Quantitative traits are shaped by networks of pleiotropic genes . To understand the mechanisms that maintain genetic variation for quantitative traits in natural populations and to predict responses to artificial and natural selection, we must evaluate pleiotropic effects of underlying quantitative trait genes and define functional allelic variation at the level of quantitative trait nucleotide...

New alleles are constantly accumulated during intentional crop selection. The molecular understanding of these alleles has stimulated new genomic approaches to mapping quantitative trait loci (QTL) and haplotype multiplicity of the genes concerned. A limited number of quantitative trait nucleotides responsible for QTL variation have been described, but an acceleration in their rate of discovery...

An F2 Japanese quail population was developed by crossing two strains (wild and white) to map quantitative trait loci (QTL) for performance and carcass traits. A total of 472 F2 birds were reared and slaughtered at 42 days of age. Performance and carcass traits were measured on all of the F2 individuals. Parental (P0), F1 and F2 individuals were genotyped with 3 microsatellites from quail chrom...

The value of anonymous genetic markers such as random DNA markers (SSRs, AFLPs, RFLPs etc.) depends for various applications on the known linkage phase between marker and target locus alleles (Lübberstedt et al. 1998). Thus, (quantitative) trait locus mapping is necessary for each cross de novo, as different subsets of QTL are polymorphic in individual populations, and linkage phases between ma...

DNA methylation plays a crucial role in establishing tissue-specific gene expression. However, our incomplete understanding of the cis elements that regulate DNA methylation prevents us from interpreting the functional effects of non-coding variants. We present CpGenie (http://cpgenie.csail.mit.edu), a deep convolutional neural network that learns a regulatory sequence code of DNA methylation a...

Single nucleotide polymorphisms (SNPs) between microarray probes and RNA targets can affect the performance of expression array by weakening the hybridization. In this paper, we examined the effect of the SNPs on Affymetrix GeneChip probe set summaries and the expression quantitative trait loci (eQTL) mapping results in two eQTL datasets, one from mouse and one from human. We showed that removi...

the construction of molecular maps and identification of genomic regions controlling quantitative traits have great significance for plant breeders. in this study, a genetic analysis of quantitative trait loci (qtls) affecting the heading date of rice was performed using an f2 population of a cross between two iranian landrace cultivars, domsephid and gerdeh, comprising 192 plants. an approxima...

Circulating angiotensin-1-converting enzyme (ACE) is a highly heritable trait, and a major component of the genetic variance maps to the region of the ACE gene. The strong effect of the locus, and the interest in ACE as a candidate gene for cardiovascular disorders, has led to extensive investigation of its relationship to the ACE phenotype, providing one of the most complete examples of quanti...

Understanding the genetic underpinnings of disease is important for screening, treatment, drug development, and basic biological insight. One way of getting at such an understanding is to find out which parts of our DNA, such as single-nucleotide polymorphisms, affect particular intermediary processes such as gene expression. Naively, such associations can be identified using a simple statistic...