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PubMed2006

Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza rufipogon Griff.).

SIL040, an introgression line (IL) developed by introgressing chromosomal segments from an accession of Oryza rufipogon into an indica cultivar Guichao 2, showed significantly less grains per panicle than the recurrent parent Guichao 2. Quantitative trait locus (QTL) analysis in F2 and F3 generations derived from the cross between SIL040 and Guichao 2 revealed that gpa7, a QTL located on the short arm of chromosome 7, was responsible of this variation. Alleles from O. rufipogon decreased grains per panicle. To fine mapping of gpa7, a high-resolution map with 1,966 F2 plants derived from the cross between SIL040 and Guichao 2 using markers flanking gpa7 was constructed, and detailed quantitative evaluation of the structure of main panicle of each of F3 families derived from recombinants screened was performed. By two-step substitution mapping, gpa7 was finally narrowed down to a 35-kb region that contains five predicted genes in cultivated rice. The fact that QTLs for five panicle traits (length of panicle, primary branches per panicle, secondary branches per panicle, grains on primary branches and grains on secondary branches) were all mapped in the same interval as that for gpa7 suggested that this locus was associated with panicle structure, showing pleiotropic effects. The characterizing of panicle structure of IL SIL040 further revealed that, during the domestication from common wild allele to cultivated rice one at gpa7, not only the number of branches and grains per panicle increased significantly, more importantly, but also the ratio of secondary branches per panicle to total branches per panicle and the ratio of grains on secondary branches per panicle to total grains per panicle increased significantly. All these results reinforced the idea that gpa7 might play an important role in the regulation of grain number per panicle and the ratio of secondary branches per panicle during the domestication of rice panicle.

Alleles↗

PubMed1993

Microsatellite mapping of the gene causing weaver disease in cattle will allow the study of an associated quantitative trait locus.

A genetic disease in cattle, progressive degenerative myeloencephalopathy (weaver disease), is associated with increased milk production. This association could result from population stratification, from a pleiotropic effect of a single gene, or from linkage disequilibrium between the gene causing weaver disease and a quantitative trait locus (QTL) for milk production. To test these hypotheses, we performed an extensive linkage study in a bovine pedigree segregating for the weaver condition and identified a microsatellite locus (TGLA116) closely linked to the weaver gene (zmax, 8.15; theta, 0.03). TGLA116 and, by extension, the weaver locus were assigned to bovine synteny group 13. This microsatellite can be used to identify weaver carriers, to select against this genetic defect, and to study the effect of the corresponding chromosomal region on milk production in Brown Swiss and other breeds of cattle.

Animals↗

PubMed2026

Quantitative trait locus qLDC5 regulates primary root branching in an auxin-dependent manner.

L-type lateral root (LLR) density determines root system architecture, affecting nutrient acquisition in rice (Oryza sativa L.), particularly under low-phosphorus conditions. Previous studies identified genotypic differences in LLR density and a quantitative trait locus (QTL) enhancing LLR density on crown roots (qLDC5). We showed that LLR densities on crown and primary roots were closely correlated and confirmed higher LLR density on primary roots in qLDC5 donor DJ123 compared with the African variety NERICA4 using X-ray micro-computed tomography. We confirmed the qLDC5 effect in a field experiment for LLR density on primary roots. LLR densities on primary and crown roots, therefore, appear under similar genetic control. Developmental analyses revealed that DJ123 and NDJ188-a derivative line harboring qLDC5-initiate more lateral root primordia than NERICA4, with a higher proportion progressing to elongation, but that exogenous auxin application reversed this ranking. Within qLDC5, auxin biosynthesis gene OsYUCCA2 and auxin response factor OsARF15 were up-regulated in DJ123. Transcriptome analysis revealed an indirect auxin-mediated regulatory network underlying LLR variation. Differentially expressed genes in DJ123 and NDJ188 were enriched for ent-kaurene and gibberellin metabolism, including the robust induction of OsGA2ox5. These findings suggest qLDC5 increases lateral root density by coordinating gibberellin, auxin, and terpene pathways.

Oryza↗

PubMed2001

Quantitative trait locus analysis for chronic pancreatitis and diabetes mellitus in the WBN/Kob rat.

A causative gene mutation is still undefined in approximately half of patients with hereditary pancreatitis, and no genetic factor has been identified in most patients with sporadic chronic pancreatitis. To identify a pancreatitis-associated gene, we performed a quantitative trait locus (QTL) analysis for the traits of chronic pancreatitis and diabetes mellitus in WBN/Kob rats. We identified two highly significant QTLs for chronic pancreatitis and/or hyperinsulinemia on chromosomes 7 and X. These QTLs were located on completely different chromosomal regions from those of causative genes that have been reported for human chronic pancreatitis: PRSS1, CFTR, and SPINK1. For these QTLs, prevalences of the WBN/Kob allele significantly increased in the rats with chronic pancreatitis. These findings indicate that chronic pancreatitis in WBN/Kob rats is controlled by multiple genes, and a genetic analysis in WBN/Kob rats might be useful for gene targeting for human chronic pancreatitis.

Animals↗

PubMed2002

Variance components models for gene-environment interaction in quantitative trait locus linkage analysis.

Gene-environment interaction (G x E) is likely to be a common and important source of variation for complex behavioral traits. Gene-environment interaction, or genetic control of sensitivity to the environment, can be incorporated into variance components twin and sib-pair analyses by partitioning genetic effects into a mean part, which is independent of the environment, and a part that is a linear function of the environment. An approach described in a companion paper (Purcell, 2002) is applied to sib-pair variance components linkage analysis in two ways: allowing for quantitative trait locus by environment interaction and utilizing information on any residual interactions detected prior to analysis. As well as elucidating environmental pathways, consideration of G x E in quantitative and molecular studies will potentially direct and enhance gene-mapping efforts.

Computer Simulation↗

PubMed1999

Two-stage selection strategies utilizing marker-quantitative trait locus information and individual performance.

Short- and long-term response to marker-assisted selection in two stages was studied using a stochastic simulation of a closed nucleus herd for beef production. First-stage selection was carried out within families based on information at a fully additive quantitative trait locus (QTL). Second-stage selection strategies were based on 1) individual phenotype, 2) individual phenotype precorrected for QTL, 3) a selection index incorporating phenotype and QTL information, 4) a standard animal model BLUP, and 5) a selection index incorporating marker-QTL information and standard animal model BLUP on records precorrected for QTL. All strategies were efficient in moving the favorable allele at the QTL to fixation, but they differed in the time to reach fixation. Mass selection was less efficient in changing allele frequencies than BLUP. Discounted accumulated response, accounting for the time response was realized and inflation rate, was proposed to rank strategies and to elude the conflict between short- and long-term response in marker-assisted selection. Discounted accumulated response at a time horizon of 20 yr for alternative two-stage selection strategies was compared with conventional BLUP carried out in second stage only. Within-family selection increased discounted accumulated response by more than 11% using Strategy 4 and by up to 12% using Strategy 5 at an inflation rate of 2%. The percentage increase in response was less for highly heritable traits and when the proportion of additive variance explained by the QTL was small. Strategy 5 gave larger response with reduced inbreeding. This strategy also resulted in the lowest cost-benefit ratio, requiring less genotyping per unit of response. Cost-benefit ratio for discounted genotyping and for discounted in vitro production of embryos for traits with low heritability was two to four times that for traits with high heritability. The use of first-stage selection slightly increased the level of inbreeding for both mass (Strategy 1) and BLUP selection (Strategies 4 and 5).

Animals↗

PubMed2001

A major quantitative trait locus on chromosome 3 controls colitis severity in IL-10-deficient mice.

Colitic lesions are much more severe in C3H/HeJBir (C3H) than C57BL/6J (B6) mice after 10 backcrosses of a disrupted interleukin-10 (Il10) gene. This study identified cytokine deficiency-induced colitis susceptibility (Cdcs) modifiers by using quantitative trait locus (QTL) analysis. A segregating F(2) population (n = 408) of IL-10-deficient mice was genotyped and necropsied at 6 weeks of age. A major C3H-derived colitogenic QTL (Cdcs1) on chromosome (Chr.) 3 contributed to lesions in both cecum [logarithm of odds ratio (LOD) = 14.6)] and colon (LOD = 26.5) as well as colitis-related phenotypes such as spleen/body weight ratio, mesenteric lymph node/body weight ratio, and secretory IgA levels. Evidence for other C3H QTL on Chr. 1 (Cdcs2) and Chr. 2 (Cdcs3) was obtained. Cdcs1 interacted epistatically or contributed additively with loci on other chromosomes. The resistant B6 background also contributed colitogenic QTL: Cdcs4 (Chr. 8), Cdcs5 (Chr. 17, MHC), and Cdcs6 (Chr. 18). Epistatic interactions between B6 QTL on Chr. 8 and 18 contributing to cecum hyperplasia were particularly striking. In conclusion, a colitogenic susceptibility QTL on Chr. 3 has been shown to exacerbate colitis in combination with modifiers contributed from both parental genomes. The complex nature of interactions among loci in this mouse model system, coupled with separate deleterious contributions from both parental strains, illustrates why detection of human inflammatory bowel disease linkages has proven to be so difficult. A human ortholog of the Chr. 3 QTL, if one exists, would map to Chr. 4q or 1p.

Animals↗

PubMed2004

A quantitative trait locus influencing fasting plasma glucose in chromosome region 18q22-23.

Fasting plasma glucose is a multigenic trait related to both diabetes and obesity. We performed a genome scan for quantitative fasting plasma glucose levels in 320 families (1,514 subjects), segregating extreme obesity and normal weight using 382 autosomal microsatellite markers. We found significant linkages on 18q22-23 using family regression (logarithm of odds [LOD] 3.67, P = 0.00002, D18S1371 at 116 cM) and variance components (LOD 4.48, P < 0.00001) methods. Evidence for linkage remained strong when restricted to European Americans (260 families, 1,258 individuals). After an additional 60 families were added, the linkage signal strengthened (LOD 6.59). The result on 18q22-23 remained significant, even after controlling for both BMI and diabetes status. We also found suggestive linkages on chromosomes 2 (LOD 1.58, 216 cM) and 7 (LOD 1.78, 163 cM). Our results suggest that there is a quantitative trait locus in chromosome region 18q22-23 that influences fasting glucose levels and may play a role in the pathogenesis of type 2 diabetes. The strength of the serum glucose results after controlling for BMI suggests that this putative gene does not influence glucose levels merely through an effect on obesity.

Blood Glucose↗

PubMed2003

FXR and ABCG5/ABCG8 as determinants of cholesterol gallstone formation from quantitative trait locus mapping in mice.

BACKGROUND & AIMS: Cholesterol gallstone formation is a complex genetic trait. To identify additional cholesterol gallstone susceptibility loci, we performed a quantitative trait locus analysis using an intercross of PERA/Ei and I/LnJ inbred strains of mice. METHODS: Mice of both sexes were examined for gallstone weight and evaluated according to a scoring system for the physical chemistry of cholelithiasis during feeding of a lithogenic diet. Intercross offspring were genotyped, and linkage analysis was performed by interval mapping. Differences in messenger RNA expression of positional candidate genes were determined using reverse-transcription and real-time polymerase chain reaction. RESULTS: We identified significant loci associated with gallstone weight on chromosomes 10 and 4, named Lith7 and Lith8, respectively (both susceptibility alleles conferred by strain I/LnJ). Positional candidate genes with higher expression in I/LnJ mice are Fxr (official symbol, Nr1h4), encoding the nuclear bile salt receptor, on chromosome 10 and Shp1 (official symbol, Nr0b2), encoding the small heterodimer partner 1, on chromosome 4. A significant locus associated with gallstone score on chromosome 17, named Lith9 (susceptibility allele conferred by strain PERA/Ei), colocalizes with the genes Abcg5 and Abcg8 that encode the canalicular cholesterol transporter. Higher hepatic messenger RNA expression of Abcg5 and Abcg8 in strain PERA/Ei correlates positively with higher biliary cholesterol levels. CONCLUSIONS: Our findings suggest a primary role of the nuclear bile salt receptor FXR and the canalicular cholesterol transporter ABCG5/ABCG8 in the genetic susceptibility and pathogenesis of cholesterol cholelithiasis in these strains of inbred mice.

ATP Binding Cassette Transporter, Subfamily G, Mem↗

PubMed2002

A quantitative-trait locus in the human factor XII gene influences both plasma factor XII levels and susceptibility to thrombotic disease.

One approach to the identification of genetic loci that influence complex diseases is through the study of quantitative risk factors correlated with disease susceptibility. Factor XII (FXII) plasma levels, a related phenotype correlated with thrombosis, is such a risk factor. We conducted the first genomewide linkage screen to localize genes that influence variation in FXII levels. Two loci were detected: one on chromosome 5 and another on chromosome 10 (LOD scores 4.73 and 3.53, respectively). On chromosome 5, the peak LOD score occurred in the 5q33-5ter region, near the FXII gene. Addition of a 46C/T mutation in the FXII gene increased the multipoint LOD score to 10.21 (P=3.6 x 10(-12)). A bivariate linkage analysis of FXII activity and thrombosis further improved the linkage signal (LOD = 11.73) and provided strong evidence that this quantitative-trait locus (QTL) has a pleiotropic effect on the risk of thrombosis (P=.004). Linkage analysis conditional on 46C/T indicated that this mutation alone cannot explain the chromosome 5 signal, implying that other functional sites must exist. These results represent the first direct genetic evidence that a QTL in or near the FXII gene influences both FXII activity and susceptibility to thrombosis and suggest the presence of one or more still unknown functional variants in FXII.

Chromosome Mapping↗

PubMed2003

Quantitative trait locus mapping of genes that regulate phospholipid transfer activity in SM/J and NZB/BlNJ inbred mice.

OBJECTIVE: Phospholipid transfer protein (PLTP), an important protein in the transfer of phospholipids between lipoprotein particles and in the remodeling of HDL, is regulated at both the transcriptional and the protein level. We performed quantitative trait locus (QTL) analysis to identify genomic loci regulating PLTP activity in mice. METHODS AND RESULTS: Plasma PLTP activity was measured in 217 male F2 progeny from a SM/J x NZB/B1NJ intercross. Two QTL for plasma PLTP activity in mice fed chow (Pltpq1 and Pltpq2) were found on chromosomes 3 (34 cM, logarithm of odds [LOD] 3.5) and 10 (66 cM, LOD 4.1); two additional QTL in mice fed atherogenic diet (Pltpq3 and Pltpq4) were found on chromosomes 9 (56 cM, LOD 4.5) and 15 (34 cM, LOD 5.0); and one QTL (Pltiq1) for the inducibility of PLTP activity was found on chromosome 4 (70 cM, LOD 3.7). Several candidate genes for these 5 QTL were tested by sequence comparison and expression studies. CONCLUSIONS: We identified five significant loci involved in PLTP activity in the mouse and provided supporting evidence for the candidacy of Nr1h4 and Apof as the genes underlying Pltpq2.

Alleles↗

PubMed2002

Mapping of the QTL (quantitative trait locus) conferring partial resistance to leaf blast in rice cultivar Chubu 32.

The rice cultivar Chubu 32 possesses a high level of partial resistance to leaf blast. The number and chromosomal location of genes conferring this resistance were detected by restriction fragment length polymorphism (RFLP) linkage mapping and quantitative trait locus (QTL) analysis. For the mapping, 149 F(3) lines derived from the cross between rice cultivar Norin 29, with a low level of partial resistance, and Chubu 32 were used, and their partial resistance to leaf blast was assessed in upland nurseries. A linkage map covering six chromosomes and consisting of 36 RFLP markers was constructed. In the map, only one significant QTL (LOD>2.0) for partial resistance was detected on chromosome 11. This QTL explained 45.6% of the phenotypic variation. The segregation ratio of the F3 lines was 3:1 for partial resistance to susceptibility. These results suggest that the partial resistance in Chubu 32 is controlled by a major gene.

Journal Article↗

PubMed1999

Quantitative-trait locus for specific language and reading deficits on chromosome 6p.

Reading disability (RD), or dyslexia, is a complex cognitive disorder manifested by difficulties in learning to read, in otherwise normal individuals. Individuals with RD manifest deficits in several reading and language skills. Previous research has suggested the existence of a quantitative-trait locus (QTL) for RD on the short arm of chromosome 6. In the present study, RD subjects' performance in several measures of word recognition and component skills of orthographic coding, phonological decoding, and phoneme awareness were individually subjected to QTL analysis, with a new sample of 126 sib pairs, by means of a multipoint mapping method and eight informative DNA markers on chromosome 6 (D6S461, D6S276, D6S105, D6S306, D6S258, D6S439, D6S291, and D6S1019). The results indicate significant linkage across a distance of at least 5 cM for deficits in orthographic (LOD = 3.10) and phonological (LOD = 2.42) skills, confirming previous findings.

Adult↗

PubMed2001

A major quantitative trait locus for resistance to Potato leafroll virus is located in a resistance hotspot on potato chromosome XI and is tightly linked to N-gene-like markers.

Potato leafroll virus (PLRV) causes one of the most widespread and important virus diseases in potato. Resistance to PLRV is controlled by genetic factors that limit plant infection by viruliferous aphids or virus multiplication and accumulation. Quantitative trait locus (QTL) analysis of resistance to virus accumulation revealed one major and two minor QTL. The major QTL, PLRV.1, mapped to potato chromosome XI in a resistance hotspot containing several genes for qualitative and quantitative resistance to viruses and other potato pathogens. This QTL explained between 50 and 60% of the phenotypic variance. The two minor QTL mapped to chromosomes V and VI. Genes with sequence similarity to the tobacco N gene for resistance to Tobacco mosaic virus were tightly linked to PLRV.1. The cDNA sequence of an N-like gene was used to develop the sequence characterized amplified region (SCAR) marker N127(1164) that can assist in the selection of potatoes with resistance to PLRV.

Chromosome Mapping↗

PubMed2006

Quantitative trait locus analysis of nonverbal communication in autism spectrum disorder.

Autism spectrum disorder (ASD) is a neurodevelopmental syndrome marked by impairments in social interactive functioning and communication skills, and the presence of repetitive and restrictive behaviors. Twin and linkage studies provide evidence that ASD is heritable and genetically complex. Genetic analyses of familial quantitative traits in those with ASD may help to reveal underlying risk genes. We report a quantitative trait locus (QTL) analysis of nonverbal communication (NVC) in 228 families from the autism genetics resource exchange (AGRE) ascertained for at least two siblings with ASD. QTL at 1p13-q12, 4q21-25, 7q35, 8q23-24, and 16p12-13 indicate that genes at these loci may contribute to the variation in NVC among those with ASD. Using the criteria of Lander and Kruglyak, the QTL at 1p13-q12 is 'suggestive', while the other four are 'possible'. To assess whether these QTL are likely to harbor genes contributing specifically to the deficits in NVC, linkage analysis of ASD sibships with the most severe NVC scores was conducted. The sibships were identified by ordered-subset analyses (OSA), and families with the most severe NVC scores displayed lod scores of 3.4 at 8q23-24 and 3.8 at 16p12-13, indicating that these two regions are likely to harbor gene(s) contributing to ASD by predisposing to deficits in NVC.

Adolescent↗

PubMed2003

Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus.

Glucosinolate profiles differ among Arabidopsis thaliana ecotypes, caused by the composition of alleles at several glucosinolate biosynthetic loci. One of these, GS-Elong, harbors a family of methylthioalkylmalate synthase (MAM) genes that determine the side chain length of aliphatic glucosinolate structures. Fine mapping reveals that GS-Elong constitutes an insect resistance quantitative trait locus, caused by variation in glucosinolate profiles conferred by polymorphism of MAM alleles in this region. A sequence survey of randomly chosen ecotypes indicates that GS-Elong is highly variable among A. thaliana ecotypes: indel polymorphisms are frequent, as well as gene conversion events between gene copies arranged in tandem. Furthermore, statistical methods of molecular population genetics suggest that one of the genes, MAM2, is subject to balancing selection. This may be caused by ecological tradeoffs, i.e., by contrasting physiological effects of glucosinolates on generalist vs. specialist insects.

Animals↗

PubMed2004

Quantitative trait locus mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits.

From simulation studies it is known that the allocation of experimental resources has a crucial effect on power of QTL detection as well as on accuracy and precision of QTL estimates. In this study, we used a very large experimental data set composed of 976 F(5) maize testcross progenies evaluated in 19 environments and cross-validation to assess the effect of sample size (N), number of test environments (E), and significance threshold on the number of detected QTL, the proportion of the genotypic variance explained by them, and the corresponding bias of estimates for grain yield, grain moisture, and plant height. In addition, we used computer simulations to compare the usefulness of two cross-validation schemes for obtaining unbiased estimates of QTL effects. The maximum, validated genotypic variance explained by QTL in this study was 52.3% for grain moisture despite the large number of detected QTL, thus confirming the infinitesimal model of quantitative genetics. In both simulated and experimental data, the effect of sample size on power of QTL detection as well as on accuracy and precision of QTL estimates was large. The number of detected QTL and the proportion of genotypic variance explained by QTL generally increased more with increasing N than with increasing E. The average bias of QTL estimates and its range were reduced by increasing N and E. Cross-validation performed well with respect to yielding asymptotically unbiased estimates of the genotypic variance explained by QTL. On the basis of our findings, recommendations for planning of QTL mapping experiments and allocation of experimental resources are given.

Chromosome Mapping↗

PubMed2006

Identification of EFHC2 as a quantitative trait locus for fear recognition in Turner syndrome.

One-third of women with Turner syndrome (45,X) have autism-like social and communication difficulties, despite normal verbal IQ. Deletion mapping of the X-chromosome implicated 5 Mb of Xp11.3-4 as critical for recognition of facial fear, a quantitative measure of social cognition. Variability in fear recognition accuracy in Turner syndrome suggested the existence of a quantitative trait locus (QTL) revealed by X-monosomy. We aimed to identify the gene(s) influencing fear recognition by dense mapping of the 5 Mb region. Initial regression-based association mapping of fear recognition in 93 women with Turner syndrome across the critical region was performed, using genotype data at 242 single nucleotide polymorphisms (SNPs). We identified three regions of interest, in which 52 additional SNPs were genotyped. The third region then contained four SNPs associated with fear recognition (0.0030 > P > 0.00046). We obtained an independent sample of 77 Turner syndrome females that we genotyped for 77 SNPs in the initial regions of interest. Region three showed association in the same direction, maximal at SNPs rs7055196 and rs7887763 (P = 0.022 each). Four SNPs in strong linkage disequilibrium (LD), including this pair, span 40 kb within a novel transcript, EF-hand domain containing 2 (EFHC2). In the combined Turner syndrome samples, the most strongly associated SNP (P = 0.00007) has frequency of 8.8% and an estimated effect size accounting for over 13% of the variance in fear recognition. EFHC2 shows genealogy and extended LD consistent with directional selection. This novel QTL may influence social cognition in the general population and in autism.

Chromosome Mapping↗