Main Quantitative Trait Loci Research Articles

Quantitative trait loci for susceptibility to tapeworm infection in the red flour beetle.

Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.

QTL analysis of bread-making quality in wheat using a doubled haploid population

A set of 187 doubled haploid lines derived from the cross between cvs. Courtot and Chinese Spring was explored for QTLs for three bread-making quality tests: hardness, protein content and strength of the dough (W of alveograph). The scores of the parental lines were quite different except for protein content, and the population showed a wide range of variation. About 350 molecular and biochemical markers were used to establish the genetic map, and technological criteria were evaluated in 1 to 3 years. QTL detection was performed by the ”marker regression” method. The most significant unlinked markers were used in the model as covariates, and the results were tested by bootstrap resampling. For hardness, we confirmed a previously tagged major QTL on chromosome 5DS, and two additional minor QTLs were found on chromosome 1A and 6D, respectively. For protein content two main QTLs were identified on chromosomes 1B and 6A, respectively. For W, three consistent QTLs were detected: two at the same location as those for hardness, on chromosomes 1A and 5D; the third one on chromosome 3B. Therefore, it appeared that except for the Glu-1A locus, storage protein loci were not clearly involved in the genetic control of the criteria studied in the present work. Despite the reasonable size of the population no QTL with interactive effects could be substantially established as measured. All computations were carried out using home-made programmes in Splus language, and these are available upon request.

Analysis of natural allelic variation at flowering time loci in the Landsberg erecta and Cape Verde Islands ecotypes of Arabidopsis thaliana.

We have analyzed the flowering behavior of two Arabidopsis ecotypes: the laboratory strain Landsberg erecta (Ler) and an ecotype from the tropical Cape Verde Islands (Cvi). They differ little in their flowering phenotypes and in their responses to photoperiod length changes and to vernalization treatment. However, segregating populations derived from crosses between them showed a much larger variation. An approach of quantitative trait locus (QTL) mapping in recombinant inbred lines (RILs) grown under three environments differing in day-length and/or vernalization treatment has been used to detect and locate flowering loci. Four main QTLs were identified, designated early day-length insensitive (EDI), flowering F, G, and H (FLF, FLG, and FLH, respectively), to which most of the flowering behavior differences could be attributed. To further characterize the individual loci, near isogenic lines were constructed by introgressing Cvi early alleles of EDI and FLH into the Ler genetic background. EDI-Cvi alleles produce earliness under both long- and short-day photoperiods, rendering Ler plants almost day-length neutral. In addition, RILs were selected to analyze FLF and FLG. These loci interact epistatically and RILs carrying late alleles at FLF and FLG were very responsive to vernalization and showed an increased response to photoperiod length changes. The possible role of these loci for the control of flowering is discussed in the context of the current Arabidopsis model.

Mapping genes controlling root morphology and root distribution in a doubled-haploid population of rice

A deep thick root system has been demonstrated to have a positive effect on yield of upland rice under water stress conditions. Molecular-marker-aided selection could be helpful for the improvement of root morphological traits, which are otherwise difficult to score. We studied a doubled-haploid population of 105 lines derived from an indica×japonica cross and mapped the genes controlling root morphology and distribution (root thickness, maximum root length, total root weight, deep root weight, deep root weight per tiller, and deep root to shoot ratio). Most putative QTL activity was concentrated in fairly compact regions on chromosomes 1, 2, 3, 6, 7, 8 and 9, but was widely spread on chromosome 5 and largely absent on chromosomes 4, 10, 11 and 12. Between three and six QTLs were identified on different chromosomes for each trait. Individual QTLs accounted for between 4 and 22% of the variation in the traits. Multiple QTL models accounted for between 14 and 49%. The main QTLs were common between traits, showing that it should be possible to modify several aspects of root morphology simultaneously. There was evidence of interaction between marker locations in determining QTL expression. Interacting locations were mostly on different chromosomes and showed antagonistic effects with magnitudes large enough to mask QTL detection. The comparison of QTL locations with another population showed that one to three common QTLs per trait were recovered, among which the most significant was in one or other population. These results will allow the derivation of isogenic lines introgressed with these common segments, separately in the indica and japonica backgrounds.

Regions of the Genome that Affect Agronomic Performance in Two‐Row Barley

Quantitative trait locus (QTL) main effects and QTL by environment (QTL × E) interactions for seven agronomic traits (grain yield, days to heading, days to maturity, plant height, lodging severity, kernel weight, and test weight) were investigated in a two‐row barley (Hordeum vulgare L.) cross, Harrington/TR306. A 127‐point base map was constructed from markers (mostly RFLP) scored in 146 random double‐haploid (DH) lines from the Harrington/TR306 cross. Field experiments involving the two parents and 145 random DH lines were grown in 1992 and/or 1993 at 17 locations in North America. Analysis of QTL was based on simple and composite interval mapping. Primary QTL were declared at positions where both methods gave evidence for QTL. The number of primary QTL ranged from three to six per trait, collectively explaining 34 to 52% of the genetic variance. None of these primary QTL showed major effects, but many showed effects that were consistent across environments. The addition of secondary QTL gave models that explained 39 to 80% of the genetic variance. The QTL were dispersed throughout the barley genome and some were detected in regions where QTL have been found in previous studies. Eight chromosome regions contained pleiotropic loci and/or linked clusters of loci that affected multiple traits. One region on chromosome 7 affected all traits except days to heading. This study was an intensive effort to evaluate QTL in a narrow‐base population grown in a large set of environments. The results reveal the types and distributions of QTL effects manipulated by plant breeders and provide opportunities for future testing of marker‐assisted selection.