AFLP analysis of genetic diversity within Saccharum officinarum and comparison with sugarcane cultivars

Molecular diversity among 421 clones of cultivated sugarcane and wild relatives was analysed using AFLP markers. Of these clones, 270 were Saccharum officinarum and 151 were either cultivars produced by the Australian breeding program or important parents used in the breeding program. The S. of. cinarum clones were obtained from a collection that contained clones from all the major regions where S. of. cinarum is grown. Five AFLP primer combinations generated 657 markers ofwhich 614 were polymorphic. All clones contained a large number of markers; a result of the polyploid nature and heterozygosity of the genome. S. of. cinarum clones from New Guinea displayed greater diversity than S. of. cinarum clones from other regions. This is in agreement with the hypothesis that New Guinea is the centre of origin of this species. The S. of. cinarum clones from Hawaii and Fiji formed a separate group and may correspond to clones that have been introgressed with other members of the ` Saccharum complex'. Greater diversity was found in the cultivars than in the S. of. cinarum clones due to the introgression of S. spontaneum chromatin. These cultivars clustered as expected based on pedigree. The major contribution of clones QN66- 2008 and Nco310 to Australian sugarcane cultivars divided the cultivars into 2 main groups. Although only a fewS. of. cinarum clones are known to have been used in the breeding of current cultivars, about 90% of markers present in the S. of. cinarum clone collection ( 2n= 80) were also present in the cultivar collection. This suggests that most of the observed genetic diversity in S. of. cinarum has been captured in Australian sugarcane germplasm.

Identification of a novel frameshift mutation in the giant muscle filament titin in a large Australian family with dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is an etiologically heterogeneous cardiac disease characterized by left ventricular dilation and systolic dysfunction. Approximately 25-30% of DCM patients show a family history of mainly autosomal dominant inheritance. We and others have previously demonstrated that mutations in the giant muscle filament titin (TTN) can cause DCM. However, the prevalence of titin mutations in familial DCM is unknown. In this paper, we report a novel heterozygous 1-bp deletion mutation (c.62890delG) in TTN that cosegregates with DCM in a large Australian pedigree (A3). The TTN deletion mutation c.62890delG causes a frameshift, thereby generating a truncated A-band titin due to a premature stop codon (p.E20963KfsX10) and the addition of ten novel amino acid residues. The clinical phenotype of DCM in kindred A3 demonstrates incomplete penetrance and variable expressivity. Finally, protein analysis of a skeletal muscle biopsy sample from an affected member did not reveal the predicted truncated titin isoform although the aberrant mRNA was present, suggesting posttranslational modification and degradation of the truncated protein. The identification of a novel disease-causing mutation in the giant titin gene in a third large family with DCM indicates that mutations in titin may account for a significant portion of the genetic etiology in familial DCM.

EPCIS Event-Based traceability in pharmaceutical supply chains via automated generation of linked pedigrees

In this paper we show how event processing over semantically annotated streams of events can be exploited, for implementing tracing and tracking of products in supply chains through the automated generation of linked pedigrees. In our abstraction, events are encoded as spatially and temporally oriented named graphs, while linked pedigrees as RDF datasets are their specific compositions. We propose an algorithm that operates over streams of RDF annotated EPCIS events to generate linked pedigrees. We exemplify our approach using the pharmaceuticals supply chain and show how counterfeit detection is an implicit part of our pedigree generation. Our evaluation results show that for fast moving supply chains, smaller window sizes on event streams provide significantly higher efficiency in the generation of pedigrees as well as enable early counterfeit detection.

Variation in parent-offspring kinship in socially monogamous systems with extra-pair reproduction and inbreeding

Peer reviewed

Heritability and genetic correlations of personality traits in a wild population of yellow-bellied marmots (Marmota flaviventris)

This article is protected by copyright. All rights reserved. Acknowledgments We thank all the marmoteers that helped collect data over the years, and specifically Amanda Lea for help with the pedigree and Leon Chong for help in the field. The comments of two anonymous reviewers helped us improve our original MS. M.B.P. was funded by two U.S. Department of Education GAANN Fellowships, an NSF GK-12 Fellowship, and the UCLA Department of Ecology and Evolutionary Biology. J.G.A.M. was supported by a Marie-Curie Fellowship. D.T.B was supported by the National Geographic Society, UCLA (Faculty Senate and the Division of Life Sciences), a Rocky Mountain Biological Laboratory research fellowship and by the NSF (IDBR-0754247 and DEB-1119660 to D.T.B., as well as DBI 0242960 and 0731346 to the Rocky Mountain Biological Laboratory).

Mandibular Torus : A Synthesis of New and Previously Reported Data and a Discusssion of its Cause

Using original data on 1,5000 mandibles, but mainly previously published data, I present a overview of the distribution characteristics of mandibular torus and a hypothesis concerning its cause. Pedigree studies have established that genetic factors influence torus development. Extrinsic factors are strongly implicated by other evidence: prevalence among Arctic peoples, effect of dietary change, age regression, preponderance in males and on the right side, effect of cranial deformation, concurrence with palatine torus and maxillary alveolar exostoses, and clinical evidence. I propose that the primary factor is masticatory stress. According to a mechanism suggested by orthodontic research, the horizontal component of bite force tips the lower canine, premolars and first molar so that their root apices exert pressure on the periodontal membrane, causing formation of new bone on the lingual cortical plate of the alveolar process. Thus formed, the hyperostosis is vulnerable to trauma and its periosteal covering becomes bruised causing additional deposition of bone. Genes influence torus indirectly through their effect on occlusion. A patern of increased expressivity with incidence suggests that a quasicontinuous model may provide a better fit to pedigree data than single locus models previously tested.

Identification des gènes modifiant l’âge d’apparition du glaucome primaire à angle-ouvert dans une famille canadienne-française fondatrice.

Le glaucome est un groupe hétérogène de maladies qui sont caractérisées par l’apoptose des cellules ganglionnaires de la rétine et la dégénérescence progressive du nerf optique. Il s’agit de la première cause de cécité irréversible, qui touche environ 60 millions de personnes dans le monde. Sa forme la plus commune est le glaucome à angle ouvert (GAO), un trouble polygénique causé principalement par une prédisposition génétique, en interaction avec d’autres facteurs de risque tels que l’âge et la pression intraoculaire élevée (PIO). Le GAO est une maladie génétique complexe, bien que certaines formes sévères sont autosomiques dominantes. Dix-sept loci ont été liés à la maladie et acceptés par la « Human Genome Organisation » (HUGO) et cinq gènes ont été identifiés à ces loci (MYOC, OPTN, WDR36, NTF4, ASB10). Récemment, des études d’association sur l’ensemble du génome ont identifié plus de 20 facteurs de risque fréquents, avec des effets relativement faibles. Depuis plus de 50 ans, notre équipe étudie 749 membres de la grande famille canadienne-française CA où la mutation MYOCK423E cause une forme autosomale dominante de GAO dont l’âge de début est fortement variable. Premièrement, il a été montré que cette variabilité de l’âge de début de l’hypertension intraoculaire possède une importante composante génétique causée par au moins un gène modificateur. Ce modificateur interagit avec la mutation primaire et altère la sévérité du glaucome chez les porteurs de MYOCK423E. Un gène modificateur candidat WDR36 a été génotypé dans 2 grandes familles CA et BV. Les porteurs de variations non-synonymes de WDR36 ainsi que de MYOCK423E de la famille CA ont montré une tendance à développer la maladie plus jeune. Un outil de forage de données a été développé pour représenter des informations connues relatives à la maladie et faciliter la priorisation des gènes candidats. Cet outil a été appliqué avec succès à la dépression bipolaire et au glaucome. La suite du projet consiste à finaliser un balayage de génome sur la famille CA et à séquencer les loci afin d’identifier les variations modificatrices du glaucome. Éventuellement, ces variations permettront d’identifier les individus dont le glaucome risque d’être plus agressif.

Large national series of patients with Xq28 duplication involving MECP2: Delineation of brain MRI abnormalities in 30 affected patients.

Xq28 duplications encompassing MECP2 have been described in male patients with a severe neurodevelopmental disorder associated with hypotonia and spasticity, severe learning disability, stereotyped movements, and recurrent pulmonary infections. We report on standardized brain magnetic resonance imaging (MRI) data of 30 affected patients carrying an Xq28 duplication involving MECP2 of various sizes (228 kb to 11.7 Mb). The aim of this study was to seek recurrent malformations and attempt to determine whether variations in imaging features could be explained by differences in the size of the duplications. We showed that 93% of patients had brain MRI abnormalities such as corpus callosum abnormalities (n = 20), reduced volume of the white matter (WM) (n = 12), ventricular dilatation (n = 9), abnormal increased hyperintensities on T2-weighted images involving posterior periventricular WM (n = 6), and vermis hypoplasia (n = 5). The occipitofrontal circumference varied considerably between >+2SD in five patients and <-2SD in four patients. Among the nine patients with dilatation of the lateral ventricles, six had a duplication involving L1CAM. The only patient harboring bilateral posterior subependymal nodular heterotopia also carried an FLNA gene duplication. We could not demonstrate a correlation between periventricular WM hyperintensities/delayed myelination and duplication of the IKBKG gene. We thus conclude that patients with an Xq28 duplication involving MECP2 share some similar but non-specific brain abnormalities. These imaging features, therefore, could not constitute a diagnostic clue. The genotype-phenotype correlation failed to demonstrate a relationship between the presence of nodular heterotopia, ventricular dilatation, WM abnormalities, and the presence of FLNA, L1CAM, or IKBKG, respectively, in the duplicated segment.

Genome-Wiide estimates of coancestry, in breeding and effective population size in the Spanish Holstein population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

Predictive ability of Genomic Estimated Family Values (GEFV).

Genomic selection (GS) has been used to compute genomic estimated breeding values (GEBV) of individuals; however, it has only been applied to animal and major plant crops due to high costs. Besides, breeding and selection is performed at the family level in some crops. We aimed to study the implementation of genome-wide family selection (GWFS) in two loblolly pine (Pinus taeda L.) populations: i) the breeding population CCLONES composed of 63 families (5-20 individuals per family), phenotyped for four traits (stem diameter, stem rust susceptibility, tree stiffness and lignin content) and genotyped using an Illumina Infinium assay with 4740 polymorphic SNPs, and ii) a simulated population that reproduced the same pedigree as CCLONES, 5000 polymorphic loci and two traits (oligogenic and polygenic). In both populations, phenotypic and genotypic data was pooled at the family level in silico. Phenotypes were averaged across replicates for all the individuals and allele frequency was computed for each SNP. Marker effects were estimated at the individual (GEBV) and family (GEFV) levels with Bayes-B using the package BGLR in R and models were validated using 10-fold cross validations. Predicted ability, computed by correlating phenotypes with GEBV and GEFV, was always higher for GEFV in both populations, even after standardizing GEFV predictions to be comparable to GEBV. Results revealed great potential for using GWFS in breeding programs that select families, such as most outbreeding forage species. A significant drop in genotyping costs as one sample per family is needed would allow the application of GWFS in minor crops.

Evolução da estrutura populacional do núcleo de conservação de ovinos da raça Morada Nova da Embrapa Caprinos e Ovinos.

2015