PubMed Health⌕ Search

Biomedical subjects

P Stam

Publications and source records attributed to P Stam.

11 recordsLinked to original sources
PubMed1999

The role of ecophysiological models in QTL analysis: the example of specific leaf area in barley

Crop modelling has so far contributed little to the genetic analysis of a quantitative trait. This study illustrates how a simple model for crop phenological development, which assumes that crop development rate is affected by daily effective temperature, can assist the identification of Quantitative Trait Loci (QTLs), using specific leaf area (SLA) in barley as an example. The SLA was measured in a field experiment six times during the growing season of 94 recombinant inbred lines (RILs) derived from a cross between cultivars Prisma and Apex. Of the six measurements, one was conducted at the same physiological age for all RILs (at flowering), four were undertaken at specific chronological days prior to flowering, and the last one was taken at 14 days after flowering. When the measured SLA was directly used as the quantitative trait, one to three QTLs were detected for SLA at each measurement time. The major dwarfing gene denso segregating in the population was found to affect SLA strongly at all measurement times except at flowering. If SLA of the different RILs was corrected for differences in physiological age at the time of measurement, by the use of the crop development model, QTLs were detected for SLA at only three stages. Furthermore, the effect of the denso gene was no longer significant during the preflowering stages. The effect of the denso gene detected in the first instance was therefore the consequence of its direct effect on the duration of the preflowering period. This demonstrates the important role that crop development models can play in QTL analysis of a trait that varies with developmental stage. Potential uses of ecophysiological crop growth models in QTL analysis are briefly discussed.

Journal Article↗
PubMed1994

High resolution of quantitative traits into multiple loci via interval mapping.

A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F1 data, which fixes the joint QTL effects and the environmental error, and (b) the use of markers as cofactors, which reduces the genetic background noise. As a result, a significant increase of QTL detection power is achieved in comparison with conventional QTL mapping. The core of the method is the completion of any missing genotypic (QTL and marker) observations, which is embedded in a general and simple expectation maximization (EM) algorithm to obtain maximum likelihood estimates of the model parameters. The method is described in detail for the analysis of an F2 generation. Because of the generality of the approach, it is easily applicable to other generations, such as backcross progenies and recombinant inbred lines. An example is presented in which multiple QTLs for plant height in tomato are mapped in an F2 progeny, using additional data from the parents and their F1 progeny.

Chromosome Mapping↗
PubMed1994

Multiple alleles for tuber shape in diploid potato detected by qualitative and quantitative genetic analysis using RFLPs.

Tuber shape in potato is commonly regarded as displaying continuous variation, yet at the diploid level phenotypes can be discerned visually, having round or long tubers. Inheritance of qualitative tuber shape can be explained by a single locus Ro, round being dominant to long. With restriction fragment length polymorphisms (RFLPs) the Ro locus was mapped on chromosome 10. Tuber shape was also studied as a quantitative trait, using the length/width ratio as trait value. The estimated broad sense heritability was h2 = 0.80. The morphologically mapped Ro locus explained 75% of the genetic variation, indicating the presence of a major quantitative trait locus (QTL) at the Ro locus and minor genetic factors. RFLP alleles linked with Ro alleles were used to divide the progeny into four genotypic classes: RofemaleRomale:Rofemalero:roRomale:roro = 1:1:1:1. The recessive ro allele is identical by descent in both parents. The significantly different effects (P = 0.0157) of the non-identical alleles Rofemale and Romale provided evidence for multiallelism at the Ro locus. Linkage mapping of the Ro locus was compared with QTL mapping. Only those markers which are polymorphic in both parents allow accurate QTL mapping when genetic factors segregate from both parents. This finding applies to QTL mapping in all outbreeders without homozygous inbred strains.

Alleles↗
PubMed1993

Integration of the classical and molecular linkage maps of tomato chromosome 6.

In the past, a classical map of the tomato genome has been established that is based on linkage data from intraspecific Lycopersicon esculentum crosses. In addition, a high density molecular linkage map has recently been constructed using a L. esculentum x L. pennellii cross. As the respective maps only partially match, they provide limited information about the relative positions of classical and molecular markers. In this paper we describe the construction of an integrated linkage map of tomato chromosome 6 that shows the position of cDNA-, genomic DNA- and RAPD markers relative to 10 classical markers. Integration was achieved by using a L. esculentum line containing an introgressed chromosome 6 from L. pennellii in crosses to a variety of L. esculentum marker lines. In addition, an improved version of the classical linkage map is presented that is based on a combined analysis of new linkage data for 16 morphological markers and literature data. Unlike the classical map currently in use, the revised map reveals clustering of markers into three major groups around the yv, m-2 and c loci, respectively. Although crossing-over rates are clearly different when comparing intraspecific L. esculentum crosses with L. esculentum x L. pennellii crosses, the clusters of morphological markers on the classical map coincide with clusters of genomic- and cDNA-markers on the molecular map constructed by Tanksley and coworkers.

Chromosome Mapping↗
PubMed1988

Interpretation of UV-survival curves of Aspergillus conidiospores.

Semi-logarithmic dose-response curves for survival of UV-irradiated conidiospores of A. nidulans have an initial shoulder (at low doses) followed by a decline which becomes linear. To explain the initial shoulder and the resulting extrapolation number (log S intercept of the linear extrapolation line) a general model is presented, which includes multi-target (n) and multi-hit (h) effects and allows for the effect of initial repair and of a compound parameter k, which stands for inherent sensitivity of the spores and for dose received inside the spores. From experiments on (a) the modification of k (spore wall colour and shelter effects), (b) a repair-deficient strain (shoulderless) and (c) preincubation during which DNA-replication takes place, it is concluded that the shoulder is generated by initial repair rather than by a multi-hit nature of the cell-killing process. In experiments where k takes different values (sub a and c), notably the position of the point of intersection of the linear lines gives conclusive information. In general, the log S intercept of the linear extrapolation line cannot be used to estimate the target number.

Aspergillus nidulans↗
PubMed1981

Clonal analysis of radiation-induced translocations in stem-cell spermatogonia of normal and T70H translocation heterozygous mice.

7 T(1;13)70H/+ and 13+/+ male mice were given 2 doses of 250 rad acute X-rays separated by 24 h. The +/+ mice were analysed in 2 groups during the first meiotic division for induced translocations, on average 177 and 233 days after irradiation, and the T70H/+ mice were analysed in parallel with the second group of +/+ males. One testis was treated with normal air-drying procedures yielding a random sample of cells. The other testis was processed according to a new technique, which enable separate analysis of the various locations along the seminiferous epithelium where groups of cells are synchronously in the diakinesis-metaphase I stage of meiosis. The number of cells in such groups was estimated. Both capita epididymes were used for a sperm count. In agreement with an earlier finding, fewer induced translocations were recovered from the T70H/+ mice than from +/+ mice (10.6 versus 19.2%, air-drying technique). Estimates of the group sizes in combination with the occurrence of induced translocations yielded the following information. A synchronously moving group of diakinesis-metaphase I cells originates from, on average, 1.25 stem cells (Appendix). We found an indication for a reduction in group size by 33% when a clone originated from a stem cell carrying an induced translocation compared with a wild-type clone (see Appendix). Both, the data on group size and the sperm counts indicate that, 7 months after the irradiation, the seminiferous epithelium has not totally recovered. Final recovery seems to be slower or absent in the T70H/+ males. The data obtained from the T70H/+ heterozygotes indicate the stem-cell spermatogonia to be responsible for the reduction of the rate or translocation induction with this karyotype, either due to a reduced formation rate or due to a diminished capacity of some of the induced translocation-carrying stem cells to proliferate into a clone reaching the meiotic divisions.

Animals↗
PubMed1975

Linkage disequilibrium causing selection at a neutral locus in pooled Tribolium populations.

The role of linkage disequilibrium with respect to the changes in allele frequencies at a marker locus in newly started polymorphic populations is demonstrated using the marker locus black in Tribolium. The experiments, jointly taken, indicate that the black locus is selectively neutral, or nearly so, under the current experimental conditions. A number of possible mechanisms for selection at the neutral marker locus, i.e. a single linked or non-linked locus and a number of linked and/or non-linked loci through which selection acts, are discussed. On the basis of the experiments some of these models can be excluded, leaving three models for further evaluation: (A) a single linked fitness locus, (B) a number of linked fitness loci and (C) a number of both linked and non-linked fitness loci. The first of these models allows estimation of parameters (recombination fraction and selection coefficients). Models B and C are described in terms of heterozygosity of chromosome pairs. It is argued that in view of the history of a laboratory mutant stock, model C fits best to the experimental results.

Alleles↗