The candidate gene, Clock, localizes to a strong spawning time quantitative trait locus region in rainbow trout

We applied a candidate gene mapping approach to an existing quantitative trait loci (QTL) data set for spawning date in rainbow trout (Oncorynchus mykiss) to ascertain whether these genes could potentially account for any observed QTL effects. Several genes were chosen for their known or suspected roles in reproduction, circadian, or circannual timing, including salmon-type gonadotropin-releasing hormone 3A and 3B (GnRH3A and GnRH3B), Clock, Period1, and arylalkylamine N-acetlytransferase-1 and -2 (AANAT-1 and AANAT-2). Genes were sequenced, and polymorphisms were identified in parents of two rainbow trout mapping families, one of which was used previously to detect spawn timing QTL. Interval mapping was used to identify associations between genetic markers and spawning date effects. Using a genetic map that was updated with 574 genetic markers (775 total), we found evidence for 11 significant or suggestive QTL regions. Most QTL were only localized within one of the parents; however, a strong QTL region was identified in both female and male parents on linkage group RT-8 that explained 20% and 50% of trait variance, respectively. The Clock gene mapped to this region. Period1 mapped to a region in the female parent associated with a marginal effect (P = .056) on spawn timing. Other candidate genes were not associated with significant QTL effects.     

A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidum ssp. durum)

Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi‐allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd‐B1, while the latter overlapped with the vernalization locus VRN‐A3. Additionally, 21 QTL with environment‐specific effects were found. Our results indicated a prevalence of environment‐specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes.     

Interval-specific congenic strains (ISCS): An experimental design for mapping a QTL into a 1-centimorgan interval

A general experimental design that allows mapping of a quantitative trait locus (QTL) into a 1-cM interval is presented. The design consists of a series of strains, termed ``interval-specific congenic strains (ISCS)'. Each ISCS is recombinant at a specific 1-cM sub-interval out of an ordered set of sub-intervals, which together comprise a wider interval, to which a QTL was previously mapped. It is shown that a specific and previously detected QTL of moderate or even small effect can be accurately mapped into a 1-cM interval in a program involving a total of no more than 1000 individuals. Consequently, ISCS can serve as the ultimate genetic mapping procedure before the application of physical mapping tools for positional cloning of a QTL. Received: 2 August 1996 / Accepted: 28 October 1996     

Quantitative Resistance to Phytophthora Infestans in Potato: A Case Study for Qtl Mapping in an Allogamous Plant Species

Phytophthora infestans is the most important fungal pathogen in the cultivated potato (Solanum tuberosum). Dominant, race-specific resistance alleles and quantitative resistance-the latter being more important for potato breeding- are found in the germplasm of cultivated and wild potato species. Quantitative trait loci (QTLs) for resistance to two races of P. infestans have been mapped in an F(1) progeny of a cross between non-inbred diploid potato parents with multiple alleles. Interval mapping methods based on highly informative restriction fragment length polymorphism markers revealed 11 chromosome segments on 9 potato chromosomes showing significant contrasts between marker genotypic classes. Whereas phenotypically no difference in quantitative resistance response was observed between the two fungal races, QTL mapping identified at least one race specific QT locus. Two QT regions coincided with two small segments on chromosomes V and XII to which the dominant alleles R1, conferring race specific resistance to P. infestans, Rx1 and Rx2, both inducing extreme resistance to potato virus X, have been allocated in independent mapping experiments. Some minor QTLs were correlated with genetic loci for specific proteins related to pathogenesis, the expression of which is induced after infection with P. infestans.     

Quantitative trait loci affecting risk for pentobarbital withdrawal map near alcohol withdrawal loci on mouse Chromosomes 1, 4, and 11

Barbiturate dependence is associated with the development of physiological dependence (withdrawal), tolerance, or a maladaptive pattern of drug use. Analysis of strain and individual differences with animal models for physiological dependence liability are useful means to identify potential genetic determinants of liability in humans. Behavioral and quantitative trait locus (QTL) mapping analyses were conducted with mice that are resistant versus sensitive to pentobarbital withdrawal. With a multi-stage genetic mapping strategy, a pentobarbital withdrawal QTL (Pbw1) was mapped to the distal region of mouse Chromosome (Chr) 1 and may be identical to an alcohol withdrawal QTL mapped to this chromosomal region. Two suggestive QTLs for pentobarbital withdrawal, both in proximity to QTLs definitely mapped for alcohol withdrawal, were also tentatively identified. These were on Chr 11 in proximity to a gene cluster including several members of the GABA_A receptor gene family, and on Chr 4 near a locus associated with β-carboline-induced seizure severity. These data represent the first detection and mapping of loci influencing risk for physiological dependence on barbiturates, and suggest the involvement of common genes in physiological dependence on pentobarbital and alcohol. Received: 14 October 1998 / Accepted: 19 January 1999     

Gene flow's effect on the genetic architecture of a local adaptation and its consequences for QTL analyses

This paper uses computer simulations to determine how gene flow between populations affects (1) the genetic architecture of a local adaptation and (2) properties of alleles segregating in quantitative trait locus (QTL) mapping populations. Results suggest that the average magnitude of an allele that causes a phenotypic difference between populations declines as the migration rate increases, but with an increase in migration, alleles of larger magnitude cause proportionally more of the phenotypic difference between populations. Gene flow between populations that are used in a QTL study tends to cause the average magnitude and percent variance explained (PVE) of an allele in a mapping population to increase. Thus, although the average magnitude of an allele causing a difference declines with migration the average magnitude or PVE of an allele in a QTL mapping population may increase. The reason is that the probability an allele is sampled for a QTL mapping population is in direct proportion to its frequency and alleles of larger magnitude tend to segregate at relatively higher frequencies than alleles of smaller effect with an increased migration. As the rate of gene flow between populations increases, the proportion of the phenotypic difference explained by alleles that are segregating in a QTL mapping population (and therefore potentially detected) decreases. Lastly, results suggest QTL alleles of large effect (>20% PVE) should be commonly found, provided the divergence time between populations is not too long or optima of populations are not too far apart.     

Identification of quantitative trait loci affecting sex determination in the Eastern treehole mosquito (Ochlerotatus triseriatus)

Laboratory colonies of the eastern treehole mosquito (Ochlerotatus triseriatus (Say)) exhibit a consistent female-biased sex ratio. This is unusual among mosquito species, in which heritable sex ratio distortion is usually male biased and mediated by meiotic drive. Quantitative trait loci (QTL) affecting sex were mapped in an F(1) intercross to better understand the genetics underlying this female bias. In P(1) and F(1) parents and in 146 F(2) individuals with a female-biased sex ratio (106 females:40 males), regions of seven cDNA loci were analyzed with single-strand conformation polymorphism (SSCP) analysis to identify and orient linkage groups. Genotypes were also scored at 73 random amplified polymorphic DNA (RAPD)-SSCP loci. In addition to the sex locus, at least four QTL affecting sex determination were detected with interval mapping on linkage groups I and II. Alleles at the sex locus cumulatively accounted for approximately 61-77% of the genetic variance in sex. Alleles at QTL adjacent to the sex locus and at a QTL on the opposite end of linkage group I increased the proportion of females, but alleles at a QTL on linkage group I and a second QTL on linkage group II increased the proportion of males. The female-biased sex ratio observed in laboratory colonies of O. triseriatus is most easily explained by the existence of multiple female biased distorter loci, as have been observed in other Diptera.     

Quantitative Trait Loci Differentiating the Outbreeding Mimulus Guttatus from the Inbreeding M. Platycalyx

Theoretical predictions about the evolution of selfing depend on the genetic architecture of loci controlling selfing (monogenic vs. polygenic determination, large vs. small effect of alleles, dominance vs. recessiveness), and studies of such architecture are lacking. We inferred the genetic basis of mating system differences between the outbreeding Mimulus guttatus and the inbreeding M. platycalyx by quantitative trait locus (QTL) mapping using random amplified polymorphic DNA and isozyme markers. One to three QTL were detected for each of five mating system characters, and each QTL explained 7.6-28.6% of the phenotypic variance. Taken together, QTL accounted for up to 38% of the variation in mating system characters, and a large proportion of variation was unaccounted for. Inferred QTL often affected more than one trait, contributing to the genetic correlation between those traits. These results are consistent with the hypothesis that quantitative variation in plant mating system characters is primarily controlled by loci with small effect.     

Quantitative trait locus mapping with background control in genetic populations of clonal F1 and double cross

In this study, we considered five categories of molecular markers in clonal F₁ and double cross populations, based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F₁ and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in inclusive composite interval mapping (ICIM) of quantitative trait locus (QTL). The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple‐QTL models and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize.     

Genetic architecture of a selection response in Arabidopsis thaliana

Quantitative trait locus (QTL) mapping has become an established and effective method for studying the genetic architecture of complex traits. In this report, we use a QTL mapping approach in combination with data from a large selection experiment in Arabidopsis thaliana to explore a response to selection of experimental populations with differentiated genetic backgrounds. Experimental populations with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were exposed to multiple generations of fertility and viability selection. This selection resulted in phenotypic shifts in a number of life-history and fitness-related characters including early development time, flowering time, dry biomass, longevity, and fruit production. Quantitative trait loci were mapped for these traits and their positions were compared to previously characterized allele frequency changes in the experimental populations (Ungerer et al. 2003). Quantitative trait locus positions largely colocalized with genomic regions under strong and consistent selection in populations with differentiated genetic backgrounds, suggesting that alleles for these traits were selected similarly in differentiated genetic backgrounds. However, one QTL region exhibited a more variable response; being positively selected on one genetic background but apparently neutral in another. This study demonstrates how QTL mapping approaches can be combined with map-based population genetic data to study how selection acts on standing genetic variation in populations.     

Morphological traits defining species differences in wild relatives of maize are controlled by multiple quantitative trait loci

We analyzed the genetic basis of morphological differences between two wild species of teosinte (Zea diploperennis and Z. mays ssp. parviglumis), which are relatives of maize. These two species differ in a number of taxonomically important traits including the structure of the tassel (male inflorescence), which is the focus of this report. To investigate the genetic inheritance of six tassel traits, quantitative trait locus (QTL) mapping with 95 RFLP markers was employed on a population of 425 F2 plants. Each trait was analyzed by interval mapping (IM) and composite interval mapping (CIM) to identify and characterize the QTL controlling the differences in tassel morphology. We detected two to eight QTL for each trait. In total, 30 QTL with IM and 33 QTL with CIM were found for tassel morphology. QTL for several of the traits mapped near each other, suggesting pleiotropy and/or linkage of QTL. The QTL showed small to moderate magnitudes of effect. No QTL of exceptionally large effect were found as seen under domestication and in the case of some other natural species. Thus, the model involving major QTL of large effect seems not to apply to the traits and species analyzed. A mixture of QTL with positive and negative allelic effects was found for most tassel traits and may suggest a history of periodic changes in the direction of selection during the divergence of Z. diploperennis and Z. mays ssp. parviglumis or fixation of QTL alleles by random genetic drift rather than selection.     

Mixed-model QTL mapping for kernel hardness and dough strength in bread wheat

Plant breeding data comprise unbalanced phenotypic data for inbreds with complex pedigrees. As traditional methods to map quantitative trait loci (QTL) cannot exploit plant breeding data, an alternative approach is QTL mapping via a mixed-model procedure. Our objective was to validate mixed-model QTL mapping for self-pollinated crops by detecting QTL for kernel hardness and dough strength from data in a bread wheat (Triticum aestivum L.) breeding program. We studied 80 parental and 373 experimental inbreds genotyped for 65 simple sequence repeat (SSR) markers and three candidate loci. The methodology involved three steps: variance component estimation, single-marker analyses, and a final multiple-marker analysis with marker effects treated as fixed effects. Two QTLs for kernel hardness were detected on chromosomes 1A (close to candidate locus GluA3) and 5D (close to candidate locus Ha). Four QTLs were detected for dough strength on chromosomes 1A, 1B, 1D, and 5B. Candidate gene GluA1, which was associated with dough strength, was the only candidate locus found significant. Results were consistent with previously reported markers and QTLs associated with kernel hardness and dough strength. Unlike previous studies that have assumed QTL effects as random, the assumption of fixed marker effects identified the favorable marker alleles to select for. We conclude that the detection of previously mapped QTL validates the usefulness of mixed-model QTL mapping in the context of a plant-breeding program.     

Mapping quantitative trait loci controlling silking date in a diallel cross among four lines of maize

 We describe and apply an interval mapping method for quantitative trait locus (QTL) detection using F₃ and testcross progenies derived from F₂ populations obtained from a diallel cross among four elite lines of maize. Linear model-based procedures were used for the test and estimation of putative QTL effects together with genetic interactions including epistasis. We mapped QTL associated with silking date and explored their genetic effects. Ten QTL were detected, and these explained more than 40% of the phenotypic variance. Most of these QTL had consistent and stable effects among genetic backgrounds and did not show significant epistasis. QTL-by-environment interaction was important for four QTL and was essentially due to changes in magnitude of allelic effects. These results show the efficiency of our method in several genetic situations as well as the power of the diallel design in detecting QTL simultaneously over several populations. Received: 2 September 1996 / Accepted: 20 December 1996     

Efficient QTL detection for nonhost resistance in wild lettuce: backcross inbred lines versus F2 population

In plants, several population types [F₂, recombinant inbred lines, backcross inbred lines (BILs), etc.] are used for quantitative trait locus (QTL) analyses. However, dissection of the trait of interest and subsequent confirmation by introgression of QTLs for breeding purposes has not been as successful as that predicted from theoretical calculations. More practical knowledge of different QTL mapping approaches is needed. In this recent study, we describe the detection and mapping of quantitative resistances to downy mildew in a set of 29 BILs of cultivated lettuce (L. sativa) containing genome segments introgressed from wild lettuce (L. saligna). Introgression regions that are associated with quantitative resistance are considered to harbor a QTL. Furthermore, we compare this with results from an already existing F₂ population derived from the same parents. We identified six QTLs in our BIL approach compared to only three in the F₂ approach, while there were two QTLs in common. We performed a simulation study based on our actual data to help us interpret them. This revealed that two newly detected QTLs in the BILs had gone unnoticed in the F₂, due to a combination of recessiveness of the trait and skewed segregation, causing a deficit of the wild species alleles. This study clearly illustrates the added value of extended genetic studies on two different population types (BILs and F₂) to dissect complex genetic traits.     

Development of microsatellite markers and comparative mapping for bovine chromosome 19

Previous research has mapped an ovulation rate quantitative trait locus (QTL) to bovine chromosome 19. In an effort to enhance comparative mapping information and develop additional markers for refined QTL mapping, microsatellite markers were developed in a targeted approach. A bovine bacterial artificial chromosome (BAC) library was screened for loci with either known or predicted locations on bovine chromosome 19. An average of 6.4 positive BAC were identified per screened locus. A total of 10 microsatellite markers were developed for five targeted loci with heterozygosity of 7-83% in a sample of reference family parents. The newly developed markers were typed on reference families along with four previously mapped marker loci and used to create a linkage map. Comparison of locus order between human and cattle provides support for previously observed rearrangement. One of the mapped loci myotubularin related protein 4 (MTMR4) potentially extends the proximal boundary of a conserved linkage group.     

Epistatic interaction between two nonstructural loci on chromosomes 7 and 3 influences hepatic lipase activity in BSB mice

BSB mice exhibit a wide range of obesity despite being produced by a backcross of lean C57BL/6J (B) x lean Mus spretus (SPRET/Pt) F1 animals x B. Previous linkage studies identified a quantitative trait locus (QTL) on mouse chromosome 7 with coincident peaks for hepatic lipase activity, obesity, and plasma cholesterol. However, these mice were not analyzed for gene x gene epistasis. Hepatic lipase activity is correlated with obesity and plasma cholesterol levels. In this study, we identified QTLs for plasma hepatic lipase activity with three statistical mapping methods: maximum likelihood interval mapping, Bayesian nonepistatic mapping, and Bayesian epistatic mapping. Bayesian epistatic mapping detected not only the QTL on chromosome 7 but also an additional QTL on chromosome 3, which has a weak main effect but a strong interaction with chromosome 7. SPRET/Pt alleles of the QTL on each chromosome promote hepatic lipase activity. The proportion of phenotypic variance explained by the epistatic effect is higher than that explained by the main effect of the QTL on chromosome 7.     

Multi-trait evolution in a cave fish, Astyanax mexicanus

SUMMARY When surface species colonize caves, a characteristic suite of traits eventually evolves over time, regardless of species. The genetic basis of the inevitable appearance of these very similar phenotypes was investigated through quantitative trait loci (QTL) mapping of 12 traits that differ significantly between the recently evolved (<1 Myr). Mexican cave tetra and its surface conspecific. The traits were a representative set, including eye size, pigment cell numbers, chemical sensitivity, body and skull morphology, standard length, and metabolism. We used both single- and multi-trait models for QTL mapping. QTL effects of these traits were significantly clustered in the genome. We mapped 13 regions in the genome with QTL effects on from three to nine traits. These clusters could be multigenic or could represent single locus with pleiotropic alleles. Given the relatively short time available to construct clusters from unlinked genes through genomic rearrangement, and the counterintuitive polarities of some of the substitution effects, we argue that at least some of the clusters must have a pleiotropic basis.     

Detection of quantitative trait loci for body weight at 10 weeks from Philippine wild mice

A genome-wide scan for quantitative trait loci (QTLs) controlling body weight at 10 weeks after birth was carried out in a population of 387 intersubspecific backcross mice derived from a cross between C57BL/6J inbred mice (Mus musculus domesticus) and wild mice (M. m. castaneus) captured in the Philippines, in order to discover novel QTLs from the wild mice that have about 60% lower body weight than C57BL/6J. By interval mapping, we detected four QTLs: a highly significant QTL on Chromosome (Chr) 2, which was common in both sexes; two significant QTLs on Chr 13, one male-specific and the other female-specific; and a suggestive male-specific QTL on X Chr. By composite interval mapping, we confirmed the presence of the three QTLs on Chrs 2 and 13, but not of the male-specific X-linked QTL. The composite interval mapping analysis newly identified three QTLs: a significant male-specific QTL on Chr 11 and two highly significant female-specific QTLs on Chrs 9 and X. Individual QTLs explained 3.8–11.6% of the phenotypic variance, and all the QTL alleles derived from the wild mice decreased body weight. A two-way analysis of variance revealed a significant epistatic interaction between the Chr 2 QTL and the background marker locus D12Mit4 on Chr 12 only in males. The interaction effect unexpectedly increased body weight. The chromosomal region containing the Chr 2 QTL did not coincide with those of growth or fatness QTLs mapped in previous studies. These results suggest that a population of wild mice may play an important role as new sources of valuable QTLs. Received: 14 January 2000 / Accepted: 14 April 2000     

Quantitative trait locus mapping in natural populations: progress, caveats and future directions

Over the last 15 years quantitative trait locus (QTL) mapping has become a popular method for understanding the genetic basis of continuous variation in a variety of systems. For example, the technique is now an integral tool in medical genetics, livestock production, plant breeding and population genetics of model organisms. Ten years ago, it was suggested that the method could be used to understand continuous variation in natural populations. In this review I: (i) clarify what is meant by natural population in the QTL context, (ii) discuss whether evolutionary biologists have successfully mapped QTL in natural populations, (iii) highlight some of the questions that have been addressed by QTL mapping in natural populations, (iv) describe how QTL mapping can be conducted in unmanipulated natural populations, (v) highlight some of the limitations of QTL mapping and (vi) try to predict some future directions for QTL mapping in natural populations.