bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for Different Origins of Sex Chromosomes in Closely Related Oryzias Fishes: Substitution of the Master Sex-Determining Gene
Authors: Tanaka Keita , Takehana Yusuke , Naruse Kiyoshi , Hamaguchi Satoshi , Sakaizumi Mitsuru 
Published: October 2007

AbstractThe medaka Oryzias latipes and its two sister species, O. curvinotus and O. luzonensis, possess an XX–XY sex-determination system. The medaka sex-determining gene DMY has been identified on the orthologous Y chromosome [O. latipes linkage group 1 (LG1)] of O. curvinotus. However, DMY has not been discovered in other Oryzias species. These results and molecular phylogeny suggest that DMY was generated recently [∼10 million years ago (MYA)] by gene duplication of DMRT1 in a common ancestor of O. latipes and O. curvinotus. We identified seven sex-linked markers from O. luzonensis (sister species of O. curvinotus) and constructed a sex-linkage map. Surprisingly, all seven sex-linked markers were located on an autosomal linkage group (LG12) of O. latipes. As suggested by the phylogenetic tree, the sex chromosomes of O. luzonensis should be “younger” than those of O. latipes. In the lineage leading to O. luzonensis after separation from O. curvinotus ∼5 MYA, a novel sex-determining gene may have arisen and substituted for DMY. Oryzias species should provide a useful model for evolution of the master sex-determining gene and differentiation of sex chromosomes from autosomes.
Analytical Description of Mutational Effects in Competing Asexual Populations
Authors: Pinkel Daniel 
Published: October 2007

Abstract
The adaptation of a population to a new environment is a result of selection operating on a suite of stochastically occurring mutations. This article presents an analytical approach to understanding the population dynamics during adaptation, specifically addressing a system in which periods of growth are separated by selection in bottlenecks. The analysis derives simple expressions for the average properties of the evolving population, including a quantitative description of progressive narrowing of the range of selection coefficients of the predominant mutant cells and of the proportion of mutant cells as a function of time. A complete statistical description of the bottlenecks is also presented, leading to a description of the stochastic behavior of the population in terms of effective mutation times. The effective mutation times are related to the actual mutation times by calculable probability distributions, similar to the selection coefficients being highly restricted in their probable values. This analytical approach is used to model recently published experimental data from a bacterial coculture experiment, and the results are compared to those of a numerical model published in conjunction with the data. Finally, experimental designs that may improve measurements of fitness distributions are suggested.
Linkage Mapping of Domestication Loci in a Large Maize–Teosinte Backcross Resource
Authors: Briggs William H , McMullen Michael D , Gaut Brandon S , Doebley John 
Published: October 2007

Abstract
An ultimate objective of QTL mapping is cloning genes responsible for quantitative traits. However, projects seldom go beyond segments &lt;5 cM without subsequent breeding and genotyping lines to identify additional crossovers in a genomic region of interest. We report on a QTL analysis performed as a preliminary step in the development of a resource for map-based cloning of domestication and improvement genes in corn. A large backcross (BC)1 population derived from a cross between maize (Zea mays ssp. mays) and teosinte (ssp. parviglumis) was grown for the analysis. A total of 1749 progenies were genotyped for 304 markers and measured for 22 morphological traits. The results are in agreement with earlier studies showing a small number of genomic regions having greater impact on the morphological traits distinguishing maize and teosinte. Despite considerable power to detect epistasis, few QTL interactions were identified. To create a permanent resource, seed of BC1 plants was archived and 1000 BC2S6 BC1-derived lines are in development for fine mapping and cloning. The identification of four BC1 progeny with crossovers in a single gene, tb1, indicated that enough derived lines already exist to clone many QTL without the need to generate and identify additional crossovers.
A Semiparametric Approach for Composite Functional Mapping of Dynamic Quantitative Traits
Authors: Yang Runqing , Gao Huijiang , Wang Xin , Zhang Ji , Zeng Zhao-Bang , Wu Rongling 
Published: October 2007

Abstract
Functional mapping has emerged as a powerful tool for mapping quantitative trait loci (QTL) that control developmental patterns of complex dynamic traits. Original functional mapping has been constructed within the context of simple interval mapping, without consideration of separate multiple linked QTL for a dynamic trait. In this article, we present a statistical framework for mapping QTL that affect dynamic traits by capitalizing on the strengths of functional mapping and composite interval mapping. Within this so-called composite functional-mapping framework, functional mapping models the time-dependent genetic effects of a QTL tested within a marker interval using a biologically meaningful parametric function, whereas composite interval mapping models the time-dependent genetic effects of the markers outside the test interval to control the genome background using a flexible nonparametric approach based on Legendre polynomials. Such a semiparametric framework was formulated by a maximum-likelihood model and implemented with the EM algorithm, allowing for the estimation and the test of the mathematical parameters that define the QTL effects and the regression coefficients of the Legendre polynomials that describe the marker effects. Simulation studies were performed to investigate the statistical behavior of composite functional mapping and compare its advantage in separating multiple linked QTL as compared to functional mapping. We used the new mapping approach to analyze a genetic mapping example in rice, leading to the identification of multiple QTL, some of which are linked on the same chromosome, that control the developmental trajectory of leaf age.
Interspecific Recombinant Congenic Strains Between C57BL/6 and Mice of the Mus spretus Species: A Powerful Tool to Dissect Genetic Control of Complex Traits
Authors: Burgio Gaëtan , Szatanik Marek , Guénet Jean-Louis , Arnau Maria-Rosa , Panthier Jean-Jacques , Montagutelli Xavier 
Published: October 2007

Abstract
Complex traits are under the genetic control of multiple genes, often with weak effects and strong epistatic interactions. We developed two new collections of mouse strains to improve genetic dissection of complex traits. They are derived from several backcrosses of the Mus spretus SEG/Pas or STF/Pas strains on the C57BL/6J background. Each of the 55 interspecific recombinant congenic strains (IRCSs) carries up to eight SEG/Pas chromosomal segments with an average size of 11.7 Mb, totalizing 1.37% of the genome. The complete series covers 39.7% of the SEG/Pas genome. As a complementary resource, six partial or complete interspecific consomic strains were developed and increased genome coverage to 45.6%. To evaluate the usefulness of these strains for QTL mapping, 16 IRCSs were compared with C57BL/6J for seven hematological parameters. Strain 66H, which carries three SEG/Pas chromosomal segments, had lower red blood cell volume and higher platelet count than C57BL/6J. Each chromosomal segment was isolated in a congenic strain to evaluate individual effects. Congenic strains were combined to assess epistasis. Our data show that both traits were controlled by several genes with complex epistatic interactions. IRCSs are therefore useful to unravel QTL with small effects and gene-by-gene interactions.
Association Analysis of Historical Bread Wheat Germplasm Using Additive Genetic Covariance of Relatives and Population Structure
Authors: Crossa José , Burgueño Juan , Dreisigacker Susanne , Vargas Mateo , Herrera-Foessel Sybil A , Lillemo Morten , Singh Ravi P , Trethowan Richard , Warburton Marilyn , Franco Jorge , Reynolds Matthew , Crouch Jonathan H , Ortiz Rodomiro 
Published: October 2007

AbstractLinkage disequilibrium can be used for identifying associations between traits of interest and genetic markers. This study used mapped diversity array technology (DArT) markers to find associations with resistance to stem rust, leaf rust, yellow rust, and powdery mildew, plus grain yield in five historical wheat international multienvironment trials from the International Maize and Wheat Improvement Center (CIMMYT). Two linear mixed models were used to assess marker–trait associations incorporating information on population structure and covariance between relatives. An integrated map containing 813 DArT markers and 831 other markers was constructed. Several linkage disequilibrium clusters bearing multiple host plant resistance genes were found. Most of the associated markers were found in genomic regions where previous reports had found genes or quantitative trait loci (QTL) influencing the same traits, providing an independent validation of this approach. In addition, many new chromosome regions for disease resistance and grain yield were identified in the wheat genome. Phenotyping across up to 60 environments and years allowed modeling of genotype × environment interaction, thereby making possible the identification of markers contributing to both additive and additive × additive interaction effects of traits.
Msc1 Acts Through Histone H2A.Z to Promote Chromosome Stability inSchizosaccharomyces pombe
Authors: Ahmed Shakil , Dul Barbara , Qiu Xinxing , Walworth Nancy C 
Published: October 2007

AbstractAs a central component of the DNA damage checkpoint pathway, the conserved protein kinase Chk1 mediates cell cycle progression when DNA damage is generated. Msc1 was identified as a multicopy suppressor capable of facilitating survival in response to DNA damage of cells mutant for chk1. We demonstrate that loss of msc1 function results in an increased rate of chromosome loss and that an msc1 null allele exhibits genetic interactions with mutants in key kinetochore components. Multicopy expression of msc1 robustly suppresses a temperature-sensitive mutant (cnp1-1) in the centromere-specific histone H3 variant CENP-A, and localization of CENP-A to the centromere is compromised in msc1 null cells. We present several lines of evidence to suggest that Msc1 carries out its function through the histone H2A variant H2A.Z, encoded by pht1 in fission yeast. Like an msc1 mutant, a pht1 mutant also exhibits chromosome instability and genetic interactions with kinetochore mutants. Suppression of cnp1-1 by multicopy msc1 requires pht1. Likewise, suppression of the DNA damage sensitivity of a chk1 mutant by multicopy msc1 also requires pht1. We present the first genetic evidence that histone H2A.Z may participate in centromere function in fission yeast and propose that Msc1 acts through H2A.Z to promote chromosome stability and cell survival following DNA damage.
The Formation of the Central Element of the Synaptonemal Complex May Occur by Multiple Mechanisms: The Roles of the N- and C-Terminal Domains of the Drosophila C(3)G Protein in Mediating Synapsis and Recombination
Authors: Jeffress Jennifer K , Page Scott L , Royer Suzanne M , Belden Elizabeth D , Blumenstiel Justin P , Anderson Lorinda K , Hawley R Scott 
Published: October 2007

Abstract
In Drosophila melanogaster oocytes, the C(3)G protein comprises the transverse filaments (TFs) of the synaptonemal complex (SC). Like other TF proteins, such as Zip1p in yeast and SCP1 in mammals, C(3)G is composed of a central coiled-coil-rich domain flanked by N- and C-terminal globular domains. Here, we analyze in-frame deletions within the N- and C-terminal regions of C(3)G in Drosophila oocytes. As is the case for Zip1p, a C-terminal deletion of C(3)G fails to attach to the lateral elements of the SC. Instead, this C-terminal deletion protein forms a large cylindrical polycomplex structure. EM analysis of this structure reveals a polycomplex of concentric rings alternating dark and light bands. However, unlike both yeast and mammals, all three proteins deleted for N-terminal regions completely abolished both SC and polycomplex formation. Both the N- and C-terminal deletions significantly reduce or abolish meiotic recombination similarly to c(3)G null homozygotes. To explain these data, we propose that in Drosophila the N terminus, but not the C-terminal globular domain, of C(3)G is critical for the formation of antiparallel pairs of C(3)G homodimers that span the central region and thus for assembly of complete TFs, while the C terminus is required to affix these homodimers to the lateral elements.
Sex-Specific Splicing of the HoneybeedoublesexGene Reveals 300 Million Years of Evolution at the Bottom of the Insect Sex-Determination Pathway
Authors: Cho Soochin , Huang Zachary Y , Zhang Jianzhi 
Published: October 2007

AbstractSex-determination mechanisms vary greatly among taxa. It has been proposed that genetic sex-determination pathways evolve in reverse order from the final step in the pathway to the first step. Consistent with this hypothesis, doublesex (dsx), the most downstream gene in the Drosophila sex-determination cascade that determines most sexual phenotypes also determines sex in other dipterans and the silk moth, while the upstream genes vary among these species. However, it is unknown when dsx was recruited to the sex-determination pathway during insect evolution. Furthermore, sex-specific splicing of dsx, by which dsx determines sex, is different in pattern and mechanism between the moth and the fly, raising an interesting question of how these insects have kept the executor of sex determination while allowing flexibility in the means of execution. To address these questions, here we study the dsx gene of the honeybee Apis mellifera, a member of the most basal lineage of holometabolous insects. We report that honeybee dsx is sex-specifically spliced and that it produces both the fly-type and moth-type splicing forms, indicating that the use of different splicing forms of Dsx in controlling sexual differentiation was present in the common ancestor of holometabolous insects. Our data suggest that in ancestral holometabolous insects the female Dsx form is the default and the male form is generated by suppressing the splicing of the female form. Thus, it is likely that the dsx splicing activator system in flies, where the male form is the default, arose during early dipteran evolution.
Circadian Rhythm Gene Regulation in the Housefly Musca domestica
Authors: Codd Veryan , Dolezel David , Stehlik Jan , Piccin Alberto , Garner Karen J , Racey Seth N , Straatman Kornelis R , Louis Edward J , Costa Rodolfo , Sauman Ivo , Kyriacou Charalambos P , Rosato Ezio 
Published: October 2007

Abstract
The circadian mechanism appears remarkably conserved between Drosophila and mammals, with basic underlying negative and positive feedback loops, cycling gene products, and temporally regulated nuclear transport involving a few key proteins. One of these negative regulators is PERIOD, which in Drosophila shows very similar temporal and spatial regulation to TIMELESS. Surprisingly, we observe that in the housefly, Musca domestica, PER does not cycle in Western blots of head extracts, in contrast to the TIM protein. Furthermore, immunocytochemical (ICC) localization using enzymatic staining procedures reveals that PER is not localized to the nucleus of any neurons within the brain at any circadian time, as recently observed for several nondipteran insects. However, with confocal analysis, immunofluorescence reveals a very different picture and provides an initial comparison of PER/TIM-containing cells in Musca and Drosophila, which shows some significant differences, but many similarities. Thus, even in closely related Diptera, there is considerable evolutionary flexibility in the number and spatial organization of clock cells and, indeed, in the expression patterns of clock products in these cells, although the underlying framework is similar.
Ninety-Six Haploid Yeast Strains With Individual Disruptions of Open Reading Frames Between YOR097C and YOR192C, Constructed for the Saccharomyces Genome Deletion Project, Have an Additional Mutation in the Mismatch Repair Gene MSH3
Authors: Lehner Kevin R , Stone Megan M , Farber Rosann A , Petes Thomas D 
Published: October 2007

Abstract
As part of the Saccharomyces Genome Deletion Project, sets of presumably isogenic haploid and diploid strains that differed only by single gene deletions were constructed. We found that one set of 96 strains (containing deletions of ORFs located between YOR097C and YOR192C) in the collection, which was derived from the haploid BY4741, has an additional mutation in the MSH3 mismatch repair gene.
Molecular Phylogeography of Domesticated Barley Traces Expansion of Agriculture in the Old World
Authors: Saisho Daisuke , Purugganan Michael D 
Published: October 2007

Abstract
Barley (Hordeum vulgare ssp. vulgare) was first cultivated 10,500 years ago in the Fertile Crescent and is one of the founder crops of Eurasian agriculture. Phylogeographic analysis of five nuclear loci and morphological assessment of two traits in &gt;250 domesticated barley accessions reveal that landraces found in South and East Asia are genetically distinct from those in Europe and North Africa. A Bayesian population structure assessment method indicates that barley accessions are subdivided into six clusters and that barley landraces from 10 different geographical regions of Eurasia and North Africa show distinct patterns of distribution across these clusters. Using haplotype frequency data, it appears that the Europe/North Africa landraces are most similar to the Near East population (FST = 0.15) as well as to wild barley (FST = 0.11) and are strongly differentiated from all other Asian populations (FST = 0.34–0.74). A neighbor-joining analysis using these FST estimates also supports a division between European, North African, and Near East barley types from more easterly Asian accessions. There is also differentiation in the presence of a naked caryopsis and spikelet row number between eastern and western barley accessions. The data support the differential migration of barley from two domestication events that led to the origin of barley—one in the Fertile Crescent and another farther east, possibly at the eastern edge of the Iranian Plateau—with European and North African barley largely originating from the former and much of Asian barley arising from the latter. This suggests that cultural diffusion or independent innovation is responsible for the expansion of agriculture to areas of South and East Asia during the Neolithic revolution.
A New Method for Haplotype Inference Including Full-Sib Information
Authors: Ding Xiang Dong , Simianer Henner , Zhang Qin 
Published: October 2007

Abstract
Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families, can be an alternative strategy in determining linkage phase and estimating haplotype frequencies. In the case of no possibility to obtain genotypes for parents, and only full-sib information being used, a new approach is suggested to infer phase and to reconstruct haplotypes. We present a maximum-likelihood method via an expectation-maximization algorithm, called FSHAP, using only full-sib information when parent information is not available. FSHAP can deal with families with an arbitrary number of children, and missing parents or missing genotypes can be handled as well. In a simulation study we compare FSHAP with another existing expectation-maximization (EM)-based approach (FAMHAP), the conditioning approach implemented in FBAT and GENEHUNTER, which is only pedigree based and assumes linkage equilibrium. In most situations, FSHAP has the smallest discrepancy of haplotype frequency estimation and the lowest error rate in haplotype reconstruction, only in some cases FAMHAP yields comparable results. GENEHUNTER produces the largest discrepancy, and FBAT produces the highest error rate in offspring in most situations. Among the methods compared, FSHAP has the highest accuracy in reconstructing the diplotypes of the unavailable parents. Potential limitations of the method, e.g., in analyzing very large haplotypes, are indicated and possible solutions are discussed.
Evolution of Fitnesses and Allele Frequencies in a Population With Spatially Heterogeneous Selection Pressures
Authors: Star Bastiaan , Stoffels Rick J , Spencer Hamish G 
Published: October 2007

Abstract
The level of gene flow considerably influences the outcome of evolutionary processes in structured populations with spatial heterogeneity in selection pressures; low levels of gene flow may allow local adaptation whereas high levels of gene flow may oppose this process thus preventing the stable maintenance of polymorphism. Indeed, proportions of fitness space that successfully maintain polymorphism are substantially larger in spatially heterogenous populations with lower to moderate levels of gene flow when compared to single-deme models. Nevertheless, the effect of spatial heterogeneity on the evolutionary construction of polymorphism is less clear. We have investigated the levels of polymorphism resulting from a simple two-deme construction model, which incorporates recurrent mutation as well as selection. We further compared fitness properties, stability of equilibria, and frequency distribution patterns emerging from the construction approach and compared these to the static fitness-space approach. The construction model either promotes or constrains the level of polymorphisms, depending on the levels of gene flow. Comparison of the fitness properties resulting from both approaches shows that they maintain variation in different parts of fitness space. The part of fitness space resulting from construction is more stable than that implied by the ahistoric fitness-space approach. Finally, the equilibrium allele-frequency distribution patterns vary substantially with different levels of gene flow, underlining the importance of correctly sampling spatial structure if these patterns are to be used to estimate population-genetic processes.
The Extent of Linkage Disequilibrium in Rice (Oryza sativa L.)
Authors: Mather Kristie A , Caicedo Ana L , Polato Nicholas R , Olsen Kenneth M , McCouch Susan , Purugganan Michael D 
Published: October 2007

Abstract
Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits using association techniques. Here we characterize LD in five 500-kb regions of the rice genome in three major cultivated rice varieties (indica, tropical japonica, and temperate japonica) and in the wild ancestor of Asian rice, Oryza rufipogon. Using unlinked SNPs to determine the amount of background linkage disequilibrium in each population, we find that the extent of LD is greatest in temperate japonica (probably &gt;500 kb), followed by tropical japonica (∼150 kb) and indica (∼75 kb). LD extends over a shorter distance in O. rufipogon (≪40 kb) than in any of the O. sativa groups assayed here. The differences in the extent of LD among these groups are consistent with differences in outcrossing and recombination rate estimates. As well as heterogeneity between groups, our results suggest variation in LD patterns among genomic regions. We demonstrate the feasibility of genomewide association mapping in cultivated Asian rice using a modest number of SNPs.