Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

BackgroundDense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. ResultsSNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. ConclusionsThis manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection

Characterisation of a Wheat Breeders’ Array suitable for high throughput SNP genotyping of global accessions of hexaploid bread wheat (<i>Triticum aestivium</i>)

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'

Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)

Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results: This 90K "SNP-Chip" was tested in several river buffalo populations and found to have ∼70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.Daniela Iamartino, Ezequiel L. Nicolazzi, Curtis P. Van Tassell, James M. Reecy, Eric R. Fritz-Waters, James E. Koltes, Stefano Biffani, Tad S. Sonstegard, Steven G. Schroeder, Paolo Ajmone-Marsan, Riccardo Negrini, Rolando Pasquariello, Paola Ramelli, Angelo Coletta, José F. Garcia, Ahmad Ali, Luigi Ramunno, Gianfranco Cosenza, Denise A.A. de Oliveira, Marcela G. Drummond, Eduardo Bastianetto, Alessandro Davassi, Ali Pirani, Fiona Brew, John L. William

Itrio en la Ría de Vigo (NO Península Ibérica): Origen, distribución y valores de fondo

9 páginas, 3 figuras, 1 tabla.[EN] Certain heavy minerals enriched in yttrium, such as monazite and xenotime, have previously been indexed in the Vigo area. The levels and spatial distribution of this element were studied in 50 surface sediment samples from the Vigo Ria. The highest levels were found along the southern margin in the middle of the ria, coinciding with the geological source of the Galiñeiro Complex. From this zone, a dilution of yttrium in the sediments was observed seaward due to the presence of calcium carbonate (outer ria) and upstream due to the input of migmatites, anatexites, and two-mica granites (inner ria). The estimated background concentration in the Vigo Ria was 14.6 ± 2.6 mg kg–1 (Sc normalized), which is close to the average concentration found in surface sediments (13.4 ± 5.4 mg kg–1). This suggests that yttrium in the Vigo Ria sediments is mainly of lithogenic origin.[ES] Con base en el registro de minerales pesados ricos en itrio tales como la monacita y la xenotima en el área de Vigo, se midieron los contenidos y la distribución de este elemento en 50 muestras de sedimento superficial de la ría de Vigo. Se encontraron los valores más altos en el margen sur de la mitad de la ría, lo cual coincide con una característica geológica procedente del Complejo del Galiñeiro. Se observó, a partir de esta zona, una dilución de itrio debida a la presencia de carbonato de calcio en la parte externa de la ría y además por la entrada de migmatitas, anatemitas y granitos de dos micas en la parte interna de la ría. El valor de fondo medio calculado para la ría de Vigo fue de 14.6 ± 2.6 mg kg–1 (normalizado con Sc) el cual es cercano a la concentración media estimada en los sedimentos superficiales 13.4 ± 5.4 mg kg–1. El origen de itrio en la ría de Vigo es principalmente litogénico.Este trabajo es una contribución al programa LOICZ-España en coordinación con el proyecto "Balance biogeoquímicos y modelado de flujos de metales en una ría Gallega (METRIA)" financiado por CICYT (ref. REN2003-04106-C03). La primera autora agradece a la COFAA-EDI-COTEPABE-IPN (Mexico) el apoyo financiero para realizar una estancia de investigación en el IIM-CSIC (España).Peer reviewe

Complications in Spinal Fusion Surgery: A Systematic Review of Clinically Used Cages

Spinal fusion (SF) comprises surgical procedures for several pathologies that affect different spinal levels, and different cages are employed in SF surgery. Few clinical studies highlight the role of cages in complications beyond the outcomes. The aim of this systematic review is to collect the last 10 years’ worth of clinical studies that include cages in SF surgery, focusing on complications. Three databases are employed, and 21 clinical studies are included. The most-performed SF procedure was anterior cervical discectomy and fusion (ACDF), followed by lumbar SF. The polyetheretherketone (PEEK) cage was the most-used, and it was usually associated with autograft or calcium phosphate ceramics (hydroxyapatite (HA) and tricalcium phosphate (βTCP)). For lumbar SF procedures, the highest percentages of subsidence and pseudoarthrosis were observed with PEEK filled with bone morphogenetic protein 2 (BMP2) and βTCP. For ACDF procedures, PEEK filled with autograft showed the highest percentages of subsidence and pseudoarthrosis. Most studies highlighted the role of surgical techniques in patient complications. There are many interacting events that contextually affect the rate of clinical success or failure. Therefore, in future clinical studies, attention should focus on cages to improve knowledge of chemical, biological and topographical characteristics to improve bone growth and to counteract complications such as cage loosening or breaking and infections

A step change in the transfer of interspecific variation into wheat from Amblyopyrum muticum

Despite some notable successes, only a fraction of the genetic variation available in wild relatives has been utilized to produce superior wheat varieties. This is as a direct result of the lack of availability of suitable high-throughput technologies to detect wheat/wild relative introgressions when they occur. Here, we report on the use of a new SNP array to detect wheat/wild relative introgressions in backcross progenies derived from interspecific hexaploid wheat/Ambylopyrum muticum F₁ hybrids. The array enabled the detection and characterization of 218 genomewide wheat/Am. muticum introgressions, that is a significant step change in the generation and detection of introgressions compared to previous work in the field. Furthermore, the frequency of introgressions detected was sufficiently high to enable the construction of seven linkage groups of the Am. muticum genome, thus enabling the syntenic relationship between the wild relative and hexaploid wheat to be determined. The importance of the genetic variation from Am. muticum introduced into wheat for the development of superior varieties is discussed

High throughput SNP discovery and genotyping in hexaploid wheat

International audienceBecause of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms(SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In wheat, most of the previous SNP discovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genome largely unexploited. Here we report on the use of whole-genome resequencing data from eight wheat lines to mine for SNPs in the genic, the repetitive and non-repetitive intergenic fractions of the wheat genome. Eventually, we identified 3.3 million SNPs, 49% being located on the B-genome, 41% on the A-genome and 10% on the D-genome. We also describe the development of the TaBW280K high-throughput genotyping array containing 280,226 SNPs. Performance of this chip was examined by genotyping a set of 96 wheat accessions representing the worldwide diversity. Sixty-nine percent of the SNPs can be efficiently scored, half of them showing a diploid-like clustering. The TaBW280K was proven to be a very efficient tool for diversity analyses, as well as for breeding as it can discriminate between closely related elite varieties. Finally, the TaBW280K array was used to genotype a population derived from a cross between Chinese Spring and Renan, leading to the construction a dense genetic map comprising 83,721 markers. The results described here will provide the wheat community with powerful tools for both basic and applied research

Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)

Background The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results This 90K ªSNP-Chipº was tested in several river buffalo populations and found to have *70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.This article is published as Iamartino D, Nicolazzi EL, Van Tassell CP, Reecy JM, Fritz-Waters ER, Koltes JE, et al. (2017) Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis). PLoS ONE 12(10): e0185220. doi: 10.1371/journal.pone.0185220.</p