LOD significance thresholds for QTL analysis in experimental populations of diploid species

Ooijen, J.W. van

doi:10.1038/sj.hdy.6886230

Cited by 242 publications

(148 citation statements)

References 21 publications

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“…For each QTL detected, the linkage group (LG), maximum LOD score, and percent of the phenotypic variance explained (PVE) are indicated. QTLs were scored as significant (asterisks) or suggestive based on conservative recommendations for genome wide linkage mapping 29 , and by permutation testing for each trait. The genome-wide LOD significance thresholds are 4.2 for gill raker number and pelvic spine length, and 4.3 for plate number and dorsal spine length.…”

Section: Qtl Mappingmentioning

confidence: 99%

The genetic architecture of divergence between threespine stickleback species

Peichel

Nereng

Ohgi

et al. 2001

Nature

443

514

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The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the threespine stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago 1 The benthic species feeds on invertebrates near shore and has a great reduction in the amount of body armor, increased body depth, and a decreased number of gill rakers for filtering ingested food. The limnetic species more closely resembles an ancestral marine fish, with more extensive body armor, a longer and more streamlined body, and an increased number of gill rakers. Despite reproductive isolation between the two species in the wild 3-6 , it is possible to establish productive matings between the two species under laboratory conditions 2 . The resulting F1 hybrids are viable and fertile, making it possible to carry out a formal genetic analysis of the number and location of loci responsible for the adaptive morphological differences between these naturally occurring vertebrate species.To develop resources for genome-wide linkage mapping in Gasterosteus aculeatus, we used large-scale library screening and sequencing to identify a collection of genomic and cDNA clones containing microsatellite repeat sequences. Initially, we sequenced of 192 kb of random genomic clones and showed that CA dinucleotides were the most common form of microsatellite in sticklebacks, occurring approximately once every 14 kb. We subsequently screened genomic and cDNA libraries with a (GT) 15 probe, sequenced 3560 clones, and identified 1176 new microsatellite loci. Primers flanking 410 new and 18 previously identified microsatellites 7-9 were designed and used to type a genetic cross between the benthic and limnetic species from Priest Lake, British Columbia (Figure 1). For this cross, an individual Priest benthic female was mated with a single Priest limnetic male, and a single F1 male (B 1 L 1 ) was crossed to a second Priest benthic female (B 2 B 3 ) to generate 103 progeny. Of the 281 markers that amplified robust bands from the F1 and benthic parent, 227 (81%) were polymorphic, and therefore informative, in one or both parents. Higher rates of polymorphism were seen in the F1 male than the benthic female parent (71% vs. 57% of 281 markers), consistent with a greater level of genetic diversity between the distinct populations of benthic and limnetic fish than within the benthic population.The segregation patterns of the 227 informative markers were scored on 92 progeny from the cross, and the 20,884 resulting genotypes were analyzed for linkage using JoinMap software 10 . The markers were ordered into 26 linkage groups co...

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Section: Qtl Mappingmentioning

confidence: 99%

The genetic architecture of divergence between threespine stickleback species

Peichel

Nereng

Ohgi

et al. 2001

Nature

443

514

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“…The computer program MapQTL version 4 (Van Ooijen et al, 2002) was used to identify and locate QTLs linked to the markers using both interval mapping and multiple QTL model mapping. A LOD score of 2.8 was set to determine the presence of a QTL using the method described by Van Ooijen (1999). This value represents a genome-wide significance of 5%.…”

Section: Discussionmentioning

confidence: 99%

“…The Arabidopsis recombinant inbred line (RIL) population derived from a cross between the Cape Verdi Islands (Cvi) accession and the Landsberg erecta (Ler) laboratory strain has been an important tool for the analysis of a number of quantitative traits of Arabidopsis and in particular aspects of seed growth and physiology (Alonso-Blanco et al, 1998a, 1999Swarup et al, 1999;Bentsink et al, 2000;El-Assal et al, 2001;Kliebenstein et al, 2001;Borevitz et al, 2002). In this paper we describe mapping of QTL for seed oil content and composition in the Ler/Cvi RIL population and show that it should be possible to use a map-based approach to clone at least one of the loci involved in controlling seed oil content.…”

mentioning

confidence: 99%

Genetic Control of Storage Oil Synthesis in Seeds of Arabidopsis

2004

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Quantitative trait loci (QTL) that control seed oil content and fatty acid composition were studied using a recombinant inbred population derived from a cross between the Arabidopsis ecotypes Landsberg erecta and Cape Verdi Islands. Multiple QTL model mapping identified two major and two minor QTL that account for 43% of the variation in oil content in the population. The most significant QTL is at the bottom of chromosome 2 and accounts for 17% of the genetic variation. Two other significant QTL, located on the upper and lower arms of chromosome 1, account for a further 19% of the genetic variation. A QTL near to the top of chomosome 3 is epistatic to that on the upper arm of chromosome 1. There are strong QTL for linoleic (18:2) and linolenic (18:3) acids contents that colocate with the FAD3 locus, another for oleic acid (18:1) that colocates with FAD2 and other less significant QTL for palmitic (16:0), stearic (18:0), and eicosaenoic (20:1) acids. The presence of the QTL for seed oil content on chromosome 2 was confirmed by the generation of lines that contain a 22-cM region of Landsberg erecta DNA at the bottom of chromosome 2 in a background containing Cape Verdi Islands in other regions of the genome that had been shown to influence oil content in the QTL analysis.

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“…These data were analyzed for QTL mapping of As(V) using the genetic map with 99 and 79 markers previously developed for the Col gl-1 x Kas-1 and Col-0 x Tsu-0 populations 18,36 . QTL were mapped by the multiple QTL mapping method implemented in MapQTL v.4.0 software 38 . QTL were detected using LOD thresholds of 3, corresponding to an approximate genomewide significance a ¼ 0.01, as estimated with the MapQTL permutation test.…”

Section: Methodsmentioning

confidence: 99%

Natural variation in arsenate tolerance identifies an arsenate reductase in Arabidopsis thaliana

et al. 2014

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The enormous amount of environmental arsenic was a major factor in determining the biochemistry of incipient life forms early in the Earth's history. The most abundant chemical form in the reducing atmosphere was arsenite, which forced organisms to evolve strategies to manage this chemical species. Following the great oxygenation event, arsenite oxidized to arsenate and the action of arsenate reductases became a central survival requirement. The identity of a biologically relevant arsenate reductase in plants nonetheless continues to be debated. Here we identify a quantitative trait locus that encodes a novel arsenate reductase critical for arsenic tolerance in plants. Functional analyses indicate that several non-additive polymorphisms affect protein structure and account for the natural variation in arsenate reductase activity in Arabidopsis thaliana accessions. This study shows that arsenate reductases are an essential component for natural plant variation in As(V) tolerance.

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LOD significance thresholds for QTL analysis in experimental populations of diploid species

Cited by 242 publications

References 21 publications

The genetic architecture of divergence between threespine stickleback species

The genetic architecture of divergence between threespine stickleback species

Genetic Control of Storage Oil Synthesis in Seeds of Arabidopsis

Natural variation in arsenate tolerance identifies an arsenate reductase in Arabidopsis thaliana

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