Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 14668406

Rank-based statistical methodologies for quantitative trait locus mapping.

Fei Zou·Brian S Yandell·Jason P Fine
View original source ↗Export metadata ↓

Abstract

This article addresses the identification of genetic loci (QTL and elsewhere) that influence nonnormal quantitative traits with focus on experimental crosses. QTL mapping is typically based on the assumption that the traits follow normal distributions, which may not be true in practice. Model-free tests have been proposed. However, nonparametric estimation of genetic effects has not been studied. We propose an estimation procedure based on the linear rank test statistics. The properties of the new procedure are compared with those of traditional likelihood-based interval mapping and regression interval mapping via simulations and a real data example. The results indicate that the nonparametric method is a competitive alternative to the existing parametric methodologies.

Explore related subjects

Crosses, GeneticLikelihood FunctionsQuantitative Trait LociJournal Article

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Fei Zou, Brian S Yandell, Jason P Fine. 2003. Rank-based statistical methodologies for quantitative trait locus mapping.. https://doi.org/10.1093/genetics%2F165.3.1599

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2004

Natural hybridization between a deciduous (Nothofagus antarctica, Nothofagaceae) and an evergreen (N. dombeyi) forest tree species: evidence from morphological and isoenzymatic traits.

BACKGROUND AND AIMS: Trees with a partial leaf-shedding pattern and other morphological features a priori considered intermediate between those of the deciduous Nothofagus antarctica (G. Forster) Oersted and the evergreen N. dombeyi (Mirb.) Oersted (Nothofagaceae) were found in natural stands. The hybridization between a deciduous and an evergreen species of Nothofagus has not been reported so far in natural communities. METHODS: The putative hybrids and the two presumed parental species were compared using 14 enzyme systems as well as shoot, leaf and reproductive morphology. KEY RESULTS: Six enzyme systems showed good resolution (MDH-B, IDH, SKDH, 6-PGDH, GOT and PGI) and in four of them (PGI, MDH-B, SKDH and 6-PGDH) the putative hybrids showed intermediate zymogram patterns between N. antarctica and N. dombeyi. Both principal coordinates analysis on isozyme data and principal components analysis (PCA) on quantitative morphological traits of shoots and leaves separated both parental species and located the putative hybrids closer to N. antarctica than to N. dombeyi. In the PCA, the number of basal cataphylls and the length : width ratio of leaves were the variables most discriminating among shoots of the three entities. The putative hybrids were intermediate between both species regarding leaf vernation, outline and venation, variation in leaf shape (length/width) with position on the parent shoot and in staminate inflorescence and cupule morphology. For other morphological traits, the putative hybrids resembled one of the parental species or differed from both species (e.g. valve morphology). CONCLUSIONS: Isoenzymatic and morphological data sets support the idea of the hybrid nature (probably F1 generation) of the semi-deciduous trees found. Nothofagus antarctica and N. dombeyi are probably more closely related than previously assumed. The relevance of pollen type in revealing evolutionary relationships between Nothofagus species is supported, and that of leaf-shedding pattern is rejected.

Crosses, Genetic↗
PubMed2004

Resistance in wheat to Fusarium infection and trichothecene formation.

The state of the art in Fusarium head blight resistance research is reviewed with reference to breeding for genetic resistance to Fusarium in wheat in practice. Fusarium graminearum and F. culmorum produce the trichothecene mycotoxin deoxynivalenol (DON). DON has phytotoxic properties and is an important aggressiveness factor in head blight. Head blight resistance in wheat is not specific for either F. graminearum or F. culmorum. Resistance components include resistance to penetration, resistance to colonization and mechanisms that influence kernel DON content. The resistance to Fusarium in wheat is a quantitative trait with relative high heritability and controlled by a few genes with major effect. A major quantitative trait locus (QTL) for head blight resistance from the Chinese variety Sumai 3 has been identified and verified by several research groups via molecular marker analysis. Research is now directed at identifying additional QTLs to make accumulation of resistance genes in elite wheat lines possible. The policy of official variety list trials may affect the head blight resistant level of future wheat varieties by excluding candidate varieties that are a too susceptible to Fusarium. A higher level of Fusarium head blight will guarantee lower risks for the farmer of crop loss due to reduced grain yield, low quality and mycotoxin contamination.

Crosses, Genetic↗
PubMed2004

Quantitative and qualitative differences in morphological traits revealed between diploid Fragaria species.

BACKGROUND AND AIMS: The aims of this investigation were to highlight the qualitative and quantitative diversity apparent between nine diploid Fragaria species and produce interspecific populations segregating for a large number of morphological characters suitable for quantitative trait loci analysis. METHODS: A qualitative comparison of eight described diploid Fragaria species was performed and measurements were taken of 23 morphological traits from 19 accessions including eight described species and one previously undescribed species. A principal components analysis was performed on 14 mathematically unrelated traits from these accessions, which partitioned the species accessions into distinct morphological groups. Interspecific crosses were performed with accessions of species that displayed significant quantitative divergence and, from these, populations that should segregate for a range of quantitative traits were raised. KEY RESULTS: Significant differences between species were observed for all 23 morphological traits quantified and three distinct groups of species accessions were observed after the principal components analysis. Interspecific crosses were performed between these groups, and F2 and backcross populations were raised that should segregate for a range of morphological characters. In addition, the study highlighted a number of distinctive morphological characters in many of the species studied. CONCLUSIONS: Diploid Fragaria species are morphologically diverse, yet remain highly interfertile, making the group an ideal model for the study of the genetic basis of phenotypic differences between species through map-based investigation using quantitative trait loci. The segregating interspecific populations raised will be ideal for such investigations and could also provide insights into the nature and extent of genome evolution within this group.

Crosses, Genetic↗