The combination of gene expression profiling with linkage analysis has become a powerful paradigm for mapping gene expression quantitative trait loci (eQTL). To date, most studies have searched for eQTL by analyzing gene expression traits one at a time. As thousands of expression traits are typically analyzed, this can reduce power because of the need to correct for the number of hypothesis tests performed. In addition, gene expression traits exhibit a complex correlation structure, which is ignored when analyzing traits individually. To address these issues, we applied two different multivariate dimension reduction techniques, the Singular Value Decomposition (SVD) and Independent Component Analysis (ICA) to gene expression traits derived from a cross between two strains of Saccharomyces cerevisiae. Both methods decompose the data into a set of meta-traits, which are linear combinations of all the expression traits. The meta-traits were enriched for several Gene Ontology categories including metabolic
Transcript abundance from cRNA hybridizations to Affymetrix microarrays can be used for simultaneous marker development and genome-wide gene expression quantitative trait locus (eQTL) analysis of crops. We have previously shown that it is easily possible to use Affymetrix expression arrays to profil …
Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. ...
The transcriptome connects genome to the gene function and ultimate phenome in biology. Sofar, transcriptomic approach was not used in peanut for performing trait mapping in bi-parentalpopulations. In this research, we sequenced the whole transcriptome in immature seeds in apeanut recombinant inbred line (RIL) population and explored thoroughly the landscape oftranscriptomic variations and its genetic basis. The comprehensive analysis identified total49 691 genes in RIL population, of which 92 genes followed a paramutation-like expressionpattern. Expression quantitative trait locus (eQTL) analysis identified 1207 local eQTLs and15 837 distant eQTLs contributing to the whole-genome transcriptomic variation in peanut.There were 94 eQTL hot spot regions detected across the genome with the dominance of distanteQTL. By integrating transcriptomic profile and annotation analyses, we unveiled a putativecandidate gene and developed a linked marker InDel02 underlying a major QTL responsible forpurple ...
Expression quantitative trait loci (eQTL) analysis is a powerful method to detect correlations between gene expression and genomic variants and is widely used to interpret the biological mechanism underlying identified genome wide association studies (GWAS) risk loci. Numerous eQTL studies have been performed on different cell types and tissues of which the majority has been based on microarray technology. We present here an eQTL analysis based on cap analysis gene expression sequencing (CAGEseq) data created from human postmortem frontal lobe tissue combined with genotypes obtained through genotyping arrays, exome sequencing, and CAGEseq. Using CAGEseq as an expression profiling technique combined with these different genotyping techniques allows measurement of the molecular effect of variants on individual transcription start sites and increases the resolution of eQTL analysis by also including the non-annotated parts of the genome. We identified 2410 eQTLs and show that non-coding transcripts are
TY - JOUR. T1 - A novel quantitative trait locus, qCL1, involved in semi-dwarfism derived from Japanese rice cultivar Nipponbare. AU - Hori, Kiyosumi. AU - Yamamoto, Toshio. AU - Ebana, Kaworu. AU - Takeuchi, Yoshinobu. AU - Yano, Masahiro. PY - 2009/10/5. Y1 - 2009/10/5. N2 - To identify quantitative trait loci (QTLs) associated with culm length in Japanese japonica rice varieties, we conducted QTL analyses using a set of reciprocal backcrossed inbred lines (BILs) from crosses between Nipponbare and Koshihikari. We detected five QTLs in the two BILs that are involved in the culm-length difference between Nipponbare and Koshihikari. A QTL located on the short arm of chromosome 1, qCL1, was commonly detected near the simple sequence repeat (SSR) marker RM8068 in both BILs in three growing seasons. The Nipponbare allele of qCL1 shortened from 1.9 to 3.0 cm of culm length. Substitution lines (SLs) of Koshihikari in which the QTL was replaced with the Nipponbare allele exhibited decreased lengths of ...
The observation that variants regulating gene expression (expression quantitative trait loci, eQTL) are at a high frequency among SNPs associated with complex traits has made the genome-wide characterization of gene expression an important tool in genetic mapping studies of such traits. As part of a study to identify genetic loci contributing to bipolar disorder and other quantitative traits in members of 26 pedigrees from Costa Rica and Colombia, we measured gene expression in lymphoblastoid cell lines derived from 786 pedigree members. The study design enabled us to comprehensively reconstruct the genetic regulatory network in these families, provide estimates of heritability, identify eQTL, evaluate missing heritability for the eQTL, and quantify the number of different alleles contributing to any given locus. In the eQTL analysis, we utilize a recently proposed hierarchical multiple testing strategy which controls error rates regarding the discovery of functional variants. Our results ...
Background: Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS). The small sample sizes of some previous eQTL studies have limited their statistical power. We conducted an eQTL investigation of microarray-based gene and exon expression levels in whole blood in a cohort of 5257 individuals, exceeding the single cohort size of previous studies by more than a factor of 2. Results: We detected over 19,000 independent lead cis-eQTLs and over 6000 independent lead trans-eQTLs, targeting over 10,000 gene targets (eGenes), with a false discovery rate (FDR) , 5%. Of previously published significant GWAS SNPs, 48% are identified to be significant eQTLs in our study. Some trans-eQTLs point toward novel mechanistic explanations for the association of the SNP with the GWAS-related phenotype. We ...
Many cancer risk loci act as expression quantitative trait loci (eQTLs) of transcripts including non-coding RNA. Long non-coding RNAs (lncRNAs) are implicated in various human cancers. However, the pathological and clinical impacts of the genetic determinants of lncRNAs in cancers remain largely unknown. In this study, we performed eQTL mapping of lncRNA expression (elncRNA) in 11 TCGA cancer types and characterized the biological processes of elncRNAs in the setting of genomic location, cancer treatment responses, and immune microenvironment. As a result, 10.86% of the cis-eQTLs and 1.67% of the trans-eQTLs of lncRNA were related to known genome-wide association studies (GWAS) cancer risk loci. The elncRNAs are significantly enriched for those which are previously annotated as predictive of drug sensitivities in cancer cell lines. We further revealed the downstream transcriptomic effectors of eQTL-elncRNA pairs. Our data specifically suggested that the genes affected by eQTL-elncRNA associations are
The present invention is in the field of plant breeding and disease resistance. More specifically, the invention includes a method for breeding soybean plants containing quantitative trait loci that are associated with resistance to Asian Soybean Rust (ASR), a fungal disease associated with Phakopsora spp. The invention further includes germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring disease resistance for introgression into elite germplasm in a breeding program for resistance to ASR.
Identifying the genes underlying genetically complex traits is of fundamental importance for medicine, agriculture, and evolutionary biology. However, the level of resolution offered by traditional quantitative trait locus (QTL) mapping is usually coarse. We analyze here a trait closely related to fitness, ovariole number. Our initial interspecific mapping between Drosophila sechellia (8 ovarioles/ovary) and D. simulans (15 ovarioles/ovary) identified a major QTL on chromosome 3 and a minor QTL on chromosome 2. To refine the position of the major QTL, we selected 1038 additional recombinants in the region of interest using flanking morphological markers (selective phenotyping). This effort generated approximately one recombination event per gene and increased the mapping resolution by approximately seven times. Our study thus shows that using visible markers to select for recombinants can efficiently increase the resolution of QTL mapping. We resolved the major QTL into two epistatic QTL, QTL3a ...
Abstract: Detecting genetic loci responsible for variation in quantitative traits is a problem of great importance to biologists. The location on a genetic map responsible for a quantitative trait is referred to as Quantitative Trait Loci, or QTL. This thesis uses a Bayesian Hierarchical Regression model which incorporates variability both within and between lines to detect the QTL. This method is applied to a simulated data set using the line information from Bay-0 × Shahdara population to find the activation probability of each genetic segment via the Gibbs sampler and Monte Carlo integration techniques. Using the activation probability, which indicates the influence of each segment within all the models, the QTL is detected. The results show that it is an effective way to detect QTL.. Bayesian hierarchical regression model to detect quantitative trait loci ...
OBJECTIVES: In sib pair studies, quantitative trait loci (QTL) identification may be adversely affected by non-normality in the phenotypic distribution, particularly when subjects falling in the tails of the distribution bias the trait mean or varian
IN the mapping of quantitative trait loci (QTL) in an experimental cross, selective genotyping (in which only the individuals at the extremes of the phenotype distribution are genotyped) can provide nearly equivalent power to complete genotyping at a reduced cost (Lander and Botstein 1989; Darvasi and Soller 1992).. Interval mapping with selectively genotyped data is best performed with consideration of all individuals, even those that were not genotyped (Lander and Botstein 1989). Consideration of only the genotyped individuals results in a biased estimate of the QTL effect. Haley-Knott regression (Haley and Knott 1992) generally provides a good approximation to standard interval mapping, but should be avoided in the case of selective genotyping, as it tends to produce inflated evidence for linkage (Feenstra et al. 2006).. Despite the common use of selective genotyping for QTL mapping and the extensive literature on significance thresholds for QTL mapping, we are not aware of any discussion of ...
Genome-wide studies of gene expression have successfully identified genetic variants that contribute to the variation of gene expression within populations [1-11]. The objective of genome-wide association studies (GWAS) is to map genotypic variation to phenotypic variation. Jansen and Nap [12] proposed extending the GWAS paradigm to deal with quantitative endophenotypes, e.g. RNA, protein and metabolite abundance in a cell. To date, consideration of RNA abundance has received most attention in the literature [1-11]. Those variants that affect gene expression are referred to as expression quantitative trait loci (eQTLs) of which thousands have been reported [1-11]. Most studies have focused on single nucleotide polymorphisms (SNPs).. The literature reports two classes of eQTL, cis-acting SNPs and trans-acting SNPs. Cis-acting SNPs lie within a gene or near the transcription start or stop site of a gene and correlate with the expression of that gene. In contrast, trans-acting SNPs can lie anywhere ...
TY - JOUR. T1 - A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. AU - Manichaikul, Ani. AU - Moon, Jee Young. AU - Sen, Śaunak. AU - Yandell, Brian S.. AU - Broman, Karl W.. PY - 2009/3. Y1 - 2009/3. N2 - The identification of quantitative trait loci (QTL) and their interactions is a crucial step toward the discovery of genes responsible for variation in experimental crosses. The problem is best viewed as one of model selection, and the most important aspect of the problem is the comparison of models of different sizes. We present a penalized likelihood approach, with penalties on QTL and pairwise interactions chosen to control false positive rates. This extends the work ofBroman and Speed to allow for pairwise interactions among QTL. A conservative version of our penalized LOD score provides strict control over the rate of extraneous QTL and interactions; a more liberal criterion is more lenient on interactions but seeks ...
TY - JOUR. T1 - Identification of quantitative trait locus for abscisic acid responsiveness on chromosome 5A and association with dehydration tolerance in common wheat seedlings. AU - Iehisa, Julio C.M.. AU - Matsuura, Takakazu. AU - Mori, Izumi C.. AU - Takumi, Shigeo. PY - 2014/1/1. Y1 - 2014/1/1. N2 - The phytohormone abscisic acid (ABA) plays important roles in response to environmental stress as well as in seed maturation and dormancy. In common wheat, quantitative trait loci (QTLs) for ABA responsiveness at the seedling stage have been reported on chromosomes 1B, 2A, 3A, 6D and 7B. In this study, we identified a novel QTL for ABA responsiveness on chromosome 5A using an F2 population derived from a cross between the common wheat cultivar Chinese Spring (CS) and a chromosome substitution line of CS with chromosome 5A of cultivar Hope (Hope5A). This QTL was found in a similar chromosomal region to previously reported QTLs for drought tolerance and seed dormancy. Physiological ...
Soybean [Glycine max (L.) Merr.] is an important oilseed crop which produces about 30 %of the worlds edible vegetable oil. The quality of soybean oil is determined by its fatty acid composition. Soybean oil high in oleic and low in linolenic fatty acids is desirable for human consumption and other uses. The objectives of this study were to identify quantitative trait loci (QTLs) for unsaturated fatty acids and to evaluate the genetic effects of single QTL and QTL combinations in soybean. A population of recombinant inbred lines derived from the cross of SD02-4-59 X A02-381100 was evaluated for fatty acid content in seven environments. In total, 516 polymorphic single nucleotide polymorphism markers, 477 polymorphic simple sequence repeat markers and three GmFAD3 geneswere used to genotype the mapping population. By using the composite interval mapping and/or the interval mapping method, a total of 15 QTLs for the three unsaturated fatty acids were detected in more than two environments. Two QTLs for
Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of pathogens and long lasting. Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. Five disease resistance QTL that colocalized with defense response genes were accumulated by marker-aided selection to develop blast-resistant varieties. One advanced backcross line carrying the major-effect QTL on chromosome (chr) 8, which included a cluster of 12 germin-like protein (OsGLP) gene members, exhibited resistance to rice (Oryza sativa) blast disease over 14 cropping seasons. To determine if OsGLP members contribute to resistance and if the resistance was broad spectrum, a highly conserved portion of the OsGLP coding region was used as an RNA interference trigger to silence a few to all expressed chr 8 OsGLP family members. Challenge with two different fungal pathogens (causal agents of rice blast and sheath ...
The accumulation of intracellular fat depots is a polygenic trait. Therefore, the extent of lipid storage in the individuals of a species covers a broad range and is determined by many genetic factors. Quantitative trait loci analysis can be used to identify those genetic differences between two strains of the same species that are responsible for the differences in a given phenotype. We used this method and complementary approaches to identify genes in the yeast Saccharomyces cerevisiae that are involved in neutral lipid storage. We selected two yeast strains, the laboratory strain BY4741 and the wine yeast AWRI1631, with a more than two-fold difference in neutral lipid content. After crossing, sporulation and germination, we used fluorescence activated cell sorting to isolate a subpopulation of cells with the highest neutral lipid content from the pool of segregants. Whole genome sequencing of this subpopulation and of the unsorted pool of segregants implicated several loci that are involved in lipid
Deerhake, Marion Elizabeth, Quantitative trait loci analysis of blood pressure in an eight intercross mouse study (2008). Summer and Academic Year Student Reports. 2234 ...
TY - JOUR. T1 - Genome-Wide Scans Reveal a Quantitative Trait Locus for Withers Height in Horses Near the ANKRD1 Gene. AU - Al Abri, Mohammed A.. AU - Posbergh, Christian. AU - Palermo, Katelyn. AU - Sutter, Nathan B.. AU - Eberth, John. AU - Hoffman, Gabriel E.. AU - Brooks, Samantha A.. PY - 2016/10/19. Y1 - 2016/10/19. N2 - Withers height is an important economic trait for the American Miniature Horses (AMHs) as the breeders primary objective is to produce small and proportionate animals. Identification of Quantitative Trait Loci (QTLs) affecting height in this breed will result in a better understanding of the genetic architecture and biological pathways contributing to skeletal development. In earlier work, we genotyped 48 horses from 16 different breeds that represent extremes in body size, using the Equine SNP50 bead chip (Illumina Inc). In this study, we applied a dominant model Genome-wide association study (GWAS), a genome-wide fixation index (FST) estimation, as well as a ...
MalaCards based summary : Bone Mineral Density Quantitative Trait Locus 12, is also known as bone mineral density qtl 12, osteoporosis. An important gene associated with Bone Mineral Density Quantitative Trait Locus 12 is UGT2B17 (UDP Glucuronosyltransferase Family 2 Member B17). Affiliated tissues include bone ...
MalaCards based summary : Bone Mineral Density Quantitative Trait Locus 11, also known as bmnd11, is related to osteoporosis. An important gene associated with Bone Mineral Density Quantitative Trait Locus 11 is BMND11 (Bone Mineral Density QTL 11). Affiliated tissues include bone ...
A four-stage approach was used to analyse epistasis based on the pre-corrected phenotypes where SNP genotypes were fitted as fixed factors: 1) single SNP regression to identify qSNPs (see above); 2) detect qSNP × qSNP pairs [9]; 3) detect qSNP × non-qSNP pairs; 4) detect non-qSNP × non-qSNP pairs. Nested tests were used to identify significant epistatic pairs; the first test compares the full model (y = μ+SNP1+SNP2+SNP1 *SNP2+e) with the NULL model (y = μ+e); the second test compares the full model with the two-SNP model (y = μ+SNP1+SNP2+e) (i.e. epistasis test). Only pairs that were significant for the first test enter the epistasis test. When either SNP1 or SNP2 is a qSNP, the first test is changed to ensure the full model is better than the single SNP model (y = μ+qSNP +e) before the epistasis test. When both SNP1 and SNP2 are qSNPs, only the epistasis test is needed. To avoid spurious interactions between closely located SNPs an arbitrary minimum distance of 10 cM was applied to any ...
TY - JOUR. T1 - Identification of porcine Lhx3 and SF1 as candidate genes for QTL affecting growth and reproduction traits in swine. AU - Smith, T. P.L.. AU - Showalter, A. D.. AU - Sloop, K. W.. AU - Rohrer, G. A.. AU - Fahrenkrug, S. C.. AU - Meier, B. C.. AU - Rhodes, S. J.. PY - 2001. Y1 - 2001. N2 - The distal portion of the long arm of porcine chromosome 1 has been shown to harbour several quantitative trait loci affecting growth and reproductive traits in swine. In order to identify potential candidate genes that might underlie these effects, a comparative mapping analysis was undertaken to define the extent of orthologous segments of human chromosome 9. A microsatellite associated with heat shock protein (HSP) A5 was used to define the proximal boundary of the quantitative trait loci (QTL) region, which suggests the human orthologue of the gene(s) responsible for the observed effects lies between HSPA5 and the q arm telomere of human chromosome 9. Examination of this region revealed two ...
Beef cattle require dietary minerals for optimal health, production and reproduction. Concentrations of minerals in tissues are at least partly genetically determined. Mapping genomic regions that affect the mineral content of bovine longissimus dorsi muscle can contribute to the identification of genes that control mineral balance, transportation, absorption and excretion and that could be associated to metabolic disorders. We applied a genome-wide association strategy and genotyped 373 Nelore steers from 34 half-sib families with the Illumina BovineHD BeadChip. Genome-wide association analysis was performed for mineral content of longissimus dorsi muscle using a Bayesian approach implemented in the GenSel software. Muscle mineral content in Bos indicus cattle was moderately heritable, with estimates ranging from 0.29 to 0.36. Our results suggest that variation in mineral content is influenced by numerous small-effect QTL (quantitative trait loci) but a large-effect QTL that explained 6.5% of the
Three quantitative trait loci (QTL) located on chromosome 1H, single QTL located on chromosomes 1H, 2H, 4H, 5H and 7H, were identified to be responsible for salinity tolerance under different environments. Waterlogging stress, daylight length and temperature showed significant effects on barley salinity tolerance. The QTL for salinity tolerance mapped on chromosomes 4H and 7H, QSlwd.YG.4H, QSlwd.YG.7H and QSlww.YG.7H were only identified in winter trials, while the QTL on chromosome 2H QSlsd.YG.2H and QSlsw.YG.2H were only detected in summer trials. Genes associated with flowering time were found to pose significant effects on the salinity QTL mapped on chromosomes 2H and 5H in summer trials. Given the fact that the QTL for salinity tolerance QSlsd.YG.1H and QSlww.YG.1H-1 reported here have never been considered in the literature, this warrants further investigation and evaluation for suitability to be used in breeding programs.. ...
Wheat (Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci (QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits including protein content (GPC); test weight (TW); single kernel characterization system (SKCS)-estimated kernel weight (SKW); kernel diameter (KD); kernel hardness measured by near-infrared reflectance spectroscopy (NIRS) hardness index (NHI); and SKCS-hardness index (SHI), a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers was developed using recombinant inbred lines (RILs) derived from Ning7840 x Clark. The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 QTL with additive effects on different traits were mapped on most wheat chromosomes, excluding 1A, 2A, 3D, 4D, 6D, and 7B. Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic ...
Serum lactate dehydrogenase (LDH) is used in diagnosing many diseases and is significantly determined by genetic factors. Three genes coding for LDH isoenzymes were mapped to chromosome 11q15 and 12p12. We used 330 Framingham Heart Study largest families for microsatellite linkage scan and 100K SNPs association scan to determine quantitative trait loci of LDH level. We estimated the heritability at 41%. Our genome-wide linkage analysis yielded several chromosomal regions, other than 11q and 12p, with LOD scores between 1 and 2.5. None of the 100K SNPs with a P-value ,10^-4 in our genome-wide association study was close to the chromosomal regions where the LDH genes reside. Our study demonstrated a strong genetic effect on the variation of LDH levels. There may not be a single gene with a large effect, instead may be several genes with small effects in controlling the variation of serum LDH. Those genes may be located on chromosomal regions that differ from where the genes encoding LDH isoenzymes ...
Breeding chickens for heat tolerance is desirable. The F18 and F19 generations of a broiler by Fayoumi advanced intercross line (AIL) was used to facilitate fine mapping of QTL. Three major phenotype collection phases were: pre-heat, acute heat, and chronic heat, with birds being exposed to daily heat cycles from 22 to 28 days of age. Body temperature was measured at all three phases; body weight at pre-heat and chronic heat phases. Breast muscle yield (as percentage of body weight) was measured after necropsy at d 28. Feed digestibility was assayed from ileal content collected at d 28. Birds were genotyped using a 600K Affymetrix chicken SNP array. Using GenSel significant QTL were found for each of the measured traits, indicating the feasibility of improving performance under hot conditions by genomic selection. This is the first GWAS using this novel AIL of chickens under heat stress.. ...
Low soil P availability is a primary constraint to common bean (Phaseolus vulgaris L.) production in Latin America and Africa. Substantial genotypic variation in bean adaptation to low phosphorus (LP) availability has been linked with root traits that enhance the efficiency of soil foraging. The objectives of this study were to identify quantitative trait loci (QTLs) for P accumulation and associated root architectural traits, to facilitate genetic improvement and to reveal physiological relationships. Eighty‐six F5.7 recombinant inbred lines (RILs) were developed from a cross between G19833, an Andean landrace with high total P accumulation, and DOR 364, a Mesoamerican cultivar with low total P accumulation in LP conditions. A genetic map constructed with restriction fragment length polymorphisms (RFLPs), microsatellites, and PCR‐based markers covering 1703 centimorgans (cM) total genetic distance and all eleven linkage groups (LGs) was used for QTL analysis. Seventy‐one RILs were ...
Genome editing (GE) is a method that enables specific nucleotides in the genome of an individual to be changed. To date, use of GE in livestock has focussed on simple traits that are controlled by a few quantitative trait nucleotides (QTN) with large effects. The aim of this study was to evaluate the potential of GE to improve quantitative traits that are controlled by many QTN, referred to here as promotion of alleles by genome editing (PAGE). Multiple scenarios were simulated to test alternative PAGE strategies for a quantitative trait. They differed in (i) the number of edits per sire (0 to 100), (ii) the number of edits per generation (0 to 500), and (iii) the extent of use of PAGE (i.e. editing all sires or only a proportion of them). The base line scenario involved selecting individuals on true breeding values (i.e., genomic selection only (GS only)-genomic selection with perfect accuracy) for several generations. Alternative scenarios complemented this base line scenario with PAGE (GS + PAGE).
Differences in floral morphologies affect pollination behaviour in many flowering plants. In the genus Oryza, several differences in the size of floral organs are known. In this study, we focused on the differences in the size of floral organs between common cultivated rice, Oryza sativa L. and its wild ancestor, O. rufipogon. We compared floral morphologies between cultivated rice O. sativa cv. Nipponbare and O. rufipogon W630. We first evaluated temporal changes in filament and anther lengths. W630 had longer filaments with rapid elongation within 15 min after spikelet opening. W630 also had longer anthers than Nipponbare, and size of anther was consistent throughout all time examined. We also analysed other six floral traits, and found that W630 had higher stigma and style length, as well as lemma and palea length, but lower lemma and palea width. Quantitative trait locus (QTL) analysis was performed to identify the loci controlling these floral traits, using backcross recombinant inbred
The whitebacked planthopper (WBPH), Sogatella furcifera Horváth, is a serious rice pest in Asia. Ovicidal resistance is a natural rice defense mechanism against WBPH and is characterized by the formation of watery lesions (WLs) and increased egg mortality (EM) at the WBPH oviposition sites. This study aimed to understand the genetic and molecular basis of rice ovicidal resistance to WBPH by combining genetic and genomic analyses. First, the ovicidal trait in doubled haploid rice lines derived from a WBPH-resistant cultivar (CJ06) and a WBPH-susceptible cultivar (TN1) were phenotyped based on the necrotic symptoms of the leaf sheaths and EM. Using a constructed molecular linkage map, 19 quantitative trait loci (QTLs) associated with WLs and EM were identified on eight chromosomes. Of them, qWL6 was determined to be a major QTL for WL. Based on chromosome segment substitution lines and a residual heterozygous population, a high-resolution linkage analysis further defined the qWL6 locus to a 122-kb region
Detecting both the majors genes that control the phenotypic mean and those controlling phenotypic variance has been raised in quantitative trait loci analysis. In order to mapping both kinds of genes, we applied the idea of the classic Haley-Knott regression to double generalized linear models. We performed both kinds of quantitative trait loci detection for a Red Jungle Fowl x White Leghorn F2 intercross using double generalized linear models. It is shown that double generalized linear model is a proper and efficient approach for localizing variance-controlling genes. We compared two models with or without fixed sex effect and prefer including the sex effect in order to reduce the residual variances. We found that different genes might take effect on the body weight at different time as the chicken grows.. ...
The genetics of sexual isolation, behavioral differences between species that prevent mating, is understood poorly. Pheromonal differences between species can influence sexual isolation in many animals and in some cases a single locus can cause large functional changes in pheromonal mating signals. Drosophila cuticular hydrocarbons (CHCs) can function as pheromones and consequently affect mate recognition. In a previous study of the two major CHCs in females that affect mating discrimination between Drosophila simulans and D. sechellia, quantitative trait loci (QTL) were identified on the X and third chromosome, and a few candidate genes were potentially implicated. Here we specifically test candidate genes for CHC biosynthesis and determine the genetic architecture of four additional CHCs that differ in abundance between D. simulans and D. sechellia females. The same QTL, and new ones, were found for additional CHCs. By examining all these CHCs and exploring their covariance, we were able to ascribe
Infectious disease has a significant economic impact in livestock production systems worldwide. Selection using DNA markers closely linked to, or within genes controlling resistance traits is increasingly prevalent. We review the state of quantitative trait loci (QTL) studies based on genome wide screens or targeted candidate gene studies for sheep and cattle. Infectious diseases considered include gastrointestinal nematodes, mastitis, trypanosomiasis, dermatophilosis, footrot, fasciolosis, tick and tickborne diseases. We discuss the problems and methods of moving from QTL results to quantitative trait nucleotides (QTN) by fine mapping, and comparative mapping. We highlight the utility of integrating QTL studies with large scale transcriptome studies to obtain positional-functional candidate genes, followed by gain/loss of function studies. We close with markers shown to have utility in industry applications.. ...
Di Nicolantonio, R., Kostka, V., Kwitek, A., Jacob, H., Thomas, W.G. and Harrap, S.B. 2006, Fine mapping of Lvm1: a quantitative trait locus controlling heart size independently of blood pressure, Pulmonary pharmacology & therapeutics, vol. 19, no. 1, pp. 70-73, doi: 10.1016/j.pupt.2005.02.010. ...
Coffee Berry Disease (CBD) is a major constraint that limits Coffea arabica production, whose resistance is governed by three genes, T, R that are dominant and recessive k in varieties Hibrido de Timor (HDT), Rume Sudan (RS) and K7 respectively. This study identified the genomic region occupied by R-gene using F2 genotypes from varieties RS and SL28; and Single Nucleotide Polymorphic (SNP) markers obtained through Genotyping by Sequencing. Redundant markers were removed and 699 markers obtained for linkage mapping and quantitative trait loci (QTL) analysis. The Linkage map spread over 5525.39 cM across eleven coffee chromosomes (Chr). The QTL was analyzed by both Interval Mapping (IM) and Inclusive Composite Interval Mapping (ICIM) using SNP markers and CBD resistance mean scores of the F2 genotypes and their parents. Three QTLs, qCBD 1-1 in Chr 1, qCBD 2-1 and qCBD 2-2 in Chr 2 were significantly associated with CBD resistance, detected by both IM and ICIM at LOD ≥ 2.5 (P≤0.05).  Two
Quantitative resistance of Salix to Melampsora larici--epitea leaf rust was studied in 2 Salix mapping populations. One population was a backcross between a S, schwerinii x S. viminalis hybrid and S. viminalis, and the other was all F-2 population between S. viminalis and S. dasyclados. A leaf disc bioassay was used to study the components of quantitative resistance (latent period, uredinia number, and uredinia size) to 3 isolates of the leaf rust. The analysis of quantitative trait loci (QTLs) revealed 9 genomic regions in the backcross population and 7 genomic regions in the F-2 population that were important for rust resistance, with QTLs explaining 8-26% of the phenotypic variation. An important genomic region was identified for the backcross population in linkage group 2, where QTLs were identified for all resistance components for 2 of the rust isolates. Four of the QTLs had overlapping mapping intervals, demonstrating a common genetic background for latent period, uredinia diameter, and ...
TY - JOUR. T1 - A polymerase chain reaction-based linkage map of broccoli and identification of quantitative trait loci associated with harvest date and head weight. AU - Brown, Allan F.. AU - Jeffery, Elizabeth H.. AU - Juvik, John A.. N1 - Copyright: Copyright 2020 Elsevier B.V., All rights reserved.. PY - 2007/7. Y1 - 2007/7. N2 - A set of 216 polymerase chain reaction-based molecular markers was screened for polymorphisms using two morphologically dissimilar broccoli (Brassica oleracea L. ssp. italica Plenck) lines, VI-158 and Brocolette Neri E. Cespuglio. Fifty-nine of these simple sequence repeat (SSR) and sequence-related amplified polymorphic (SRAP) primer pairs generated 69 polymorphisms that were used to construct a linkage map of broccoli from a population of 162 F2:3 families derived from the cross between these two lines. Ten linkage groups were generated that spanned a distance of 468 cM with an average interval width of 9.4 cM. The map was used to identify quantitative trait ...
Limb bone lengths and bone mineral density (BMD) have been used to assess the bone growth and the risk of bone fractures in pigs, respectively. It has been suggested that limb bone lengths and BMD are under genetic control. However, the knowledge about the genetic basis of the limb bone lengths and mineralisatinon is limited in pigs. The aim of this study was to identify quantitative trait loci (QTL) affecting limb bone lengths and BMD of the distal femur in a White Duroc × Erhualian resource population. Limb bone lengths and femoral bone mineral density (fBMD) were measured in a total of 1021 and 116 F2 animals, respectively. There were strong positive correlations among the lengths of limb bones and medium positive correlations between the lengths of limb bones and fBMD. A whole-genome scan involving 183 microsatellite markers across the pig genome revealed 35 QTL for the limb bone lengths and 2 for femoral BMD. The most significant QTL for the lengths of five limb bones were mapped on two
TY - JOUR. T1 - Regulatory Network Identification by Genetical Genomics: Signaling Downstream of the Arabidopsis Receptor-Like Kinase ERECTA. AU - Terpstra, I.R.. AU - Snoek, L.B.. AU - Keurentjes, J.J.B.. AU - Peeters, A.J.M.. AU - van den Ackerveken, G.. PY - 2010. Y1 - 2010. N2 - Gene expression differences between individuals within a species can be largely explained by differences in genetic background. The effect of genetic variants (alleles) of genes on expression can be studied in a multifactorial way by application of genetical genomics or expression quantitative trait locus (eQTL) mapping. In this paper we present a strategy to construct regulatory networks by application of genetical genomics in combination with transcript profiling of mutants that are disrupted in single genes. We describe the network identification downstream of the receptor-like kinase ERECTA in Arabidopsis (Arabidopsis thaliana). Extending genetical genomics on the Landsberg erecta/Cape Verde islands (Ler/Cvi) ...
In previous work, we identified genetic correlations between cAMP accumulation in the cerebellum and sensitivity to the incoordinating effects of ethanol. A genetic correlation suggests that common genes underlie the phenotypes investigated. One method for provisionally identifying genes involved in a given phenotypic measure is quantitative trait locus (QTL) analysis. Using a panel of 30 BXD recombinant inbred strains of mice and the progenitors (DBA/2J and C57BL/6J), and the dowel test for ataxia, we measured the blood ethanol concentrations at the time an animal first fell from the dowel and acute functional tolerance (AFT), and investigated cAMP signaling in the cerebellum. Cyclic AMP accumulation was measured in whole-cell preparations of cerebellar minces from individual mice under basal or stimulated conditions. We conducted a genome-wide QTL analysis of the behavioral and biochemical measures with >2000 genetic markers to identify significant associations. Western blot and comparative ...
TY - JOUR. T1 - Quantitative trait loci and molecular markers associated with wheat allelopathy. AU - Wu, Hanwen. AU - Pratley, James. AU - Ma, W. AU - Haig, Terrence. N1 - Imported on 12 Apr 2017 - DigiTool details were: Journal title (773t) = Theoretical and Applied Genetics: international journal of plant breeding research. ISSNs: 0040-5752; PY - 2003. Y1 - 2003. N2 - Wheat (Triticum aestivum L.) has been examined for allelopathic potential against annual ryegrass (Lolium rigidum). The bioassay technique, equal-compartment-agar-method, was employed to evaluate seedling allelopathy in a doubled-haploid (DH) population derived from cv Sunco (weakly allelopathic) and cv Tasman (strongly allelopathic). A significant difference in allelopathic activity was found among the DH lines, which inhibited the root length of ryegrass across a range from 23.7 to 88.3%. The phenotypic data showed that wheat allelopathic activity was distributed normally within this DH population and a substantial ...
In dairy cattle, quantitative trait nucleotides (QTNs) underlying quantitative trait loci (QTL) for milk production traits have been identified in bovine DGAT1, GHR and ABCG2 genes. The SPP1 gene has also been proposed to be a regulator of lactation. In sheep, QTL underlying milk production traits h …
3C technologies have enabled studies of the dynamics of high-order chromatin structures and long-range chromatin interactions (26-30). However, how these long-range interactions contribute to biological processes and human diseases is not well understood. Our research has focused on an enhancer containing the PCa risk-associated rs55958994 SNP, integrating higher-order chromatin structure data, gene expression profiling, and functional assays. Our results suggest that the rs55958994-containing enhancer regulates PCa progression through long-range interactions with multiple genes. Among these genes, ITGA5, CDH23, and CNTN1 were verified to be both regulated by the rs55958994-containing enhancer and associated with PCa progression; deletion of the enhancer region in PCa cells induced down-regulation of these target genes and led to defects in tumor initiation and migration and loss of CSCs.. Previous eQTL (expression quantitative trait locus) analyses suggested that rs55958994 is linked to KRT8 ...
Shirali M., Miraei‐Ashtiani S.R., Pakdel A., Haley C., Navarro P. and Pong‐Wong R, 2015, A Comparison of the Sensitivity of the BayesC and Genomic Best Linear Unbiased Prediction (GBLUP) Methods of Estimating Genomic Breeding Values under Different Quantitative Trait Locus (QTL) Model Assumptions, Iranian Journal of Applied Animal Science, 5(1), 41-46 Shirali M., Miraei‐Ashtiani S.R., Pakdel A., Haley C., Navarro P. and Pong‐Wong R, 2015, A Comparison of the Sensitivity of the BayesC and Genomic Best Linear Unbiased Prediction (GBLUP) Methods of Estimating Genomic Breeding Values under Different Quantitative Trait Locus (QTL) Model Assumptions, Iranian Journal of Applied Animal Science, 5(1), 41-46
BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is associated with obesity and the metabolic syndrome and affects over one third of American adults. A subset of NAFLD patients develop advanced disease associated with liver injury, scar tissue (fibrosis), and cirrhosis, increasing risk for liver-related mortality, including primary liver cancer. Several genes have been associated with NAFLD, but determination of their function in the disease process has been difficult. We hypothesized that expression quantitative trait loci (eQTL) analysis would improve the identification of causally related genetic variants by integrating single nucleotide polymorphisms (SNPs) with gene expression. METHODS: Patients with biopsy-proven NAFLD were selected based on fibrosis stage (mild NAFLD: stage F0-F1 vs. advanced NAFLD: stage F3-F4). Genomic data, including genotype (Cardiometabolic SNP array, Illumina), methylation (Human Methylation450 BeadChip, Illumina) and expression (Human U133 Plus 2.0 GeneChip, ...
ILs and advanced backcross QTL approaches are now well-established tools for dissecting the genetic basis of complex polygenic traits in plant populations. In this study, S. pennellii ILs were used to identify a fruit firmness QTL located to an 8.6-Mb region on tomato chromosome 2. A prior study had identified a firmness QTL, fir2.1 in Solanum pimpinellifolium (Doganlar et al., 2002), mapping within this region. Conservation of QTLs within the Solanaceace family has been demonstrated for a number of traits including fruit size, shape, and weight (Saliba-Colombani et al., 2001; Frary et al., 2004). However, QTL fir2.1 in S. pimpinellifolium has not been further resolved by fine-mapping. In this work, we have used a composite mapping population of M82 × IL 2-3 F2 and M82 × IL 2-4 F3 to resolve the S. pennellii firmness QTL on chromosome 2 and report that at least several major firmness effects occur within a mapping interval of approximately 8.6 Mb, delineated by markers CT255 and TG527. Other ...
CONTEXT: Recently, a quantitative trait locus for stature was reported on chromosome 3p26 in patients with type 2 diabetes. OBJECTIVE: Given that ghrelin is a peptide involved in GH release and located on 3p26, we hypothesized that variation within its gene (GHRL) may be responsible for the quantitative trait locus on 3p26. DESIGN: The evidence for linkage around GHRL was refined with the genotyping of an additional four microsatellites (D3S4545, D3S1537, D3S1597, and D3S3611), giving a total of 27 markers, followed by multipoint variance components linkage analysis. Probands from the linkage families were typed for five common single nucleotide polymorphisms (SNPs) within GHRL and tested for association with adult stature using haplotype trend regression. RESULTS: The maximum multipoint evidence for linkage between adult stature and the 27 microsatellites yielded an LOD score of 2.58 (P = 0.0003) between D3S1297 and D3S1304. Five common (frequency of | or =5%) SNPs were typed in the probands [two
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作 者:Kun Li, Hongwu Wang, Xiaojiao Hu, Feiqian Ma, Yujin Wu, Qi Wang, Zhifang Liu, and Changling Huang. 影响因子: 4.298. 刊物名称: Frontiers in plant science. 出版年份: 2017. 卷: 8 期:24 August 页码: 1472. 文章摘要 : The plant cell wall plays vital roles in various aspects of the plant life cycle. It provides a basic structure for cells and gives mechanical rigidity to the whole plant. Some complex cell wall components are involved in signal transduction during pathogenic infection and pest infestations. Moreover, the lignification level of cell walls strongly influences the digestibility of forage plants. To determine the genetic bases of cell wall components and digestibility, quantitative trait locus (QTL) analyses for six related traits were performed using a recombinant inbred line (RIL) population from a cross between Zheng58 and HD568. Eight QTL for in vitro neutral detergent fiber (NDF) digestibility were observed, out of which only two increasing alleles came ...
Abundant contribution of short tandem repeats to gene expression variation in humans Melissa Gymrek , Thomas Willems , Haoyang Zeng , Barak Markus , Mark J Daly , Alkes L Price , Jonathan Pritchard , Yaniv Erlich doi: http://dx.doi.org/10.1101/017459 Expression quantitative trait loci (eQTLs) are a key tool to dissect cellular processes mediating complex diseases.…
Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the
Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent ...
Schizophrenia is a complex, highly heritable and heterogeneous disease with estimated heritability ranging up to 80%. It affects approximately 0.5-1% of the world population. During the past decade, numerous schizophrenia-associated variants and loci in world-wide populations have been identified, but most of the risk single-nucleotide polymorphisms (SNPs) or variants identified by GWASs were located in intergenic, intronic or other non-coding regions. To identify the causal genes at the reported risk loci and to elucidate how these risk genes influence the pathogenesis of schizophrenia remains a daunting task. Previous studies showed that most complex disease-associated variants confer risk for the illnesses by acting as eQTL to influence gene expression in cis or in trans. By integrating a large-scale schizophrenia GWAS data and brain prefrontal cortex expression quantitative trait loci (eQTL) data, a team of scientists from the Kunming Institute of Zoology (KIZ) of the Chinese Academy of ...
Brassica napus L. is a widely cultivated oil crop and provides important resources of edible vegetable oil, and its quality is determined by fatty acid composition and content. To explain the genetic basis and identify more minor loci for fatty acid content, the multi-locus random-SNP-effect mixed linear model (mrMLM) was used to identify genomic regions associated with fatty acid content in a genetically diverse population of 435 rapeseed accessions, including 77 winter-type, 55 spring-type, and 303 semi-winter-type accessions grown in different environments. A total of 149 quantitative trait nucleotides (QTNs) were found to be associated with fatty acid content and composition, including 34 QTNs that overlapped with the previously reported loci, and 115 novel QTNs. Of these, 35 novel QTNs, located on chromosome A01, A02, A03, A05, A06, A09, A10, and C02, respectively, were repeatedly detected across different environments. Subsequently, we annotated 95 putative candidate genes by BlastP ...
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THIS PROPOSED RESEARCH REPRESENTS A UNIQUE COMBINATION OF TECHNOLOGIES AND SUBSEQUENT OPPORTUNITY TO EXAMINE THE MOLECULAR BASIS OF TRAITS EXHIBITING QUANTITATIVE EXPRESSIONAND INHERITANCE. IT HAS BEEN OBSERVED THAT THERE ARE OFTEN STRONG ASSOCIATIONS BETWEEN PATTERNS OF VARIATION OF ISOZYME MARKERS AND PLANT MORPHOLOGICAL CHARACTERS WHICH SHOW QUANTITATIVE INHERITANCE. RECENTLY, HELENTJARIS, EDWARDS, AND STUBER (UNPUBLISHED DATA) HAVE EXTENDED THIS TYPE OF ANALYSIS USING RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLP). SEVERAL RFLP LOCI WERE IDENTIFIED WHICH WERE PREDICTIVE FOR PLANT HEIGHT. ROBERTSON HAS SUGGESTED THAT GENETIC LOCI RESULTING IN DWARF PLANTS ARE GOOD CANDIDATES FOR LOCI INVOLVED IN THE QUANTITATIVE INHERITANCE OF PLANT HEIGHT. THE DWARF LOCUS, D3, MAPS IN ONE OF THE AREAS OF THE GENOME IDENTIFIED AS SIGNIFICANTLY CONTRIBUTING TO PLANT HEIGHT. WE PROPOSE TO TAKE ADVANTAGE OF THIS EASILY RECOGNIZABLE PHENOTYPE TO CLONE A DWARF ALLELE USING THE STRATEGY OF INSERTION MUTAGENESIS ...
A genome-wide association study (GWAS) was conducted to identify expression quantitative trait loci (eQTLs) for the genes involved in phosphatidylinositol-3-kinase/v-akt murine thymoma viral oncogene homolog (PI3K/AKT) pathway.Data on mRNA expression of 341 genes in lymphoblastoid cell lines of 373 Europeans recruited by the 1000 Genomes Project using Illumina HiSeq2000 were utilized. We used their genotypes at 5,941,815 nucleotide variants obtained by Genome Analyzer II and SOLiD.The association analysis revealed 4166 nucleotide variants associated with expression of 85 genes (P < 5 × 10). A total of 73 eQTLs were identified as association signals for the expression of multiple genes. They included 9 eQTLs for both of the genes encoding collagen type I alpha 1 (COL1A1) and integrin alpha 11 (ITGA11), which synthesize a major complex of plasma membrane. They also included eQTLs for type IV collagen molecules; 13 eQTLs for both collagen type IV alpha 1 (COL4A1) and collagen type IV alpha 2 ...
Annual fish of the genus Nothobranchius show large variations in lifespan and expression of age-related phenotypes between closely related populations. We studied N. kadleci and its sister species N. furzeri GRZ strain, and found that N.kadleci is longer-lived than the N. furzeri. Lipofuscin and apoptosis measured in the liver increased with age in N. kadleci with different profiles: lipofuscin increased linearly, while apoptosis declined in the oldest animals. More lipofuscin (P,0.001) and apoptosis (P,0.001) was observed in N. furzeri than in N. kadleci at 16w age. Lipofuscin and apoptotic cells were then quantified in hybrids from the mating of N. furzeri to N. kadleci. F₁individuals showed heterosis for lipofuscin but additive effects for apoptosis. These two age-related phenotypes were not correlated in F₂ hybrids. Quantitative trait loci analysis of 287 F₂ fish using 237 markers identified two QTL accounting for 10% of lipofuscin variance (P,0.001) with overdominance effect. ...
Individual kernel weight is an important trait for maize yield determination. We have identified genomic regions controlling this trait by using the B73xMo17 population; however, the effect of genetic background on control of this complex trait and its physiological components is not yet known. The objective of this study was to understand how genetic background affected our previous results. Two nested stable recombinant inbred line populations (N209xMo17 and R18xMo17) were designed for this purpose. A total of 408 recombinant inbred lines were genotyped and phenotyped at two environments for kernel weight and five other traits related to kernel growth and development. All traits showed very high and significant (P , 0.001) phenotypic variability and medium-to-high heritability (0.60−0.90). When N209xMo17 and R18xMo17 were analyzed separately, a total of 23 environmentally stable quantitative trait loci (QTL) and five epistatic interactions were detected for N209xMo17. For R18xMo17, 59 ...
TY - JOUR. T1 - Exploring hepsin functional genetic variation association with disease specific protein expression in bipolar disorder. T2 - Applications of a proteomic informed genomic approach. AU - Nassan, Malik. AU - Jia, Yun Fang. AU - Jenkins, Greg. AU - Colby, Colin. AU - Feeder, Scott. AU - Choi, Doo Sup. AU - Veldic, Marin D. AU - McElroy, Susan L.. AU - Bond, David J.. AU - Weinshilboum, Richard M. AU - Biernacka, Joanna M. AU - Frye, Mark A. PY - 2017/12/1. Y1 - 2017/12/1. N2 - In a prior discovery study, increased levels of serum Growth Differentiation Factor 15 (GDF15), Hepsin (HPN), and Matrix Metalloproteinase-7 (MMP7) were observed in bipolar depressed patients vs controls. This exploratory post-hoc analysis applied a proteomic-informed genomic research strategy to study the potential functional role of these proteins in bipolar disorder (BP). Utilizing the Genotype-Tissue Expression (GTEx) database to identify cis-acting blood expression quantitative trait loci (cis-eQTLs), five ...
Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through ...
|i|SLC30A8|/i| encodes zinc transporter 8 which is involved in packaging and release of insulin. Evidence for the association of|i| SLC30A8|/i| variants with type 2 diabetes (T2D) is inconclusive. We interrogated single nucleotide polymorphisms (SNPs) around|i| SLC30A8|/i| for association with T2D in high-risk, pedigreed individuals from extended Mexican American families. This study of 118 SNPs within 50 kb of the|i| SLC30A8|/i| locus tested the association with eight T2D-related traits at four levels: (i) each SNP using measured genotype approach (MGA); (ii) interaction of SNPs with age and sex; (iii) combinations of SNPs using Bayesian Quantitative Trait Nucleotide (BQTN) analyses; and (iv) entire gene locus using the gene burden test. Only one SNP (rs7817754) was significantly associated with incident T2D but a summary statistic based on all T2D-related traits identified 11 novel SNPs. Three SNPs and one SNP were weakly but interactively associated with age and sex, respectively. BQTN analyses could
Beamer WG, Shultz KL, Churchill GA, Frankel WN, Baylink DJ, Rosen CJ, Donahue LR. Quantitative trait loci for bone density in C57BL/6J and CAST/EiJ inbred mice. Mamm Genome. 1999 Nov;10(11):1043-9. PubMed 10556421 Ackert-Bicknell CL, Karasik D, Li Q, Smith RV, Hsu YH, Churchill GA, Paigen BJ, Tsaih SW. Mouse BMD quantitative trait loci show improved concordance with human genome-wide association loci when recalculated on a new, common mouse genetic map. J Bone Miner Res. 2010 Aug;25(8):1808-20. PubMed 20200990 ...
Mediators of Inflammation is a peer-reviewed, Open Access journal that publishes original research and review articles on all types of inflammatory mediators, including cytokines, histamine, bradykinin, prostaglandins, leukotrienes, PAF, biological response modifiers and the family of cell adhesion-promoting molecules.
Increasingly, baseline peripheral blood cell counts are implicated as risk factors for common complex diseases. While genetic influences on these hematologic parameters are firmly established, the gen
Non-insulin-dependent diabetes mellitus (NIDDM) is a prototypical multifactorial disease. Genetic predisposition and obesity are major risk factors for NIDDM development and the interactions between these factors are likely to be important in the eti
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints ...
The study was conducted to investigate genetic variability among 113 aromatic and fine local rice genotypes of which five were exotic in origin. The test genotypes were evaluated for 19 growth traits, yield components, and yield. All the quantitative traits varied significantly among the test genotypes. High heritability along with high genetic advance was observed for flag leaf area, secondary branches per panicle, filled grains per panicle, grain length, grain breadth, grain length breadth ratio, and 1000 grain weight. Such findings suggested preponderance of additive gene action in gene expression for these characters. Grain yield was significantly and positively correlated with days to flowering, days to maturity, panicle length, filled grains per panicle, and 1000 grain weight. According to D2 cluster analysis, 113 test genotypes formed 10 clusters. Selection of parents from the clusters V and X followed by hybridization would possibly result in desirable heterosis for the development of ...
A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal genomes of individual patients and to facilitate the development of personalized treatment or therapeutic approaches. Leveraging deep neural network on the TensorFlow framework, we developed a computational tool, integrated Mental-disorder GEnome Score (iMEGES), for analyzing whole genome/exome sequencing data on personal genomes. iMEGES takes as input genetic mutations and phenotypic information from a patient with mental disorders, and outputs the rank of whole genome susceptibility variants and the prioritized disease-specific genes for mental disorders by integrating contributions from coding and non-coding variants, structural variants (SVs), known brain expression quantitative trait loci (eQTLs),
In a first-of-its-kind study, NC State researchers applied a new approach to examine how members of two different species - a plant and a pathogen, for example, or a bacterium and a human - interact at the molecular level, and whether slight genetic changes in one species could affect gene expression in the other.. In a paper published in the journal Genetics, NC State plant pathologists, biologists and statisticians use a genetic mapping method - expression quantitative trait locus, or eQTL, mapping - applied in a novel way to describe these interactions, opening the door for further work on these complex relationships.. Were really trying to get to the genetics behind the interactions between two different organisms, said David McK. Bird, a NC State plant pathology professor and co-corresponding author of the paper. Genetics gives us causality more than just correlation.. We used an interactive system to see if DNA changes in one species would affect the characteristics in another ...
Alzheimers disease (AD) is the most common neurodegenerative disease in the elderly and the leading cause of dementia in humans. Evidence shows that cellular trafficking and recycling machineries are associated with AD risk. A recent study found that the coat protein complex I (COPI)-dependent trafficking in vivo could significantly reduce amyloid plaques in the cortex and hippocampus of neurological in the AD mouse models and identified 12 single-nucleotide polymorphisms in COPI genes to be significantly associated with increased AD risk using 6,795 samples. Here, we used a large-scale GWAS dataset to investigate the potential association between the COPI genes and AD susceptibility by both SNP and gene-based tests. The results showed that only rs9898218 was associated with AD risk with P = 0.017. We further conducted an expression quantitative trait loci (eQTLs) analysis and found that rs9898218 G allele was associated with increased COPZ2 expression in cerebellar cortex with P = 0.0184. Importantly,
Differential HLA-C levels influence several human diseases, but the mechanisms responsible are incompletely characterized. Using a validated prediction algorithm, we imputed HLA-C cell surface levels in 228 individuals from the 1000 Genomes dataset.. We tested 68,726 SNPs within the MHC for association with HLA-C level. The HLA-C promoter region variant, rs2395471, 800 bp upstream of the transcription start site, gave the most significant association with HLA-C levels (p = 4.2 x 10-66). This imputed expression quantitative trait locus, termed impeQTL, was also shown to associate with HLA-C expression in a genome-wide association study of 273 donors in which HLA-C mRNA expression levels were determined by quantitative PCR (qPCR) (p = 1.8 x 10-20) and in two cohorts where HLA-C cell surface levels were determined directly by flow cytometry (n = 369 combined, p < 10-15).. rs2395471 is located in an Oct1 transcription factor consensus binding site motif where the A allele is predicted to have higher ...
BACKGROUND: Complex etiology and pathogenesis of pathophysiological components of the cardio-metabolic syndrome have been demonstrated in humans and animal models. METHODOLOGY/PRINCIPAL FINDINGS: We have generated extensive physiological, genetic and genome-wide gene expression profiles in a congenic strain of the spontaneously diabetic Goto-Kakizaki (GK) rat containing a large region (110 cM, 170 Mb) of rat chromosome 1 (RNO1), which covers diabetes and obesity quantitative trait loci (QTL), introgressed onto the genetic background of the normoglycaemic Brown Norway (BN) strain. This novel disease model, which by the length of the congenic region closely mirrors the situation of a chromosome substitution strain, exhibits a wide range of abnormalities directly relevant to components of the cardio-metabolic syndrome and diabetes complications, including hyperglycaemia, hyperinsulinaemia, enhanced insulin secretion both in vivo and in vitro, insulin resistance, hypertriglyceridemia and altered pancreatic
We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available,
We will work to validate, dissect and characterize a QTL for kernel weight (KW) located on chromosome 6A. The QTL was identified in a RIL population derived the cross SS-MPV 57 x Massey when grown at Raleigh, NC for three years. The QTL has an additive effect of 1.75 mg. In this population, the KW QTL coincides with plant height QTL having an additive effect of 3.78 cm. Heterozygous plants were identified in F5-derived RIL for development of fine-mapping populations. This QTL region is physically large and spans the centromere. Observed recombination in the HIFs has been localized towards the ends of the QTL interval.. A second population of 358 RIL from the cross SS-MPV57 x LA95135 is being used to validate the KW QTL effect. This population is also being targeted for identification of additional QTL in regions more amenable to fine-mapping and cloning.. ...
We have examined the genetics of nonhost resistance in Arabidopsis, using the bean pathogen Pseudomonas syringae pv. phaseolicola race 6 1448A to probe accessions for natural variation in basal defense. Symptoms rarely developed in leaves of Niedersenz (Nd), some yellowing and occasional necrosis developed in Columbia (Col), whereas tissue collapse was observed in Wassilewskija (Ws) after inoculation by infiltration. Analysis of F2 progeny and recombinant inbred lines (RIL) from a cross between Col and Nd revealed a pattern of continuous symptom increase, indicating the operation of quantitative determinants of resistance. By mapping quantitative trait loci (QTL), significant linkage was determined for resistance (low symptom score) to markers on chromosome 4. Segregation in the F2 cross from Nd × Ws indicated the operation of two dominant genes for resistance, one of which was FLS2 encoding the flagellin receptor. The requirement for FLS2 to confer resistance was confirmed by transgenic ...
This timely text presents a comprehensive guide to genetic association, a new and rapidly expanding field that aims to elucidate how our genetic code (genotypes) influences the traits we possess (phenotypes). The book provides a detailed review of methods of gene mapping used in association with experimental crosses, as well as genome-wide association studies. Emphasis is placed on model selection procedures for analyzing data from large-scale genome scans based on specifically designed modifications of the Bayesian information criterion. Topics and features: Presents a thorough introduction to the theoretical background to studies of genetic association (both genetic and statistical) Reviews the latest advances in the field, highlighting the advantages and shortcomings of the currently most commonly used methods Illustrates the properties of methods for mapping quantitative trait loci using computer simulations and the analysis of real data Discusses open challenges that remain to be solved in ...