Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Trait mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,693 records · Page 94Linked to original sources
PubMed2005

A major gene mapped on chromosome XII is the main factor of a quantitatively inherited resistance to Meloidogyne fallax in Solanum sparsipilum.

Meloidogyne fallax is an emerging pest in Europe and represents a threat for potato production. We report the mapping of genetic factors controlling a quantitative resistance against M. fallax identified in the Solanum sparsipilum genotype 88S.329.15. When infected, this genotype develops a necrotic reaction at the feeding site of the juveniles and totally prevents their development to the female stage. A "F1" diploid progeny consisting of 128 individuals was obtained using the potato (S. tuberosum) dihaploid genotype BF15 H1 as female progenitor. Sixty-eight hybrid genotypes displayed necrosis at the feeding site of the juveniles and 60 other genotypes showed no defence reaction. This suggested a monogenic control of the resistance. However, when considering the number of nematode females developed in their roots, a continuous distribution was observed for both "necrotic" and "non-necrotic" hybrid genotypes, indicating a polygenic control of the resistance. A linkage map of each parental genotype was constructed using AFLP markers. The necrotic reaction (NR) was mapped as a qualitative trait on chromosome XII of the resistant genotype 88S.329.15. Quantitative trait locus (QTL) analysis for the number of nematode females developed per "F1" plant genotype was performed using the QTL cartographer software. No QTL was detected on the linkage map of the susceptible parent. A QTL explaining 94.5% of the phenotypic variation was mapped on chromosome XII of the resistant progenitor. This QTL, named MfaXIIspl, was mapped in a genomic region collinear to the map position of the Mi-3 gene conferring resistance to Meloidogyne incognita in tomato. It corresponds to the NR locus.

Animals↗
PubMed1999

Overview of QTL mapping software and introduction to map manager QT.

At least ten software packages are available for marker-based detection and localization of loci contributing to quantitative traits in experimental animals and plants. Many of these have unique strengths or situations in which they are particularly useful. Six were developed by or in collaboration with plant geneticists and may not be well known to mammalian geneticists. These software packages are reviewed here and compared with a previously undescribed program, Map Manager QT, a Mac OS microcomputer program for mapping quantitative trait loci in populations derived from backcrosses, intercrosses, and recombinant inbred lines. Map Manager QT is an enhanced version of Map Manager Classic (Map Manager v2.6.5, Manly 1993), designed for mapping Mendelian loci. This review describes the methods Map Manager QT uses for mapping quantitative trait loci and describes other features that differ from those in Map Manager Classic. A complete description of both Map Manager Classic and Map Manager QT is available in the user manual, the on-line version of which can be found at http://mcbio.med.buffalo.edu/MMM/MMM.ht ml.

Animals↗
PubMed2003

Physiological and molecular basis of susceptibility and tolerance of rice plants to complete submergence.

Rice plants are much damaged by several days of total submergence. The effect can be a serious problem for rice farmers in the rainfed lowlands of Asia, and runs contrary to a widespread belief amongst plant biologists that rice is highly tolerant of submergence. This article assesses the characteristics of the underwater environment that may damage rice plants, examines various physiological mechanisms of injury, and reviews recent progress achieved using linkage mapping to locate quantitative traits loci (QTL) for tolerance inherited from a submergence-tolerant cultivar FR13A. Progress towards identifying the gene(s) involved through physical mapping of a dominant tolerance locus on chromosome 9 is also summarized. Available physiological evidence points away from responses to oxygen shortage as being inextricably involved in submergence injury. An imbalance between production and consumption of assimilates is seen as being especially harmful, and is exacerbated by strongly accelerated leaf extension and leaf senescence that are ethylene-mediated and largely absent from FR13A and related cultivars. DNA markers for a major QTL for tolerance are shown to be potentially useful in breeding programmes designed to improve submergence tolerance.

Adaptation, Physiological↗
PubMed2005

Natural allelic variation in the temperature-compensation mechanisms of the Arabidopsis thaliana circadian clock.

Temperature compensation is a defining feature of circadian oscillators, yet no components contributing to the phenomenon have been identified in plants. We tested 27 accessions of Arabidopsis thaliana for circadian leaf movement at a range of constant temperatures. The accessions showed varying patterns of temperature compensation, but no clear associations to the geographic origin of the accessions could be made. Quantitative trait loci (QTL) were mapped for period and amplitude of leaf movement in the Columbia by Landsberg erecta (CoL) and Cape Verde Islands by Landsberg erecta (CvL) recombinant inbred lines (RILs) at 12 degrees , 22 degrees , and 27 degrees . Six CvL and three CoL QTL were located for circadian period. All of the period QTL were temperature specific, suggesting that they may be involved in temperature compensation. The flowering-time gene GIGANTEA and F-box protein ZEITLUPE were identified as strong candidates for two of the QTL on the basis of mapping in near isogenic lines (NILs) and sequence comparison. The identity of these and other candidates suggests that temperature compensation is not wholly determined by the intrinsic properties of the central clock proteins in Arabidopsis, but rather by other genes that act in trans to alter the regulation of these core proteins.

Arabidopsis↗
PubMed2003

Mapping of genetic loci predisposing to hypertriglyceridaemia in the hereditary hypertriglyceridaemic rat: analysis of genetic association with related traits of the insulin resistance syndrome.

AIMS/HYPOTHESIS: Hypertriglyceridaemia is an important risk factor for coronary heart disease, especially in the context of the insulin resistance syndrome where it often occurs with hypertension. The two phenotypes are also associated in the hereditary hypertriglyceridaemic (hHTg) rat. The aim of this study was to map quantitative trait loci that affect plasma triglyceride concentration in the hHTg rat and determine whether they co-localize with loci for blood pressure. METHODS: Second filial generation progeny (n=189) from a cross of the hHTg rat with the Brown Norway rat were phenotyped for fasting plasma triglyceride, glucose and insulin concentrations, and direct unrestrained resting blood pressure. A partial genome-scan was conducted using 153 microsatellite markers that were polymorphic between the two strains. RESULTS: A major locus (lod score 6.5) influencing plasma triglyceride concentration in a co-dominant fashion was mapped to chromosome 4 between D1Mit 5 and D1Mit17. Chromosome 8 contained multiple peaks with a lod score greater than 4.0 influencing triglyceride concentration. Importantly, none of the triglyceride loci had an effect on blood pressure. The triglyceride locus on chromosome 4 co-localized with a locus for fasting plasma insulin (lod score 4.1), although the effect on insulin concentration was in the opposite direction to that on triglyceride. CONCLUSION/INTERPRETATION: We have mapped the major loci that affect plasma triglyceride concentration in the hHTg rat. These loci do not influence blood pressure suggesting that these commonly associated phenotypes of the insulin resistance syndrome are not be due to pleiotropic effects of the same gene(s).

Animals↗
PubMed2003

QTLs for agronomic traits in the Mediterranean environment identified in recombinant inbred lines of the cross 'Arta' x H. spontaneum 41-1.

A genetic linkage map has been developed for recombinant inbred lines (RILs) of the cross 'Arta' x Hordeum spontaneum 41-1. One hundred and ninety four RILs, randomly chosen from a population of 494 RILs, were mapped with 189 markers including one morphological trait ( btr = brittle rachis locus). The linkage map extended to 890 cM. Agronomic traits such as grain yield, biological yield, days to heading, plant height, cold tolerance and others were evaluated at the ICARDA research stations Tel Hadya and Breda during the years 1996-97 and 1997-98. QTLs for agronomic traits related to drought resistance were localized. For the most-important character 'plant height under drought stress', QTLs on 2H, 3H and 7H were detected. The 'plant height' QTLs, specially the one on 3H, showed pleiotropic effects on traits such as days to heading, grain yield and biological yield. QTLs were also identified for other traits associated with adaptation to the Mediterranean environment such as cold tolerance, days to heading and tiller number. The identification of QTLs for agronomic traits is a first step to analyze and to dissect complex characters such as adaptation to drought tolerance.

Adaptation, Physiological↗
PubMed2005

Identification of candidate markers associated with agronomic traits in rice using discriminant analysis.

Plant genetic mapping strategies routinely utilize marker genotype frequencies obtained from progeny of controlled crosses to declare presence of a quantitative trait locus (QTL) on previously constructed linkage maps. We have evaluated the potential of discriminant analysis (DA), a multivariate statistical procedure, to detect candidate markers associated with agronomic traits among inbred lines of rice (Oryza sativa L.). A total of 218 lines originating from the US and Asia were planted in field plots near Alvin, Texas, in 1996 and 1997. Agronomic data were collected for 12 economically important traits, and DNA profiles of each inbred line were produced using 60 SSR and 114 RFLP markers. Model-based methods revealed population structure among the lines. Marker alleles associated with all traits were identified by DA at high levels of correct percent classification within subpopulations and across all lines. Associated marker alleles pointed to the same and different regions on the rice genetic map when compared to previous QTL mapping experiments. Results from this study suggest that candidate markers associated with agronomic traits can be readily detected among inbred lines of rice using DA combined with other methods described in this report.

Asia↗
PubMed1997

Genetic and molecular dissection of quantitative traits in rice.

Recent progress in the generation of a molecular genetic map and markers for rice has made possible a new phase of mapping individual genes associated with complex traits. This type of analysis is often referred to as quantitative trait locus (QTL) analysis. Increasing numbers of QTL analyses are providing enormous amounts of information about QTLs, such as the numbers of loci involved, their chromosomal locations and gene effects. Clarification of genetic bases of complex traits has a big impact not only on fundamental research on rice plant development, but it also has practical benefits for rice breeding. In this review, we summarize recent progress of QTL analysis of several complex traits in rice. A strategy for positional cloning of genes at QTLs is also discussed.

Chromosome Mapping↗
PubMed2004

Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa).

BACKGROUND AND AIMS: Seedling vigour is one of the major determinants for stable stand establishment in rice (Oryza sativa), especially in a direct seeding cropping system. The objectives of this study were to identify superior alleles with consistent effects on seedling vigour across different temperature conditions and to investigate genotype x environmental temperature interactions for seedling vigour QTL. METHODS: A set of 282 F13 recombinant inbred lines (RILs) derived from a rice cross were assessed for four seedling vigour traits at three temperatures (25 degrees C, 20 degrees C and 15 degrees C). Using a linkage map with 198 marker loci, the main-effect QTL for the traits were mapped by composite interval mapping. KEY RESULTS: A total of 34 QTL for the four seedling vigour traits were identified. Of these QTL, the majority (82%) were clustered within five genomic regions, designated as QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2. All of these five QTL had small individual effects on the traits, explaining 3.1-15.8 % of the phenotypic variation with a mean of 7.3 %. QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all three temperatures while qSV-5 and qSV-8-2 had effects mainly at the 'normal' temperatures of 20 degrees C and 25 degrees C. Among the five QTL identified, all and four showed additive effects on shoot length and germination rate, respectively. The contributions of these five QTL to shoot length and germination rate were also much larger than those to the other two traits. CONCLUSIONS: A few of genomic regions (or QTL) were identified as showing effects on seedling vigour. For these QTL, significant genotype x environmental temperature interactions were found and these interactions appeared to be QTL-specific. Among the four seedling vigour traits measured, shoot length and germination rate could be used as relatively good indicators to evaluate the level of seedling vigour in rice.

Chromosome Mapping↗
PubMed1996

An ordered yeast artificial chromosome library covering over half of rice chromosome 6.

Yeast artificial chromosome (YAC) clones carrying DNA marker sequences located on the rice genetic map of chromosome 6 were ordered for physical mapping. A total of 122 restriction fragment length polymorphism markers, 16 sequence-tagged site markers, and five random amplified polymorphic DNA markers located, on average, at 0.9-cM intervals, were used for YAC clone screening by colony/Southern hybridization and PCR screening, respectively. A total of 216 individual YACs were selected from our YAC library of 7000 clones covering six genome equivalents. Each DNA marker could select, on average, 4.8 YAC clones, with 11 clones being the maximum. The YACs localized to the corresponding linkage map positions form 43 contigs and encompass about 60% of rice chromosome 6. This is the first step in constructing a physical map covering the whole rice genome by chromosome landing with YAC clones. These YACs and data will be used soon to isolate phenotypical trait genes by map-based cloning.

Blotting, Southern↗
PubMed2003

Preliminary investigation of QTLs associated with seedling resistance to ascochyta blight from Cicer echinospermum, a wild relative of chickpea.

Accessions from Cicer echinospermum, a wild relative of chickpea (Cicer arietinum L.), contain resistance to the fungal disease ascochyta blight, a devastating disease of chickpea. A linkage map was constructed based on an interspecific F(2) population, derived from a cross between a susceptible chickpea cultivar (Lasseter) and a resistant C. echinospermum accession (PI 527930). The linkage map incorporated 83 molecular markers, that included RAPD, ISSR, STMS and RGA markers; eight markers remained unlinked. The map comprised eight linkage groups and covered a map distance of 570 cM. Six out of the eight linkage groups were correlated to linkage groups from the integrated Cicer map using STMS markers. Quantitative trait loci (QTLs) associated with ascochyta blight resistance were detected using interval mapping and single-point analysis. The F(2) population was evaluated for seedling and stem resistance in glasshouse trials. At least two QTLs were identified for seedling resistance, both of which were located within linkage group 4. Five markers were associated with stem resistance, four of which were also associated with seedling resistance. QTLs from previous studies also mapped to LG 4, suggesting that this linkage group is an important region of the Cicer genome for resistance to ascochyta blight.

Ascomycota↗
PubMed2003

Two loci on chromosome 5H determine low-temperature tolerance in a 'Nure' (winter) x 'Tremois' (spring) barley map.

Barley ( Hordeum vulgare subsp. vulgare) is an economically important diploid model for the Triticeae; and a better understanding of low-temperature tolerance mechanisms could significantly improve the yield of fall-sown cereals. We developed a new resource for genetic analysis of winter hardiness-related traits, the 'Nure' x 'Tremois' linkage map, based on a doubled-haploid population that is segregating for low-temperature tolerance and vernalization requirement. Three measures of low-temperature tolerance and one measure of vernalization requirement were used and, for all traits, QTLs were mapped on chromosome 5H. The vernalization response QTL coincides with previous reports at the Vrn-1/Fr1 region of the Triticeae. We also found coincident QTLs at this position for all measures of low-temperature tolerance. Using Composite Interval Mapping, a second proximal set, of coincident QTLs for low-temperature tolerance, and the accumulation of two different COR proteins (COR14b and TMC-Ap3) was identified. The HvCBF4 locus, or another member of the CBF loci clustered in this region, is the candidate gene underlying this QTL. There is a CRT/DRE recognition site in the promoter of cor14b with which a CBF protein could interact. These results support the hypothesis that highly conserved regulatory factors, such as members of the CBF gene family, may regulate the stress responses of a wide range of plant species.

Acclimatization↗
PubMed2005

Linkage analysis of alcohol dependence using MOD scores.

Alcohol dependence is a typical example of a complex trait that is governed by several genes and for which the mode of inheritance is unknown. We analyzed the microsatellite markers and the Affymetrix single-nucleotide polymorphisms (SNPs) for a subset of the Collaborative Study on the Genetics of Alcoholism family sample, 93 pedigrees of Caucasian ancestry comprising 919 persons, 390 of whom are affected according to DSM III-R and Feighner criteria. In particular, we performed parametric single-marker linkage analysis using MLINK of the LINKAGE package (for the microsatellite data), as well as multipoint MOD-score analysis with GENEHUNTER-MODSCORE (for the microsatellite and SNP data). By use of two liability classes, different penetrances were assigned to males and females. In order to investigate parent-of-origin effects, we calculated MOD scores under trait models with and without imprinting. In addition, for the microsatellite data, the MOD-score analysis was performed with sex-averaged as well as sex-specific maps. The highest linkage peaks were obtained on chromosomes 1, 2, 7, 10, 12, 13, 15, and 21. There was evidence for paternal imprinting at the loci on chromosomes 2, 10, 12, 13, 15, and 21. A tendency to maternal imprinting was observed at two loci on chromosome 7. Our findings underscore the fact that an adequate modeling of the genotype-phenotype relation is crucial for the genetic mapping of a complex trait.

Alcoholism↗
PubMed2004

Limitations of a two-step moment method for mapping linked multiple QTL.

As an alternative to multiple-interval mapping a two-step moment method was recently proposed to map linked multiple quantitative trait loci (QTLs). The advantage of this moment method was supposed to be its simplicity and computational efficiency, especially in detecting closely linked QTLs within a marker bracket, but also in mapping QTLs in different marker intervals. Using simulations it is shown that the two-step moment method may give poor results compared with multiple-interval mapping, irrespective of whether the QTLs are in the same or in different marker intervals, especially if linked QTLs are in repulsion. The criteria of comparison are number of identified QTLs, likelihood ratio test statistics, means and empirical standard errors of the QTL position and QTL effects estimates, and the accuracy of the residual variance estimates. Further, the joint conditional probabilities of QTL genotypes for two putative QTLs within a marker interval were derived and compared with the unmodified approach ignoring the non-independence of the conditional probabilities.

Analysis of Variance↗
PubMed2002

Congenic rat strains are important tools for the genetic dissection of essential hypertension.

The identification of mutated genes and the characterization of disease pathways in monogenetic forms of human arterial hypertension has been very successful during the past decade, although only little progress has been made with regard to the genetic analysis of essential hypertension. Inbred rat strains that display hypertension as an inherited trait represent an attractive substitute for the dissection of the polygenetic basis of human essential hypertension. The power of studying these inbred models with natural allelic variation is that each strain can be thought of as a different subtype of essential hypertension. Thus, to study the genetics of hypertension using a potpourri of inbred hypertensive rat strains may help to identify a set of genes that can give rise to hypertension in the heterogeneous clinical situation of essential hypertension. Indeed, multiple blood pressure quantitative trait loci (QTL) have been identified in the rat genome and a few of those have been implicated in the human disease by homology mapping already. Here, we discuss the role of congenic breeding strategies to further dissect the genetics of hypertension in the rat. Based on recent accomplishments it can be anticipated that by using congenic strains, the genetic sifting of the collection of blood pressure QTLs identified so far will lead to the identification of additional and new candidate genes. This will open the possibility for the development of new diagnostic and therapeutic means contributing to a better control of human essential hypertension.

Animals↗
PubMed2003

Primary factors affecting the evaluation accuracy of animal model MBLUP.

Marker-assisted best linear unbiased prediction (MBLUP) is one important method of implementing marker-assisted selection (MAS). The computer stochastic simulation method was used to study the effects of heritability of trait, QTL variance and map distance between two adjacent markers on the evaluation accuracy of animal model MBLUP. With the higher heritability, the smaller QTL variance and the shorter map distance between two adjacent markers, the evaluation accuracy of animal model MBLUP would be increased. On the contrary, the evaluation accuracy of animal model MBLUP would be decreased when the heritability was lower, QTL variance was larger and map distance between two adjacent markers was longer.

Animals↗
PubMed1993

The goals and status of the bovine gene map.

The bovine genome map has developed rapidly in recent years. The synteny and chromosomal maps are sufficiently developed to identify chromosomal conservation with other mammals, which is especially useful for the extrapolation of data to cattle from the better developed maps of mouse and human. The rapid development of microsatellite and other hypervariable markers in several laboratories around the world and the availability of a common set of reference families for linkage analysis will produce a 20-cM map in 2 yr. Immediate needs for development are 1) markers to anchor physical maps to linkage maps, 2) resource families segregating economic trait loci, and 3) chromosome-specific libraries to develop densely saturated linkage maps over genomic regions shown to contain economic trait loci.

Animals↗
PubMed2005

A genetic map of Cottus gobio (Pisces, Teleostei) based on microsatellites can be linked to the physical map of Tetraodon nigroviridis.

To initiate QTL studies in the nonmodel fish Cottus gobio we constructed a genetic map based on 171 microsatellite markers. The mapping panel consisted of F1 intercrosses between two divergent Cottus lineages from the River Rhine System. Basic local alignment search tool (BLAST) searches with the flanking sequences of the microsatellite markers yielded a significant (e < 10(-5)) hit with the Tetraodon nigroviridis genomic sequence for 45% of the Cottus loci. Remarkably, most of these hits were due to short highly conserved noncoding stretches. These have an average length of 40 bp and are on average 92% conserved. Comparison of the map locations between the two genomes revealed extensive conserved synteny, suggesting that the Tetraodon genomic sequence will serve as an excellent genomic reference for at least the Acanthopterygii, which include evolutionarily interesting fish groups such as guppies (Poecilia), cichlids (Tilapia) or Xiphophorus (Platy). The apparent high density of short conserved noncoding stretches in these fish genomes will highly facilitate the identification of genes that have been identified in QTL mapping strategies of evolutionary relevant traits.

Animals↗