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Bone density in sheep: genetic variation and quantitative trait loci localisation.

Bone density (BD) is an important factor in osteoporotic fracture risk in humans. However, BD is a complex trait confounded by environmental influences and polygenic inheritance. Sheep provide a potentially useful model for studying differences in BD, as they provide a means of circumventing complex environmental factors and are a similar weight to humans. The aims of this study were to establish whether there is genetic variation in BD in sheep and then to localise quantitative trait loci (QTLs) associated with this variation. We also aimed to evaluate the relationship between fat and muscle body components and BD in sheep. Results showed that there was significant (P < 0.01) genetic variation among Coopworth sheep sires for BD. This genetic difference was correlated (P < 0.01) with body weight and muscle mass. A number of QTLs exceeding the suggestive threshold were identified (nine in total). Of these, two (chromosomes 1, P < 0.05; chromosome 24, P < 0.01) were significant using genome-wide permutation significance thresholds (2000 iterations). The position of the QTL on chromosome 24 coincided with a number of other body composition QTLs, indicating possible pleiotropic effects or the presence of multiple genes affecting body composition at that site. This study shows that sheep are potentially a useful model for studying the genetics of BD.

Animals↗

Mapping of quantitative trait loci underlying ethanol metabolism in BXD recombinant inbred mouse strains.

BACKGROUND: Genetic factors are well known to play an important role in determining individual differences in the metabolism of ethanol (EtOH), and several specific polymorphic loci have been identified that significantly contribute to the variability of EtOH metabolism in humans. However, these variant genes are either alcohol or aldehyde dehydrogenases, and the identification of new gene products that contribute to variation in alcohol metabolism would be useful. METHODS: To identify quantitative trait loci (QTLs), we correlated variation in polymorphic markers with blood EtOH concentration and the rate of EtOH metabolism (beta) in C57BL/6J and DBA/2J strains and in 25 of their recombinant inbred strains after 2 and 3 g/kg of EtOH intraperitoneally. RESULTS: A QTL associated with beta values for both doses was definitively mapped to the proximal region of chromosome 17, syntenic with human chromosome 6q25-27. Seven to 12 chromosomal regions were provisionally identified for each phenotype; several were associated with 2 or more phenotypes. Each QTL suggests the location of a gene or genes affecting EtOH pharmacokinetics. Candidate genes suggested by these analyses included several whose gene products are known to be induced by EtOH (e.g., superoxide dismutase, glutathione transferase, and cytochrome P450 2E1), as well as several whose gene products have signaling functions likely to contribute to this induction. CONCLUSIONS: These studies provide evidence for the existence of genes affecting EtOH metabolism in multiple chromosomal regions. Future studies will be required to identify the chromosome 17 gene product. Use of other genetic populations, such as B6D2F2 crosses, will be required to determine which of the provisional loci represent true and which represent false-positive associations.

Animals↗

Resistance gene analogues in sugarcane and sorghum and their association with quantitative trait loci for rust resistance.

Fifty-four different sugarcane resistance gene analogue (RGA) sequences were isolated, characterized, and used to identify molecular markers linked to major disease-resistance loci in sugarcane. Ten RGAs were identified from a sugarcane stem expressed sequence tag (EST) library; the remaining 44 were isolated from sugarcane stem, leaf, and root tissue using primers designed to conserved RGA motifs. The map location of 31 of the RGAs was determined in sugarcane and compared with the location of quantitative trait loci (QTL) for brown rust resistance. After 2 years of phenotyping, 3 RGAs were shown to generate markers that were significantly associated with resistance to this disease. To assist in the understanding of the complex genetic structure of sugarcane, 17 of the 31 RGAs were also mapped in sorghum. Comparative mapping between sugarcane and sorghum revealed syntenic localization of several RGA clusters. The 3 brown rust associated RGAs were shown to map to the same linkage group (LG) in sorghum with 2 mapping to one region and the third to a region previously shown to contain a major rust-resistance QTL in sorghum. These results illustrate the value of using RGAs for the identification of markers linked to disease resistance loci and the value of simultaneous mapping in sugarcane and sorghum.

Chromosome Mapping↗

Quantitative trait loci for insulin-like growth factor I, leptin, thyroxine, and corticosterone in genetically heterogeneous mice.

Genotype information was collected at 87 loci in a group of 1,108 UM-HET3 mice bred as the progeny of [BALB/cJ x C57BL/6J]F1 mothers and [C3H/HeJ x DBA/2J]F1 fathers, for which thyroxine (T4), insulin-like growth factor I (IGF-I), and leptin levels had been measured at 4 and 15 mo of age. The data provided significant evidence for quantitative trait loci (QTL) modulating IGF-I levels on chromosomes 1, 3, 8, 10, and 17; for loci affecting T4 on chromosomes 4, 15, and 17; and for leptin on chromosome 3. Fecal levels of corticosterone at 17 mo of age were influenced by a QTL on chromosome 1. Nine other gene/hormone associations reached a nominal P < 0.01, providing suggestive but not statistical evidence for additional QTL. QTL with an influence on a given hormone were in nearly all cases additive, with little or no evidence for epistasis. Of the 12 strongest QTL, 5 had effects that were age dependent, having more effect in 15-mo-old than in 4-mo-old mice in all but one case; the other QTL had effects that were apparently age-independent. These results show that the genetic controls over late-life hormone levels are complex and dependent on effects of genes that act both early and late in the life course.

Aging↗

Genetic analysis of quantitative traits in highly ascertained samples: total serum IgE in families with asthma.

The objective of this study was to compare the effect of an approximate ascertainment correction using proband phenotypes with heuristic corrections based on sample trait means and on published "standard" population values. Data were from the Collaborative Study on the Genetics of Asthma, which comprises 225 families ascertained through sib pairs affected with asthma. In variance component linkage analysis of IgE no lod scores greater than 3.0 were observed, either with or without several attempted corrections for ascertainment. The ascertained nature of the sample may have compromised the power to detect linkage to a quantitative trait (IgE) associated with the focal phenotype (asthma).

Adult↗

Genetic regulation of plasma von Willebrand factor levels: quantitative trait loci analysis in a mouse model.

BACKGROUND: The genetic factors responsible for the wide variation in plasma von Willebrand factor (VWF) levels observed among individuals are largely unknown, although these genes are also likely to contribute to variability in the severity of von Willebrand disease (VWD) and other bleeding and thrombotic disorders. We have previously mapped two genes contributing to the regulation of plasma VWF levels in mice (Mvwf1 on chromosome 11 and Mvwf2 on chromosome 6). OBJECTIVE: To identify additional quantitative trait loci (QTL) contributing to the genetic regulation of murine plasma VWF levels. METHODS: To map genetic loci contributing to the > 7-fold difference in plasma VWF levels between two mouse strains (A/J and CASA/RkJ), high-density individual genotyping and R/qtl analyses were applied to a previously generated set of approximately 200 F2 mice obtained from an intercross of these two inbred lines. RESULTS: Genomic loci for two additional candidate VWF modifier genes were identified: Mvwf3 on chromosome 4 and Mvwf4 on chromosome 13. These loci demonstrate primarily epistatic effects when co-inherited with two CASA/RkJ Vwf alleles, although Mvwf4 may also exert a small, independent, additive effect. CONCLUSIONS: Mvwf3 and Mvwf4, combined with the effect of Mvwf2, explain approximately 45% of the genetic variation in plasma VWF level among the A/J and CASA/RkJ strains. Mvwf3 and Mvwf4 exhibit homology of synteny to three human chromosomal segments (on chromosomes 1, 5 and 6) previously reported by the Genetic Analysis of Idiopathic Thrombophilia (GAIT) study, suggesting that orthologs of Mvwf3 and Mvwf4 may also encode important VWF modifier genes in humans.

Animals↗

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↗

Heart rate and blood pressure quantitative trait loci for the airpuff startle reaction.

The airpuff startle reaction is a probe of sensori-autonomic processing and is useful for studies of genetic control of stress-induced cardiovascular activity. Using a Wistar-Kyoto-Spontaneously Hypertensive Rat F2 cross, we reported an airpuff-elicited strain-dependent and trial-dependent bradycardia, the absence of which cosegregated with hypertension. Here, we use the mapping power of the HXB-BXH recombinant inbred rat strains (n=23) to locate quantitative trait loci (QTL) for this and associated cardiovascular phenotypes. Rats (12 weeks old), with indwelling femoral arterial catheters, were subjected to repeated airpuff startle stimuli (100 ms, 12.5 psi, 28 trials). Basal mean arterial pressure (MAP), delta MAP, and delta heart rate response to airpuff stimuli were analyzed as the average over 28 trials. There was a significant strain effect on the cardiovascular phenotypes measured. One QTL for the bradycardia elicited by the first airpuff stimulus was identified on chromosome 2 (D2rat 62/63; logarithm of odds [LOD] 2.9) mapping near a reported blood pressure locus. Further QTL were identified for basal MAP (RN08), stimulus-elicited tachycardia on trials 2 to 5 (RNO1 and RNO10), and delta MAP (RNO6). Our results indicate that chromosomes 1, 2, and 10 are involved in heart rate responses to airpuff startle stimulus, and chromosomes 6 and 8 are involved in pressor responses. This study is the first to identify stress-related heart rate loci and provides additional support for our prior cosegregation results. Furthermore, we have established the utility of this experimental paradigm to identify loci responsible for cardiovascular regulation during stress in genetic hypertensive models.

Animals↗

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↗

Quantitative trait linkage analysis of longitudinal change in body weight.

One of the great strengths of the Framingham Heart Study data, provided for the Genetic Analysis Workshop 13, is the long-term survey of phenotypic data. We used this unique data to create new phenotypes representing the pattern of longitudinal change of the provided phenotypes, especially systolic blood pressure and body weight. We performed a linear regression of body weight and systolic blood pressure on age and took the slopes as new phenotypes for quantitative trait linkage analysis using the SOLAR package. There was no evidence for heritability of systolic blood pressure change. Heritability was estimated as 0.15 for adult life "body weight change", measured as the regression slope, and "body weight gain" (including only individuals with a positive regression slope), and as 0.22 for body weight "change up to 50" (regression slope of weight on age up to an age of 50). With multipoint analysis, two regions on the long arm of chromosome 8 showed the highest LOD scores of 1.6 at 152 cM for "body weight change" and of >1.9 around location 102 cM for "body weight gain" and "change up to 50". The latter two LOD scores almost reach the threshold for suggestive linkage. We conclude that the chromosome 8 region may harbor a gene acting on long-term body weight regulation, thereby contributing to the development of the metabolic syndrome.

Adult↗

Interactions among quantitative traits in the course of sympatric speciation.

Sympatric speciation, the origin of two or more species from a single local population, has almost certainly been involved in formation of several species flocks, and may be fairly common in nature. The most straightforward scenario for sympatric speciation requires disruptive selection favouring two substantially different phenotypes, and consists of the evolution of reproductive isolation between them followed by the elimination of all intermediate phenotypes. Here we use the hypergeometric phenotypic model to show that sympatric speciation is possible even when fitness and mate choice depend on different quantitative traits, so that speciation must involve formation of covariance between these traits. The increase in the number of variable loci affecting fitness facilitates sympatric speciation, whereas the increase in the number of variable loci affecting mate choice has the opposite effect. These predictions may enable more cases of sympatric speciation to be identified.

Animals↗

Aod1 controlling day 3 thymectomy-induced autoimmune ovarian dysgenesis in mice encompasses two linked quantitative trait loci with opposing allelic effects on disease susceptibility.

Day 3 thymectomy (D3Tx) leads to a paucity of CD4(+)CD25(+) suppressor T cells, a loss of peripheral tolerance, and the development of organ-specific autoimmune disease in adult mice. Importantly, D3Tx does not lead to autoimmune disease in all mouse strains, indicating that this process is genetically controlled. Previously, we reported linkage of D3Tx-induced autoimmune ovarian dysgenesis (AOD) and its intermediate phenotypes, antiovarian autoantibody responsiveness, oophoritis, and atrophy, to five quantitative trait loci (QTL), designated Aod1 through Aod5. We also showed interaction between these QTL and H2 as well as Gasa2, a QTL controlling susceptibility to D3Tx-induced autoimmune gastritis. To physically map Aod1, interval-specific bidirectional recombinant congenic strains of mice were generated and studied for susceptibility to D3Tx-induced AOD. Congenic mapping studies revealed that Aod1 controls susceptibility to oophoritis and comprises two linked QTL with opposing allelic effects. Aod1a resides between D16Mit211 (23.3 cM) and D16Mit51 (66.75 cM) on chromosome 16. Aod1b maps proximal of Aod1a between D16Mit89 (20.9 cM) and D16Mit211 (23.3 cM) and includes the candidate genes stefin A1, A2, and A3 (Stfa1-Stfa3), inhibitors of cathepsin S, a cysteine protease required for autoantigen presentation, and the development of autoimmune disease of the salivary and lacrimal glands following D3Tx. cDNA sequencing revealed the existence of structural polymorphisms for both Stfa1 and Stfa2. Given the roles of cathepsins in Ag processing and presentation, Stfa1 and Stfa2 alleles have the potential to control susceptibility to autoimmune disease at the level of both CD4(+)CD25(+) suppressor and CD4(+)CD25(-) effector T cells.

Alleles↗

Mapping of quantitative trait loci for seminal vesicle mass and litter size to rat chromosome 8.

The spontaneously hypertensive rat (SHR) and the Brown Norway (BN) rat differ significantly in litter size (7.6 versus 4.5 pups). In the HXB and BXH sets of recombinant inbred (RI) strains derived from SHR and BN rats, heritability of litter size and of selected male reproductive parameters such as sperm production, sperm count, sperm morphology and motility, and the mass of the testis, epididymides, and seminal vesicles were estimated and a search was undertaken for quantitative trait loci (QTL) associated with these phenotypes. The mass of seminal vesicles was significantly associated with a QTL near the D8Cebr204S21 marker on chromosome 8 (LOD score = 4.1, P = 0.00001); this QTL was responsible for 46% of the genetic variability of the trait. The same gene marker on chromosome 8 also showed a suggestive association with the litter size. Litter size was significantly correlated with the mass of seminal vesicles (r = 0.58, P = 0.003). These findings indicate that the variability in litter size among RI strains may be due in part to differences in the mass of seminal vesicles and it is possible that both mass of seminal vesicles and litter size are determined by a pleiotropic effect of the same QTL on rat chromosome 8.

Animals↗

Natural selection for salt tolerance quantitative trait loci (QTLs) in wild sunflower hybrids: implications for the origin of Helianthus paradoxus, a diploid hybrid species.

For a new diploid or homoploid hybrid species to become established, it must diverge ecologically from parental genotypes. Otherwise the hybrid neospecies will be overcome by gene flow or competition. We initiated a series of experiments designed to understand how the homoploid hybrid species, Helianthus paradoxus, was able to colonize salt marsh habitats, when both of its parental species (H. annuusxH. petiolaris) are salt sensitive. Here, we report on the results of a quantitative trait locus (QTL) analysis of mineral ion uptake traits and survivorship in 172 BC2 hybrids between H. annuus and H. petiolaris that were planted in H. paradoxus salt marsh habitat in New Mexico. A total of 14 QTLs were detected for mineral ion uptake traits and three for survivorship. Several mineral ion QTLs mapped to the same position as the survivorship QTLs, confirming previous studies, which indicated that salt tolerance in Helianthus is achieved through increased Ca uptake, coupled with greater exclusion of Na and related mineral ions. Of greater general significance was the observation that QTLs with effects in opposing directions were found for survivorship and for all mineral ion uptake traits with more than one detected QTL. This genetic architecture provides an ideal substrate for rapid ecological divergence in hybrid neospecies and offers a simple explanation for the colonization of salt marsh habitats by H. paradoxus. Finally, selection coefficients of +0.126, -0.084 and -0.094 for the three survivorship QTLs, respectively, are sufficiently large to account for establishment of new, homoploid hybrid species.

Adaptation, Biological↗

Phenotypic variation and quantitative trait locus identification for osmotic potential in an interspecific hybrid inbred F2 poplar pedigree grown in contrasting environments.

Elucidation of the mechanisms of dehydration tolerance in poplar (Populus sp.) trees will permit development of biochemical and molecular indicators to identify dehydration-tolerant genotypes during genetic selection. The objectives of this study were to characterize the degree of phenotypic variation in osmotic potential (a determinant of dehydration tolerance), determine the relationship between osmotic potential at full turgor and relative growth rate, and identify quantitative trait loci (QTL) for osmotic potential in an advanced-generation, interspecific poplar pedigree established in contrasting environments. A three-generation, sib-mated black cottonwood (Populus trichocarpa Torr. & Gray) and eastern cottonwood (P. deltoides Bartr.) segregating F(2) family (Family 331) was analyzed at a dry site east of the Cascade Mountain Range (Boardman, OR) and at a wet site west of the mountains (Clatskanie, OR). At the Boardman site, 2-year-old trees (59 clones) were either irrigated everyday (wet) or every other day (dry), whereas 3- and 4-year-old trees (58 clones) at the Clatskanie site were unirrigated. At the Boardman site, the typically narrow range of osmotic potentials exhibited by grandparents and parents was greatly expanded in the F(2) population, spanning from -1.38 to -2.35 MPa under wet conditions, with a similar range under dry conditions (-1.40 to -2.15 MPa). Clones that had osmotic potentials < or = -1.90 MPa generally displayed full maintenance of stem relative growth rates under dry conditions in contrast to clones with osmotic potentials that were < or = -1.60 MPa, in which stem relative growth rates were reduced by an average of 38% in the dry treatment relative to the wet treatment. Although osmotic adjustments of 0.13 to 0.36 MPa were observed in nine out of 59 clones, adjustment typically occurred from relatively high baseline osmotic potentials. The range in osmotic potential at the wetter Clatskanie site at age three was higher (-1.27 to -1.84 MPa) and was further expanded the following year (-1.14 to -1.94 MPa), which had a wetter spring than the previous year, followed by a typically dry July. Seven QTL for osmotic potential were identified that each explained > 7.5% of the variation in osmotic potential. Given that four clones (7%) had osmotic potentials of -2.00 MPa or less and that QTL for osmotic potential have been identified, we suggest that there are opportunities to extend the limit of dehydration tolerance in Populus.

Adaptation, Physiological↗

Mapping of quantitative trait loci affecting organ weights and blood variables in a broiler layer cross.

1. A genome scan was performed to locate genomic regions associated with traits that are known to vary in birds (most commonly broilers) suffering from heart, lung or muscular dysfunction and for weight of the dressed carcass and some internal organs. 2. The F2 population studied was derived from a cross between a broiler and a layer line and consisted of over 460 birds that were genotyped for 101 markers. 3. There was strong support for segregation of quantitative trait loci (QTL) for carcass and organ weights and blood variables. We identified 11 genome-wide significant QTL (most of them for dressed carcass weight) and several genome-wide suggestive QTL. 4. The results point to some genome regions that may be associated with health-related traits and merit further study, with the final aim of identifying linked genetic markers that could be used in commercial breeding programmes to decrease the incidence of muscular and metabolic disorders in broiler populations.

Animals↗

Quantitative trait loci associated with AutoFOM grading characteristics, carcass cuts and chemical body composition during growth of Sus scrofa.

A three-generation full-sib resource family was constructed by crossing two commercial pig lines. Genotypes for 37 molecular markers covering chromosomes SSC1, SSC6, SSC7 and SSC13 were obtained for 315 F2 animals of 49 families and their parents and grandparents. Phenotypic records of traits including carcass characteristics measured by the AutoFOM grading system, dissected carcass cuts and meat quality characteristics were recorded at 140 kg slaughter weight. Furthermore, phenotypic records on live animals were obtained for chemical composition of the empty body, protein and lipid accretion (determined by the deuterium dilution technique), daily gain and feed intake during the course of growth from 30 to 140 kg body weight. Quantitative trait loci (QTL) detection was conducted using least-squares regression interval mapping. Highest significance at the 0.1% chromosome-wise level was obtained for five QTL: AutoFOM belly weight on SSC1; ham lean-meat weight, percentage of fat of primal cuts and daily feed intake between 60 and 90 kg live weight on SSC6; and loin lean-meat weight on SSC13. QTL affecting daily gain and protein accretion were found on SSC1 in the same region. QTL for protein and lipid content of empty body at 60 kg liveweight were located close to the ryanodine receptor 1 (RYR1) locus on SSC6. On SSC13, significant QTL for protein accretion and feed conversion ratio were detected during growth from 60 to 90 kg. In general, additive genetic effects of alleles originating from the Piétrain line were associated with lower fatness and larger muscularity as well as lower daily gain and lower protein accretion rates. Most of the QTL for carcass characteristics were found on SSC6 and were estimated after adjustment for the RYR1 gene. QTL for carcass traits, fatness and growth on SSC7 reported in the literature, mainly detected in crosses of commercial lines x obese breeds, were not obtained in the present study using crosses of only commercial lines, suggesting that these QTL are not segregating in the analysed commercial lines.

Alleles↗

Quantitative trait loci analysis for the differences in susceptibility to atherosclerosis and diabetes between inbred mouse strains C57BL/6J and C57BLKS/J.

Mice from the inbred strain C57BLKS/J (BKS) exhibit increased susceptibility to both diabetes and atherosclerosis compared to C57BL/6J (B6) mice. To determine whether the differences in diabetes and atherosclerosis are related, we carried out a cross between B6-db/db and BKS. We selected 99 female F2-db/db progeny, tested the progeny for plasma lipids, plasma glucose, and fatty-streak lesions, and used quantitative trait loci (QTL) analysis to identify the chromosomal regions associated with these phenotypes. No major QTL were found for total cholesterol, VLDL-cholesterol, or triglycerides. Two suggestive QTL were found for HDL-cholesterol (LOD scores of 2. 7 and 2.8), and two suggestive loci were found for plasma glucose (LOD scores of 2.3 and 2.0). Lesion size was not correlated with plasma lipid levels or glucose. Lesion size was determined by a locus at D12Mit49 with a LOD score of 2.5 and a significant likelihood ratio statistic. The gene for apolipoprotein apoB lies within the region, but apoB levels were similar in strains B6 and BKS. The QTL on Chr 12 was confirmed by constructing a congenic strain with BKS alleles in the QTL region on a B6 genetic background. We conclude that susceptibilities to diabetes and atherosclerosis are not conferred by the same genes in these strains and that a major gene on Chr 12, which we name Ath6, determines the difference in atherosclerosis susceptibility.

Alleles↗