bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Candidate Genes With Flowering Time and Water-Soluble Carbohydrate Content in Lolium perenne (L.)
Authors: Skøt Leif , Humphreys Jan , Humphreys Mervyn O , Thorogood Danny , Gallagher Joe , Sanderson Ruth , Armstead Ian P , Thomas Ian D 
Published: July 2007

Abstract
We describe a candidate gene approach for associating SNPs with variation in flowering time and water-soluble carbohydrate (WSC) content and other quality traits in the temperate forage grass species Lolium perenne. Three analysis methods were used, which took the significant population structure into account. First, a linear mixed model was used enabling a structured association analysis to be incorporated with the nine populations identified in the structure analysis as random variables. Second, a within-population analysis of variance was performed. Third, a tree-scanning method was used, in which haplotype trees were associated with phenotypes on the basis of inferred haplotypes. Analysis of variance within populations identified several associations between WSC, nitrogen (N), and dry matter digestibility with allelic variants within an alkaline invertase candidate gene LpcAI. These associations were only detected in material harvested in one of the two years. By contrast, consistent associations between the L. perenne homolog (LpHD1) of the rice photoperiod control gene HD1 and flowering time were identified. One SNP, in the immediate upstream region of the LpHD1 coding sequence (C-4443-A), was significant in the linear mixed model. Within-population analysis of variance and tree-scanning analysis confirmed and extended this result to the 2118 polymorphisms in some of the populations. The merits of the tree-scanning method are compared to the single SNP analysis. The potential usefulness of the 4443 SNP in marker-assisted selection is currently being evaluated in test crosses of genotypes from this work with turf-grass varieties.
Bird and Mammal Sex-Chromosome Orthologs Map to the Same Autosomal Region in a Salamander (Ambystoma)
Authors: Smith Jeramiah J , Voss S Randal 
Published: July 2007

AbstractWe tested hypotheses concerning the origin of bird and mammal sex chromosomes by mapping the location of amniote sex-chromosome loci in a salamander amphibian (Ambystoma). We found that ambystomatid orthologs of human X and chicken Z sex chromosomes map to neighboring regions of a common Ambystoma linkage group 2 (ALG2). We show statistically that the proportion of human X and chicken Z orthologs observed on ALG2 is significantly different from the proportion that would be expected by chance. We further show that conserved syntenies between ALG2 and amniote chromosomes are identified as overlapping conserved syntenies when all available chicken (N = 3120) and human (N = 14,922) RefSeq orthologs are reciprocally compared. In particular, the data suggest that chromosomal regions from chicken chromosomes (GGA) Z and 4 and from human chromosomes (HSA) 9, 4, X, 5, and 8 were linked ancestrally. A more distant outgroup comparison with the pufferfish Tetraodon nigroviridis reveals ALG2/GGAZ/HSAX syntenies among three pairs of ancestral chromosome duplicates. Overall, our results suggest that sex chromosomal regions of birds and mammals were recruited from a common ancestral chromosome, and thus our findings conflict with the currently accepted hypothesis of separate autosomal origins. We note that our results were obtained using the most immediate outgroup to the amniote clade (mammals, birds, and other reptiles) while the currently accepted hypothesis is primarily based upon conserved syntenies between in-group taxa (birds and mammals). Our study illustrates the importance of an amphibian outgroup perspective in identifying ancestral amniote gene orders and in reconstructing patterns of vertebrate sex-chromosome evolution.
On the Choice of Genetic Distance in Spatial-Genetic Studies
Authors: Fearnhead Paul 
Published: July 2007

Abstract
We look at how to choose genetic distance so as to maximize the power of detecting spatial structure. We answer this question through analyzing two population genetic models that allow for a spatially structured population in a continuous habitat. These models, like most that incorporate spatial structure, can be characterized by a separation of timescales: the history of the sample can be split into a scattering and a collecting phase, and it is only during the scattering phase that the spatial locations of the sample affect the coalescence times. Our results suggest that the optimal choice of genetic distance is based upon splitting a DNA sequence into segments and counting the number of segments at which two sequences differ. The size of these segments depends on the length of the scattering phase for the population genetic model.
Natural Variation for Alleles Under Epigenetic Control by the Maize ChromomethylaseZmet2
Authors: Makarevitch Irina , Stupar Robert M , Iniguez A Leonardo , Haun William J , Barbazuk W Brad , Kaeppler Shawn M , Springer Nathan M 
Published: July 2007

AbstractThe contribution of epigenetic alterations to natural variation for gene transcription levels remains unclear. In this study, we investigated the functional targets of the maize chromomethylase ZMET2 in multiple inbred lines to determine whether epigenetic changes conditioned by this chromomethylase are conserved or variable within the species. Gene expression microarrays were hybridized with RNA samples from the inbred lines B73 and Mo17 and from near-isogenic derivatives containing the loss-of-function allele zmet2-m1. A set of 126 genes that displayed statistically significant differential expression in zmet2 mutants relative to wild-type plants in at least one of the two genetic backgrounds was identified. Analysis of the transcript levels in both wild-type and mutant individuals revealed that only 10% of these genes were affected in zmet2 mutants in both B73 and Mo17 genetic backgrounds. Over 80% of the genes with expression patterns affected by zmet2 mutations display variation for gene expression between wild-type B73 and Mo17 plants. Further analysis was performed for 7 genes that were transcriptionally silent in wild-type B73, but expressed in B73 zmet2-m1, wild-type Mo17, and Mo17 zmet2-m1 lines. Mapping experiments confirmed that the expression differences in wild-type B73 relative to Mo17 inbreds for these genes were caused by cis-acting regulatory variation. Methylation-sensitive PCR and bisulfite sequencing demonstrated that for 5 of these genes the CpNpG methylation in the wild-type B73 genetic background was substantially decreased in the B73 zmet2-m1 mutant and in wild-type Mo17. A survey of eight maize inbreds reveals that each of these 5 genes exhibit transcriptionally silent and methylated states in some inbred lines and unmethylated, expressed states in other inbreds, providing evidence for natural variation in epigenetic states for some maize genes.
A Genomic Screen in Yeast Reveals Novel Aspects of Nonstop mRNA Metabolism
Authors: Wilson Marenda A , Meaux Stacie , van Hoof Ambro 
Published: July 2007

Abstract
Nonstop mRNA decay, a specific mRNA surveillance pathway, rapidly degrades transcripts that lack in-frame stop codons. The cytoplasmic exosome, a complex of 3′–5′ exoribonucleases involved in RNA degradation and processing events, degrades nonstop transcripts. To further understand how nonstop mRNAs are recognized and degraded, we performed a genomewide screen for nonessential genes that are required for nonstop mRNA decay. We identified 16 genes that affect the expression of two different nonstop reporters. Most of these genes affected the stability of a nonstop mRNA reporter. Additionally, three mutations that affected nonstop gene expression without stabilizing nonstop mRNA levels implicated the proteasome. This finding not only suggested that the proteasome may degrade proteins encoded by nonstop mRNAs, but also supported previous observations that rapid decay of nonstop mRNAs cannot fully explain the lack of the encoded proteins. Further, we show that the proteasome and Ski7p affected expression of nonstop reporter genes independently of each other. In addition, our results implicate inositol 1,3,4,5,6-pentakisphosphate as an inhibitor of nonstop mRNA decay.
Comparisons Among Two Fertile and Three Male-Sterile Mitochondrial Genomes of Maize
Authors: Allen James O , Fauron Christiane M , Minx Patrick , Roark Leah , Oddiraju Swetha , Lin Guan Ning , Meyer Louis , Sun Hui , Kim Kyung , Wang Chunyan , Du Feiyu , Xu Dong , Gibson Michael , Cifrese Jill , Clifton Sandra W , Newton Kathleen J 
Published: July 2007

Abstract
We have sequenced five distinct mitochondrial genomes in maize: two fertile cytotypes (NA and the previously reported NB) and three cytoplasmic-male-sterile cytotypes (CMS-C, CMS-S, and CMS-T). Their genome sizes range from 535,825 bp in CMS-T to 739,719 bp in CMS-C. Large duplications (0.5–120 kb) account for most of the size increases. Plastid DNA accounts for 2.3–4.6% of each mitochondrial genome. The genomes share a minimum set of 51 genes for 33 conserved proteins, three ribosomal RNAs, and 15 transfer RNAs. Numbers of duplicate genes and plastid-derived tRNAs vary among cytotypes. A high level of sequence conservation exists both within and outside of genes (1.65–7.04 substitutions/10 kb in pairwise comparisons). However, sequence losses and gains are common: integrated plastid and plasmid sequences, as well as noncoding “native” mitochondrial sequences, can be lost with no phenotypic consequence. The organization of the different maize mitochondrial genomes varies dramatically; even between the two fertile cytotypes, there are 16 rearrangements. Comparing the finished shotgun sequences of multiple mitochondrial genomes from the same species suggests which genes and open reading frames are potentially functional, including which chimeric ORFs are candidate genes for cytoplasmic male sterility. This method identified the known CMS-associated ORFs in CMS-S and CMS-T, but not in CMS-C.
Segregation Analyses of Partial Self-Incompatibility in Self and Cross Progeny of Solanum carolinense Reveal a Leaky S-Allele
Authors: Mena-Ali Jorge I , Stephenson Andrew G 
Published: July 2007

Abstract
Natural populations of self-incompatible species often exhibit marked phenotypic variation among individuals in the strength of self-incompatibility (SI). In previous studies, we found that the strength of the SI response in Solanum carolinense, a weedy invasive with RNase-mediated SI, is a plastic trait. Selfing can be particularly important for weeds and other successional species that typically undergo repeated colonization and local extinction events and whose population sizes are often small. We applied a PCR-based protocol to identify the S-alleles present in 16 maternal genotypes and their offspring and performed a two-generation greenhouse study to determine whether variation in the strength of SI is due to the existence of weak and strong S-alleles differing in their ability to recognize and reject self-pollen. We found that allele S9 sets significantly more self seed than the other S-alleles in the population we sampled and that its ability to self is not dependent on interactions with other S-alleles. Our data suggest that the observed variations in self-fertility are likely due to factors that directly influence the expression of SI by altering the translation, turnover, or activity of the S-RNase. The variability in the strength of SI among individuals that we have observed in this and our previous studies raises the possibility that plasticity in the strength of SI in S. carolinense may play a role in the colonization and establishment of this weedy species.
Meiotic Pairing and Disjunction of Mini-X Chromosomes in Drosophila Is Mediated by 240-bp rDNA Repeats and the Homolog Conjunction Proteins SNM and MNM
Authors: Thomas Sharon E , McKee Bruce D 
Published: July 2007

Abstract
In most eukaryotes, segregation of homologous chromosomes during meiosis is dependent on crossovers that occur while the homologs are intimately paired during early prophase. Crossovers generate homolog connectors known as chiasmata that are stabilized by cohesion between sister-chromatid arms. In Drosophila males, homologs pair and segregate without recombining or forming chiasmata. Stable pairing of homologs is dependent on two proteins, SNM and MNM, that associate with chromosomes throughout meiosis I until their removal at anaphase I. SNM and MNM localize to the rDNA region of the X–Y pair, which contains 240-bp repeats that have previously been shown to function as cis-acting chromosome pairing/segregation sites. Here we show that heterochromatic mini-X chromosomes lacking native rDNA but carrying transgenic 240-bp repeat arrays segregate preferentially from full-length sex chromosomes and from each other. Mini-X pairs do not form autonomous bivalents but do associate at high frequency with the X–Y bivalent to form trivalents and quadrivalents. Both disjunction of mini-X pairs and multivalent formation are dependent on the presence of SNM and MNM. These results imply that 240-bp repeats function to mediate association of sex chromosomes with SNM and MNM.
Positive Selection Near an Inversion Breakpoint on the Neo-XChromosome ofDrosophila americana
Authors: Evans Amy L , Mena Paulina A , McAllister Bryant F 
Published: July 2007

AbstractUnique features of heteromorphic sex chromosomes are produced as a consequence of sex-linked transmission. Alternative models concerning the evolution of sex chromosomes can be classified in terms of genetic drift or positive selection being the primary mechanism of divergence between this chromosomal pair. This study examines early changes on a newly acquired chromosomal arm of the X in Drosophila americana, which was derived from a centromeric fusion between the ancestral X and previously autosomal chromosome 4 (element B). Breakpoints of a chromosomal inversion In(4)a, which is restricted to the neo-X, are identified and used to guide a sequence analysis along chromosome 4. Loci flanking the distal breakpoint exhibit patterns of sequence diversity consistent with neutral evolution, yet loci near the proximal breakpoint reveal distinct imprints of positive selection within the neo-X chromosomal class containing In(4)a. Data from six separate positions examined throughout the proximal region reveal a pattern of recent turnover driven by two independent sweeps among chromosomes with the inverted gene arrangement. Selection-mediated establishment of an extended haplotype associated with recombination-suppressing inversions on the neo-X indicates a pattern of active coadaptation apparently initiated by X-linked transmission and potentially sustained by intralocus sexual conflict.
Haplotype Inference in General Pedigrees Using the Cluster Variation Method
Authors: Albers Cornelis A , Heskes Tom , Kappen Hilbert J 
Published: July 2007

Abstract
We present CVMHAPLO, a probabilistic method for haplotyping in general pedigrees with many markers. CVMHAPLO reconstructs the haplotypes by assigning in every iteration a fixed number of the ordered genotypes with the highest marginal probability, conditioned on the marker data and ordered genotypes assigned in previous iterations. CVMHAPLO makes use of the cluster variation method (CVM) to efficiently estimate the marginal probabilities. We focused on single-nucleotide polymorphism (SNP) markers in the evaluation of our approach. In simulated data sets where exact computation was feasible, we found that the accuracy of CVMHAPLO was high and similar to that of maximum-likelihood methods. In simulated data sets where exact computation of the maximum-likelihood haplotype configuration was not feasible, the accuracy of CVMHAPLO was similar to that of state of the art Markov chain Monte Carlo (MCMC) maximum-likelihood approximations when all ordered genotypes were assigned and higher when only a subset of the ordered genotypes was assigned. CVMHAPLO was faster than the MCMC approach and provided more detailed information about the uncertainty in the inferred haplotypes. We conclude that CVMHAPLO is a practical tool for the inference of haplotypes in large complex pedigrees.
Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower
Authors: Kolkman Judith M , Berry Simon T , Leon Alberto J , Slabaugh Mary B , Tang Shunxue , Gao Wenxiang , Shintani David K , Burke John M , Knapp Steven J 
Published: July 2007

AbstractGenetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression−the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (θ = 0.0094) than wild populations (θ = 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome (∼3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping.
Structure/Function Analysis of the Phosphatidylinositol-3-Kinase Domain of Yeast Tra1
Authors: Mutiu A Irina , Hoke Stephen M T , Genereaux Julie , Hannam Carol , MacKenzie Katherine , Jobin-Robitaille Olivier , Guzzo Julie , Côté Jacques , Andrews Brenda , Haniford David B , Brandl Christopher J 
Published: July 2007

Abstract
Tra1 is an essential component of the Saccharomyces cerevisiae SAGA and NuA4 complexes. Using targeted mutagenesis, we identified residues within its C-terminal phosphatidylinositol-3-kinase (PI3K) domain that are required for function. The phenotypes of tra1-P3408A, S3463A, and SRR3413-3415AAA included temperature sensitivity and reduced growth in media containing 6% ethanol or calcofluor white or depleted of phosphate. These alleles resulted in a twofold or greater change in expression of ∼7% of yeast genes in rich media and reduced activation of PHO5 and ADH2 promoters. Tra1-SRR3413 associated with components of both the NuA4 and SAGA complexes and with the Gal4 transcriptional activation domain similar to wild-type protein. Tra1-SRR3413 was recruited to the PHO5 promoter in vivo but gave rise to decreased relative amounts of acetylated histone H3 and histone H4 at SAGA and NuA4 regulated promoters. Distinct from other components of these complexes, tra1-SRR3413 resulted in generation-dependent telomere shortening and synthetic slow growth in combination with deletions of a number of genes with roles in membrane-related processes. While the tra1 alleles have some phenotypic similarities with deletions of SAGA and NuA4 components, their distinct nature may arise from the simultaneous alteration of SAGA and NuA4 functions.
Genomewide Discovery and Classification of Candidate Ovarian Fertility Genes in the Mouse
Authors: Gallardo Teresa D , John George B , Shirley Lane , Contreras Cristina M , Akbay Esra A , Haynie J Marshall , Ward Samuel E , Shidler Meredith J , Castrillon Diego H 
Published: July 2007

AbstractFemale infertility syndromes are among the most prevalent chronic health disorders in women, but their genetic basis remains unknown because of uncertainty regarding the number and identity of ovarian factors controlling the assembly, preservation, and maturation of ovarian follicles. To systematically discover ovarian fertility genes en masse, we employed a mouse model (Foxo3) in which follicles are assembled normally but then undergo synchronous activation. We developed a microarray-based approach for the systematic discovery of tissue-specific genes and, by applying it to Foxo3 ovaries and other samples, defined a surprisingly large set of ovarian factors (n = 348, ∼1% of the mouse genome). This set included the vast majority of known ovarian factors, 44% of which when mutated produce female sterility phenotypes, but most were novel. Comparative profiling of other tissues, including microdissected oocytes and somatic cells, revealed distinct gene classes and provided new insights into oogenesis and ovarian function, demonstrating the utility of our approach for tissue-specific gene discovery. This study will thus facilitate comprehensive analyses of follicle development, ovarian function, and female infertility.
Distinctly Different Sex Ratios in African and European Populations ofDrosophila melanogasterInferred From Chromosomewide Single Nucleotide Polymorphism Data
Authors: Hutter Stephan , Li Haipeng , Beisswanger Steffen , De Lorenzo David , Stephan Wolfgang 
Published: July 2007

AbstractIt has been hypothesized that the ratio of X-linked to autosomal sequence diversity is influenced by unequal sex ratios in Drosophila melanogaster populations. We conducted a genome scan of single nucleotide polymorphism (SNP) of 378 autosomal loci in a derived European population and of a subset of 53 loci in an ancestral African population. On the basis of these data and our already available X-linked data, we used a coalescent-based maximum-likelihood method to estimate sex ratios and demographic histories simultaneously for both populations. We confirm our previous findings that the African population experienced a population size expansion while the European population suffered a population size bottleneck. Our analysis also indicates that the female population size in Africa is larger than or equal to the male population size. In contrast, the European population shows a huge excess of males. This unequal sex ratio and the bottleneck alone, however, cannot account for the overly strong decrease of X-linked diversity in the European population (compared to the reduction on the autosome). The patterns of the frequency spectrum and the levels of linkage disequilibrium observed in Europe suggest that, in addition, positive selection must have acted in the derived population.
Reduced Levels of Su(var)3-9 But Not Su(var)2-5 (HP1) Counteract the Effects on Chromatin Structure and Viability in Loss-of-Function Mutants of the JIL-1 Histone H3S10 Kinase
Authors: Deng Huai , Bao Xiaomin , Zhang Weiguo , Girton Jack , Johansen Jørgen , Johansen Kristen M 
Published: July 2007

Abstract
It has recently been demonstrated that activity of the essential JIL-1 histone H3S10 kinase is a major regulator of chromatin structure and that it functions to maintain euchromatic domains while counteracting heterochromatization and gene silencing. In the absence of JIL-1 kinase activity, the major heterochromatin markers histone H3K9me2 and HP1 spread in tandem to ectopic locations on the chromosome arms. In this study, we show that the lethality as well as some of the chromosome morphology defects associated with the null JIL-1 phenotype to a large degree can be rescued by reducing the dose of the Su(var)3-9 gene. This effect was observed with three different alleles of Su(var)3-9, strongly suggesting it is specific to Su(var)3-9 and not to second site modifiers. This is in contrast to similar experiments performed with alleles of the Su(var)2-5 gene that codes for HP1 in Drosophila where no genetic interactions were detectable between JIL-1 and Su(var)2-5. Taken together, these findings indicate that while Su(var)3-9 histone methyltransferase activity is a major factor in the lethality and chromatin structure perturbations associated with loss of the JIL-1 histone H3S10 kinase, these effects are likely to be uncoupled from HP1.