Quantitative Trait Loci Alleles Research Articles

Mapping and validation of quantitative trait loci for resistance to Cercospora zeae-maydis infection in tropical maize (Zea mays L.)

Breeding for resistance to gray leaf spot, caused by Cercospora zeae-maydis (Cz) is paramount for many maize environments, in particular under warm and humid growing conditions. In this study, we mapped and characterized quantitative trait loci (QTL) involved in the resistance of maize against Cz. We confirmed the impact of the QTL on disease severity using near-isogenic lines (NILs), and estimated their effects on three major agronomic traits using their respective near isogenic hybrids (NIHs), which we obtained by crossing the NILs with an inbred from a complementary heterotic pool. We further validated three of the four QTL that were mapped using the Multiple Interval Mapping approach and showed LOD values>2.5. NILs genotype included all combinations between favorable alleles of the two QTL located in chromosome 1 (Q1 in bin 1.05 and Q2 in bin 1.07), and the allele in chromosome 3 (Q3 in bin 3.07). Each of the three QTL separately significantly reduced the severity of Cz. However, we found an unfavorable epistatic interaction between Q1 and Q2: presence of the favorable allele at one of the QTL allele effectively nullified the effect of the favorable allele at the other. In contrast, the interaction between Q2 and Q3 was additive, promoting the reduction of the severity to a greater extent than the sum of their individual effects. When evaluating the NIH we found significant individual effects for Q1 and Q3 on gray leaf spot severity, for Q2 on stalk lodging and grain yield, and for Q3 on grain moisture and stalk lodging. We detected significant epitasis between Q1 and Q2 for grain moisture and between Q1 and Q3 for stalk lodging. These results suggest that the combination of QTL impacts the effectiveness of marker-assisted selection procedures in commercial product development programs.

Strategies for Estimating Genetic Parameters in Marker-Assisted Best Linear Unbiased Predictor Models in Dairy Cattle

An appropriate strategy to estimate variance components and breeding values in genetic models with quantitative trait loci (QTL) was developed for a dairy cattle breeding scheme by utilizing simulated data. Reliable estimates for variance components in QTL models are a prerequisite in fine-mapping experiments and for marker-assisted genetic evaluations. In cattle populations, only a small fraction of the population is genotyped at genetic markers, and only these animals are included in marker-assisted genetic evaluation models. Phenotypic information in these models are precorrected phenotypes [daughter yield deviations (DYD) for bulls, yield deviations (YD) for cows] estimated by standard animal models from the entire population. Because DYD and YD may represent different amounts of information, the problem of weighting these 2 types of information appropriately arises. To detect the best combination of phenotypes and weighting factors, a stochastic simulation for a trait representing milk yield was used. The results show that DYD models are generally optimal for estimating QTL variance components, but properties of estimates depend strongly on weighting factors. An example for the benefit in selection of using YD is shown for the selection among paternal half-sibs inheriting alternative QTL alleles. Even if QTL effects are small, marker-assisted best unbiased linear prediction can improve the selection among half-sibs, because the Mendelian sampling variance within family can be exploited, especially in DYD-YD models. Marker-assisted genetic evaluation models should also include YD for cows to ensure that marker-assisted selection improves selection even for moderate QTL effects (≥10%). A useful strategy for practical implementation is to estimate variance components in DYD models and breeding values in DYD-YD models.

On the detection of imprinted quantitative trait loci in line crosses: effect of linkage disequilibrium.

Imprinted quantitative trait loci (QTL) are commonly reported in studies using line-cross designs, especially in livestock species. It was previously shown that such parent-of-origin effects might result from the nonfixation of QTL alleles in one or both parental lines, rather than from genuine molecular parental imprinting. We herein demonstrate that if linkage disequilibrium exists between marker loci and nonfixed QTL, spurious detection of pseudo-imprinting is increased by an additional 40-80% in scenarios mimicking typical livestock situations. This is due to the fact that imprinting can be tested only in F(2) offspring whose sire and dam have distinct marker genotypes. In the case of linkage disequilibrium between markers and QTL, such parents have a higher chance to have distinct QTL genotypes as well, thus resulting in distinct padumnal and madumnal allele substitution effects, i.e., QTL pseudo-imprinting.

The genetic mosaic suggests a new role for hitchhiking in ecological speciation.

Early in ecological speciation, the genomically localized effects of divergent selection cause heterogeneity among loci in divergence between incipient species. We call this pattern of genomic variability in divergence the 'genetic mosaic of speciation'. Previous studies have used F(ST) outliers as a way to identify divergently selected genomic regions, but the nature of the relationship between outlier loci and quantitative trait loci (QTL) involved in reproductive isolation has not yet been quantified. Here, we show that F(ST) outliers between a pair of incipient species are significantly clustered around QTL for traits that cause ecologically based reproductive isolation. Around these key QTL, extensive 'divergence hitchhiking' occurs because reduced inter-race mating and negative selection decrease the opportunity for recombination between chromosomes bearing different locally adapted QTL alleles. Divergence hitchhiking is likely to greatly increase the opportunity for speciation in populations that are sympatric, regardless of whether initial divergence was sympatric or allopatric. Early in ecological speciation, analyses of population structure, gene flow or phylogeography based on different random or arbitrarily chosen neutral markers should be expected to conflict--only markers in divergently selected genomic regions will reveal the evolutionary history of adaptive divergence and ecologically based reproductive isolation. Species retain mosaic genomes for a very long time, and gene exchange in hybrid zones can vary dramatically among loci. However, in hybridizing species, the genomic regions that affect ecologically based reproductive isolation are difficult to distinguish from regions that have diverged for other reasons.

On the Genetic Control of Heterosis for Fruit Shape in Melon (Cucumis Melo L.)

The objective of the present work is to study the genetic basis of heterosis for fruit shape (FS) in melon observed in a cross between the Spanish cultivar "Piel de Sapo" (PS) and the Korean accession PI 161375 (Songwang Charmi [SC]) using a set of near-isogenic lines (NILs) with contrasting phenotypes for FS, each carrying a single chromosomal introgression from SC within the genetic background of PS. We investigated the FS of homozygous NILs, hybrids NIL x PS, and all 2-way crosses between NILs to test the main heterosis hypotheses (dominance, overdominance, and epistatic interactions). Gene action of alleles of quantitative trait loci inducing fruit enlargement was dominance, whereas those inducing rounder fruit were additive or recessive. Only minor epistatic interactions were found. Therefore, the most plausible explanation for FS heterosis in this cross is in agreement with the dominance complementation hypothesis. Over 70% of the hybrid heterosis could be achieved by combining just 2 loci, indicating that the genetic control of FS heterosis in this cross is relatively simple. FS is proposed as a reproductive trait in melon because of the high correlation to the number of seeds produced along the fruit longitudinal axis.

Quantitative trait loci underlying domestication- and yield-related traits in anOryza sativa ×Oryza rufipogonadvanced backcross population

To understand the genetic characteristics of the traits related to differentiation between cultivated rice and its wild progenitor, genetic factors controlling domestication- and yield-related traits were identified using a BC3F2 population derived from an accession of common wild rice (donor, Oryza rufipogon Griff.) collected from Yuanjiang, Yunnan province, China, and an indica cultivar, Teqing (recipient, Oryza sativa L.). A genetic linkage map consisting of 125 simple sequence repeat (SSR) markers was constructed. Based on the phenotypes of the 383 BC3F2 families evaluated in two environments, two domestication-related morphological traits, panicle shape and growth habit, were found to be controlled by single Mendelian factors. This implies that the recessive mutations of single genes controlling some morphological traits could have been easily selected during early domestication. By single-point analysis and interval mapping, 59 putative quantitative trait loci (QTLs) that influence 11 quantitative traits were detected at two sites, and 37.5% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield-related traits in the Teqing background. Regions with significant QTLs for domestication- and yield-related traits were detected on chromosomes 1, 4, 5, 7, 8, and 12. Fine mapping and cloning of these domestication-related genes and QTLs will be useful in elucidating the origin and differentiation of Asian cultivated rice in the future.

The genetic architecture of complex behaviors: lessons from Drosophila

Complex behaviors are affected by multiple interacting loci with individually small and environmentally sensitive effects. Understanding the genetic architecture of behavioral traits begins with identifying the genes regulating these traits, mapping the subset of genetically varying quantitative trait loci (QTLs) in natural populations, and pinpointing the molecular polymorphisms defining QTL alleles. Drosophila brings an impressive toolkit to the challenge of genetically dissecting complex traits: P transposable element mutagenesis to identify genes regulating these traits; artificial selection from natural populations to create extreme trait phenotypes; high resolution mapping to identify positional candidate genes corresponding to QTLs; linkage disequilibrium mapping to identify molecular polymorphism(s) that functionally define QTL alleles; and whole genome transcriptional profiling to postulate networks of interacting genes affecting complex traits. Studies in Drosophila have revealed large numbers of pleiotropic genes that interact epistatically to regulate behavioral traits, and that can have sex- and environment-specific effects. These observations offer valuable lessons for understanding the genetic basis of variation for complex behaviors in other organisms, including humans.

Quantitative trait loci affecting stomatal density and growth in a Quercus robur progeny: implications for the adaptation to changing environments

AbstractStomatal traits are important to cope with changes in levels of atmospheric carbon dioxide (CO2) and with changing availability of water. Thus, they are expected to be involved in the reactions of plants to climate change. They are known to show a plastic physiological response to environmental factors such as elevated CO2 concentrations, but they are also under genetic control and should undergo evolutionary change if selection differs among environments. Stomatal development is regulated by several environmental and genetic signals suggesting a polygenic inheritance. In the present study, F1 progeny derived from a cross between Quercus robur and Q. robur subsp. slavonica were used to map QTLs (quantitative trait loci) for stomatal densities and growth parameters under nonwater stress conditions in 2 and 3 consecutive years, respectively. The positions of QTLs for stomatal density and growth coincided on six linkage groups. The QTL allele associated with the higher stomatal density was generally associated with taller plants and size increment indicating pleiotropic gene effects or close linkage. The phenotypic effects of the individual QTLs were mostly moderate in terms of phenotypic variance explained. However, a considerable amount of the genetically determined variation was explained by QTLs for stomatal density (from 63.6% to 94.4%). Especially, the QTL on linkage group 11 had a strong and highly significant effect on stomatal densities and growth parameters in all years suggesting a major QTL on this linkage group. The importance to analyse the genetic variation controlling complex adaptive traits in keystone species as oaks is discussed with regard to a better understanding of the reactions of ecosystems to global change.

Phenological Characterization of Near‐Isogenic Sunflower Families Bearing Two QTLs for Photoperiodic Response

Understanding the effects of environment and genotype on crop phenology is critical to achieving appropriate adaptation of cultivars to targeted production areas. The main objective of this work is to examine the phenology of near‐isogenic sunflower (Helianthus annuus L.) families bearing all combinations of alleles for quantitative trait loci (QTLs) A and B associated with photoperiodic response growing in controlled environment chambers under short and extended photoperiods. Plants were harvested at intervals, the apices dissected out, and apex development from the start (apex transformation) to the end of floral differentiation scored using a 10‐point scale of floral stages. Parental lines showed significant (p < 0.05) contrasting responses to photoperiod. The genotypes exhibited significant (p < 0.0001) effects of photoperiod, QTL, QTL × photoperiod, and QTL × QTL interactions for the timing of apex transformation (B0) and for the inverse of rate of development during floral differentiation (B1). The strong QTL A × QTL B interaction for both B0 and B1 reflects the much greater delay in development under both photoperiods when QTL A was derived from HA89 and QTL B from ZenB8. This effect on B1, but not on B0, increased under extended photoperiod in the same family, reflecting a three‐factor (QTL A × QTL B × photoperiod) interaction acting on rate of development during the floral differentiation process. Given the weight of direct and interaction contributions associated with the two QTLs to the nonerror variability of both B0 and B1 across genotypes and photoperiods, we conclude both QTLs are important effectors in the photoperiodic control of flowering in sunflower.

Pathogen-Specific Effects of Quantitative Trait Loci Affecting Clinical Mastitis and Somatic Cell Count in Danish Holstein Cattle

The aim of this study was to investigate whether quantitative trait loci (QTL) affecting the risk of clinical mastitis (CM) and QTL affecting somatic cell score (SCS) exhibit pathogen-specific effects on the incidence of mastitis. Bacteriological data on mastitis pathogens were used to investigate pathogen specificity of QTL affecting treatments of mastitis in first parity (CM1), second parity (CM2), and third parity (CM3), and QTL affecting SCS. The 5 most common mastitis pathogens in the Danish dairy population were analyzed: Streptococcus dysgalactiae, Escherichia coli, coagulase-negative staphylococci, Staphylococcus aureus, and Streptococcus uberis. Data were analyzed using 2 approaches: an independence test and a generalized linear mixed model. Three different data sets were used to investigate the effect of data sampling: all samples, only samples that were followed by antibiotic treatment, and samples from first-crop daughters only. The results showed with high certainty that 2 QTL affecting SCS exhibited pathogen specificity against Staph. aureus and E. coli, respectively. The latter result might be explained by a pleiotropic QTL that also affects CM2 and CM3. Less certain results were found for QTL affecting CM. A QTL affecting CM1 was found to be specific against Strep. dysgalactiae and Staph. aureus, a QTL affecting CM2 was found to be specific against E. coli, and finally a QTL affecting CM3 was found to be specific against Staph. aureus. None of the QTL analyzed was found to be specific against coagulase-negative staphylococci and Strep. uberis. Our results show that particular mastitis QTL are highly likely to exhibit pathogen-specificity. However, the results should be interpreted carefully because the results are sensitive to the sampling method and method of analysis. Field data were used in this study. These kind of data may be heavily biased because there is no standard procedure for collecting milk samples for bacteriological analysis in Denmark. Furthermore, using only the mean SCS from d 10 to 180 after parturition may lead to truncated effects of SCS-QTL when samples collected after d 180 are used. Additionally, repeated samples were used, which could boost the difference in incidence of pathogens between daughters of sires inheriting the positive and negative QTL allele, respectively. However, the magnitude of these effects in this study is unclear.

Detection of QTL on Bovine X Chromosome by Exploiting Linkage Disequilibrium

A fine-mapping method exploiting linkage disequilibrium was used to detect quantitative trait loci (QTL) on the X chromosome affecting milk production, body conformation and productivity traits. The pedigree comprised 22 paternal half-sib families of Black-and-White Holstein bulls in the Netherlands in a grand-daughter design for a total of 955 sons. Twenty-five microsatellite markers were genotyped to construct a linkage map on the chromosome X spanning 170 Haldane cM with an average inter-marker distance of 7.1 cM. A covariance matrix including elements about identical-by-descent probabilities between haplotypes regarding QTL allele effects was incorporated into the animal model, and a restricted maximum-likelihood method was applied for the presence of QTL using the LDVCM program. Significance thresholds were obtained by permuting haplotypes to phenotypes and by using a false discovery rate procedure. Seven QTL responsible for conformation types (teat length, rump width, rear leg set, angularity and fore udder attachment), behavior (temperament) and a mixture of production and health (durable prestation) were detected at the suggestive level. Some QTL affecting teat length, rump width, durable prestation and rear leg set had small numbers of haplotype clusters, which may indicate good classification of alleles for causal genes or markers that are tightly associated with the causal mutation. However, higher maker density is required to better refine the QTL position and to better characterize functionally distinct haplotypes which will provide information to find causal genes for the traits.

Across-Family Marker-Assisted Selection Using Selective Genotyping Strategies in Dairy Cattle Breeding Schemes

This study investigated the potential loss expected from marker-assisted selection (MAS) when only a proportion of animals are genotyped using several selective genotyping strategies. A population resembling a commercial dairy cattle population over 25 yr was simulated, and the most informative individuals for genotyping were identified among the potential breeding candidates (young bulls and bull-dams). Two strategies were used to identify the most informative animals. The first genotyping strategy was based on selecting individuals for genotyping with predicted total genetic effect [sum of the predicted quantitative trait locus (QTL) and polygenic effects] close to the truncation point for selection. The second strategy used an index that extended the previous strategy to include the variance due to segregation of the QTL in the parents. The 2 strategies for selective genotyping were applied at the 2 different genotyping levels and compared with random selection of candidates for genotyping and complete genotyping of the potential candidates. All selective genotyping strategies at the same proportion of genotyping showed similar cumulative genetic level. The frequency of the favorable QTL allele increased faster with more animals genotyped. Extra response in total genetic effect (polygenic and QTL) was not significantly different between genotyping all candidates (100%), 20%, and 50% genotyping (except for yr 13), but all MAS strategies resulted in significantly higher response than BLUP until yr 18. With 50% (20%) genotyping of candidates for selection within a population, 95% (89%) of maximum cumulative QTL response was achieved in yr 13. All MAS schemes resulted in a 19% decrease in the rate of inbreeding compared with the BLUP scheme. Therefore, it is possible to use selective genotyping in practical dairy cattle breeding and decrease the genotyping costs with a minimal loss of response compared with complete genotyping of the potential candidates.

Model‐based linkage analysis with imprinting for quantitative traits: ignoring imprinting effects can severely jeopardize detection of linkage

Genes with imprinting (parent-of-origin) effects express differently when inheriting from the mother or from the father. Some genes for development and behavior in mammals are known to be imprinted. We developed parametric linkage analysis that accounts for imprinting effects for continuous traits, implementing it in MORGAN. To study misspecification of imprinting on linkage analysis, we simulated eight markers over a 35 cM region with phenotypes where imprinting contributes 0, 25, 50, and 75% of the variance of a quantitative trait locus (QTL) effect and analyzed them under all four models. Multipoint lod scores were computed and maximized over the same 35 cM region. Our most important finding is the dramatic lod score improvement under the correct imprinting model over the no-imprinting model. For data with minor QTL allele frequency 0.05, the correct model provided the highest lod scores with maximum expected lod scores over 4 in all settings. Ignoring imprinting provided the lowest lod scores with maximum expected lod scores between -9.9 and 2.4. In the extreme scenario, cases with max lod > or =3 from the correct imprinting model and max lod < or =-2 from the no-imprinting model occurred in 86% of replications. Models with misspecified imprinting produced lod scores intermediate between those with correct imprinting and with no imprinting. The effects of model misspecification were less pronounced for singlepoint analysis. Our multipoint results illustrate that ignoring true imprinting severely impairs detection of linkage and erroneously excludes genomic regions (with max lod <-2), whereas accounting for it can substantially improve linkage detection.

AB-QTL analysis in winter wheat: II. Genetic analysis of seedling and field resistance against leaf rust in a wheat advanced backcross population

The present study aimed to localize exotic quantitative trait locus (QTL) alleles for the improvement of leaf rust (P.triticina) resistance in an advanced backcross (AB) population, B22, which is derived from a cross between the winter wheat cultivar Batis (Triticumaestivum) and the synthetic wheat accession Syn022L. The latter was developed from hybridization of T.turgidum ssp. dicoccoides and T.tauschii. Altogether, 250 BC2F3 lines of B22 were assessed for seedling resistance against the leaf rust isolate 77WxR under controlled conditions. In addition, field resistance against leaf rust was evaluated by assessing symptom severity under natural infestation across multiple environments. Simultaneously, population B22 was genotyped with a total of 97 SSR markers, distributed over the wheat A, B and D genomes. The phenotype and genotype data were subjected to QTL analysis by applying a 3-factorial mixed model analysis of variance including the marker genotype as a fixed effect and the environments, the lines and the marker by environment interactions as random effects. The QTL analysis revealed six putative QTLs for seedling resistance and seven for field resistance. For seedling resistance, the effects of exotic QTL alleles improved resistance at all detected loci. The maximum decrease of disease symptoms (−46.3%) was associated with marker locus Xbarc149 on chromosome 1D. For field resistance, two loci had stable main effects across environments and five loci exhibited marker by environment interaction effects. The strongest effects were detected at marker locus Xbarc149 on chromosome 1D, at which the exotic allele decreased seedling symptoms by 46.3% and field symptoms by 43.6%, respectively. Some of the detected QTLs co-localized with known resistance genes, while others appear to be as novel resistance loci. Our findings indicate, that the exotic wheat accession Syn022L may be useful for the improvement of leaf rust resistance in cultivated wheat.

Biphasic survival analysis of trypanotolerance QTL in mice

A marker-assisted introgression (MAI) experiment was conducted to transfer trypanotolerance quantitative trait loci (QTL) from a donor mouse strain, C57BL/6, into a recipient mouse strain, A/J. The objective was to assess the effect of three previously identified chromosomal regions on mouse chromosomes 1 (MMU1), 5 (MMU5) and 17 (MMU17) in different genetic backgrounds on the survival pattern following infection with Trypanosoma congolense. An exploratory data analysis revealed a biphasic pattern of time to death, with highly distinct early and late mortality phases. In this paper, we present survival analysis methods that account for the biphasic mortality pattern and results of reanalyzing the data from the MAI experiment. The analysis with a Weibull mixture model confirmed the biphasic pattern of time to death. Mortality phase, an unobserved variable, appears to be an important factor influencing survival time and is modeled as a binary outcome variable using logistic regression analysis. Accounting for this biphasic pattern in the analysis reveals that a previously observed sex effect on average survival is rather an effect on proportion of mice in the two mortality phases. The C57BL/6 (donor) QTL alleles on MMU1 and MMU17 act dominantly in the late mortality phase while the A/J (recipient) QTL allele on MMU17 acts dominantly in the early mortality phase. From this study, we found clear evidence for a biphasic survival pattern and provided models for its analysis. These models can also be used when studying defense mechanisms against other pathogens. Finally, these approaches provide further information on the nature of gene actions.

Introgressing multiple QTL in breeding programmes of limited size

The ability to enrich a breed with favourable alleles from multiple unlinked quantitative trait loci (QTL) of a donor breed through marker-assisted introgression (MAI) in a population of limited size was evaluated by considering the effects of the proportion selected, the size of the marker intervals, the number of introgressed QTL and the uncertainty of QTL position. Informative flanking markers were used to select progeny with the largest expected number of donor QTL alleles over five generations of backcrossing and five generations of intercrossing. In the backcrossing phase, with 5% selected and 20 cM marker intervals for three QTL, there were sufficient backcross progeny that were heterozygous for all markers, and QTL frequencies dropped below 0.5 only because of double recombinants. For higher fractions selected, longer marker intervals, and more QTL, frequency reductions from 0.5 were greater and increased with additional generations of backcrossing. However, even with 20% selected, three QTL, and marker intervals of 5 or 20 cM, mean QTL frequencies in generation 5 were 0.35 and 0.30, sufficient to allow subsequent selection of QTL in the intercrossing phase. After five generations of intercrossing, over 90% of individuals were homozygous for all QTL, and 85% when five QTL were introgressed. The higher the proportions selected, the longer the marker intervals, and larger numbers of introgressed QTL increased the number of intercrossing generations required to achieve fixation of QTL. Location of the QTL in the marked intervals did not affect QTL frequencies or the proportion of QTL lost at the end of the introgression programme. In conclusion, introgressing multiple QTL can be accomplished in a MAI programme of limited size without requiring that all individuals selected during the backcrossing phase to be carriers of favourable alleles at all QTL.

Detection of quantitative trait loci controlling extremely early heading in rice

To clarify the genetic basis of extremely early heading in rice, we conducted quantitative trait locus (QTL) analyses using F2 populations from two genetically wide cross combinations, Hayamasari/Kasalath (HaF2) and Hoshinoyume/Kasalath (HoF2). Hayamasari and Hoshinoyume are extremely early-heading japonica cultivars. Photoperiod sensitivity is completely lost in Hayamasari and weak in Hoshinoyume. Three QTLs, QTL(chr6), QTL(chr7), and QTL(chr8), for days-to-heading (DTH) in HaF2 were detected on chromosomes 6, 7, and 8, respectively, and QTL(chr6) and QTL(chr7) were detected in HoF2. On the basis of the chromosomal locations, QTL(chr6), QTL(chr7), and QTL(chr8) may be likely to be Hd1, Hd4, and Hd5, respectively, which had been detected previously as QTLs for DTH in an F2 population of NipponbarexKasalath. Alleles of QTL(chr7) decreased DTH dramatically in both Hayamasari and Hoshinoyume, suggesting that QTL(chr7) has a major role in determining extremely early heading. In addition, allele-specific interactions were detected between QTL(chr6), QTL(chr7) and QTL(chr8). This result suggests that not only allelic differences but also epistatic interactions contribute to extremely early heading. QTL(chr8) was detected in HaF2, but not in HoF2, suggesting that it determines the difference in DTH between Hayamasari and Hoshinoyume. A major QTL was also detected in the region of QTL(chr8) in QTL analysis using an F2 population of HayamasarixHoshinoyume. This result supports the idea that QTL(chr8) is a major factor that determines the difference in DTH between Hayamasari and Hoshinoyume, and is involved in photoperiod sensitivity.

Detection of quantitative trait loci for teat number and female reproductive traits in Meishan × Large White F2 pigs

A quantitative trait locus (QTL) analysis of female reproductive data from a three-generation experimental cross between Meishan (MS) and Large White (LW) pig breeds is presented. Six F1 boars and 23 F1 sows, progeny of six LW boars and six MS sows, produced 573 F2 females and 530 F2 males. Six traits, i.e. teat number (TN), age at puberty (AP), ovulation rate (OR), weight at mating (WTM), number of viable embryos (NVE) and embryo survival (ES) at 30 days of gestation were analysed. Animals were genotyped for a total of 137 markers covering the entire porcine genome. Analyses were carried out based on interval mapping methods, using a line-cross (LC) regression and a half–full sib (HFS) maximum likelihood test. Genome-wide (GW) highly significant (P < 0.001) QTL were detected for WTM on SSC 7 and for AP on SSC 13. They explained, respectively, 14.5% and 8.9% of the trait phenotypic variance. Other GW significant (P < 0.05) QTL were detected for TN on SSC 3, 7, 8, 16 and 17, for OR on SSC 4 and 5, and for ES on SSC 9. Two additional chromosome-wide significant (P < 0.05) QTL were detected for TN, three for WTM, four for AP, three for OR, three for NVE and two for ES. With the exception of the two above-mentioned loci, the QTL explained from 1.2% to 4.6% of trait phenotypic variance. QTL alleles were in most cases not fixed in the grand-parental populations and Meishan alleles were not systematically associated with higher reproductive performance.

Quantitative trait locus analysis of hybrid pedigrees: variance-components model, inbreeding parameter, and power

BackgroundFor the last years reliable mapping of quantitative trait loci (QTLs) has become feasible through linkage analysis based on the variance-components method. There are now many approaches to the QTL analysis of various types of crosses within one population (breed) as well as crosses between divergent populations (breeds). However, to analyse a complex pedigree with dominance and inbreeding, when the pedigree's founders have an inter-population (hybrid) origin, it is necessary to develop a high-powered method taking into account these features of the pedigree.ResultsWe offer a universal approach to QTL analysis of complex pedigrees descended from crosses between outbred parental lines with different QTL allele frequencies. This approach improves the established variance-components method due to the consideration of the genetic effect conditioned by inter-population origin and inbreeding of individuals. To estimate model parameters, namely additive and dominant effects, and the allelic frequencies of the QTL analysed, and also to define the QTL positions on a chromosome with respect to genotyped markers, we used the maximum-likelihood method. To detect linkage between the QTL and the markers we propose statistics with a non-central χ2-distribution that provides the possibility to deduce analytical expressions for the power of the method and therefore, to estimate the pedigree's size required for 80% power. The method works for arbitrarily structured pedigrees with dominance and inbreeding.ConclusionOur method uses the phenotypic values and the marker information for each individual of the pedigree under observation as initial data and can be valuable for fine mapping purposes. The power of the method is increased if the QTL effects conditioned by inter-population origin and inbreeding are enhanced. Several improvements can be developed to take into account fixed factors affecting trait formation, such as age and sex.

AB-QTL analysis in winter wheat: I. Synthetic hexaploid wheat (T. turgidum ssp. dicoccoides × T. tauschii) as a source of favourable alleles for milling and baking quality traits

The advanced backcross QTL (AB-QTL) strategy was utilised to locate quantitative trait loci (QTLs) for baking quality traits in two BC(2)F(3) populations of winter wheat. The backcrosses are derived from two German winter wheat cultivars, Batis and Zentos, and two synthetic, hexaploid wheat accessions, Syn022 and Syn086. The synthetics originate from hybridisations of wild emmer (T. turgidum spp. dicoccoides) and T. tauschii, rather than from durum wheat and T. tauschii and thus allowed for the first time to test for exotic QTL effects on wheat genomes A and B in addition to genome D. The investigated quality traits comprised hectolitre weight, grain hardness, flour yield Type 550, falling number, grain protein content, sedimentation volume and baking volume. One hundred and forty-nine SSR markers were applied to genotype a total of 400 BC(2)F(3) lines. For QTL detection, a mixed-model ANOVA was conducted, including the effects DNA marker, BC(2)F(3) line, environment and marker x environment interaction. Overall 38 QTLs significant for a marker main effect were detected. The exotic allele improved trait performance at 14 QTLs (36.8%), while the elite genotype contributed the favourable effect at 24 QTLs (63.2%). The favourable exotic alleles were mainly associated with grain protein content, though the greatest improvement of trait performance due to the exotic alleles was achieved for the traits falling number and sedimentation volume. At the QTL on chromosome 4B the exotic allele increased the falling number by 19.6% and at the QTL on chromosome 6D the exotic allele led to an increase of the sedimentation volume by 21.7%. The results indicate that synthetic wheat derived from wild emmer x T. tauschii carries favourable QTL alleles for baking quality traits, which might be useful for breeding improved wheat varieties by marker-assisted selection.