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The North American (NA) Atlantic salmon typically has 27 pairs of chromosomes, whereas the European (EU) subspecies typically has 29. We investigated within-family recombination within three previously identified chromosome rearrangements (Ssa01p/23, Ssa08/29, and Ssa26/28) in NA Atlantic salmon by creating high-density linkage maps using a custom 50K SNP chip developed for the Saint John River aquaculture strain. Linkage maps created for individual purebred and EU hybrid parents in 10 full-sibling families averaged 14337 SNPs per cross, covering 43033 SNPs from the 50K SNP chip. Chromosomal translocation Ssa01p/23 was fixed except in one hybrid female map. In contrast, fusion Ssa08/29 was present in maps in 4 out of 10 females and 8 out of 10 males, whereas fusion Ssa26/28 was present in maps in 6 out of 10 females and 8 out of 10 males. The orientation of Ssa08/29 differed from the previous map; the short arm of the metacentric Ssa08 was fused to the centromere of the acrocentric Ssa29. We detected large regions of recombination suppression in female maps at the fusion of Ssa08 to Ssa29. This suppression may reduce the impacts of aneuploidy resulting from pairing of fused and unfused chromosomes, thereby allowing the persistence of chromosomal polymorphisms in this population. Key words: SNP array, SNP linkage map, chromosome polymorphism, recombination suppression, sex locus, Introduction Recombination between chromosomes with different structural variants can facilitate genome evolution (Bertolotti et al. 2020). Large inversions cause reduced recombination in specific areas of the genome, thereby facilitating local [...]

The purpose of this study was to study the genetic mechanism of low hydrocyanic acid (HCN) content. The segregation of HCN content trait in fresh stems and leaves was determined in the sorghum (Sorghum bicolor (L.) Moench)--sudangrass (Sorghum sudanense (Piper) Stapf) hybrid [F.sub.2] population (N = 1200), also used to detect a quantitative trait locus (QTL) for HCN content. Our hypothesis was that the additive effect of QTL was negative, showing that QTL was associated with low HCN. In the present research, a total of 11 simple sequence repeats (SSR) polymorphic primers were screened, and four SSR markers associated with low HCN content were developed based on the bulked segregant analysis method. A high-resolution genetic linkage group of the previously known qPA7-1 locus of the low HCN trait was constructed by analyzing different populations, families, and recombinants. Then, the QTL qPA7-1 of sorghum--sudangrass hybrid was fine-mapped to a 203.6 kb region between markers SORBI4G4-120 and SORBI4G4-680, and seven candidate genes for low HCN were predicted in this region based on sequence comparison with the sorghum reference genome. According to gene annotation, the candidate genes related to low HCN content may be different from those involved in the known regulation mode of sorghum dhurrin biosynthesis and metabolism. Key words: sorghum--sudangrass hybrid, low hydrocyanic acid, QTL qPA7-1, fine mapping, candidate genes Le but de cette etude etait d'examiner le determinisme genetique de la faible teneur en cyanure d'hydrogene (HCN). La segregation pour la teneur en HCN chez les tiges et feuilles fraiches a ete determinee au sein d'une population [F.sub.2] ( N = 1200) issue d'un croisement interspecifique sorgho ( Sorghum bicolor (L.) Moench)--sorgho du Soudan ( Sorghum sudanense (Piper) Stapf) ; ces memes donnees ont aussi ete employees pour detecter un QTL pour ce caractere. L'hypothese des auteurs etait que l'efet additif du QTL etait negatif, montrant que le QTL etait associe a une faible teneur en HCN. Dans le present travail, 11 marqueurs microsatellites (SSR) ont ete examines et quatre marqueurs SSR se sont reveles associes a la faible teneur en HCN par le biais d'une analyse BSA (<< bulked segregant analysis >>). Une carte genetique a haute resolution de la region qPA1-7 , deja connue comme etant associee a une faible teneur en HCN, a ete produite en analysant diferentes populations, familles et recombinants. Ensuite, le QTL qPA1-7 au sein de cet hybride sorgho--sorgho du Soudan a ete cartographie finement et logeait au sein d'un intervalle de 203,6 kb entre les marqueurs SORBI4G4-120 et SORBI4G4-680. Au sein de cette region, sept genes candidats pour la faible teneur en HCN ont ete predits sur la base de la comparaison de sequences avec le genome de reference du sorgho. Selon l'annotation de ces genes, il semblerait que les genes candidats impliques dans cette faible teneur en HCN seraient diferents de ceux impliques dans le mode connu de regulation de la synthese et du metabolisme de la dhurrine chez le sorgho. [Traduit par la Redaction] Mots-cles : hybride sorgho--sorgho du Soudan, faible teneur en cyanure d'hydrogene, QTL qPA7-1, cartographie fine, genes candidats, Introduction Sorghum--sudangrass hybrid is an annual grass of the genus Sorghum in the Poaceae family, which is derived from the cross between sorghum (Sorghum bicolor (L.) Moench, 2n = 2x [...]

Fusarium wilt, caused by Fusarium oxysporum f. sp. ricini, is the most destructive disease in castor. Host plant resistance is the best strategy for the management of wilt. Identification of molecular markers linked to wilt resistance will enhance the efficiency and effectiveness of breeding for wilt resistance. In the present study, genomic regions linked to wilt resistance were mapped using a bi-parental population of 185 [F.sub.6]-RILs and a genetically diverse panel of 300 germplasm accessions. Quantitative trait loci (QTL) analysis performed using a linkage map consisting of 1090 SNP markers identified a major QTL on chromosome 7 with an LOD score of 18.7, which explained 44% of the phenotypic variance. The association mapping performed using genotypic data from 3465 SNP loci revealed 69 significant associations (p < 1 x [10.sup.-4]) for wilt resistance. The phenotypic variance explained by the individual SNPs ranged from 0.063 to 0.210. The QTL detected in the bi-parental mapping population was not identified in the association analysis. Thus, the results of this study indicate the possibility of vast gene diversity for Fusarium wilt resistance in castor. Key words: Fusarium oxysporum f. sp. ricini, Ricinus communis L., genome-wide association study, QTL mapping, SNP markers. La flétrissure fusarienne causée par le Fusarium oxysporum f. sp. ricini est la maladie la plus importante chez le ricin. La résistance de l'hôte est la meilleure stratégie pour lutter contre la flétrissure. L'identification de marqueurs moléculaires liés à la résistance à la flétrissure permettra d'augmenter l'efficience et l'efficacité de la sélection pour la résistance à la flétrissure. Dans le présent travail, les auteurs ont tenté d'identifier des régions génomiques liées à la résistance à la flétrissure au sein d'une population biparentale composée de 185 [F.sub.6] - RIL ainsi qu'au sein d'une collection de 300 accessions. L'analyse QTL a été réalisée au moyen d'une carte génétique comprenant 1090 marqueurs SNP et a permis d'identifier un QTL majeur sur le chromosome 7 qui présentait un score LOD de 18,7 et qui expliquait 44% de la variance phénotypique. L'analyse d'association a été réalisée à l'aide des données génotypiques pour 3465 SNP et a révélé 69 associations significatives (p < 1 x [10.sup.-4]) avec la résistance à la flétrissure. La variance phénotypique expliquée par les SNP variait entre 0,063 et 0,210. Le QTL détecté au sein de la population de cartographie biparentale n'a pas été identifié dans l'analyse d'association. Ainsi, les résultats de ce travail suggèrent une grande diversité génique pour la résistance à la flétrissure fusarienne chez le ricin. [Traduit par la Rédaction] Mots-clés : Fusarium oxysporum f. sp. ricini, Ricinus communis L., analyse d'association pangénomique, cartographie QTL, marqueurs SNP., Introduction Castor (Ricinus communis L.) is an important oilseed crop grown in arid and semi-arid regions of the world. Its oil is an important raw material for several industrial products [...]

Most deaths from cancer are explained by metastasis, and yet large-scale metastasis research has been impractical owing to the complexity of in vivo models. Here we introduce an in vivo barcoding strategy that is capable of determining the metastatic potential of human cancer cell lines in mouse xenografts at scale. We validated the robustness, scalability and reproducibility of the method and applied it to 500 cell lines.sup.1,2 spanning 21 types of solid tumour. We created a first-generation metastasis map (MetMap) that reveals organ-specific patterns of metastasis, enabling these patterns to be associated with clinical and genomic features. We demonstrate the utility of MetMap by investigating the molecular basis of breast cancers capable of metastasizing to the brain--a principal cause of death in patients with this type of cancer. Breast cancers capable of metastasizing to the brain showed evidence of altered lipid metabolism. Perturbation of lipid metabolism in these cells curbed brain metastasis development, suggesting a therapeutic strategy to combat the disease and demonstrating the utility of MetMap as a resource to support metastasis research. A method in which pooled barcoded human cancer cell lines are injected into a mouse xenograft model enables simultaneous mapping of the metastatic potential of multiple cell lines, and shows that breast cancer cells that metastasize to the brain have altered lipid metabolism., Author(s): Xin Jin [sup.1] , Zelalem Demere [sup.1] , Karthik Nair [sup.1] , Ahmed Ali [sup.1] [sup.2] , Gino B. Ferraro [sup.3] , Ted Natoli [sup.1] , Amy Deik [sup.1] [...]

Purpose: Specific language impairment (SLI) is characterized by a delay in language acquisition despite a lack of other developmental delays or hearing loss. Genetics of SLI is poorly understood. The purpose of this study is to identify SLI genetic loci through family-based linkage mapping. Method: We performed genome-wide parametric linkage analysis in six families segregating with SLI. An age-appropriate standardized omnibus language measure was used to categorically define the SLI phenotype. Results: A suggestive linkage region replicated a previous region of interest with the highest logarithm of odds (LOD) score of 2.40 at 14q11.2-q13.3 in Family 489. A paternal parent-of-origin effect associated with SLI and language phenotypes on a nonsynonymous single nucleotide polymorphism (SNP) in NOP9 (14q12) was reported previously. Linkage analysis identified a new SLI locus at 15q24.3-25.3 with the highest parametric LOD score of 3.06 in Family 315 under a recessive mode of inheritance. Suggestive evidence of linkage was also revealed at 4q31.23-q35.2 in Family 300, with the highest LOD score of 2.41. Genetic linkage was not identified in the other three families included in parametric linkage analysis. Conclusions: These results are the first to report genomewide suggestive linkage with a total language standard score on an age-appropriate omnibus language measure across a wide age range. Our findings confirm previous reports of a language-associated locus on chromosome 14q, report new SLI loci, and validate the pedigree-based parametric linkage analysis approach to mapping genes for SLI. Supplemental Material: https://doi.org/10.23641/asha. 13203218, Most children acquire language without any formal instruction. Contrary to common expectations, language does not come easily to all children. Specific language impairment (SLI) is a language disorder that delays [...]

Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic analysis identified a monogenic dominant inheritance of one dwarfing gene from WAOAT2132, temporarily designated DwWA. A simple sequence repeat (SSR) marker (AME117) that was already available and a new codominant PCR-based marker (bi17) developed by homologous cloningin the present study were both associated with the dwarfing gene. The two markers were located 21 and 1.2 cM from DwWA, respectively. The bi17 marker was mapped to neighboring SNP markers on chromosome 18D of the oat consensus map. Since Dw6 was previously mapped on chromosome 18, and since our new marker bi17 is also diagnostic for NILs generated for Dw6, there is strong evidence that the dwarfing gene identified in WAOAT2132 is Dw6. The newly developed markers could find applications in the identification of this gene in oat germplasm and in the fine mapping or positional cloning of the gene. Key words: Avena sativa, dwarfing gene, SSR, consensus map, chromosome location. Une paille courte est un caractère souhaité chez l'avoine cultivée hexaploïde (Avena sativa L.) dans certains environnements. La sélection assistée par marqueurs, un outil important pour l'atteinte de cet objectif, est limitée par le manque de données de cartographie et par le manque de marqueurs. Dans ce travail, une analyse de ségrégants en composite (BSA, << bulked segregant analysis >>) a été employée pour identifier des marqueurs PCR associés à un gène de nanisme. L'analyse génétique a permis d'identifier un gène de nanisme à hérédité monogénique et dominante chez l'avoine WAOAT2132 ; ce gène a temporairement été nomméDwWA.Unmarqueur microsatellite (AME117), lequel était déjà disponible, ainsi qu'un nouveau marqueur PCR codominant (bi17), mis au point suite à un clonage homologue au cours du présent travail, étaient tous deux associés au gène de nanisme. Les deux marqueurs étaient situés respectivement à 21 et 1,2 cM de DwWA. Le marqueur bi17 a été positionné à proximité de marqueurs SNP sur le chromosome 18D sur la carte consensus de l'avoine. Puisque le locus Dw6 avait déjà était placé sur le chromosome 18, et parce que le nouveau marqueur bi17 était diagnostique au sein de lignées quasi-isogéniques pour Dw6, cela suggère fortement que le gène de nanisme identifié chez WAOAT2132 est en fait Dw6. Ces nouveaux marqueurs pourront servir à l'identification de ce gène au sein du germoplasme de l'avoine et à la cartographie fine ou au clonage positionnel de ce gène. [Traduit par la Rédaction] Mots-clés : Avena sativa, gène de nanisme, SSR, carte consensus, position chromosomique., Introduction Cereal crops, the world's primary food source, have been domesticated from a diverse array of grass species. One of these cereals, cultivated hexaploid oat (Avena sativa L.; hereafter oat), [...]

Much effort has been directed at identifying sources of resistance to Fusarium head blight (FHB) in wheat. We sought to identify molecular markers for what we hypothesized was a new major FHB resistance locus originating from the wheat cultivar 'Freedom' and introgressed into the susceptible wheat cultivar 'USU-Apogee'. An [F.sub.2:3] mapping population from a cross between Apogee and A30, its BC4 near-isoline exhibiting improved FHB resistance, was evaluated for resistance. The distribution of FHB resistance in the population approximated a 1:3 moderately resistant : moderately susceptible + susceptible ratio. Separate disease evaluations established that A30 accumulated less deoxynivalenol and yielded a greater proportion of sound grain than Apogee. Molecular mapping revealed that the FHB resistance of A30 is associated with molecular markers on chromosome arm 3DL that exhibit a null phenotype in A30 but are present in both Apogee and Freedom, indicating a spontaneous deletion occurred during the development of A30. Aneuploid analysis revealed that the size of the deleted segment is approximately 19% of the arm's length. Our results suggest that the deleted interval of chromosome arm 3DL in Apogee may harbor FHB susceptibility genes that promote disease spread in infected spikes, and that their elimination increases FHB resistance in a novel manner. Keywords: Fusarium, susceptibility, breeding, genetics, mapping. Des efforts considerables ont ete consacres a l'identification de sources de resistance a la fusariose de l'epi (FHB) chez le ble. Les auteurs ont cherche a identifier des marqueurs moleculaires associes a un presume nouveau gene de resistance majeur provenant du cultivar de ble 'Freedom'. Parallelement, ce gene a ete introgresse dans le cultivar de ble sensible 'USU-Apogee'. Une population de cartographie [F.sub.2:3] derivee d'un croisement entre Apogee et A30, une lignee BC4 quasi-isogenique affichant une resistance accrue a la FHB, a ete evaluee pour la resistance. La distribution de la resistance a la FHB au sein de la population s'approchait d'un ratio 1:3 (moderement resistants : moderement sensibles + sensibles). Des evaluations distinctes de la maladie ont montre que la lignee A30 accumulait moins de desoxynivalenol et produisait une plus grande proportion de grains sains que le cultivar Apogee. La cartographie genetique a revele que la resistance a la FHB chez A30 est associee a des marqueurs moleculaires sur le bras chromosomique 3DL qui presentent un phenotype nul chez A30, mais qui sont presents tant chez Apogee que chez Freedom. Cela suggere qu'une deletion spontanee serait survenue au cours du developpement de la lignee A30. Une analyse de l'aneuplo'idie a revele que le segment manquant representerait environ 19 % de la taille de ce bras. Ces resultats suggerent que cet intervalle du bras chromosomique 3DL chez Apogee porterait des genes de sensibilite a la FHB qui favoriseraient la propagation de la maladie sur des epis infectes et que leur elimination accroit la resistance a la FHB d'une maniere inedite. [Traduit par la Redaction] Mots-cles : Fusarium, sensibilite, amelioration genetique, genetique, cartographie., Introduction The disease Fusarium head blight (FHB), caused by members of the fungal genus Fusarium, reduces yields and erodes grain quality in wheat and other small grains. The principal species [...]

In soybean, asynaptic and desynaptic mutants lead to abnormal meiosis and fertility reduction. Several male-sterile, female-sterile mutants have been identified and studied in soybean, however, some of these mutants have not been mapped to locations on soybean chromosomes. The objectives of this study were to molecularly map five male-sterile, female-sterile genes (st2, st4, st5, st6, and st7) in soybean and compare the map locations of these genes with already mapped sterility genes. Microsatellite markers were used in bulked segregant analyses to locate all five malesterile, female-sterile genes to soybean chromosomes, and markers from the corresponding chromosomes were used on F2 populations to generate genetic linkage maps. The st2, st4, st5, st6, and st7 genes were located on molecular linkage group (MLG) B1 (chromosome 11), MLG D1a (chromosome 01), MLG F (chromosome 13), MLG B2 (chromosome 14), and D1b (chromosome 02), respectively. The st2, st4, st5, st6, and st7 genes were flanked to 10.3 (~399 kb), 6.3 (~164 kb), 3.9 (~11.8 Mb), 11.0 (~409 kb), and 5.3 cM (~224 kb), and the flanked regions contained 57,17, 362, 52, and 17 predicted genes, respectively. Future characterization of candidate genes should facilitate identification of the male- and female-fertility genes, which may provide vital insights on structure and function of genes involved in the reproductive pathway in soybean. Key words: Glycine max, sterility, simple sequence repeat, genetic linkage map, male-sterile female-sterile. Chez le soya, des mutants asynaptiques et desynaptiques presentent des anomalies meiotiques et une reduction de la fertilite. Plusieurs mutants presentant une sterilite male et femelle ont ete identifies et etudies, mais certains de ceux-ci n'ont pas ete situes sur les chromosomes du soya. Les objectifs de ce travail etaient de realiser la cartographie de cinq genes de sterilite male et femelle (st2, st4, st5, st6 et st7) chez le soya et de comparer la position de ces genes avec celle d'autres genes de sterilite deja positionnes. Des marqueurs microsatellites ont ete employes dans le cadre d'analyses de segregants en melange afin d'assigner une position chromosomique aux cinq genes de sterilite male et femelle. Les marqueurs situes sur ces chromosomes ont ete employes sur des populations F2 afin de generer des cartes genetiques. Les genes st2, st4, st5, st6 et st7 ont ete assignes respectivement aux groupes de liaison moleculaires (MLG) B1 (chromosome 11), MLG D1a (chromosome 01), MLG F (chromosome 13), MLG B2 (chromosome 14) et MLG D1b (chromosome 2). Les genes st2, st4, st5, st6 et st7 ont ete assignes a des intervalles de 10,3 (~399 kb), 6,3 (~164 kb), 3,9 (~11,8 Mb), 11,0 (~409 kb) et 5,3 cM (~224 kb); ces intervalles contenaient respectivement 57,17, 362, 52 et 17 genes predits. Une future caracterisation de genes candidats devrait faciliter l'identification des genes de fertilite male et femelle, laquelle fournira un eclairage important sur la structure et la fonction des genes impliques dans la reproduction chez le soya. [Traduit par la Redaction] Mots-cles: Glycine max, sterilite, sequence simple repetee, carte genetique, sterilite male et femelle., Introduction In soybean, asynaptic and desynaptic mutants lead to abnormal meiosis and fertility reduction. This is caused by abnormal pairing of chromosomes during the first meiotic prophase, also known as [...]

Genome-wide association studies have identified loci underlying human diseases, but the causal nucleotide changes and mechanisms remain largely unknown. Here we developed a fine-mapping algorithm to identify candidate causal variants for 21 autoimmune diseases from genotyping data. We integrated these predictions with transcription and cis-regulatory element annotations, derived by mapping RNA and chromatin in primary immune cells, including resting and stimulated [CD4.sup.+] T-cell subsets, regulatory T cells, [CD8.sup.+] T cells, Bcells, and monocytes. We find that ~90% of causal variants are non-coding, with ~60% mapping to immune-cell enhancers, many of which gain histone acetylation and transcribe enhancer-associated RNA upon immune stimulation. Causal variants tend to occur near binding sites for master regulators of immune differentiation and stimulus-dependent gene activation, but only 10- 20% directly alter recognizable transcription factor binding motifs. Rather, mostnon-codingriskvariants, including those that alter gene expression, affect non-canonical sequence determinants not well-explained by current gene regulatory models., Genome-wide association studies (GWAS) have revolutionized the study of complex human traits by identifying thousands of genetic loci that contribute susceptibility for a diverse set of diseases (1,2). However, progress [...]

Three methods for gene-expression profiling have now been combined to produce spatially defined single-cell maps of developing human organs from limited sample material, overcoming a major hurdle in studying human development. A framework for spatially resolved single-cell maps of human organs., Author(s): Ragini Phansalkar, Kristy Red-Horse Author Affiliations: Techniques converge to map the developing human heart at single-cell level People are often curious about how their bodies work. So, it is [...]

The mitotic checkpoint plays an important role in preventing chromo-some segregation errors and the production of aneuploid progeny. In this issue, Zhang et al. examine mice and cells lacking the deubiquitinat-ing enzyme USP44. Surprisingly, they find that USP44 prevents chromo-some segregation errors through a function independent of its previously identified role in the mitotic checkpoint. Usp44-null animals develop aneuploidy and experience increased rates of tumorigenesis, implicating USP44 as novel tumor suppressor., Ubiquitination is a reversible posttransla-tional modification that regulates a broad range of cellular processes. Ubiquitin is a small, 76-amino-acid protein that can be covalently conjugated with the aid of ubiquitin [...]

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations., Recent efforts to map human genetic variation by sequencing exomes (1) and whole genomes (2-4) have characterized the vast majority of common single nucleotide polymorphisms (SNPs) and many structural variants [...]

DNA barcodes help to detail the genomic architecture and sequence of an unbroken cell or even an entire embryo. DNA barcodes help to detail the genomic architecture and sequence of an unbroken cell or even an entire embryo., Author Affiliations: Genomic techniques can be used to specify the DNA sequence of cells in an entire mouse embryo (pictured). Credit: Meng Zhu, Zernicka-Goetz Laboratory, Cambridge University/SPL Eight-cell mouse embryo, [...]

Chromosomal instability (CIN) is a hallmark of human neoplasms. Despite its widespread prevalence, knowledge of the mechanisms and contributions of CIN in cancer has been elusive. It is now evident that the role of CIN in tumor initiation and growth is more complex than previously thought. Furthermore, distinguishing CIN, which consists of elevated rates of chromosome missegregation, from aneuploidy, which is a state of abnormal chromosome number, is crucial to understanding their respective contributions in cancer. Collectively, experimental evidence suggests that CIN enables tumor adaptation by allowing tumors to constantly sample the aneuploid fitness landscape. This complex relationship, together with the potential to pharmacologically influence chromosome missegregation frequencies in cancer cells, offers previously unrecognized means to limit tumor growth and its response to therapy., Introduction Adaptation is a hallmark of human neoplasms, and the ability of tumors to adapt to external pressures stems from tumor cell heterogeneity (1). Mechanisms responsible for this heterogeneity include [...]

The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200-300 million years (1-3). The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes' genes owing to genetic decay (4,5). This evolutionary decay was driven by a series of five 'stratification' events. Each event suppressed X-Y crossing over within a chromosome segment or 'stratum', incorporated that segment into the MSY and subjected its genes to the erosive forces that attend the absence of crossing over (2,6). The last of these events occurred 30 million years ago, 5 million years before the human and Old World monkey lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome (7-10), remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage. To investigate this question, we sequenced the MSY of the rhesus macaque, an Old World monkey, and compared it to the human MSY. We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. In the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 million years ago. Likewise, the rhesus MSY has not lost any older genes (from strata 1-4) during the past 25 million years, despite its major structural differences to the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection., The human Y chromosome no longer engages in crossing over with its once-identical partner, the X chromosome, except in its pseudoautosomal regions. During evolution, X-Y crossing over was suppressed in [...]

Intact proteins yield to proteomics Conventional 'bottom-up' proteomics, in which mass spectrometry is used to analyse peptide mixtures made by tryptic digestion of target proteins, is a powerful way of characterizing complex proteomes. However, the technique has limitations when considering different protein isoforms and combinations of post-translational modifications. The 'top-down' approach is generally thought to be impractical because of the limitations of mass spectrometry and difficulties with automation. A new top-down system presented here avoids these problems by using a four-dimensional separation system that achieves greater proteome coverage than conventional methods. A proof-of-principle experiment shows that the method is capable of identifying previously undetected isoforms and isoform-specific post-translational modifications caused by cellular senescence. A full description of the human proteome relies on the challenging task of detecting mature and changing forms of protein molecules in the body. Large-scale proteome analysis.sup.1 has routinely involved digesting intact proteins followed by inferred protein identification using mass spectrometry.sup.2. This 'bottom-up' process affords a high number of identifications (not always unique to a single gene). However, complications arise from incomplete or ambiguous.sup.2 characterization of alternative splice forms, diverse modifications (for example, acetylation and methylation) and endogenous protein cleavages, especially when combinations of these create complex patterns of intact protein isoforms and species.sup.3. 'Top-down' interrogation of whole proteins can overcome these problems for individual proteins.sup.4,5, but has not been achieved on a proteome scale owing to the lack of intact protein fractionation methods that are well integrated with tandem mass spectrometry. Here we show, using a new four-dimensional separation system, identification of 1,043 gene products from human cells that are dispersed into more than 3,000 protein species created by post-translational modification (PTM), RNA splicing and proteolysis. The overall system produced greater than 20-fold increases in both separation power and proteome coverage, enabling the identification of proteins up to 105 kDa and those with up to 11 transmembrane helices. Many previously undetected isoforms of endogenous human proteins were mapped, including changes in multiply modified species in response to accelerated cellular ageing (senescence) induced by DNA damage. Integrated with the latest version of the Swiss-Prot database.sup.6, the data provide precise correlations to individual genes and proof-of-concept for large-scale interrogation of whole protein molecules. The technology promises to improve the link between proteomics data and complex phenotypes in basic biology and disease research.sup.7., Author(s): John C. Tran [sup.1] [sup.2] , Leonid Zamdborg [sup.1] , Dorothy R. Ahlf [sup.1] [sup.2] , Ji Eun Lee [sup.1] [sup.3] , Adam D. Catherman [sup.1] [sup.2] , Kenneth [...]

This paper describes two joint linkage--linkage disequilibrium (LD) mapping approaches: parallel mapping (independent linkage and LD analysis) and integrated mapping (datasets analyzed in combination). These approaches were achieved using 2,052 single nucleotide polymorphism (SNP) markers, including 659 SNPs developed from drought-response candidate genes, screened across three recombinant inbred line (RIL) populations and 305 diverse inbred lines, with anthesis-silking interval (ASI), an important trait for maize drought tolerance, as the target trait. Mapping efficiency was improved significantly due to increased population size and allele diversity and balanced allele frequencies. Integrated mapping identified 18 additional quantitative trait loci (QTL) not detected by parallel mapping. The use of hapl0types improved mapping efficiency, with the sum of phenotypic variation explained (PVE) increasing from 5.4% to 23.3% for single SNP-based analysis. Integrated mapping with haplotype further improved the mapping efficiency, and the most significant QTL had a PVE of up to 34.7%. Normal allele frequencies for 113 of 277 (40.8%) SNPs with minor allele frequency ( anthesis-silking interval | drought resistance | haplotype loci | integrated quantitative trait locus mapping doi/ 10.1073/pnas.1006105107

QTL mapping by association analysis has recently gained interest in plant breeding research as an alternative to QTL mapping in segregating populations from biparental crosses. In a first experiment on whole-genome association analysis in rapeseed, 684 mapped AFLP markers were tested for association with 14 traits in a set of 84 canola quality winter rapeseed cultivars. For association analysis a general linear model was used. By testing significance of marker-trait associations against a false discovery rate of 0.2, between 1 and 34 associated markers were found for 10 of the 14 traits. Taking into account linkage disequilibrium between the significant markers, these markers represent between 1 and 22 putative QTL for the respective traits. The minimum phenotypic variance explained by the QTL for the different traits ranged from 15% to 53%. A subset of 27 markers were significantly associated with two or more traits. These markers were predominantly shared between traits that were significantly correlated at the phenotypic level. The results show clearly that in rapeseed, QTL mapping by association analysis is a viable alternative to QTL mapping in segregating populations. Key words: Brassica napus, quantitative trait loci, association analysis. Resume : La cartographie QTL par analyse d'association a recemment suscite beaucoup d'interet en amelioration gene-etique comme alternative a la cartographie QTL au sein de populations en segregation issues de croisements biparentaux. Dans une premiere experience d'analyse d'association a l'echelle du genome chez le colza, 684 marqueurs AFLP de position connue ont ete examinees pour leur association avec 14 caracteres au sein d'un jeu de 84 cultivars de canola d'automne. Pour l'analyse d'association, un modele lineaire general a ete employee. En testant le degree de signification des associations entre les marqueurs et les caracteres de telle facjon que la fraction de faux positifs (FDR) soit de 0,2, entre 1 et 34 marqueurs associes ont ete observes pour 10 des 14 caracteres. En tenant compte du desequilibre de liaison entre les marqueurs significatifs, ces marqueurs representent entre 1 et 22 QTL potentiels pour ces caracteres. La variance phenotypique minimale expliquee par ces QTL variait entre 15 et 53 %. Un sous-ensemble de 27 marqueurs etait significativement associe avec deux caracteres ou plus. Ces marqueurs etaient majoritairement partages entre des caracteres dont les phenotypes etaient significativement correles. Ces resultats montrent clairement que la cartographie QTL par analyse d'association chez le colza est une alternative viable a la cartographie QTL sur populations biparentales. Mots-cles : Brassica napus, QTL, analyse d'association. [Traduit par la Redaction], Introduction In rapeseed (Brassica napus L.), genetic mapping of quantitative trait loci (QTL) is well established and has been used to identify and localize QTL for quality traits such as [...]

Association mapping has been used increasingly in natural populations with rich genetic diversity to detect DNA-based markers that are associated with important agronomic traits. Brassica napus is an important oil crop with limited genetic diversity. 'New-type' B. napus that is introgressed with subgenomic components from related species has been developed to broaden the genetic basis of 'traditional' B. napus. In this study, new-type B. napus lines and a collection of traditional B. napus varieties from different countries were used as two different populations to evaluate seed oil content and to determine the efficacy of association mapping by comparison with previous study of linkage mapping. Relatively rich genetic diversity, but a higher level of linkage disequilibrium was observed in the new-type B. napus as compared with the traditional B. napus. Similarly, a larger variation in oil content and a greater number of associated markers were detected in the population of new-type B. napus. Meanwhile, more than half of the genetic loci, to which the associated markers corresponded, were located within the quantitative trait loci intervals identified previously in linkage mapping experiments, which demonstrated the power of association mapping in B. napus. Key words: Brassica napus, genetic diversity, seed oil content, quantitative trait loci (QTL), association mapping. Resume : L'analyse d'association est de plus en plus utiliseee au sein de populations naturelles riches en diversite genetique pour deetecter des marqueurs genetiques qui sont associes a des caracteres agronomiques. Le Brassica napus est une culture oleagineuse importante qui presente une diversite genetique restreinte. Des B. napus de << type nouveau >>, obtenus par introgression de composantes sub-genomiques provenant d'especes apparentees, ont ete developpees pour elargir l'assise genetique des B. napus << traditionnels >>. Dans ce travail, des lignees du B. napus de << type nouveau >> ainsi qu'une collection de cultivars du B. napus de type << traditionnel >> provenant de divers pays ont ete employees pour former deux populations au sein desquelles la teneur en huile des graines a ete mesuree et l'efficacite des analyses d'association a ete comparee aux etudes anterieures fondees sur des cartes de liaison genetique. Une diversite; genetique relativement elevee et un plus grand desequilibre de liaison ont ete observes au sein des B. napus de type << nouveau >> par rapport au type << traditionnel >>. Pareillement, une plus grande variation pour la teneur en huile et un plus grand nombre de marqueurs associes ont ete detectes chez les B. napus de type << nouveau >>. Plus de la moitie des locus genetiques auxquels correspondaient les marqueurs associees etaient situees au sein d'intervalles QTL identifies lors d'experiences anterieures, ce qui demontre la puissance des analyses d'association chez le B. napus. Mots-cles : Brassica napus, diversite; genetique, teneur en huile dans les graines, locus de caractere quantitatif (QTL), analyse d'association., [Traduit par la Redaction] Introduction Mapping of quantitative trait loci (QTL) has proven to be a reliable way to dissect complex traits that are controlled by multiple genes (Salvi and [...]

Aluminium ([Al.sup.3+]) toxicity restricts productivity and profitability of wheat (Triticum aestivum L.) crops grown on acid soils worldwide. Continued gains will be obtained by identifying superior alleles and novel [Al.sup.3+] resistance loci that can be incorporated into breeding programs. We used association mapping to identify genomic regions associated with [Al.sup.3+] resistance using 1055 accessions of common wheat from different geographic regions of the world and 178 polymorphic diversity arrays technology (DArT) markers. Bayesian analyses based on genetic distance matrices classified these accessions into 12 subgroups. Genome-wide association analyses detected markers that were significantly associated with [Al.sup.3+] resistance on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5B, 6A, 6B, 7A, and 7B. Some of these genomic regions correspond to previously identified loci for [Al.sup.3+] resistance, whereas others appear to be novel. Among the markers targeting TaALMTl (the major [Al.sup.3+]-resistance gene located on chromosome 4D), those that detected alleles in the promoter explained most of the phenotypic variance for [Al.sup.3+] resistance, which is consistent with this region controlling the level of TaALMTl expression. These results demonstrate that genome-wide association mapping cannot only confirm known [Al.sup.3+]-resistance loci, such as those on chromsomes 4D and 4B, but they also highlight the utility of this technique in identifying novel resistance loci. Key words: genetic diversity, wheat, germplasm, DArT, genetic structure, linkage disequilibrium, association mapping. La toxicite de l'aluminium ([Al.sup.3+]) limite la productivite et la profitabilite du blee (Triticum aestivum L.) cultive sur sols acides partout dans le monde. Des gains continus ont ete realises en identifiant des alleles superieurs et de nouveaux locus de resistance a la toxicite; de l'[Al.sup.3+], lesquels sont ensuite incorpores dans des programmes d'ameelioration genetique. Les auteurs ont employee l'analyse d'association pour identifier de nouvelles regions genomiques associeees a la resistance a l'[Al.sup.3+] chez une collection de 1055 accessions du ble tendre provenant de diverses regions du monde et 178 marqueurs DArT polymorphes. Des analyses Bayesiennes fondeees sur les matrices de distance geneetique ont permis de classer ces accessions en 12 sous-groupes. Un balayage genomique a detecte des marqueurs significativement associesa la resistance a l'[Al.sup.3+] sur les chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5B, 6A, 6B, 7A et 7B. Certaines de ces regions correspondaient a des locus identifies anteerieurement pour la resistance a l'[Al.sup.3+] tandis que d'autres etaient rapporteees pour la premiere fois. Parmi les marqueurs ciblant TaALMT1, le principal locus de resistance a l'[Al.sup.3+] situe sur 4D, ceux situes au sein du promoteur expliquaient la plus grande part de la variance phenotypique pour la resistance a l'[Al.sup.3+], ce qui suggere que cette region determine le niveau d'expression de TaALMT1. Ces resultats montrent qu'un balayage genomique peut non seulement confirmer l'existence de locus connus de resistance a l'[Al.sup.3+], comme ceux situes sur 4D et 4B, mais demontre aussi l'utilite de cette approche en vue d'identifier des locus de resistance nouveaux. Mots-cles: diversite geneetique, ble, ressources genetiques, DArT, structure geneetique, deseequilibre de liaison, analyse d'assocation. [Traduit par la Redaction], Introduction Aluminium ([Al.sup.3+]) toxicity continues to restrict the productivity and profitability of wheat (Triticum aestivum L. subsp. aestivum;2n = 6x = 42, AABBDD) grown on acidic soils. Under low pH [...]

The architecture of the Brassica napus genome is marked by its evolutionary origins. The genome of B. napus was formed from the hybridization of two closely related diploid Brassica species, both of which evolved from an hexaploid ancestor. The extensive whole genome duplication events in its near and distant past result in the allotetraploid genome of B. napus maintaining multiple copies of most genes, which predicts a highly complex and redundant transcriptome that can confound any expression analyses. A stringent assembly of 142 399 B. napus expressed sequence tags allowed the development of a well-differentiated set of reference transcripts, which were used as a foundation to assess the efficacy of available tools for identifying and distinguishing transcripts in B. napus; including microarray hybridization and 3' anchored sequence tag capture. Microarray platforms cannot distinguish transcripts derived from the two progenitors or close homologues, although observed differential expression appeared to be biased towards unique transcripts. The use of 3' capture enhanced the ability to unambiguously identify homologues within the B. napus transcriptome but was limited by tag length. The ability to comprehensively catalogue gene expression in polyploid species could be transformed by the application of cost-efficient next generation sequencing technologies that will capture millions of long sequence tags. Key words: polyploid, homologues, next generation sequencing, expressed sequence tags, single nucleotide polymorphism, Brassica. La structure du genome chez le Brassica napus est marquee par ses origines evolutives. Le genome du B. napus aete forme suite a l'hybridation de deux especes diploi'des de Brassica tres apparenteees, toutes deux deerivees d'ancetres hexaploldes. Ces importants eveenements de duplication survenus a l'eechelle du genome entier, tant dans un passe recent que plus ancien, font en sorte que le genome alloteetraplolde du B. napus a conserve de multiples copies de la plupart des genes. Cette situation permet de penser que le transcriptome de cette espece est a la fois complexe et redondant, ce qui peut entrainer de la confusion dans les analyses d'expression. Un assemblage rigoureux de 142 399 etiquettes de sequences exprimeees chez le B. napus a permis de developper un jeu de transcrits de reference bien differencies, lesquels ont permis de mesurer l'efficacite des outils disponibles pour l'identification et la discrimination entre transcrits chez le B. napus. Les outils examinesetaient l'hybridation sur puces a ADN et la capture d'etiquettes de sequences ancrees a l'extreemitee 3'. Les puces a ADN n'arrivent pas a distinguer les transcrits provenant des deux especes progenitrices ou d'homologues proches, bien que les cas d'expression diffeerentielle observes semblaient biaisees en faveur de transcrits uniques. L'emploi d'etiquettes capturees en 3' a permis d'ameeliorer la capacite a identifier sans ambigui'te les homologues au sein du transcriptome du B. napus, mais etait limite par la taille des etiquettes. Les nouvelles technologies de sequencjage a faible coflt permettant de geenerer des millions d'etiquettes plus longues pourraient revolutionner notre capacite; a cataloguer de maniere exhaustive l'expression geenique chez des especes polyploi'des. Mots-cles: polyploldie, homologues, sequencage de seconde generation, etiquettes de sequences exprimees, variation SNP, Brassica., [Traduit par la Redaction] Introduction The study of global gene expression analysis is a powerful tool for understanding complex biological phenomena, deciphering interacting pathways, and uncovering novel genes controlling traits [...]

This study describes the use of regional association analyses to delineate a sequenced region of a Brassica napus chromosome with a significant effect on antinutritive seed meal compounds in oilseed rape. A major quantitative trait locus (QTL) influencing seed colour, fibre content, and phenolic compounds was mapped to the same position on B. napus chromosome A9 in biparental mapping populations from two different yellow-seeded x black-seeded B. napus crosses. Sequences of markers spanning the QTL region identified synteny to a sequence contig from the corresponding chromosome A9 in Brassica rapa. Remapping of sequence-derived markers originating from the B. rapa sequence contig confirmed their position within the QTL. One of these markers also mapped to a seed colour and fibre QTL on the same chromosome in a black-seeded x black-seeded B. napus cross. Consequently, regional association analysis was performed in a genetically diverse panel of dark-seeded, winter-type oilseed rape accessions. For this we used closely spaced simple sequence repeat (SSR) markers spanning the sequence contig covering the QTL region. Correction for population structure was performed using a set of genome-wide SSR markers. The identification of QTL-derived markers with significant associations to seed colour, fibre content, and phenolic compounds in the association panel enabled the identification of positional and functional candidate genes for B. napus seed meal quality within a small segment of the B. rapa genome sequence. Key words: Brassica napus, seed meal quality, association analysis, QTL mapping. Cette etude decrit une analyse d'association regionale pour delimiter une region seequencee d'un chromosome du Brassica napus qui a un effet significatif sur la teneur en composes antinutritionnels dans le tourteau de colza. Un QTL majeur influencjant la couleur des graines, la teneur en fibres et les composes phenoliques a ete localise a une meme position sur le chromosome A9 chez le Brassica napus au sein de populations biparentales issues de deux croisements entre colzas a graines jaunes et colzas a graines noires. Les sequences des marqueurs distribuees au sein de cette region ont permis d'observer de la synteenie avec un contig de sequence provenant de la region correspondante du chromosome A9 du Brassica rapa. La cartographie de marqueurs provenant du contig de sequences du B. rapa a permis de confirmer leur localisation au sein du QTL. Un de ces marqueurs s'est eegalement aveeree lie; a un QTL determinant la couleur des graines et la teneur en fibres sur le meme chromosome au sein d'un croisement entre un B. napus a graines noires et un autre a graines jaunes. En consequence, une analyse d'association regionale a ete; realisee sur un groupe varie d'accessions de colzas okeagineux d'automne a graines noires. Des marqueurs microsatellites (SSR) trees proches les uns des autres et couvrant le contig de sequence de la region QTL ont ete employees. Une correction pour la structure de la population a etee realiseea l'aide d'un jeu de marqueurs SSR distribues sur l'ensemble du genome. L'identification de marqueurs derives du QTL et affichant des associations significatives avec la couleur des graines, la teneur en fibres et en composes phenoliques au sein de ce groupe d'accessions a permis d'identifier des genes candidats pour la qualitee du tourteau chez le B. napus sur une base positionnelle et fonctionnelle au sein d'un petit segment du genome du B. rapa. Mots-cles : Brassica napus, qualite; du tourteau, analyse d'association, cartographie QTL., Introduction Detection of marker-trait associations based on linkage disequilibrium (LD) in genetically diverse materials can identify markers with direct linkage to genes showing significant effects on the trait. Association mapping [...]

Transgenic manipulation of subsets of brain cells is increasingly used for studying behaviors and their underlying neural circuits. In Drosophila, the GAL4--upstream activating sequence (UAS) binary system is powerful for gene manipulation, but GAL4 expression is often too broad for fine mapping of neural circuits. Here, we describe the development of unique molecular genetic tools to restrict GAL4 expression patterns. Building on the GAL4-UAS system, our method adds two components: a collection of enhancer-trap recombinase, Flippase (ET-FLP), transgenic lines that provide inheritable, reproducible, and tissue-specific FLP and an FRT-dependent GAL80 'flip-in' construct that converts FLP expression into tissue-specific repression of GAL4 by GAL80. By including a UAS-encoded fluorescent protein, circuit morphology can be simultaneously marked while the circuit function is assessed using another UAS transgene. In a proof-of-principle analysis, we applied this ET-FLP-induced intersectional GAL80/GAL4 repression (FINGR) method to map the neural circuitry underlying fly wing inflation. The FINGR system is versatile and powerful in combination with the vast collection of GAL4 lines for neural circuit mapping as well as for clonal analysis based on the infusion of the yeast-derived FRT/FLP system of mitotic recombination into Drosophila. The strategies and tactics underlying our FINGR system are also applicable to other genetically amenable organisms in which transgenes including the GAL4, UAS, GAL80, and FLP factors can be applied. behavior | intersection | Flippase mosaicism | GAL4 | GAL80 www.pnas.org/cgi/doi/ 10.1073/pnas.1004669107

Despite its fundamental nature, bacterial chromosome segregation remains poorly understood. Viewing segregation as a single process caused multiple proposed mechanisms to appear in conflict and failed to explain how asymmetrically dividing bacteria break symmetry to move only one of their chromosomes. Here, we demonstrate that the ParA ATPase extends from one cell pole and pulls the chromosome by retracting upon association with the ParB DNA-binding protein. Surprisingly, ParA disruption has a specific effect on chromosome segregation that only perturbs the latter stages of this process. Using quantitative high-resolution imaging, we demonstrate that this specificity results from the multistep nature of chromosome translocation. We propose that Caulobacter chromosome segregation follows an ordered pathway of events with distinct functions and mechanisms. Initiation releases polar tethering of the origin of replication, distinction spatially differentiates the two chromosomes, and commitment irreversibly translocates the distal centromeric locus. Thus, much as eukaryotic mitosis involves a sequence of distinct subprocesses, Caulobacter cells also segregate their chromosomes through an orchestrated series of steps. We discuss how the multistep view of bacterial chromosome segregation can help to explain and reconcile outstanding puzzles and frame future investigation. Par system | quantitative image analysis | bacterial cell biology doi/ 10.1073/pnas.1005274107

The objective of this study was to evaluate the effects of mutations in 2 genes [IGF2 and cathepsin D (CTSD)] that map on the telomeric end of the p arm of SSC2. In this region, an imprinted QTL affecting muscle mass and fat deposition was reported, and the IGF2 intron3-g.3072G>A substitution was identified as the causative mutation. In the same chromosome region, we assigned, by linkage mapping, the CTSD gene, a lysosomal proteinase, for which we previously identified an SNP in the 3'-untranslated region (AM933484, g.70G>A). We have already shown strong effects of this CTSD mutation on several production traits in Italian Large White pigs, suggesting a possible independent role of this marker in fatness and meat deposition in pigs. To evaluate this hypothesis, after having refined the map position of the CTSD gene by radiation hybrid mapping, we analyzed the IGF2 and the CTSD polymorphisms in 270 Italian Large White and 311 Italian Duroc pigs, for which EBV and random residuals from fixed models were calculated for several traits. Different association analyses were carried out to distinguish the effects of the 2 close markers. In the Italian Large White pigs, the results for IGF2 were highly significant for all traits when using either EBV or random residuals (e.g., using EBV: lean cuts, P = 2.2 x [10.sup.-18]; ADG, P = 2.6 x [10.sup.-16]; backfat thickness, P = 2.2 x [10.sup.-9]; feed:gain ratio, P = 2.3 x [10.sup.-9]; ham weight, P = 1.5 x [10.sup.-6]). No effect was observed for meat quality traits. The IGF2 intron3-g.3072G>A mutation did not show any association in the Italian Duroc pigs, probably because of the small variability at this polymorphic site for this breed. However, a significant association was evident for the CTSD marker (P < 0.001) with EBV of all carcass and production traits in Italian Duroc pigs (lean content, ADG, backfat thickness, feed:gain ratio) after excluding possible confounding effects of the IGF2 mutation. The effects of the CTSD g.70G>A mutation were also confirmed in a subset of Italian Large White animals carrying the homozygous genotype IGF2 intron3-g.3072GG, and by haplotype analysis between the markers of the 2 considered genes in the complete data set. Overall, these results indicate that the IGF2 intron3-g.3072G>A mutation is not the only polymorphism affecting fatness and muscle deposition on SSC2p. Therefore, the CTSD g.70G>A polymorphism could be used to increase selection efficiency in marker-assisted selection programs that already use the IGF2 mutation. However, for practical applications, because the CTSD gene should not be imprinted (we obtained this information from expression analysis in adult skeletal muscle), the different modes of inheritance of the 2 genes have to be considered. Key words: association study, cathepsin D gene, insulin-like growth factor 2 gene, Italian heavy pig, production trait, quantitative trait locus doi: 10.2527/jas.2009-2560

White clover (Trifolium repens L.) is a highly outcrossing heterozygous allotetraploid species, for which classic inheritance studies have been inconclusive. With the aid of molecular markers, it is now possible to study the genes controlling morphological traits. The objectives of this study were to catalog the leaf marks in white clover and map the location of leaf morphological traits based on cosegregation with molecular markers. A mapping population segregating for eight morphological traits consisting of leaf marks and number of leaflets was developed and phenotyped at two different locations during the summer and winter seasons. A confirmation population, derived by selfing one of the mapping population parents, was produced and phenotyped in one location at two different times of the year. Through the use of previously published simple sequence repeat (SSR) marker maps, linkages between the mapped molecular markers and genes for three different morphological traits was identified. The red midrib and red fleck traits were found to be controlled by two closely linked dominant genes on linkage group (LG) B1. The trifoliolate trait is controlled by at least one gene on LG H1. The identification of molecular markers linked to loci affecting leaf morphology traits resolves conflicting hypotheses on the genetics of these complex traits and has potential for molecular breeding improvement of white clover. doi: 10.2135/cropsci2009.08.0457

This study was conducted to develop and test new markers for use in molecular characterization of oat (Avena spp.). Results are presented for two polymerase chain reaction (PCR)-based markers targeting multiple avenin protein loci and 16 new m crosatellite or simple sequence repeat (SSR) markers. The markers were mapped in two segregating oat (Avena sativa L.) populations, 'Kanota' x 'Ogle' (KxO) and 'Terra' x 'Marion' (TxM), and were also tested across a diversity panel consisting of 35 cultivated varieties of oat and representatives of five other Avena species. All markers were robust, multiallelic, and highly polymorphic. The SSR markers, some highlighting multiple loci, mapped throughout the genome, and the avenin markers mapped to their expected locations in KxO and TxM. Also as expected, the avenin markers were shown to be linked to the stem rust resistance gene Pg9 in the population 'OT328' x 'Dumont' (OTxDu). Practical applications in variety identification and germplasm diagnostic assays were explored. The markers were able to distinguish closely related lines for fingerprinting purposes and were also useful for determining whether variation within a line was the result of residual heterozygosity or contamination. In addition, the markers were found to be useful for forensic purposes and for determining whether crossing and backcrossing had been successful. doi: 10.2135/cropsci2009.09.0474

Seed dormancy, the main factor contributing to preharvest sprouting (PHS) resistance, is a complex trait and is strongly influenced by environmental growth conditions. In this study, three sets of single chromosome substitution lines, including 36 genotypes, in a durum wheat [Triticum turgidum L. ssp. durum (Desf.) Husn.] background with donor chromosomes originating from three wild emmer [T. turgidum L. ssp. dicoccoides (Korn. ex Asch. and Graebn.) Thell.] accessions were grown in nine field environments and evaluated for seed dormancy and PHS resistance. The substitution lines involving chromosome 3A were among the most dormant genotypes. Germination tests indicated that five chromosomes contained genes influencing seed dormancy at a level comparable to 3A. Results from PHS tests showed that PHS was affected by at least eight T. dicoccoides chromosomes including 3A. The chromosomes harboring genes for seed dormancy did not fully correspond with those for PHS resistance. The weak correlations between PHS and dormancy observed in this study indicate that different genes are affecting these traits and they may be differentially influenced by the environment. Nonetheless, our results revealed that genes present on five chromosomes, 2A, 2B, 3A, 4A, and 7B, were found to affect both PHS resistance and seed dormancy. These genotypes thus provide useful resources for further studies on genetic interactions that contribute to the overall phenotypic variation and on genetic dissection of quantitative trait loci underlying PHS resistance. doi: 10.2135/cropsci2009.10.0589

The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some [10.sup.8] synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinema and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi. basidiomycete | dikaryon formation | gene families | kinase meiotic recombination doi/ 10.1073/pnas.1003391107

Variation in genome structure is an important source of human genetic polymorphism: It affects a large proportion of the genome and has a variety of phenotypic consequences relevant to health and disease. In spite of this, human genome structure variation is incompletely characterized due to a lack of approaches for discovering a broad range of structural variants in a global, comprehensive fashion. We addressed this gap with Optical Mapping, a high-throughput, high-resolution single-molecule system for studying genome structure. We used Optical Mapping to create genome-wide restriction maps of a complete hydatidiform mole and three lymphoblast-derived cell lines, and we validated the approach by demonstrating a strong concordance with existing methods. We also describe thousands of new variants with sizes ranging from kb to Mb. structural variation | copy number variation | optical mapping | single-molecule genomics | genome assembly doi/ 10.1073/pnas.0914638107

Despite the key role of the linker histone H1 in chromatin structure and dynamics, its location and interactions with nucleosomal DNA have not been elucidated. In this work we have used a combination of electron cryomicroscopy, hydroxyl radical footprinting, and nanoscale modeling to analyze the structure of precisely positioned mono-, di-, and trinucleosomes containing physiologically assembled full-length histone H1 or truncated mutants of this protein. Single-base resolution OH footprinting shows that the globular domain of histone H1 (GH1) interacts with the DNA minor groove located at the center of the nucleosome and contacts a 10-bp region of DNA localized symmetrically with respect to the nucleosomal dyad. In addition, GH1 interacts with and organizes about one helical turn of DNA in each linker region of the nucleosome. We also find that a seven amino acid residue region (121-127) in the COOH terminus of histone H1 was required for the formation of the stem structure of the linker DNA. A molecular model on the basis of these data and coarse-grain DNA mechanics provides novel insights on how the different domains of H1 interact with the nucleosome and predicts a specific HI-mediated stem structure within linker DNA. nucleosome structure | chromatin higher order structure www.pnas.org/cgi/doi/10.1073/pnas.1000309107

Chromosome segregation and cell division are essential, highly ordered processes that depend on numerous protein complexes. Results from recent RNA interference screens indicate that the identity and composition of these protein complexes is incompletely understood. Using gene tagging on bacterial artificial chromosomes, protein localization, and tandem-affinity purification--mass spectrometry, the MitoCheck consortium has analyzed about 100 human protein complexes, many of which had not or had only incompletely been characterized. This work has ted to the discovery of previously unknown, evolutionarily conserved subunits of the anaphase-promoting complex and the [gamma]-tubutin ring complex--large complexes that are essential for spindle assembly and chromosome segregation. The approaches we describe here are generally applicable to high-throughput follow-up analyses of phenotypic screens in mammalian cells. doi: 10.1126/science.1181348

ABSTRACT Genetic linkage maps were constructed for the noble scallop Chlamys nobilis Reeve on the basis of 373 amplified fragment length polymorphisms (AFLPs) and 9 microsatellite markers. The pseudo test-cross [...]

It is well established that all of the cis-acting sequences required for fully regulated human [alpha]-globin expression are contained within a region of [approximately equal to]120 kb of conserved synteny. Here, we show that activation of this cluster in erythroid cells dramatically affects expression of apparently unrelated and noncontiguous genes in the 500 kb surrounding this domain, including a gene (NME4) located 300 kb from the [alpha]-globin cluster. Changes in NME4 expression are mediated by physical cis-interactions between this gene and the [alpha]-globin regulatory elements. Polymorphic structural variation within the globin cluster, altering the number of [alpha]-globin genes, affects the pattern of NME4 expression by altering the competition for the shared [alpha]-globin regulatory elements. These findings challenge the concept that the genome is organized into discrete, insulated regulatory domains. In addition, this work has important implications for our understanding of genome evolution, the interpretation of genome-wide expression, expression-quantitative trait loci, and copy number variant analyses. chromosome looping | copy number variants | globin gene expression | allele-specific expression | 4C doi/10.1073/pnas.0909331106

Chronic inflammation predisposes to a variety of human cancers. Affected tissues slowly accumulate mutations, some of which affect growth regulation and drive successive waves of clonal evolution, whereas a far greater number are functionally neutral and serve only to passively mark expanding clones. Ulcerative colitis (UC) is an inflammatory bowel disease, in which up to 10% of patients eventually develop colon cancer. Here we have mapped mutations in hypermutable intergenic and intronic polyguanine tracts in patients with UC to delineate the extent of clonal expansions associated with carcinogenesis. We genotyped colon biopsies for length altering mutations at 28 different polyguanine markers. In eight patients without neoplasia, we detected only two mutations in a single individual from among 37 total biopsies. In contrast, for 11 UC patients with neoplasia elsewhere in the colon, we identified 63 mutations in 51 nondysplastic biopsies, and every patient possessed at least one mutant clone. A subset of clones were large and extended over many square centimeters of colon. Of these, some occurred as isolated populations in nondysplastic tissue, considerably distant from neoplastic lesions. Other large clones included regions of cancer, suggesting that the tumor arose within a preexisting clonal field. Our results demonstrate that neutral mutations in polyguanine tracts serve as a unique tool for identifying fields of clonal expansions, which may prove clinically useful for distinguishing a subset of UC patients who are at risk for developing cancer. field effect | lineage mapping | neoplastic evolution doi/10.1073/pnas.0909428106

The human MHC represents the strongest susceptibility locus for autoimmune diseases. However, the identification of the true predisposing gene(s) has been handicapped by the strong linkage disequilibrium across the region. Furthermore, most studies to date have been limited to the examination of a subset of the HLA and non-HLA genes with a marker density and sample size insufficient for mapping all independent association signals. We genotyped a panel of 1,472 SNPs to capture the common genomic variation across the 3.44 megabase (Mb) classic MHC region in 10,576 DNA samples derived from patients with systemic lupus erythematosus, Crohn's disease, ulcerative colitis, rheumatoid arthritis, myasthenia gravis, selective IgA deficiency, multiple sclerosis, and appropriate control samples. We identified the primary association signals for each disease and performed conditional regression to identify independent secondary signals. The data demonstrate that MHC associations with autoimmune diseases result from complex, multilocus effects that span the entire region. autoimmunity | genes | genetics www.pnas.org/cgi/doi/10.1073/pnas.0909307106

Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among 'orphan crops' with limited genomic resources such as cowpea [Vigna unguiculata (L.) Walp.] (2n = 2x = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded [approximately equal to] 10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean (Glycine max) and Medicago truncatula, revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with Arabidopsis revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes. legume | diploid | recombinant inbred lines | segregating traits | 1536-plex genotyping doi/10.1073/pnas.0905886106

Upon detection of antigen, [CD4.sup.+] T helper (Th) cells can differentiate into a number of effector types that tailor the immune response to different pathogens. Alternative Th1 and Th2 cell fates are specified by the transcription factors T-bet and GATA-3, respectively. Only a handful of target genes are known for these two factors and because of this, the mechanism through which T-bet and GATA-3 induce differentiation toward alternative cell fates is not fully understood. Here, we provide a genomic map of T-bet and GATA-3 binding in primary human T cells and identify their target genes, most of which are previously unknown. In Th1 cells, T-bet associates with genes of diverse function, including those with roles in transcriptional regulation, chemotaxis and adhesion. GATA-3 occupies genes in both Th1 and Th2 cells and, unexpectedly, shares a large proportion of targets with T-bet. Re-complementation of T-bet alters the expression of these genes in a manner that mirrors their differential expression between Th1 and Th2 lineages. These data show that the choice between Th1 and Th2 lineage commitment is the result of the opposing action of T-bet and GATA-3 at a shared set of target genes and may provide a general paradigm for the interaction of lineage-specifying transcription factors. Genomic map | T helper differentiation | cytokines doi/ 10.1073/pnas.0909357106

We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and dosed chromatin to form two genome-wide compartments. At the megabase scare, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes. 10.1126/science.1181369