Uncovering genetic control of variation in ethanol tolerance in natural populations of yeast Saccharomyces cerevisiae is essential for understanding the evolution of fermentation, the dominant lifestyle of the species, and for improving efficiency of selection for strains with high ethanol tolerance, a character of great economic value for the brewing and biofuel industries. To date, as many as 251 genes have been predicted to be involved in influencing this character. Candidacy of these genes was determined from a tested phenotypic effect following gene knockout, from an induced change in gene function under an ethanol stress condition, or by mutagenesis. This article represents the first genomics approach for dissecting genetic variation in ethanol tolerance between two yeast strains with a highly divergent trait phenotype. We developed a simple but reliable experimental protocol for scoring the phenotype and a set of STR/SNP markers evenly covering the whole genome.We created a mapping population comprising 319 segregants from crossing the parental strains. On the basis of the data sets, we find that the tolerance trait has a high heritability and that additive genetic variance dominates genetic variation of the trait. Segregation at five QTL detected has explained ~50% of phenotypic variation; in particular, the major QTL mapped on yeast chromosome 9 has accounted for a quarter of the phenotypic variation. We integrated the QTL analysis with the predicted candidacy of ethanol resistance genes and found that only a few of these candidates fall in the QTL regions.

Purpose: Reduced expression of the transforming growth factor ? receptor type II (TGF ? RII), a key inhibitor of epithelial cell growth and tumor suppressor gene, was reported frequently in many types of tumors including nonsmall cell lung cancer (NSCLC). This study explored the significance of the TGF RII gene in NSCLC carcinogenesis. Experimental Design: With 43 independent pairs of tumor and paracarcinoma tissue samples from patients with primary NSCLC, we carried out PCR-denaturing gradient gel electrophoresis screening for DNA variants over the coding sequence of the TGF ? RII gene, immunohistochemical assay of TGF ? RII expression, methylation-specific PCR analysis, and semiquantitative reverse transcription-PCR.

Linkage analysis in autotetraploid species has been an historical challenge in quantitative genetics theory and is a stumbling block that urgently needs to be removed in the rapidly emerging genome research on this species, such as cultivated potato. This article presents theory of a full model of tetrasomic linkage and develops a statistical framework for the linkage analysis. The model considers both double reduction and recombination, the most essential features of tetrasomic inheritance with linked loci, whereas the statistical method takes appropriate account of the major complexities in analyzing both dominant and codominant molecular marker data during map reconstruction in tetraploid species. These complexities include the problems arising from multiple dosage of allelic inheritance, the null allele, allelic segregation distortion, mixed bivalent and quadrivalent pairing in meiosis, and incomplete information of marker phenotype data. The theoretical analysis established the relationship between the coefficients of double reduction at linked loci, which is essential in the present tetrasomiclinkage analysis and in assessing the impact of double reduction on the evolution of tetraploid populations. The statistical method, based on the combination of theoretical analysis and a computerbased algorithm, provided analytical tools for predicting the maximum-likelihood estimates of the model parameters. A simulation study showed the feasibility of a practical implementation of the method, detailed the procedure of the analysis, validated the power and reliability in the parameter estimation, and compared the present method with those proposed in the current literature.

An international consortium has launched the whole-genome sequencing of potato, the fourth most important food crop in the world. Construction of genetic linkage maps is an inevitable step for taking advantage of the genome projects for the development of novel cultivars in the autotetraploid crop species. However, linkage analysis in autopolyploids, the kernel of linkage map construction, is theoretically challenging and methodologically unavailable in the current literature. We present here a theoretical analysis and a statistical method for tetrasomic linkage analysis with dominant and/or codominant molecular markers. The analysis reveals some essential properties of the tetrasomic model. The method accounts properly for double reduction and incomplete information of marker phenotype in regard to the corresponding phenotype in estimating the coefficients of double reduction and recombination frequency and in testing their significance by using the marker phenotype data. Computer simulation was developed to validate the analysis and the method and a case study with 201 AFLP and SSR markers scored on 228 full-sib individuals of autotetraploid potato is used to illustrate the utility of the method in map construction in autotetraploid species.

Gene elongation is recognized as one of the most important steps in the evolution of functional complexities of genes (Li 1997) and in the evolution of new genes (Long et al. 2003). Zhang (2000) calculated the mean and median of the proteins from 22 species including several representative organisms such as Escherichia coli, yeast, nematode, Drosophila, humans, and Arabidopsis of which the genome sequence information was available at the time. He observed that orthologous genes are longer in eukaryotes than in prokaryotes and that eukaryote-specific proteins are longer on average than prokaryote-specific proteins. Wang, Hsieh, and Li (2005) analyzed orthologous protein data in detail by reconstructing the ancestral states among the eukaryotes under question. They found that proteins in yeast, nematode, Drosophila, humans, and Arabidopsis are, on average, longer than their orthologs in E. coli and observed conservation of protein sequence length across eukaryotic kingdoms. We present here a more general pattern of the size of coding sequence of prokaryotic and eukaryotic genes and show that the mean length of genic coding sequence (MLGCS) is highly conserved in prokaryotes and eukaryotes but diverges between the two kingdoms.