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PubMed2004

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

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.

Computer Simulation↗
PubMed2005

Genetic epidemiology of osteoporosis: past, present, and future.

Research during the past several decades has unequivocally established a role of heredity in the etiology of osteoporosis. Major efforts are currently underway to identify the genes and allelic variants that confer genetic susceptibility to this common and disabling condition. Genome-wide linkage mapping in families, candidate gene association studies in unrelated individuals, and quantitative trait locus mapping in animal models are the primary strategies being used to search for the genetic contributors to osteoporosis. Genome-wide mapping efforts have identified the low-density lipoprotein receptor-related protein 5, bone morphogenetic protein 2, and 15-lipoxygenase as potential susceptibility genes for osteoporosis in the past few years, providing a rich new base for understanding bone biology. Candidate gene association analyses have also provided evidence for a modest role of allelic variants in several additional genes including collagen type Ialpha1, vitamin D receptor, and estrogen receptor-alpha. With the development of a high-density genome-wide polymorphism and haplotype map and continued improvements in high-throughput and cost-effective genotyping technologies, many more genetic contributors to osteoporosis will probably be identified in the near future. The results of this research should facilitate the development of new methods for diagnosing, preventing, and treating the growing clinical and public health problem of osteoporosis.

Animals↗
PubMed1997

Epistasis for three grain yield components in rice (Oryza sativa L.).

The genetic basis for three grain yield components of rice, 1000 kernel weight (KW), grain number per panicle (GN), and grain weight per panicle (GWP), was investigated using restriction fragment length polymorphism markers and F4 progency testing from a cross between rice subspecies japonica (cultivar Lemont from USA) and indica (cv. Tequing from China). Following identification of 19 QTL affecting these traits, we investigated the role of epistasis in genetic control of these phenotypes. Among 63 markers distributed throughout the genome that appeared to be involved in 79 highly significant (P < 0.001) interactions, most (46 or 73%) did not appear to have "main" effects on the relevant traits, but influenced the trait(s) predominantly through interactions. These results indicate that epistasis is an important genetic basis for complex traits such as yield components, especially traits of low heritability such as GN and GWP. The identification of epistatic loci is an important step toward resolution of discrepancies between quantitative trait loci mapping and classical genetic dogma, contributes to better understanding of the persistence of quantitative genetic variation in populations, and impels reconsideration of optimal mapping methodology and marker-assisted breeding strategies for improvement of complex traits.

Adaptation, Physiological↗
PubMed2003

Extent of linkage disequilibrium in a Sardinian sub-isolate: sampling and methodological considerations.

The extent of linkage disequilibrium (LD) is an important factor when designing experiments for mapping disease or trait loci using LD mapping methods. It depends on the population history and hence is a characteristic of each population. Here, we have assessed the extent of LD in a sub-isolate of the general Sardinian population (775 members of one village) using 22 polymorphic markers on chromosome 19. We found high levels of disequilibrium that extended to 8 cM, when based on D', and 11 cM when based on the significance level of the allelic association. The fact that conclusions based on both methods are similar suggests that the estimates are quite robust. We have also shown, through a simple resampling technique, that small sample sizes can overestimate both the mean value of D' and its variance up to a factor of about 2 and 16, respectively, when the number of diplotypes (the pair of haplotypes that compose the genotype) decreased from 186 to 26. We evaluated the effect on D' of the depth of the pedigree available when using phased founders, and compared the estimates with those obtained when using unphased founders, and also the effect of grouping alleles on the value of D' and the significance level. Owing to the high sampling variance of LD, we recommend the use of at least 200 unrelated individuals when characterizing the extent of LD.

Alleles↗
PubMed2001

Genetic analysis of amino acid accumulation in opaque-2 maize endosperm.

The opaque-2 mutation in maize (Zea mays) is associated with an increased level of free amino acids (FAA) in the mature endosperm. In particular, there is a high concentration of lysine, the most limiting essential amino acid. To investigate the basis for the high-FAA phenotype of opaque-2 maize, we characterized amino acid accumulation during endosperm development of several wild-type and opaque-2 inbreds. Oh545o2 was found to have an exceptionally high level of FAA, in particular those derived from aspartate (Asp) and intermediates of glycolysis. The FAA content in Oh545o2 is 12 times greater than its wild-type counterpart, and three and 10 times greater than in Oh51Ao2 and W64Ao2, respectively. We crossed Oh545o2 to Oh51Ao2 and analyzed the F(2:3) progeny to identify genetic loci linked with the high FAA level in these mutants. Quantitative trait locus mapping identified four significant loci that account for about 46% of the phenotypic variance. One locus on the long arm of chromosome 2 is coincident with genes encoding a monofunctional Asp kinase 2 and a bifunctional Asp kinase-homo-Ser dehydrogenase-2, whereas another locus on the short arm of chromosome 3 is linked with a cytosolic triose phosphate isomerase 4. The results suggest an alternation of amino acid and carbon metabolism leads to overproduction and accumulation of FAA in opaque-2 mutants.

Amino Acids↗
PubMed2002

Linkage mapping of genes controlling resistance to white rust (Albugo candida) in Brassica rapa (syn. campestris) and comparative mapping to Brassica napus and Arabidopsis thaliana.

Genes for resistance to white rust (Albugo candida) in oilseed Brassica rapa were mapped using a recombinant inbred (RI) population and a genetic linkage map consisting of 144 restriction fragment length polymorphism (RFLP) markers and 3 phenotypic markers. Young seedlings were evaluated by inoculating cotyledons with A. candida race 2 (AC2) and race 7 (AC7) and scoring the interaction phenotype (IP) on a 0-9 scale. The IP of each line was nearly identical for the two races and the population showed bimodal distributions, suggesting that a single major gene (or tightly linked genes) controlled resistance to the two races. The IP scores were converted to categorical resistant and susceptible scores, and these data were used to map a single Mendelian gene controlling resistance to both races on linkage group 4 where resistance to race 2 had been mapped previously. A quantitative trait loci (QTL) mapping approach using the IP scores detected the same major resistance locus for both races, plus a second minor QTL effect for AC2 on linkage group 2. These results indicate that either a dominant allele at a single locus (Acal) or two tightly linked loci control seedling resistance to both races of white rust in the biennial turnip rape cultivar Per. The map positions of white rust resistance genes in B. rapa and Brassica napus were compared and the results indicate where additional loci that have not been mapped may be located. Alignment of these maps to the physical map of the Arabidopsis genome identified regions to target for comparative fine mapping using this model organism.

Arabidopsis↗
PubMed1994

Conformation polymorphisms and targeted marker development.

Genetic markers were developed for three targeted bovine loci using both single-stranded and double-stranded DNA conformation polymorphisms. Eight of nine DNA fragments exhibited single-stranded conformation polymorphisms while only one of nine exhibited a double-strand conformation polymorphism. All but one of the polymorphic fragments exhibited two allelic forms, with the exception being a single-stranded conformation polymorphism with three alleles. Utility of conformation polymorphisms relative to microsatellite markers for linkage map development and quantitative trait loci (QTL) mapping was assessed by comparing frequency of heterozygote parents from reference and resource families. Heterozygosity was greater for microsatellite markers (P < 0.01) and reference family parents (P < 0.01), though the disparity between marker types tended to be less dramatic for the reference family parents (P < 0.09). These results suggest conformation polymorphisms will be a useful tool for targeted marker development in linkage map and comparative map development provided genetically diverse families are studied.

Animals↗
PubMed2005

Inheritance of field resistance to Stagonospora nodorum leaf and glume blotch and correlations with other morphological traits in hexaploid wheat (Triticum aestivum L.).

Breeding for wheat varieties resistant to Stagonospora nodorum blotch (SNB) is the most sustainable strategy for controlling the disease. In order to map quantitative trait loci (QTLs) for SNB resistance we analysed 204 recombinant inbred lines of the cross between the winter wheat (Triticum aestivum L.) variety Forno and the winter spelt (Triticum spelta L.) variety Oberkulmer. We determined the level of resistance of adult plants to leaf blotch (SNL) and glume blotch (SNG) as well as morphological traits for 2 years after artificial inoculation with S. nodorum. Using composite interval mapping and LOD > 3.7, we detected ten QTLs for SNG blotch resistance (six inherited from the susceptible parent Forno) and 11 QTLs for SNL resistance (four inherited from Forno) across 2 years. Both resistance traits were moderately correlated (r = 0.52) and had only one common QTL. For SNL resistance, seven QTLs were not associated with QTLs for morphological traits. Among them, QSnl.eth-2D, QSnl.eth-4B and QSnl.eth-7B3 had major effects (R(2) > 13%) and were potential candidates for marker-assisted selection. For SNG, the major QTL on chromosome 5A, explaining 36% of the phenotypic variance for resistance, was associated with the q locus conferring the spelt morphology (long lax ear, long culm and hard glumes). Only QSng.eth-1BS, which explained 7% of the variance for resistance to SNG blotch, was not associated with QTLs for morphological traits. The consequences for breeding programmes are discussed.

Analysis of Variance↗
PubMed2006

A method for identification of the expression mode and mapping of QTL underlying embryo-specific characters.

Embryos of crop seeds are one of the major sources of the plant protein and lipid for human nutrition. The genetic expression for embryo-specific characters in crop seeds can be controlled exclusively by the embryo or the maternal genotypes and sometimes by both simultaneously. However, current methods for mapping quantitative trait loci (QTLs) underlying characters of maternal plants have not been effective in dealing with the QTL analysis of embryo characters. On the basis of the expression feature of embryo, a statistical method was proposed for the identification of expression mode and mapping of QTL controlling embryo traits. The maximum likelihood method implemented via the expectation maximization algorithm was used to estimate parameters of a putative embryo-specific QTL. The QTL expression mode was identified by the likelihood ratio test statistic. Statistical power and other properties of the proposed method were investigated under a variety of scenarios through simulation studies. The results showed that the mapping method neglecting the effects of embryo genotype or maternal effects could neither identify the expression mode of QTL nor estimate its genetic effects accurately, whereas the proposed method could effectively map the embryo-specific QTL of various expression modes.

Algorithms↗
PubMed2006

Porcine OGN and ASPN: mapping, polymorphisms and use for quantitative trait loci identification for growth and carcass traits in a Meishan x Piétrain intercross.

The porcine orthologues of human chromosome HSA9q22.31 genes osteoglycin (OGN) and asporin (ASPN) were mapped to porcine chromosome SSC3 using linkage analysis and a somatic cell hybrid panel. This mapping was refined to SSC3q11 using fluorescence in situ hybridization. These results confirm the existence of a small conserved synteny group between SSC3 and HSA9. Polymorphisms were revealed in both genes, including a pentanucleotide microsatellite (SCZ003) in OGN and two single nucleotide polymorphisms (AM181682.1:g.780G>T and AM181682.1:g.825T>C) in ASPN. The two genes were included in a set of markers for quantitative trait loci (QTL) mapping on SSC3 in the Hohenheim Meishan x Piétrain F2 family. Major QTL for growth and carcass traits were centred in the ASPN-SW902 region.

Animals↗
PubMed2005

The full EM algorithm for the MLEs of QTL effects and positions and their estimated variances in multiple-interval mapping.

The advent of complete genetic linkage maps of DNA markers has made systematic studies of mapping quantitative trait loci (QTL) in experimental organisms feasible. The method of multiple-interval mapping provides an appropriate way for mapping QTL using genetic markers. However, efficient algorithms for the computation involved remain to be developed. In this article, a full EM algorithm for the simultaneous computation of the MLEs of QTL effects and positions is developed. EM-based formulas are derived for computing the observed Fisher information matrix. The full EM algorithm is compared with an ECM algorithm developed by Kao and Zeng (1997, Biometrics 53, 653-665). The validity of the inverted observed Fisher information matrix as an estimate of the variance matrix of the MLEs is demonstrated by a simulation study.

Algorithms↗
PubMed2005

A QTL resource and comparison tool for pigs: PigQTLDB.

During the past decade, efforts to map quantitative trait loci (QTL) in pigs have resulted in hundreds of QTL being reported for growth, meat quality, reproduction, disease resistance, and other traits. It is a challenge to locate, interpret, and compare QTL results from different studies. We have developed a pig QTL database (PigQTLdb) that integrates available pig QTL data in the public domain, thus, facilitating the use of this QTL data in future studies. We also developed a pig trait classification system to standardize names of traits and to simplify organization and searching of the trait data. These steps made it possible to compare primary data from diverse sources and methods. We used existing pig map databases and other publicly available data resources (such as PubMed) to avoid redundant developmental work. The PigQTLdb was also designed to include data representing major genes and markers associated with a large effect on economically important traits. To date, over 790 QTL from 73 publications have been curated into the database. Those QTL cover more than 300 different traits. The data have been submitted to the Entrez Gene and the Map Viewer resources at NCBI, where the information about markers was matched to marker records in NCBI's UniSTS database. Having these data in a public resource like NCBI allows regularly updated automatic matching of markers to public sequence data by e-PCR. The submitted data, and the results of these calculations, are retrievable from NCBI via Entrez Gene, Map Viewer, and UniSTS. Efforts were undertaken to improve the integrated functional genomics resources for pigs.

Animals↗
PubMed1995

Molecular genetics of growth and development in populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree.

We have mapped quantitative trait loci (QTLs) for commercially important traits (stem growth and form) and an adaptive trait (spring leaf flush) in a Populus F2 generation derived from a cross between interspecific F1 hybrids (P. trichocarpa x P. deltoides). Phenotypic data were collected over a 2-year period from a replicated clonal trial containing ramets of the parental, F1, and F2 trees. Contrary to the assumptions of simple polygenic models of quantitative trait inheritance, 1-5 QTLs of large effect are responsible for a large portion of the genetic variance in each of the traits measured. For example, 44.7% of the genetic variance in stem volume after 2 years of growth is controlled by just two QTLs. QTLs governing stem basal area were found clustered with QTLs for sylleptic branch leaf area, sharing similar chromosomal position and mode of action and suggesting a pleiotropic effect of QTLs ultimately responsible for stem diameter growth.

Chromosome Mapping↗
PubMed2002

A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus).

Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

Animals↗
PubMed2005

Fine mapping of Lvm1: a quantitative trait locus controlling heart size independently of blood pressure.

We have previously reported a quantitative trait locus (QTL) on rat chromosome 2 that influences heart size independently of blood pressure (Left Ventricular Mass Locus 1; Lvm1). The recent release of the rat genome sequence allowed us to retest and refine this relatively broad QTL with a view to identifying within it candidate genes worthy of structural investigation. We sought to achieve this 'fine mapping' by increasing the marker density within the interval and undertaking a linkage analysis in a previously defined population of F2 hybrids generated from inbred spontaneously hypertensive rats (SHR) of the Okamoto strain and Fischer rat (F344) progenitors. We were able to reconfirm and resolve Lvm1 from its original width of approximately 45 to 15 cM. By reference to the ENSEBL rat genome data bank, we identified within Lvm1 27 known genes, 109 predicted genes and 7 pseudogenes. Of the known genes, candidates include potential regulators of cardiac growth, a sodium channel and calcium channel as well as the fibroblast growth factor 2 gene. Located nearby the Lvm1 locus was the gene for the angiotensin Type 1B receptor. Given the evidence that the ligand for the angiotensin Type 1B receptor-angiotensin II-is a potent cardiotroph, we also consider this gene a potential candidate. The identification of the precise allelic variant(s) within Lvm1 involved in the control of pressure-independent cardiac growth awaits further molecular studies.

Animals↗
PubMed2002

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.

Chromosome Mapping↗
PubMed2000

A quantitative-trait locus controlling peripheral B-cell deficiency maps to mouse Chromosome 15.

Peripheral B-lymphocyte homeostasis is determined through incompletely defined positive and negative regulatory processes. The A/WySnJ mouse, but not the related A/J strain, has disturbed homeostasis leading to peripheral B-lymphocyte deficiency. B lymphopoeisis is normal in A/WySnJ mice, but the B cells apoptose rapidly in the periphery. This B cell-intrinsic defect segregated as a single locus, Bcmd, in (A/WySnJxA/J)F2 mice. Here we mapped a quantitative-trait locus (QTL) that contributes to the A/WySnJ B-cell deficiency by examining the F2 progeny of a cross between strains A/WySnJ and CAST/Ei. In this cross, minimally 1.9 QTLs controlling peripheral B lymphocyte deficiency segregated. The (A/WySnJxCAST/Ei)F2 mice were phenotyped for splenic B-cell percentage and the DNA from progeny with extreme phenotypes was used to map the QTL by the simple-sequence length polymorphism method. A genome scan showed linkage between peripheral B-cell deficiency and Chromosome (Chr) 15 markers. When closely spaced Chr 15 markers were analyzed, the 99% confidence interval for the QTL map position extended along the entire chromosome length. The peak lod scores >17 occurred between 30 and 45 cM. We conclude that a significant QTL segregating in (A/WySnJxCAST/Ei)F2 mice resides in this middle region of Chr 15.

Animals↗
PubMed1998

Unusual EEG pattern linked to chromosome 3p in a family with idiopathic generalized epilepsy.

OBJECTIVE: To map the gene causing an unusual EEG pattern of delta bursts that appears to segregate as an autosomal dominant trait in an Italian family. The EEG pattern was observed in four family members affected by idiopathic generalized epilepsy (IGE) and in six other clinically unaffected members. METHODS: All available family members underwent clinical and EEG examination. DNA samples were obtained and used to perform a whole-genome scan with 270 microsatellite markers. After the first linked marker was identified, 12 additional markers in the same chromosomal region were tested to confirm linkage and define a candidate interval. RESULTS: The gene responsible for the EEG trait was mapped to an 11-cM interval on the proximal short arm of chromosome 3 (3p14.2-p12.1). CONCLUSION: In this family, a characteristic EEG activity is due to the effect of a single gene on chromosome 3p. A gene encoding a Ca2+ channel subunit maps in the interval and is a potential candidate for the trait. The clinical expression of epilepsy in four family members may reflect the interaction of additional genes, though environmental or other factors cannot be excluded.

Chromosome Mapping↗