Genetics, Vol. 179, June 2008, Copyright © 2008
ISSUE HIGHLIGHTS
Inferring causal phenotype networks from segregating populations, pp. 1089–1100
Elias Chaibub Neto, Christine T. Ferrara, Alan D. Attie and Brian S. Yandell
This article describes approaches for inferring causal networks among phenotypes segregating in a population. The approach builds causal direction into an undirected network of phenotypes by including causal QTL for each phenotype. This approach can be applied to inbred and outbred crosses as well as to natural populations. Simulations show that the method accurately identifies network edges and infers causal direction. The method is illustrated with an example involving gene expression and metabolite traits from experimental crosses.
Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites, pp. 965–976
Li-zhi Gao and Hideki Innan
Controversy over the origins of the Asian cultivated rice Oryza sativa from its wild ancestor O. rufipogon has centered on a monophyletic or polyphyletic origin. These authors examine microsatellite genotypes of 92 individual plants from the two O. sativa subspecies and O. rufipogon. They find that the japonica subspecies suffered a more severe bottleneck than did the indica subspecies. These results suggest that indica and japonica subspecies were not independently domesticated; the two subspecies seem to be at least partially derived from the same ancestral populations.
Recurrent deletion and gene presence/absence polymorphism: Telomere dynamics dominate DNA evolution at the tip of 3L in Drosophila melanogaster and D. simulans, pp. 1021–1027
Andrew D. Kern and David J. Begun
Drosophila melanogaster has been the subject of intensive analysis of DNA polymorphism and divergence, but little is known about the distribution of variation at the ends of chromosomes. This article reports on a survey of genetic variation on the tip of 3L in D. melanogaster and D. simulans that finds reduced levels of nucleotide polymorphism but abundant deletion polymorphism. Most surprising were frequent polymorphisms due to deletions of up to two single copy genes in the region.
Regulation of neurogenesis and epidermal growth factor receptor signaling by the insulin receptor/target of rapamycin pathway in Drosophila, pp. 843–853
Helen McNeill, Gavin M. Craig and Joseph M. Bateman
Insulin receptor (InR) signaling is a highly conserved pathway that regulates cell growth and proliferation. The authors had previously shown that this pathway, unexpectedly, is also involved in neuronal differentiation in Drosophila. They now make a novel connection between the InR and epidermal growth factor receptor (EGFR) signaling pathways. Activation of the InR pathway in photoreceptor (PR) neurons upregulates several components of the EGFR pathway, and the two pathways genetically interact in controlling PR differentiation. The significance of these findings is likely to be broad, because the highly conserved nature of these pathways means that such interactions may occur in other contexts.
Sites of recombination are local determinants of meiotic homolog pairing in Saccharomyces cerevisiae, pp. 773–784
Joshua Chang Mell, Bethany L. Wienholz, Asmaa Salem and Sean M. Burgess
How do homologous chromosomes find each other during meiosis? This study of budding yeast supports the simple idea that recombination serves to loosely coalign homologous chromosomes and locally stabilize interactions between allelic sites.
Proliferating cell nuclear antigen and ASF1 modulate silent chromatin in Saccharomyces cerevisiae via lysine 56 on histone H3, pp. 793–809
Andrew Miller, Bo Yang, Tiaunn Foster and Ann L. Kirchmaier
Post-translational modifications of histones are usually associated with transcription, but this article demonstrates that K56-acetylated histone H3 affects gene silencing in yeast through the replication factors proliferating cell nuclear antigen and RF-C and the chromatin assembly factor Asf1. Thus, defects in DNA replication factors can affect epigenetic processes even though DNA replication is not required to establish gene silencing. These findings imply that DNA damage phenotypes (of some replication fork mutants) may be caused by perturbations in replication-coupled modifications on histones.
Independent origin of sex chromosomes in two species of the genus Silene, pp. 1129–1133
Martina Mrackova, Michael Nicolas, Roman Hobza, Ioan Negrutiu, Françoise Monéger, Alexander Widmer, Boris Vyskot and Bohuslav Janousek
Several examples of differences in sex determination between related animal species are caused either by transfer of the master sex determining gene from the original sex chromosome to an autosome, or by recruitment of a new master sex determining gene. This article shows that both the sex chromosomes and the sex determining pathways of two related plant species evolved independently from different pairs of autosomes.
A mutation in the putative MLH3 endonuclease domain confers a defect in both mismatch repair and meiosis in Saccharomyces cerevisiae, pp. 747–755
K. T. Nishant, Aaron J. Plys and Eric Alani
Interference-dependent chromosome crossing over during yeast and mammalian meioses involves the mismatch repair protein homologs Msh4-Msh5 and Mlh1-Mlh3. Mlh3 contains a conserved metal binding motif found in a subset of Mlh proteins predicted to have endonuclease activities. The authors show that mutations altering this motif cause defects in meiotic spore viability and crossing over, suggesting that the putative endonuclease domain of MLH3 plays a role in mismatch repair and meiotic crossing over.
Phenotypic plasticity and genotype by environment interaction for olfactory behavior in Drosophila melanogaster, pp. 1079–1088
Deepa Sambandan, Mary Anna Carbone, Robert R. H. Anholt and Trudy F. C. Mackay
Genotype by environment interactions (GEI) confound genetic studies. It is generally not known what proportion of phenotypic variation is due to GEI and how many and which genes contribute to GEI. The authors use olfactory behavior in Drosophila as a model trait for a systematic analysis of GEI, using a combination of behavioral measurements and whole genome transcript analysis in 41 inbred lines. The authors find that a small number of genes account for extensive GEI and that GEI at the level of gene expression is correlated with GEI at the level of phenotype.
Schizosaccharomyces pombe Bub3 is dispensable for mitotic arrest following perturbed spindle formation, pp. 785–792
Yoshie Tange and Osami Niwa
The core proteins of the spindle assembly checkpoint (SAC), Mads, Bubs, and Mps1, are thought to be functionally and structurally conserved through evolution. However, this article reports that Bub3 is not required for the SAC in fission yeast. Rather, Bub3 in fission yeast functions in sister centromere association during mitosis, consistent with its localization to the kinetochore.
Related articles in Genetics:
Recurrent Deletion and Gene Presence/Absence Polymorphism: Telomere Dynamics Dominate Evolution at the Tip of 3L in Drosophila melanogaster and D. simulans
Andrew D. Kern and David J. Begun
Genetics 2008 179: 1021-1027.
Phenotypic Plasticity and Genotype by Environment Interaction for Olfactory Behavior in Drosophila melanogaster
Deepa Sambandan, Mary Anna Carbone, Robert R. H. Anholt, and Trudy F. C. Mackay
Genetics 2008 179: 1079-1088.
Inferring Causal Phenotype Networks From Segregating Populations
Elias Chaibub Neto, Christine T. Ferrara, Alan D. Attie, and Brian S. Yandell
Genetics 2008 179: 1089-1100.
Independent Origin of Sex Chromosomes in Two Species of the Genus Silene
Martina Mrackova, Michael Nicolas, Roman Hobza, Ioan Negrutiu, Françoise Monéger, Alexander Widmer, Boris Vyskot, and Bohuslav Janousek
Genetics 2008 179: 1129-1133.
A Mutation in the Putative MLH3 Endonuclease Domain Confers a Defect in Both Mismatch Repair and Meiosis in Saccharomyces cerevisiae
K. T. Nishant, Aaron J. Plys, and Eric Alani
Genetics 2008 179: 747-755.
Sites of Recombination Are Local Determinants of Meiotic Homolog Pairing in Saccharomyces cerevisiae
Joshua Chang Mell, Bethany L. Wienholz, Asmaa Salem, and Sean M. Burgess
Genetics 2008 179: 773-784.
Schizosaccharomyces pombe Bub3 Is Dispensable for Mitotic Arrest Following Perturbed Spindle Formation
Yoshie Tange and Osami Niwa
Genetics 2008 179: 785-792.
Proliferating Cell Nuclear Antigen and ASF1 Modulate Silent Chromatin in Saccharomyces cerevisiae via Lysine 56 on Histone H3
Andrew Miller, Bo Yang, Tiaunn Foster, and Ann L. Kirchmaier
Genetics 2008 179: 793-809.
Regulation of Neurogenesis and Epidermal Growth Factor Receptor Signaling by the Insulin Receptor/Target of Rapamycin Pathway in Drosophila
Helen McNeill, Gavin M. Craig, and Joseph M. Bateman
Genetics 2008 179: 843-853.
Nonindependent Domestication of the Two Rice Subspecies, Oryza sativa ssp. indica and ssp. japonica, Demonstrated by Multilocus Microsatellites
Li-zhi Gao and Hideki Innan
Genetics 2008 179: 965-976.