What is a QTL? A Quantitative Trait Locus a region of the genome that is associated with an effect on a quantitative trait. Conceptually, a QTL can be a single gene, or it may be a cluster of linked genes that affect the trait. Using the methods for QTL detection to be discussed below, it is not possible to resolve the difference, and use the term “locus” to refer to a chromosomal region. Are Q...

Bayesian shrinkage analysis is arguably the state-of-the-art technique for large-scale multiple quantitative trait locus (QTL) mapping. However, when the shrinkage model does not involve indicator variables for marker inclusion, QTL detection remains heavily dependent on significance thresholds derived from phenotype permutation under the null hypothesis of no phenotype-to-genotype association....

The process of locating quantitative trait loci (QTLs) using genetic linkage maps, an ordered array of genetic markers placed along the chromosome, could be facilitated by applying e cient computer software packages. Construction of linkage maps requires that the rate of recombination be converted to distance in cM using appropriate mapping functions. However, computer software packages di er w...

A high-density genetic map is essential for comparative genomic studies and fine mapping of QTL, and can also facilitate genome sequence assembly. Here, a high density genetic map of Asian seabass was constructed with 3321 SNPs generated by sequencing 144 individuals in a F2 family. The length of the map was 1577.67 cM with an average marker interval of 0.52 cM. A high level of genomic synteny ...

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of...

Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]-a widely adapted cereal crop-we developed a nested association mapping (NAM) population using 10 diverse g...

Abstract Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum bicolor Tx7000. Using low-coverage Illumina sequencing bin-mapping...

A whole genome scan of Finnish Ayrshire was conducted to map quantitative trait loci (QTL) affecting milk production. The analysis included 12 half-sib families containing a total of 494 bulls in a granddaughter design. The families were genotyped with 150 markers to construct a 2764 cM (Haldane) male linkage map. In this study interval mapping with multiple-marker regression approach was exten...

BACKGROUND Improved genetic resolution and availability of sequenced genomes have made positional cloning of moderate-effect QTL realistic in several systems, emphasizing the need for precise and accurate derivation of positional confidence intervals (CIs) for QTL. Support interval (SI) methods based on the shape of the QTL likelihood curve have proven adequate for standard interval mapping, bu...

Body weight (BW) and carcass traits are complex and important economic traits that may benefit from the implementation of MAS. The objective of the current study was to identify QTL associated with BW and carcass traits in an experimental half-sib cross of Japanese quails selected for BW at 4 weeks of age. Body weight and carcass traits were measured in the F2 population. Total F2 individuals a...