightforward analysis and interpretations. fullsibQTL is an R open source package with C and R source code (GPLv3). It is multiplatform and can be installed from https://github.com/augusto-garcia/fullsibQTL.

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Effective Intelligent Data Mining Using Dempster-Shafer Theory

Data Warehousing and Mining ◽

10.4018/978-1-59904-951-9.ch188 ◽

2008 ◽

pp. 2943-2963

Author(s):

Malcolm J. Beynon

Keyword(s):

Data Mining ◽

Missing Values ◽

Uncertain Reasoning ◽

Worst Case ◽

Data Mining Techniques ◽

Imperfect Data ◽

Dempster Shafer Theory ◽

External Management ◽

Shafer Theory

The efficacy of data mining lies in its ability to identify relationships amongst data. This chapter investigates that constraining this efficacy is the quality of the data analysed, including whether the data is imprecise or in the worst case incomplete. Through the description of Dempster-Shafer theory (DST), a general methodology based on uncertain reasoning, it argues that traditional data mining techniques are not structured to handle such imperfect data, instead requiring the external management of missing values, and so forth. One DST based technique is classification and ranking belief simplex (CaRBS), which allows intelligent data mining through the acceptance of missing values in the data analysed, considering them a factor of ignorance, and not requiring their external management. Results presented here, using CaRBS and a number of simplex plots, show the effect of managing and not managing of imperfect data.

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