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Results for “QTL mapping”

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PubMed2002

QTLs involved in the restriction of cucumber mosaic virus (CMV) long-distance movement in pepper.

Partial restriction of cucumber mosaic virus (CMV) long-distance movement originating from the Capsicum annuum inbred line 'Vania' was assessed in a doubled-haploid progeny using two screening methods: the first allowed one to assess the resistance of adult plants decapitated above the fourth leaf and inoculated on the third leaf using a common CMV strain, and the second allowed one to assess CMV resistance to long-distance movement on seedlings inoculated using an atypical CMV strain. For both resistance tests, the behavior of the F(1) hybrid between 'Vania' and the susceptible line 'H3' indicated that partial resistance is inherited as a dominant trait. Phenotypic data from the two screening methods were correlated but the one performed on seedlings was much more severe. A subset of 184 molecular markers well-distributed over the pepper genome was selected for QTL mapping using the composite interval mapping (CIM) method. A total of seven genomic regions, including one major effect and several minor effect QTLs, were shown to be associated with partial restriction of CMV long-distance movement. These results are compared with those already obtained in pepper and also in other solanaceous crops, potato and tomato.

Journal Article↗

PubMed2002

Detection of modifier loci influencing the lung phenotype of cystic fibrosis knockout mice.

The variable severity of lung disease associated with cystic fibrosis (CF) cannot be explained by the genotype of the cystic fibrosis transmembrane conductance regulator (CFTR) locus alone. Lung disease has been reported in a congenic CF mouse model of C57BL/6J genetic background (B6 CF), in the absence of detectable infection, but not in CF mice of mixed genetic background, nor in wild-type animals maintained in identical environments. In this report, studies are presented to show that the same CF mutation in mice of a BALB/c background (BALB CF) results in minimal lung disease. By 12 weeks of age B6 CF mice developed a lung disease consisting of mononuclear cell interstitial infiltrate and fibrosis, and BALB CF or littermate control mice developed minimal histopathology. Therefore, it is possible to identify the chromosomal locations of genes that can contribute to the susceptibility to lung disease in B6 CF mice compared with BALB CF mice by means of a quantitative trait loci (QTL) mapping strategy based on the variable histology of the (B6 x BALB) F2 CF mice. Significant linkage of the fibrotic lung phenotype was detected for a region on Chromosome (Chr) 6, defined by markers D6Mit194 to D6Mit201, and suggestive linkage was found for regions on Chr 1, 2, 10, and 17. Additional loci, suggestive of linkage, were also detected for the interstitial thickening phenotype. Most of these putative loci are specific to the sex of the animals. These results suggest that multiple genes can influence the severity of CF lung disease in mice.

Animals↗

PubMed2000

Different functions of QTL for estrogen-dependent tumor growth of the rat pituitary.

Estrogen treatment to rats of the Fischer 344 (F344) strain induces growth of pituitary tumors that exhibit accelerated cell proliferation, breakdown of basement membrane, and formation of hemorrhagic lakes. Estrogen-dependent pituitary growth is due to variation in a group of quantitative trait loci (QTL), called Edpm for estrogen-dependent pituitary mass, that we previously identified in an F(2) intercross of F344 and the tumor-resistant Brown Norway strain. We previously identified 5 QTL, and microsatellite markers developed since our earlier work have allowed us to scan new chromosomal regions, resulting in two new QTL for estrogen-dependent pituitary mass: Edpm9-2 and a possible QTL on the X Chromosome (Chr). Here we report evidence that these QTL differ from each other in how they affect growth. To examine the effect of the Edpm QTL on biochemical components of tumor growth, we tested their effects in 138 progeny of a backcross to the F344 strain which were given a 10-week chronic estrogen treatment. Hemoglobin/DNA ratio (a measure of blood volume relative to cell number) and total pituitary DNA (a measure of cell number) correlated only weakly, and very large pituitaries were observed which had a low hemoglobin/DNA ratio resembling a normal gland. Through QTL mapping, we found that Edpm2-1, Edpm3, Edpm5, and Edpm9-2 all had significant effects on pituitary mass, but Edpm2-1 and Edpm9-2 primarily affected DNA content, Edpm5 primarily affected hemoglobin/DNA ratio, and Edpm3 affected all traits equally.

Animals↗

PubMed1997

Evidence for individual and between-family variability of the recombination rate in cattle.

We have conducted a study based on single sperm typing in a family design to assess patterns of variability of the male recombination rate in cattle. 2214 sperm of 37 bulls were typed for 11 loci on bovine Chromosomes (Chrs) 6, 23, and the sex chromosomes. Statistically significant individual variability of the recombination rate was observed for one interval in the pseudoautosomal region (PAR) of the bovine sex chromosomes; one marker interval on bovine Chr 23 exhibited individual variability that was close to significance. Thirty-five of the bulls were members of six paternal halfsib groups, and highly significant variability between families was found for one interval in the PAR. This variability may be due to DNA sequence differences in the PAR or to a genetic control of the recombination activity in this region. It is demonstrated that differences in the recombination rate of the magnitude observed in the present study may have a considerable impact on the power of QTL mapping experiments as well as on the sustainability of marker-assisted selection strategies.

Animals↗

PubMed2005

Locomotion and the pollen hoarding behavioral syndrome of the honeybee (Apis mellifera L.).

Honeybees selected for the colony level phenotype of storing large quantities of pollen (pollen hoarding) in the nest exhibit greater walking activity than those selected against pollen hoarding. In this study, we use a simple walking assay to demonstrate that walking activity increases with the proportion of high pollen-hoarding alleles in pure and backcrossed strains of bees (high-strain bees > offspring generated from a high backcross > offspring generated from a low backcross > low-strain bees). The trait is heritable but is not associated with markers linked to three quantitative trait loci (QTL) mapped for their effects on pollen hoarding with demonstrated pleiotropic effects on pollen and nectar foraging and learning behavior. However, locomotion in non-selected bees is correlated with responsiveness to sucrose, a trait that correlates with foraging and learning behavior. We propose that pollen-hoarding behavior involves a syndrome of behavioral traits with complex genetic and regulatory architectures that span sensory sensitivity, foraging behavior, and learning. We propose that locomotor activity is the component of this syndrome and reflects the early maturation of the bees that become pollen foragers.

Animals↗

PubMed2026

Esketamine multi-omic biomarker evaluation in major depressive disorder (EMBER-MDD): concept, objectives and methodologies of a non-clinical investigator-initiated study.

Treatment resistance (TR) in major depressive disorder (MDD) affects a substantial minority of patients and is hard to recognize early, delaying intensified care. The Esketamine multi-omic biomarker evaluation in MDD (EMBER-MDD) is a non-interventional, investigator-initiated, in-vitro study within the EU Psych-STRATA programme, analyzing biospecimens collected in the randomized INTENSIFY study and the mirror OBS-TR cohort after participants complete treatment. EMBER-MDD aims to discover individual-omic and integrated multi-omic (hypothesis-free) biomarkers and signatures associated with TR risk, and molecular correlates of clinical response to esketamine nasal spray versus treatment as usual (TAU). Biomaterials will derive from approximately 420 adults with MDD (estimated n = 210 esketamine; n = 210 TAU) and include whole blood, RNA-stabilized whole blood, plasma and serum, sampled at baseline and, when feasible, during and after treatment (up to ~ 5,040 aliquots stored at - 80 °C). Genomics will use baseline DNA genotyping on Illumina Infinium GSA v3.0+MD arrays; epigenomics will profile genome-wide DNA methylation across time points using MethylationEPIC v2.0; transcriptomics will employ mRNA-seq (NovaSeq X/ X Plus); and proteomics/ metabolomics will be generated using high-throughput Olink and/ or Biocrates platforms. Each layer will undergo state-of-the-art preprocessing and analyses (e.g., GWAS/ PRS, EWAS, differential expression, WGCNA, pathway and network analyses), followed by integrative strategies including QTL mapping (meQTL/ eQTL/ pQTL/ mQTL) and intermediate-fusion machine learning with nested cross-validation, explainable AI (SHAP/ LIME) and treatment-effect modelling. All outputs are research-only and will not support individual efficacy, tolerability, or clinical decision-making. The study will deliver robust biosignatures and mechanistic hypotheses to guide future validation and inform stratified, molecularly guided intervention strategies in subsequent prospective trials. Trial registration number: 2023-506617-21-00 and 2025-178-f-S.

Humans↗

PubMed2026

Holistic approaches for improvement of maize resistance against lodging stress: current status and future perspective.

Lodging is a major constraint in maize production, causing significant yield losses, reduced grain quality, and harvesting inefficiencies, thereby posing a serious challenge to global food security and climate-resilient agriculture. This review synthesizes current knowledge on the genetic, physiological, and agronomic determinants of maize lodging resistance and evaluates holistic strategies for improving tolerance to lodging stress. Recent advances in quantitative trait locus (QTL) mapping, genome-wide association studies (GWAS), functional gene characterization, genome editing, high-throughput phenotyping, and precision agronomy have provided powerful tools to enhance stalk biomechanics, root anchorage, and adaptive plant architecture. Integrating genomic discovery with advanced phenomics and optimized agronomic management offers a scalable framework for accelerating the development of high-yielding, lodging-resilient maize cultivars. However, critical gaps remain in understanding the genetic coordination between stalk strength and root system architecture, integrating multi-omics approaches to unravel regulatory networks, validating genome-editing interventions across diverse agro-ecologies, and developing environment-responsive predictive breeding models and cost-effective phenotyping tools, particularly for stress-prone regions. Addressing these challenges through coordinated multi-environment trials and integrative molecular-agronomic strategies will facilitate the translation of genomic discoveries into climate-resilient, high-performing maize cultivars. By consolidating molecular insights with applied breeding and management practices, this review provides a comprehensive framework that guides researchers in designing genome-informed and field-validated approaches to improve maize resistance to lodging stress and support sustainable crop production systems.

Zea mays↗

PubMed2026

Integrating genomics, multi-omics, CRISPR and speed breeding for stress-resilient vegetable legume improvement.

Vegetable legumes are nutritionally and ecologically important crops. However, their genetic improvement has not kept pace with the increasing challenges posed by climate change due to the polygenic nature of stress tolerance, narrow genetic diversity, and the persistent gap between molecular discoveries and field-level cultivar development. Although recent reviews have examined individual genomic tools or specific stress responses, a comprehensive synthesis integrating genomics-assisted breeding, multi-omics technologies, genome editing, and speed breeding within a unified crop improvement framework has been lacking. This review addresses that gap by critically evaluating how these complementary approaches can accelerate the development of stress-resilient vegetable legumes, including pea, common bean, cowpea, faba bean, cluster bean, yard-long bean, and hyacinth bean. This review synthesizes advances in QTL mapping, genome-wide association studies, transcriptomics, metabolomics, and CRISPR-based functional genomics that have identified key regulators and pathways underlying resistance to major biotic and abiotic stresses. Rather than considering these technologies independently, the review emphasizes their convergence into a systems-level breeding framework integrating genomic discovery, functional validation, predictive breeding, and accelerated generation advancement to improve breeding efficiency. Speed breeding, enabling up to seven to eight generations annually under optimized controlled-environment experimental conditions in cowpea, is discussed as a complementary strategy with genomic selection and genome editing. The review further identifies major translational bottlenecks, including transformation recalcitrance, limited genomic resources for underutilized vegetable legumes, inadequate multi-environment validation, and fragmented omics integration, and presents an integrated systems-breeding framework to bridge the gap between gene discovery and cultivar development.

Fabaceae↗

PubMed2006

QTL analysis of behavioral and morphological differentiation between wild and laboratory zebrafish (Danio rerio).

The zebrafish is an important model organism for neuro-anatomy and developmental genetics. It also offers opportunities for investigating the functional and evolutionary genetics of behaviour but these have yet to be exploited. The ecology of anti-predator behaviour has been widely studied in fish and has been shown to vary among populations and between wild and domesticated (laboratory) fish. Here, we utilise the strong behavioural differences present between a wild-derived strain of fish from Bangladesh and the laboratory strain AB. In total, 184 F2 fish were generated and tested for shoaling tendency and willingness to approach an unfamiliar object ('boldness'). Our results indicate the existence of QTL for boldness on chromosomes 9 and 16 and suggest another genomic region that influences anti-predator behaviour on chromosome 21. QTL for growth rate, weight and fat content, all of which are elevated in laboratory fish, were detected on chromosome 23. These initial results confirm the potential for QTL mapping of behavioural traits in zebrafish and also for dissecting the consequences of selection during domestication.

Animals↗

PubMed2005

Polyploidy, evolutionary opportunity, and crop adaptation.

The finding that even the smallest of plant genomes has incurred multiple genome-wide chromatin duplication events, some of which may predate the origins of the angiosperms and therefore shape all of flowering plant biology, adds new importance to the molecular analysis of polyploidization/diploidization cycles and their phenotypic consequences. Early clues as to the possible phenotypic consequences of polyploidy derive from recent QTL mapping efforts in a number of diverse crop plants of recent and well-defined polyploid origins. A small sampling examples of the role(s) of polyploidy in conferring crop adaptation from human needs include examples of (1) dosage effects of multiple alleles in autopolyploids, and (2) 'intergenomic heterosis' conferring novel traits or transgressive levels of existing traits, associated with merging divergent genomes in a common allopolyploid nucleus. A particularly interesting manifestation of #2 is the evolution of complementary alleles at corresponding ('homoeologous') loci in divergent polyploid taxa derived from a common ancestor. Burgeoning genomic data for both botanical models and major crops offer new avenues for investigation of the molecular and phenotypic consequences of polyploidy, promising new insights into the role of this important process in the evolution of botanical diversity.

Adaptation, Biological↗

PubMed2026

Molecular mechanisms underlying low glycemic index in rice: Insights from Indian landrace diversity.

The rising prevalence of diabetes mellitus, especially among populations with high rice consumption, underscores the need for functional staple crops with a low glycemic index (GI). This review examines the molecular and genetic factors influencing low-GI traits in rice, highlighting the importance of diversity within Indian landraces. Traditional cultivars like Mappillai Samba, Karuppu Kavuni and Kattuyanam contains high level of Resistant starch, dietary fiber and bioactive phytochemicals. The Waxy (Wx) gene, which codes for granule-bound starch synthase I (GBSSI), is very important for controlling the production of amylose. For example, functional alleles like Wxa and Wxlv are linked to higher amylose levels and lower starch digestibility. Moreover, secondary metabolites, such as anthocyanins and phytosterols like stigmasterol, play a role in regulating blood sugar levels by stopping the activities of α-amylase and α-glucosidase. Interactions within the starch-dietary matrix, including starch-protein, starch-lipid, and starch-polyphenol complexes, further influence enzymatic hydrolysis and glucose release kinetics. Recent advancements in genomics, encompassing QTL mapping and gene editing techniques, offer innovative prospects for the creation of biofortified, low-GI rice cultivars. The integration of these molecular insights into rice breeding programs can facilitate the development of low-glycemic, nutritionally enhanced rice cultivars that contribute to improved metabolic health and food security.

Oryza↗

PubMed2006

Nicotinamide nucleotide transhydrogenase: a key role in insulin secretion.

The C57BL/6J mouse displays glucose intolerance and reduced insulin secretion. QTL mapping identified Nicotinamide Nucleotide Transhydrogenase (Nnt), a nuclear-encoded mitochondrial protein thought to be involved in free radical detoxification, as a candidate gene. To investigate its functional role, we used siRNA to knock down Nnt in insulin-secreting MIN6 cells. This produced a dramatic reduction in insulin secretion and the rise in [Ca2+]i evoked by glucose, but not tolbutamide. We identified two ENU-induced point mutations in Nnt (N68K, G745D). Nnt mutant mice were glucose intolerant and secreted less insulin during a glucose tolerance test. Isolated islets showed impaired insulin secretion in response to glucose, but not to tolbutamide, and glucose failed to enhance ATP levels. Glucose utilization and production of reactive oxygen species were increased in Nnt beta cells. We hypothesize that Nnt mutations/deletion uncouple beta cell mitochondrial metabolism leading to less ATP production, enhanced KATP channel activity, and consequently impaired insulin secretion.

Adenosine Triphosphate↗

PubMed2004

Genetic analysis of inherited hydrocephalus in a rat model.

Congenital hydrocephalus is a serious neurological disorder with a diverse etiology. Although there is strong evidence for genetic causes, few genes have been identified in humans. The rodent model, the H-Tx rat, has hydrocephalus with an onset in late gestation and a complex mode of inheritance. Ventricular dilatation is associated with abnormalities in the cerebral aqueduct and subcommissural organ. Quantitative trait locus (QTL) mapping was performed on DNA from the progeny of a backcross with the non-hydrocephalic Fischer F344 strain, using DNA microsatellite markers. The hydrocephalus trait was quantified by measuring the severity of the ventricular dilatation. Four chromosomes, each with a locus for hydrocephalus (Chrs 9, 10, 11, and 17), were mapped using additional markers and DNA from four subsets of backcross progeny with allelic recombination at or near each locus. The genetic positions for the markers and the loci were located using the Ensemble Rat Genome Browser. For each chromosome studied, the interval containing the locus was examined for known rat genes and for human genes identified from human-rat homology. Genes expressed in brain and with a function associated with known causes of hydrocephalus were identified as possible candidate genes. Future studies to characterize the causative genes in this animal model will improve the understanding of genetic causes in humans.

Animals↗

PubMed2005

Correlation of susceptibility to 6-aminonicotinamide and hydrocortisone-induced cleft palate.

Our previous genome-wide Quantitative Trait Locus (QTL) mapping study using mouse A/J by C57BL/6J recombinant inbred (RI) lines suggested several chromosomal regions contain genes influencing susceptibility to phenytoin (PT)-induced cleft lip with or without cleft palate [CL(P)] and 6-aminonicotinamide (6-AN)-induced isolated cleft palate (CP). Importantly, the same chromosomal regions but different RI parental strain alleles were sometimes implicated in susceptibility to these different kinds of orofacial clefting. Here we report the susceptibility to hydrocortisone (HC)-induced CP in these RI lines. We treated pregnant females with HC and studied the incidence of CP in day 17 fetuses. RI lines showed highly correlated responses to HC and 6-AN. The A/J parental line and five RI lines showed very high levels of clefting in response to both of these teratogens. The C57BL/6J parental line and five other RI lines exhibited low incidence of CP for these teratogens. In contrast, there was no significant correlation between incidence of PT-induced CL(P) and HC-induced CP.

6-Aminonicotinamide↗

PubMed2005

Inbred mouse strain survey of sucrose intake.

Mouse strain differences for intake of sucrose and saccharin have been reported across studies, and some of these differences have been related to variants of the Tas1r3 taste receptor gene. However, several methodological concerns remain, including use of relatively few strains and/or a limited number of palatable concentrations in previous analyses. The present study examined strain differences in sucrose intake among 11 inbred (A/J, AKR/J, BALB/cJ, CBA/J, C3H/HeJ, C57BL6/J, C57BL10/J, DBA/2J, SJL/J, SWR/J, 129P3/J) and one outbred (CD-1) mouse strains across nine different sucrose concentrations (0.0001-20%) using two-bottle 24-h preference tests which controlled for sucrose concentration presentation effects, sucrose and water bottle positions, and measurement of kilocalorie intake as sucrose or chow. A/J, C57BL/6J, CD-1 and SWR/J strains consumed the greatest (11.6-22 ml) amount of sucrose, whereas the A/J, C57BL/10J, SJL/J and SWR/J strains consumed the greatest (44-56%) percentages of kilocalories as sucrose. The AKR/J, CBA/J, C3H/HeJ and DBA/2J strains consumed the least (6.9-7.9 ml) amount of sucrose, and displayed lower (20-30%) percentages of kilocalories consumed as sucrose. Whereas A/J, C57BL/6J, C57BL/10J, CD-1, SWR/J and SJL/J strains all displayed the most pronounced compensatory decreases in chow intake as the percentage of kilocalories consumed as sucrose increased, the AKR/J, C3H/HeJ and DBA/2J strains failed to significantly alter chow intake even at high sucrose concentrations. There was a paucity of significant correlations in the percentage of sucrose intake between sucrose concentrations, but percentage of sucrose intake at lower concentrations did correlate with previous descriptions of saccharin intake and variants of the Tas1r3 taste receptor gene. These data demonstrate clear mouse strain differences across a range of measures in sucrose intake across a wide range of concentrations, but caution against extrapolating between extremely high and low concentrations. The identification of strains with diverging abilities to regulate kilocalorie intake when presented with high sucrose concentrations may lead to the successful QTL mapping of this trait.

Animals↗

PubMed1998

Quantitative trait loci implicated in corpus callosum midsagittal area in mice.

The midsagittal area of the corpus callosum expressed as the percentage of the hemispheric surface is smaller in the NZB/BlNJ than in the C57BL/6By inbred strain of mice. We performed a QTL mapping analysis using 284 F2s. Two loci linked to this measure were found: the CCrSQTL1 and CCrSQTL2 at 87 and 67 centiMorgans from the centromere on chromosomes 1 and 4 respectively. The two loci interacted significantly. The total source of genetic variation contributed to 25% of the observed variance.

Animals↗

PubMed2002

Complexities in the genetic dissection of quantitative trait loci.

The analysis of complex traits, including those involved in many common diseases, has encountered significant difficulties, and, despite major efforts during the past decade, has had little success. Current advances in genomics, however, promise to change this. Recently, Steinmetz et al. used a new technique to produce the first complete quantitative trait locus (QTL) analysis of a complex trait from phenotype to gene to be published entirely in a single report. This marks a significant advance over previous QTL analyses, which took several years. The work exemplifies some of the complexities of QTL mapping and demonstrates a novel method to resolve the underlying genetic architecture of QTLs in yeast. Here we discuss this work in the general context of genetic dissection of complex traits and QTLs.

Chromosome Mapping↗

PubMed1999

AFLP genotyping and fingerprinting.

Amplified fragment length polymorphisms (AFLPs) are polymerase chain reaction (PCR)-based markers for the rapid screening of genetic diversity. AFLP methods rapidly generate hundreds of highly replicable markers from DNA of any organism; thus, they allow high-resolution genotyping of fingerprinting quality. The time and cost efficiency, replicability and resolution of AFLPs are superior or equal to those of other markers [allozymes, random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), microsatellites], except that AFLP methods primarily generate dominant rather than co-dominant markers. Because of their high replicability and ease of use, AFLP markers have emerged as a major new type of genetic marker with broad application in systematics, pathotyping, population genetics, DNA fingerprinting and quantitative trait loci (QTL) mapping.

Journal Article↗