Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm

Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs.The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species

Patogenicidad in vitro de Beauveria brongniartii (Sacc.) Petch en Musca domestica (L.) como posible estrategia de control biológico en áreas ganaderas

An experiment was carried out in order to study, in laboratory condition, the pathogenicity of Beauveria brongniartii (strain LF-05) against Musca domestica . The conidia of B. brongniartii were obtained from Perú. The fungus was propagated in potato-dextrose-agar culture medium, and later in semi-crude sterilized rice. F1 flies were obtained from wild specimens which were captured with mesh in a poultry breeding farm (Betijoque, Trujillo state, Venezuela). In the laboratory, one hundred and sixty adult flies from 3 days of age, divided into 8 lots with 17 to 40 per bottle flies were anesthetized with ether, and then applied B. brongniartii suspensions diluted in water from 108 conidia/mL, resulting in sis treatments: control, 1.2 x 103 , 1.2 x 104 , 1.2 x 105 , 1.2 x 106 , and 1.2 x 107 conidia/mL. Healthy controls with 100 flies were used with only ether as anesthesia. The counting of fallen flies, both in the experimental and bottles at checkpoints, it was up to 24 days. Using the Probit® methodology, it was found that the LT50 and LT95 were 11.08 and 13.25 days earlier than control group, respectively. Results showed that spores of B. brongniartii (strain LF-05), at 1.2 x107 conidia/mL, resulted in 95% mortality of M. domestica in 9.27 days. The use of nebulizations with similar concentration of spores to fly control in local production units of poultry and cattle were speculated.Se realizó un experimento con el objetivo de evaluar en condiciones de laboratorio la patogenicidad de Beauveria brongniartii (cepa LF-05) en Musca domestica . Las conidias de B. brongniartii se obtuvieron a partir de una cepa introducida desde Perú. El hongo fue propagado en medio de cultivo agar-papa-dextrosa y luego en arroz semicrudo esterilizado. Las moscas F1 se obtuvieron a partir de especimenes silvestres, los cuales fueron capturados en una granja avícola (Betijoque, Venezuela). Ciento sesenta moscas adultas de 3 días de edad, distribuidas en 8 lotes con 17 hasta 40 moscas por frasco fueron anestesiadas con éter, para posteriormente aplicar suspensiones de B. brongniartii diluida en agua a partir una suspensión madre de 108 conidias/mL, resultando seis tratamientos, en función de la concentración: sin aplicación del hongo; 1,2 x 103 ; 1,2 x 104 ; 1,2 x 105 ; 1,2 x 106 y 1,2 x 107 conidias/ mL. Se utilizaron además frascos controles con 100 moscas sanas que se sometieron únicamente a la anestesia con éter. El recuento de las moscas caídas, tanto en los frascos experimentales como en los controles, se hizo hasta el día 24. Mediante la metodología Probit® se determinó que los TL50 y TL95 se obtuvieron 11,08 y 13,25 días antes que en el control, respectivamente. Los resultados permiten concluir que esporas de B. brongniartii a 1,2 x 107 conidias/mL, produjeron 95% de mortalidad en M. domestica en 9,27 días. Se especula su uso en nebulizaciones con similar concentración del preparado para el control de la mosca en unidades de producción avícola, porcina y vacuna

Theoretical study of bulk and surface oxygen and aluminium vacancies in (alpha)-Al2O3

The formation energy, geometry, and electronic structure of isolated oxygen and aluminum vacancies in bulk and on the (0001) surface of corundum ( α − Al 2 O 3 ) have been investigated by means of periodic calculations in the framework of density functional theory within the generalized gradient approximation and large supercells. The energy cost to form an oxygen vacancy in the bulk is estimated to be of the order of 10 eV, whereas that corresponding to the formation of Al vacancies is found to be at least a 30% larger. The relaxation of the material is rather small for both defects. The removal of an oxygen atom in bulk α − Al 2 O 3 is accompanied by the appearance of an impurity level in the gap, which is a strong indication of electron localization. This has been further confirmed by integration of the density of states in the energy interval corresponding to the impurity level and by several other theoretical analyses. For the α − Al 2 O 3 ( 0001 ) surface, the formation of oxygen and aluminum vacancies exhibits many similarities with the bulk; the energy cost to form Al vacancies is much larger than for O vacancies and, in both cases, it is accompanied by rather small atomic displacements. However, there are also significant differences between bulk and surface oxygen and aluminum vacancies. Thus the formation energy of one of these point defects in the surface is rather smaller as expected and, more importantly, the degree of electronic delocalization is also larger

Transancestral mapping and genetic load in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disease with marked gender and ethnic disparities. We report a large transancestral association study of SLE using Immunochip genotype data from 27,574 individuals of European (EA), African (AA) and Hispanic Amerindian (HA) ancestry. We identify 58 distinct non-HLA regions in EA, 9 in AA and 16 in HA (similar to 50% of these regions have multiple independent associations); these include 24 novel SLE regions (P < 5 x 10(-8)), refined association signals in established regions, extended associations to additional ancestries, and a disentangled complex HLA multigenic effect. The risk allele count (genetic load) exhibits an accelerating pattern of SLE risk, leading us to posit a cumulative hit hypothesis for autoimmune disease. Comparing results across the three ancestries identifies both ancestry-dependent and ancestry-independent contributions to SLE risk. Our results are consistent with the unique and complex histories of the populations sampled, and collectively help clarify the genetic architecture and ethnic disparities in SLE.We gratefully acknowledge the Alliance for Lupus Research for funding and support. The research was supported in part by awards from the Arthritis Research UK Special Strategic Award (ref. 19289) and from George Koukis (T.J.V.). In addition, the research was funded/supported by the National Institute for Health Research (NIHR) Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust and King's College London (T.J.V.). The work would not be possible without funding from the NIH grants AR049084 (RPK, EEB); the International Consortium on the Genetics of Systemic Lupus Erythematosus (SLEGEN) AI083194 (J.B.H.); CA141700, AR058621 Proyecto de Excelencia, Consejeria de Andalucia (M.E.A.R.); AR043814 and AR-065626 (B.P.T.); AR060366, MD007909, AI107176 (S.K.N.); AR-057172 (C.O.J.); RC2 AR058959, U19 A1082714, R01 AR063124, P30 GM110766, R01 AR056360 (P.M.G.); P60 AR053308 (L.A.C.), MUSC part is from UL1RR029882 (G.S.G., D.L.K.) and 5P60AR062755 (G.S.G., D.L.K., P.R.R.). Oklahoma Samples U19AI082714, U01AI101934, P30GM103510, U54GM104938 and P30AR053483 (J.A.J., J.M.G.); Northwestern P60 AR066464 and 1U54TR001018 (R.R.G.); This study was supported by the US National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health (NIH) under Award Numbers K01 AR067280 and P60 AR062755 (PSR); N01AR22265 (funded collection of APPLE samples) (LES) and the APPLE Investigators; R01AR43727, NIH AR 043727 and 069572 (M.P.); NIAMS/NIH P50-AR055503 (D.R.K.). We would like to also thank the RILITE foundation for financial support (C.D.L.). Additional funding for Immunochip genotyping was provided by Genentech.Peer reviewe

Clinical risk assessment of organ manifestations in systemic sclerosis: A report from the EULAR Scleroderma Trials and Research group database

Background: Systemic sclerosis (SSc) is a multisystem autoimmune disease, which is classified into a diffuse cutaneous (dcSSc) and a limited cutaneous (IcSSc) subset according to the skin involvement. In order to better understand the vascular, immunological and fibrotic processes of SSc and to guide its treatment, the EULAR Scleroderma Trials And Research (EUSTAR) group was formed in June 2004. Aims and methods: EUSTAR collects prospectively the Minimal Essential Data Set (MEDS) on all sequential patients fulfilling the American College of Rheumatology diagnostic criteria in participating centres. We aimed to characterise demographic, clinical and laboratory characteristics of disease presentation in SSc and analysed EUSTAR baseline visits. Results: In April 2006, a total of 3656 patients (1349 with dcSSc and 2101 with IcSSc) were enrolled in 102 centres and 30 countries. 1330 individuals had autoantibodies against Scl70 and 1106 against anticentromere antibodies. 87% of patients were women. On multivariate analysis, scleroderma subsets (dcSSc vs IcSSc), antibody status and age at onset of Raynaud&apos;s phenomenon, but not gender, were found to be independently associated with the prevalence of organ manifestations. Autoantibody status in this analysis was more closely associated with clinical manifestations than were SSc subsets. Conclusion: dcSSc and IcSSc subsets are associated with particular organ manifestations, but in this analysis the clinical distinction seemed to be superseded by an antibody-based classification in predicting some scleroderma complications. The EUSTAR MEDS database facilitates the analysis of clinical patterns in SSc, and contributes to the standardised assessment and monitoring of SSc internationally