Wheat Landrace Genome Diversity [Genetics of Complex Traits]
Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focusing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating biparental populations was developed, mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic d...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Wingen, L. U., West, C., Leverington-Waite, M., Collier, S., Orford, S., Goram, R., Yang, C.-Y., King, J., Allen, A. M., Burridge, A., Edwards, K. J., Griffiths, S. Tags: Genetics of Complex Traits Source Type: research
X-Chromosome Control of Genome-Scale Recombination Rates in House Mice [Genetics of Complex Traits]
Sex differences in recombination are widespread in mammals, but the causes of this pattern are poorly understood. Previously, males from two interfertile subspecies of house mice, Mus musculus musculus and M. m. castaneus, were shown to exhibit a ~30% difference in their global crossover frequencies. Much of this crossover rate divergence is explained by six autosomal loci and a large-effect locus on the X chromosome. Intriguingly, the allelic effects at this X-linked locus are transgressive, with the allele conferring increased crossover rate being transmitted by the low crossover rate M. m. castaneus parent. Despite the ...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Dumont, B. L. Tags: Genetics of Complex Traits Source Type: research
Mobile Introns Shape the Genetic Diversity of Their Host Genes [Population and Evolutionary Genetics]
Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose nonrandom patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approac...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Repar, J., Warnecke, T. Tags: Population and Evolutionary Genetics Source Type: research
Role of Ectopic Gene Conversion in the Evolution of a Candida krusei Pleiotropic Drug Resistance Transporter Family [Population and Evolutionary Genetics]
In this study, we employed the eukaryotic model organism Saccharomyces cerevisiae to clone and functionally characterize all 30 alleles of an important pair of tandem-duplicated multidrug efflux pump genes, ABC1 and ABC11, from seven strains of the diploid pathogenic yeast Candida krusei. Discovery and functional characterization of their closest ancestor, C. krusei ABC12, helped elucidate the evolutionary history of the entire gene family. Our data support the proposal that the pleiotropic drug resistance (PDR) transporters Abc1p and Abc11p have evolved by concerted evolution for ~134 MY. While >90% of their seque...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Lamping, E., Zhu, J.-y., Niimi, M., Cannon, R. D. Tags: Population and Evolutionary Genetics Source Type: research
Inference of Gene Flow in the Process of Speciation: An Efficient Maximum-Likelihood Method for the Isolation-with-Initial-Migration Model [Population and Evolutionary Genetics]
This article is concerned with the isolation-with-initial-migration (IIM) model, which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to ob...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Costa, R. J., Wilkinson-Herbots, H. Tags: Population and Evolutionary Genetics Source Type: research
Requirements for Driving Antipathogen Effector Genes into Populations of Disease Vectors by Homing [Population and Evolutionary Genetics]
There is a need for new interventions against the ongoing burden of vector-borne diseases such as malaria and dengue. One suggestion has been to develop genes encoding effector molecules that block parasite development within the vector, and then use the nuclease-based homing reaction as a form of gene drive to spread those genes through target populations. If the effector gene reduces the fitness of the mosquito and does not contribute to the drive, then loss-of-function mutations in the effector will eventually replace functional copies, but protection may nonetheless persist sufficiently long to provide a public health ...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Beaghton, A., Hammond, A., Nolan, T., Crisanti, A., Godfray, H. C. J., Burt, A. Tags: Population and Evolutionary Genetics Source Type: research
Soft Selective Sweeps in Evolutionary Rescue [Population and Evolutionary Genetics]
Evolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued from extinction by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics, and the study of evolutionary rescue is critical to understanding processes ranging from species conservation to the evolution of drug and pesticide resistance. While most population-genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when ...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Wilson, B. A., Pennings, P. S., Petrov, D. A. Tags: Population and Evolutionary Genetics Source Type: research
Sequential, Divergent, and Cooperative Requirements of Foxl2a and Foxl2b in Ovary Development and Maintenance of Zebrafish [Developmental and Behavioral Genetics]
In this study, we first identified two transcript variants of foxl2a and its homologous gene foxl2b in zebrafish, and revealed their specific expression in follicular layer cells in a sequential and divergent fashion during ovary differentiation, maturation, and maintenance. Then, homozygous foxl2a mutants (foxl2a–/–) and foxl2b mutants (foxl2b–/–) were constructed and detailed comparisons, such as sex ratio, gonadal histological structure, transcriptome profiling, and dynamic expression of gonadal development-related genes, were carried out. Initial ovarian differentiation and oocyte development oc...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Yang, Y.-J., Wang, Y., Li, Z., Zhou, L., Gui, J.-F. Tags: Developmental and Behavioral Genetics Source Type: research
Genetic Basis of Melanin Pigmentation in Butterfly Wings [Developmental and Behavioral Genetics]
Despite the variety, prominence, and adaptive significance of butterfly wing patterns, surprisingly little is known about the genetic basis of wing color diversity. Even though there is intense interest in wing pattern evolution and development, the technical challenge of genetically manipulating butterflies has slowed efforts to functionally characterize color pattern development genes. To identify candidate wing pigmentation genes, we used RNA sequencing to characterize transcription across multiple stages of butterfly wing development, and between different color pattern elements, in the painted lady butterfly Vanessa c...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Zhang, L., Martin, A., Perry, M. W., van der Burg, K. R. L., Matsuoka, Y., Monteiro, A., Reed, R. D. Tags: Developmental and Behavioral Genetics Source Type: research
Transfer of Dorsoventral and Terminal Information from the Ovary to the Embryo by a Common Group of Eggshell Proteins in Drosophila [Developmental and Behavioral Genetics]
The Drosophila eggshell is an extracellular matrix that confers protection to the egg and also plays a role in transferring positional information from the ovary to pattern the embryo. Among the constituents of the Drosophila eggshell, Nasrat, Polehole, and Closca form a group of proteins related by sequence, secreted by the oocyte, and mutually required for their incorporation into the eggshell. Besides their role in eggshell integrity, Nasrat, Polehole, and Closca are also required for embryonic terminal patterning by anchoring or stabilizing Torso-like at the eggshell. Here, we show that they are also required for dorso...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Mineo, A., Furriols, M., Casanova, J. Tags: Developmental and Behavioral Genetics Source Type: research
Studies of an Androgen-Binding Protein Knockout Corroborate a Role for Salivary ABP in Mouse Communication [Developmental and Behavioral Genetics]
The house mouse Androgen-binding protein (Abp) gene family is comprised of 64 paralogs, 30 Abpa and 34 Abpbg, encoding the alpha (ABPA) and beta-gamma (ABPBG) protein subunits that are disulfide-bridged to form dimers in secretions. Only 14 Abp genes are expressed in distinct patterns in the lacrimal (11) and submandibular glands (3). We created a knockout mouse line lacking two of the three genes expressed in submandibular glands, Abpa27 and Abpbg27, by replacing them with the neomycin resistance gene. The knockout genotype (–/–) showed no Abpa27 or Abpbg27 transcripts in submandibular gland complementary DNA ...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Chung, A. G., Belone, P. M., Bimova, B. V., Karn, R. C., Laukaitis, C. M. Tags: Developmental and Behavioral Genetics Source Type: research
Endogenous RNAi Pathways Are Required in Neurons for Dauer Formation in Caenorhabditis elegans [Developmental and Behavioral Genetics]
This study highlights a mechanism whereby RNAi pathways mediate the link between environmental stress and adaptive phenotypic plasticity in animals. (Source: Genetics)
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Bharadwaj, P. S., Hall, S. E. Tags: Developmental and Behavioral Genetics Source Type: research
Editing of Mitochondrial Transcripts nad3 and cox2 by Dek10 Is Essential for Mitochondrial Function and Maize Plant Development [Cellular Genetics]
Respiration, the core of mitochondrial metabolism, depends on the function of five respiratory complexes. Many respiratory chain-related proteins are encoded by the mitochondrial genome and their RNAs undergo post-transcriptional modifications by nuclear genome-expressed factors, including pentatricopeptide repeat (PPR) proteins. Maize defective kernel 10 (dek10) is a classic mutant with small kernels and delayed development. Through positional cloning, we found that Dek10 encodes an E-subgroup PPR protein localized in mitochondria. Sequencing analysis indicated that Dek10 is responsible for the C-to-U editing at nad3-61, ...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Qi, W., Tian, Z., Lu, L., Chen, X., Chen, X., Zhang, W., Song, R. Tags: Cellular Genetics Source Type: research
Reliance of Wolbachia on High Rates of Host Proteolysis Revealed by a Genome-Wide RNAi Screen of Drosophila Cells [Cellular Genetics]
Wolbachia are gram-negative, obligate, intracellular bacteria carried by a majority of insect species worldwide. Here we use a Wolbachia-infected Drosophila cell line and genome-wide RNA interference (RNAi) screening to identify host factors that influence Wolbachia titer. By screening an RNAi library targeting 15,699 transcribed host genes, we identified 36 candidate genes that dramatically reduced Wolbachia titer and 41 that increased Wolbachia titer. Host gene knockdowns that reduced Wolbachia titer spanned a broad array of biological pathways including genes that influenced mitochondrial function and lipid metabolism. ...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: White, P. M., Serbus, L. R., Debec, A., Codina, A., Bray, W., Guichet, A., Lokey, R. S., Sullivan, W. Tags: Cellular Genetics Source Type: research
Mismatch Repair Incompatibilities in Diverse Yeast Populations [Genome Integrity and Transmission]
An elevated mutation rate can provide cells with a source of mutations to adapt to changing environments. We identified a negative epistatic interaction involving naturally occurring variants in the MLH1 and PMS1 mismatch repair (MMR) genes of Saccharomyces cerevisiae. We hypothesized that this MMR incompatibility, created through mating between divergent S. cerevisiae, yields mutator progeny that can rapidly but transiently adapt to an environmental stress. Here we analyzed the MLH1 and PMS1 genes across 1010 S. cerevisiae natural isolates spanning a wide range of ecological sources (tree exudates, Drosophila, fruits, and...
Source: Genetics - March 30, 2017 Category: Genetics & Stem Cells Authors: Bui, D. T., Friedrich, A., Al-Sweel, N., Liti, G., Schacherer, J., Aquadro, C. F., Alani, E. Tags: Genome Integrity and Transmission Source Type: research
