Regression has always been an important tool for quantitative geneticists. The use of maximum likelihood (ML) has been advocated for the detection of quantitative trait loci (QTL) through linkage with molecular markers, and this approach can be very effective. However, linear regression models have also been proposed which perform similarly to ML, while retaining the many beneficial features of...

Several issues pertinent to study designs employing extreme sibpairs (ESP) methods to detect complex oligogenic quantitative trait loci (QTL) are investigated in the setting of genome-wide multipoint scans. We demonstrate that when stringent alpha-levels are imposed (e.g., alpha = 0.00022 as recommended by Landers and Kruglyak), the power to detect a susceptibility locus could drop from 83.6% u...

Many plants flower in response to seasonal changes in daylength. This response often varies between accessions of a single species. We studied the variation in photoperiod response found in the model species Arabidopsis (Arabidopsis thaliana). Seventy-two accessions were grown under six daylengths varying in 2-h intervals from 6 to 16 h. The typical response was sigmoidal, so that plants flower...

Once linkage is detected to a quantitative trait locus (QTL), the next step towards localizing the gene involved may be to identify those families, or individuals, in whom the putative mutations are segregating. In this paper, we describe a jackknife procedure for identifying individuals (and families) who contribute disproportionately to the linkage. Following initial detection of linkage to a...

Bayesian shrinkage analysis is the state-of-the-art method for whole genome analysis of quantitative traits. It can estimate the genetic effects for the entire genome using a dense marker map. The technique is now called genome selection. A nice property of the shrinkage analysis is that it can estimate effects of QTL as small as explaining 2% of the phenotypic variance in a typical sample size...

We develop a mixed model approach of quantitative trait locus (QTL) mapping for a hybrid population derived from the crosses of two or more distinguished outbred populations. Under the mixed model, we treat the mean allelic value of each source population as the fixed effect and the allelic deviations from the mean as random effects so that we can partition the total genetic variance into betwe...

To mitigate the effects of heat and drought stress, a better understanding of the genetic control of physiological responses to these environmental conditions is needed. To this end, we evaluated an upland cotton (Gossypium hirsutum L.) mapping population under water-limited and well-watered conditions in a hot, arid environment. The elemental concentrations (ionome) of seed samples from the po...

Quantitative trait loci (QTL) with small effects on phenotypic variation can be difficult to detect and analyze. Because of this a large fraction of the genetic architecture of many complex traits is not well understood. Here we use sporulation efficiency in Saccharomyces cerevisiae as a model complex trait to identify and study small-effect QTL. In crosses where the large-effect quantitative t...

This article presents a method for QTL interval mapping in autotetraploid species for a full-sib family derived by crossing two parents. For each offspring, the marker information on each chromosome is used to identify possible configurations of chromosomes inherited from the two parents and the locations of crossovers on these chromosomes. A branch and bound algorithm is used to identify confi...

Association-mapping methods promise to overcome the limitations of linkage-mapping methods. The main objectives of this study were to (i) evaluate various methods for association mapping in the autogamous species wheat using an empirical data set, (ii) determine a marker-based kinship matrix using a restricted maximum-likelihood (REML) estimate of the probability of two alleles at the same locu...