Quantitative trait loci (QTL) detection in multicross inbred designs: recovering QTL identical-by-descent status information from marker data.

Abstract:

:Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of the genetic architecture of the trait. In addition, the effects of only two alleles are characterized, which is of limited interest to the breeder, while common pedigree breeding material remains unexploited for QTL mapping. In this study, we extend QTL mapping methodology to a generalized framework, based on a two-step IBD variance component approach, applicable to any type of breeding population obtained from inbred parents. We then investigate with simulated data mimicking conventional breeding programs the influence of different estimates of the IBD values on the power of QTL detection. The proposed method would provide an alternative to the development of specifically designed recombinant populations, by utilizing the genetic variation actually managed by plant breeders. The use of these detected QTL in assisting breeding would thus be facilitated.

journal_name

Genetics

journal_title

Genetics

authors

Crepieux S,Lebreton C,Servin B,Charmet G

doi

10.1534/genetics.104.028993

keywords:

subject

Has Abstract

pub_date

2004-11-01 00:00:00

pages

1737-49

issue

3

eissn

0016-6731

issn

1943-2631

pii

168/3/1737

journal_volume

168

pub_type

杂志文章

相关文献

GENETICS文献大全
  • Meiotic origin of triploidy in the frog detected by genetic analysis of enzyme polymorphisms.

    abstract::A female frog heterozygous at two unlinked loci, specifying electrophoretic forms of mannosephosphate isomerase (MPI) and malate dehydrogenase (MDH) was crossed to male frogs homozygous for different alleles at each locus. In the offspring approximately ten percent proved to be triploid according to nucleolar and chro...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Wright DA,Huang CP,Chuoke BD

    更新日期:1976-10-01 00:00:00

  • The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors.

    abstract::To develop a catalog of regulatory sites in two major model organisms, Drosophila melanogaster and Caenorhabditis elegans, the modERN (model organism Encyclopedia of Regulatory Networks) consortium has systematically assayed the binding sites of transcription factors (TFs). Combined with data produced by our predecess...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.117.300657

    authors: Kudron MM,Victorsen A,Gevirtzman L,Hillier LW,Fisher WW,Vafeados D,Kirkey M,Hammonds AS,Gersch J,Ammouri H,Wall ML,Moran J,Steffen D,Szynkarek M,Seabrook-Sturgis S,Jameel N,Kadaba M,Patton J,Terrell R,Corson M,Dur

    更新日期:2018-03-01 00:00:00

  • Position effect on the directionality of silencer function in Saccharomyces cerevisiae.

    abstract::In Saccharomyces cerevisiae, silencers flanking the HML and HMR loci initiate the establishment of transcriptional silencing. We demonstrate that the activity of a silencer pertaining to its potency and directionality is dependent on its genomic position. The context of the HML-E silencer is more permissive to silence...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.106.055525

    authors: Zou Y,Yu Q,Chiu YH,Bi X

    更新日期:2006-09-01 00:00:00

  • Linkage mapping in experimental crosses: the robustness of single-gene models.

    abstract::The robustness of parametric linkage mapping against model misspecification is considered in experimental breeding designs, with a focus on localization of the gene. By examining the expected LOD across the genome, it is shown that single-gene models are quite robust, even for polygenic traits. However, when the marke...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Wright FA,Kong A

    更新日期:1997-05-01 00:00:00

  • Genetic and nongenetic bases for the L-shaped distribution of quantitative trait loci effects.

    abstract::The L-shaped distribution of estimated QTL effects (R(2)) has long been reported. We recently showed that a metabolic mechanism could account for this phenomenon. But other nonexclusive genetic or nongenetic causes may contribute to generate such a distribution. Using analysis and simulations of an additive genetic mo...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Bost B,de Vienne D,Hospital F,Moreau L,Dillmann C

    更新日期:2001-04-01 00:00:00

  • amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development.

    abstract::Biosynthesis of most peptide hormones and neuropeptides requires proteolytic excision of the active peptide from inactive proprotein precursors, an activity carried out by subtilisin-like proprotein convertases (SPCs) in constitutive or regulated secretory pathways. The Drosophila amontillado (amon) gene encodes a hom...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Rayburn LY,Gooding HC,Choksi SP,Maloney D,Kidd AR 3rd,Siekhaus DE,Bender M

    更新日期:2003-01-01 00:00:00

  • The Combined Action of Duplicated Boron Transporters Is Required for Maize Growth in Boron-Deficient Conditions.

    abstract::The micronutrient boron is essential in maintaining the structure of plant cell walls and is critical for high yields in crop species. Boron can move into plants by diffusion or by active and facilitated transport mechanisms. We recently showed that mutations in the maize boron efflux transporter ROTTEN EAR (RTE) caus...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.116.198275

    authors: Chatterjee M,Liu Q,Menello C,Galli M,Gallavotti A

    更新日期:2017-08-01 00:00:00

  • Insight into the RNA Exosome Complex Through Modeling Pontocerebellar Hypoplasia Type 1b Disease Mutations in Yeast.

    abstract::Pontocerebellar hypoplasia type 1b (PCH1b) is an autosomal recessive disorder that causes cerebellar hypoplasia and spinal motor neuron degeneration, leading to mortality in early childhood. PCH1b is caused by mutations in the RNA exosome subunit gene, EXOSC3 The RNA exosome is an evolutionarily conserved complex, con...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.116.195917

    authors: Fasken MB,Losh JS,Leung SW,Brutus S,Avin B,Vaught JC,Potter-Birriel J,Craig T,Conn GL,Mills-Lujan K,Corbett AH,van Hoof A

    更新日期:2017-01-01 00:00:00

  • An ancient retrovirus-like element contains hot spots for SINE insertion.

    abstract::Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Cantrell MA,Filanoski BJ,Ingermann AR,Olsson K,DiLuglio N,Lister Z,Wichman HA

    更新日期:2001-06-01 00:00:00

  • The genetic basis of rapidly evolving male genital morphology in Drosophila.

    abstract::The external genitalia are some of the most rapidly evolving morphological structures in insects. The posterior lobe of the male genital arch shows striking differences in both size and shape among closely related species of the Drosophila melanogaster species subgroup. Here, we dissect the genetic basis of posterior ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.111.130815

    authors: Masly JP,Dalton JE,Srivastava S,Chen L,Arbeitman MN

    更新日期:2011-09-01 00:00:00

  • Genetic and developmental analysis of the locus vnd in Drosophila melanogaster.

    abstract::Genetic and developmental analysis of an X-linked vital locus vnd was undertaken. Embryos hemizygous for the original allele vnd did not hatch and exhibited a disorganized ventral nervous system (VNS). The mutation maps in the region 1B6-7 to 1B9-10, a subregion of an area previously shown to be essential to normal ne...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: White K,DeCelles NL,Enlow TC

    更新日期:1983-07-01 00:00:00

  • Temporal allele frequency change and estimation of effective size in populations with overlapping generations.

    abstract::In this paper we study the process of allele frequency change in finite populations with overlapping generations with the purpose of evaluating the possibility of estimating the effective size from observations of temporal frequency shifts of selectively neutral alleles. Focusing on allele frequency changes between su...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Jorde PE,Ryman N

    更新日期:1995-02-01 00:00:00

  • Is esterase-P encoded by a cryptic pseudogene in Drosophila melanogaster?

    abstract::We have amplified and sequenced the gene encoding Esterase-P (Est-P) in 10 strains of Drosophila melanogaster. Three premature termination codons occur in the coding region of the gene in two strains. This observation, together with other indirect evidence, leads us to propose that Est-P may be a pseudogene in D. mela...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Balakirev ES,Ayala FJ

    更新日期:1996-12-01 00:00:00

  • Saccharomyces cerevisiae BUB2 prevents mitotic exit in response to both spindle and kinetochore damage.

    abstract::The spindle assembly checkpoint-mediated mitotic arrest depends on proteins that signal the presence of one or more unattached kinetochores and prevents the onset of anaphase in the presence of kinetochore or spindle damage. In the presence of either damage, bub2 cells initiate a preanaphase delay but do not maintain ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Krishnan R,Pangilinan F,Lee C,Spencer F

    更新日期:2000-10-01 00:00:00

  • Assembly of the mitochondrial membrane system: nuclear suppression of a cytochrome b mutation in yeast mitochondrial DNA.

    abstract::In a previous study, a mitochondrial mutant expressing a specific enzymatic deficiency in co-enzyme QH2-cytochrome c reductase was described (TZAGO-LOFF, FOURY and AKAI 1976). Analysis of the mitochondrially translated proteins revealed the absence in the mutant of the mitochondrial product corresponding to cytochrome...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Coruzzi G,Tzagoloff A

    更新日期:1980-08-01 00:00:00

  • Tissue culture-induced novel epialleles of a Myb transcription factor encoded by pericarp color1 in maize.

    abstract::Plants regenerated from tissue culture often display somaclonal variation, that is, somatic and often meiotically heritable phenotypic variation that can result from both genetic and epigenetic modifications. To better understand the molecular basis of somaclonal variation, we have characterized four unique tissue cul...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.110.117929

    authors: Rhee Y,Sekhon RS,Chopra S,Kaeppler S

    更新日期:2010-11-01 00:00:00

  • Temperature-sensitive pleiotropic revertants from a mutant in the arom gene cluster of Neurospora crassa.

    abstract::Genetical and biochemical studies have been performed with revertants induced in a polyaromatic mutant (No. 58) in the arom gene cluster of Neurospora crassa. In addition to complete and partial revertants able to grow on minimal at both 25 degrees and 35 degrees , temperature-sensitive revertants capable of growth on...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Case ME,Giles NH

    更新日期:1974-04-01 00:00:00

  • The inheritance of chemical phenotype in Cannabis sativa L.

    abstract::Four crosses were made between inbred Cannabis sativa plants with pure cannabidiol (CBD) and pure Delta-9-tetrahydrocannabinol (THC) chemotypes. All the plants belonging to the F(1)'s were analyzed by gas chromatography for cannabinoid composition and constantly found to have a mixed CBD-THC chemotype. Ten individual ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: de Meijer EP,Bagatta M,Carboni A,Crucitti P,Moliterni VM,Ranalli P,Mandolino G

    更新日期:2003-01-01 00:00:00

  • Distinguishing the forces controlling genetic variation at the Xdh locus in Drosophila pseudoobscura.

    abstract::Fifty-eight isochromosomal lines sampled from two natural populations of Drosophila pseudoobscura in California and one from Bogota, Colombia, were examined using four-cutter restriction mapping. A 4.6-kb region of the xanthine dehydrogenase locus was probed and 66 of 135 restriction sites scored were polymorphic. Thi...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Riley MA,Hallas ME,Lewontin RC

    更新日期:1989-10-01 00:00:00

  • Control of germline torso expression by the BTB/POZ domain protein pipsqueak is required for embryonic terminal patterning in Drosophila.

    abstract::Early embryogenesis in Drosophila melanogaster is controlled by maternal gene products, which are deposited in the egg during oogenesis. It is not well understood how maternal gene expression is controlled during germline development. pipsqueak (psq) is a complex locus that encodes several nuclear protein variants con...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.110.121624

    authors: Grillo M,Furriols M,Casanova J,Luschnig S

    更新日期:2011-02-01 00:00:00

  • Cloning by gene amplification of two loci conferring multiple drug resistance in Saccharomyces.

    abstract::Yeast DNA fragments that confer multiple drug resistance when amplified were isolated. Cells containing a yeast genomic library cloned in the high copy autonomously replicating vector, YEp24, were plated on medium containing cycloheximide. Five out of 100 cycloheximide-resistant colonies were cross-resistant to the un...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Leppert G,McDevitt R,Falco SC,Van Dyk TK,Ficke MB,Golin J

    更新日期:1990-05-01 00:00:00

  • The multivulva phenotype of certain Caenorhabditis elegans mutants results from defects in two functionally redundant pathways.

    abstract::We previously identified Caenorhabditis elegans mutants in which certain of the six vulval precursor cells adopt fates normally expressed by other vulval precursor cells. These mutants define genes that appear to function in the response to an intercellular signal that induces vulval development. The multivulva (Muv) ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Ferguson EL,Horvitz HR

    更新日期:1989-09-01 00:00:00

  • Structure, expression and phylogenetic analysis of the gene encoding actin I in Pneumocystis carinii.

    abstract::Actin is a major component of the cytoskeleton and one of the most abundant proteins found in eukaryotic cells. Comparative sequence analysis shows that this essential gene has been highly conserved throughout eukaryotic evolution making it useful for phylogenetic analysis. Complete cDNA clones for the actin-encoding ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Fletcher LD,McDowell JM,Tidwell RR,Meagher RB,Dykstra CC

    更新日期:1994-07-01 00:00:00

  • The Roles of β-Oxidation and Cofactor Homeostasis in Peroxisome Distribution and Function in Arabidopsis thaliana.

    abstract::Key steps of essential metabolic pathways are housed in plant peroxisomes. We conducted a microscopy-based screen for anomalous distribution of peroxisomally targeted fluorescence in Arabidopsis thaliana This screen uncovered 34 novel alleles in 15 genes affecting oil body mobilization, fatty acid β-oxidation, the gly...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.116.193169

    authors: Rinaldi MA,Patel AB,Park J,Lee K,Strader LC,Bartel B

    更新日期:2016-11-01 00:00:00

  • Bayesian quantitative trait locus mapping using inferred haplotypes.

    abstract::We describe a fast hierarchical Bayesian method for mapping quantitative trait loci by haplotype-based association, applicable when haplotypes are not observed directly but are inferred from multiple marker genotypes. The method avoids the use of a Monte Carlo Markov chain by employing priors for which the likelihood ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.109.113183

    authors: Durrant C,Mott R

    更新日期:2010-03-01 00:00:00

  • Partial exclusion between T-even bacteriophages: an incipient genetic isolation mechanism.

    abstract::Conditional lethal mutant systems developed in T-even bacteriophages T2, T4 and T6 have been used to study the partial exclusion which characterizes mixed infections of these phages. In bacteria mixedly infected with T2 and T4, the dominant phage (T4) acts against localized exclusion sensitivity determinants in the ge...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Russell RL,Huskey RJ

    更新日期:1974-12-01 00:00:00

  • High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline.

    abstract::Since the publication of the first comprehensive linkage map for the laboratory mouse, the architecture of recombination as a basic biological process has become amenable to investigation in mammalian model organisms. Here we take advantage of high-density genotyping and the unique pedigree structure of the incipient ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.114.161653

    authors: Liu EY,Morgan AP,Chesler EJ,Wang W,Churchill GA,Pardo-Manuel de Villena F

    更新日期:2014-05-01 00:00:00

  • Quantitative trait loci for grain yield and adaptation of durum wheat (Triticum durum Desf.) across a wide range of water availability.

    abstract::Grain yield is a major goal for the improvement of durum wheat, particularly in drought-prone areas. In this study, the genetic basis of grain yield (GY), heading date (HD), and plant height (PH) was investigated in a durum wheat population of 249 recombinant inbred lines evaluated in 16 environments (10 rainfed and 6...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.107.077297

    authors: Maccaferri M,Sanguineti MC,Corneti S,Ortega JL,Salem MB,Bort J,DeAmbrogio E,del Moral LF,Demontis A,El-Ahmed A,Maalouf F,Machlab H,Martos V,Moragues M,Motawaj J,Nachit M,Nserallah N,Ouabbou H,Royo C,Slama A,Tubero

    更新日期:2008-01-01 00:00:00

  • The promotion of gonadal cell divisions by the Caenorhabditis elegans TRPM cation channel GON-2 is antagonized by GEM-4 copine.

    abstract::The initiation of postembryonic cell divisions by the gonadal precursors of C. elegans requires the activity of gon-2. gon-2 encodes a predicted cation channel (GON-2) of the TRPM subfamily of TRP proteins and is likely to mediate the influx of Ca(2+) and/or Mg(2+). We report here that mutations in gem-4 (gon-2 extrag...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Church DL,Lambie EJ

    更新日期:2003-10-01 00:00:00

  • Alternate-2 disjunction in the german cockroach.

    abstract::The evidence in support of two types of alternate disjunction in translocation heterozygotes from the German cockroach, Blattella germanica (L.), is reviewed. When unique cytomorphological features occur in the translocation figure, the two types of alternate disjunction are identifiable regardless of the angle of obs...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Cochran DG

    更新日期:1983-05-01 00:00:00