High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology

Background: Single-nucleotide polymorphisms (SNPs) are the most abundant type of DNA sequence polymorphisms. Their higher availability and stability when compared to simple sequence repeats (SSRs) provide enhanced possibilities for genetic and breeding applications such as cultivar identification, construction of genetic maps, the assessment of genetic diversity, the detection of genotype/phenotype associations, or marker-assisted breeding. In addition, the efficiency of these activities can be improved thanks to the ease with which SNP genotyping can be automated. Expressed sequence tags (EST) sequencing projects in grapevine are allowing for the in silico detection of multiple putative sequence polymorphisms within and among a reduced number of cultivars. In parallel, the sequence of the grapevine cultivar Pinot Noir is also providing thousands of polymorphisms present in this highly heterozygous genome. Still the general application of those SNPs requires further validation since their use could be restricted to those specific genotypes. Results: In order to develop a large SNP set of wide application in grapevine we followed a systematic re-sequencing approach in a group of 11 grape genotypes corresponding to ancient unrelated cultivars as well as wild plants. Using this approach, we have sequenced 230 gene fragments, what represents the analysis of over 1 Mb of grape DNA sequence. This analysis has allowed the discovery of 1573 SNPs with an average of one SNP every 64 bp (one SNP every 47 bp in non-coding regions and every 69 bp in coding regions). Nucleotide diversity in grape ( = 0.0051) was found to be similar to values observed in highly polymorphic plant species such as maize. The average number of haplotypes per gene sequence was estimated as six, with three haplotypes representing over 83% of the analyzed sequences. Short-range linkage disequilibrium (LD) studies within the analyzed sequences indicate the existence of a rapid decay of LD within the selected grapevine genotypes. To validate the use of the detected polymorphisms in genetic mapping, cultivar identification and genetic diversity studies we have used the SNPlex genotyping technology in a sample of grapevine genotypes and segregating progenies. Conclusion: These results provide accurate values for nucleotide diversity in coding sequences and a first estimate of short-range LD in grapevine. Using SNPlex genotyping we have shown the application of a set of discovered SNPs as molecular markers for cultivar identification, linkage mapping and genetic diversity studies. Thus, the combination a highly efficient re-sequencing approach and the SNPlex high throughput genotyping technology provide a powerful tool for grapevine genetic analysis. © 2007 Lijavetzky et al; licensee BioMed Central Ltd

Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15, 309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production

Gauging Away the Strong CP Problem

We propose a new solution to the strong-CP problem. It involves the existence of an unbroken gauged $U(1)_X$ symmetry whose gauge boson gets a Stuckelberg mass term by combining with a pseudoscalar field $\eta (x)$. The latter has axion-like couplings to $F_{QCD}\wedge F_{QCD}$ so that the theta parameter may be gauged away by a $U(1)_X$ gauge transformation. This system leads to mixed gauge anomalies and we argue that they are cancelled by the addition of an appropriate Wess-Zumino term, so that no SM fermions need to be charged under $U(1)_X$. We discuss scenarios in which the above set of fields and couplings appear. The mechanism is quite generic, but a natural possibility is that the the $U(1)_X$ symmetry arises from bulk gauge bosons in theories with extra dimensions or string models. We show that in certain D-brane Type-II string models (with antisymmetric tensor field strength fluxes) higher dimensional Chern-Simons couplings give rise to the required D=4 Wess-Zumino terms upon compactification. In one of the possible string realizations of the mechanism the $U(1)_X$ gauge boson comes from the Kaluza-Klein reduction of the eleven-dimensional metric in M-theory.Comment: 21 pages, latex, one eps figure; v2 improved discussio

Paleopatología en la necrópolis mudéjar de El Raval (Crevillent, Alicante)

X Congreso Nacional de Paleopatología. Univesidad Autónoma de Madrid, septiembre de 200

Tres posibles casos de lepra en la Plaza del Castillo (Pamplona, Navarra)

X Congreso Nacional de Paleopatología. Univesidad Autónoma de Madrid, septiembre de 200

Exponential-Potential Scalar Field Universes I: The Bianchi I Models

We obtain a general exact solution of the Einstein field equations for the anisotropic Bianchi type I universes filled with an exponential-potential scalar field and study their dynamics. It is shown, in agreement with previous studies, that for a wide range of initial conditions the late-time behaviour of the models is that of a power-law inflating FRW universe. This property, does not hold, in contrast, when some degree of inhomogeneity is introduced, as discussed in our following paper II.Comment: 16 pages, Plain LaTeX, 1 Figure to be sent on request, to appear in Phys. Rev.

Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip

[EN] Background: The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. Results: Three generations (F3, Backcross 1 and Backcross 2) of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes. Conclusions: The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine genome annotation.This work was funded by MICINN projects AGL2008-04818-C03/GAN and CSD2007-00036. DPM was funded by a FPI Ph.D grant from the Spanish Ministerio de Educacion (BES-2009-025417). YR was funded by a FPU Ph.D grant from the Spanish Ministerio de Educacion (AP2008-01450). We want to thanks to Dr. Martien Groenen (Wageningen, NL) for the SNP annotation on porcine genome assembly, to Anna Mercade for her technical assistance with the SNPs genotyping and to Rita Benitez and Fabian Garcia for technical support.Fernández, A.; Pérez-Montarelo, D.; Barragan, C.; Ramayo-Caldas, Y.; Ibáñez-Escriche, N.; Castelló, A.; Noguera, J.... (2012). Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip. BMC Genetics. 13:1-11. https://doi.org/10.1186/1471-2156-13-41S11113Van Laere, A.-S., Nguyen, M., Braunschweig, M., Nezer, C., Collette, C., Moreau, L., … Andersson, L. (2003). A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature, 425(6960), 832-836. doi:10.1038/nature02064John, S., Shephard, N., Liu, G., Zeggini, E., Cao, M., Chen, W., … Kennedy, G. C. (2004). Whole-Genome Scan, in a Complex Disease, Using 11,245 Single-Nucleotide Polymorphisms: Comparison with Microsatellites. The American Journal of Human Genetics, 75(1), 54-64. doi:10.1086/422195Mercadé, A., Estellé, J., Noguera, J. L., Folch, J. M., Varona, L., Silió, L., … Pérez-Enciso, M. (2005). On growth, fatness, and form: A further look at porcine Chromosome 4 in an Iberian × Landrace cross. Mammalian Genome, 16(5), 374-382. doi:10.1007/s00335-004-2447-4Óvilo, C., Pérez-Enciso, M., Barragán, C., Clop, A., Rodríguez, C., Oliver, M. A., … Noguera, J. L. (2000). A QTL for intramuscular fat and backfat thickness is located on porcine Chromosome 6. Mammalian Genome, 11(4), 344-346. doi:10.1007/s003350010065Cristina, Ó., Oliver, A., Noguera, J. L., Clop, A., Barragán, C., Varona, L., … Silió, L. (2002). Test for positional candidate genes for body composition on pig chromosome 6. Genetics Selection Evolution, 34(4). doi:10.1186/1297-9686-34-4-465ÓVILO, C., FERNÁNDEZ, A., NOGUERA, J. L., BARRAGÁN, C., LETÓN, R., RODRÍGUEZ, C., … TORO, M. (2005). Fine mapping of porcine chromosome 6 QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross. Genetical Research, 85(1), 57-67. doi:10.1017/s0016672305007330Óvilo, C., Fernández, A., Fernández, A. I., Folch, J. M., Varona, L., Benítez, R., … Silió, L. (2010). Hypothalamic expression of porcine leptin receptor (LEPR), neuropeptide Y (NPY), and cocaine- and amphetamine-regulated transcript (CART) genes is influenced by LEPR genotype. Mammalian Genome, 21(11-12), 583-591. doi:10.1007/s00335-010-9307-1Estellé, J., Fernández, A. I., Pérez-Enciso, M., Fernández, A., Rodríguez, C., Sánchez, A., … Folch, J. M. (2009). A non-synonymous mutation in a conserved site of theMTTPgene is strongly associated with protein activity and fatty acid profile in pigs. Animal Genetics, 40(6), 813-820. doi:10.1111/j.1365-2052.2009.01922.xEstellé, J., Pérez-Enciso, M., Mercadé, A., Varona, L., Alves, E., Sánchez, A., & Folch, J. M. (2006). Characterization of the porcine FABP5 gene and its association with the FAT1 QTL in an Iberian by Landrace cross. Animal Genetics, 37(6), 589-591. doi:10.1111/j.1365-2052.2006.01535.xMercadé, A., Pérez-Enciso, M., Varona, L., Alves, E., Noguera, J. L., Sánchez, A., & Folch, J. M. (2006). Adipocyte fatty-acid binding protein is closely associated to the porcine FAT1 locus on chromosome 41. Journal of Animal Science, 84(11), 2907-2913. doi:10.2527/jas.2005-663Evans, D. M., & Cardon, L. R. (2004). Guidelines for Genotyping in Genomewide Linkage Studies: Single-Nucleotide–Polymorphism Maps Versus Microsatellite Maps. The American Journal of Human Genetics, 75(4), 687-692. doi:10.1086/424696Gonzalez-Neira, A., Rosa-Rosa, J., Osorio, A., Gonzalez, E., Southey, M., Sinilnikova, O., … Benitez, J. (2007). Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studies. BMC Genomics, 8(1), 299. doi:10.1186/1471-2164-8-299Chioza, B. A., Aicardi, J., Aschauer, H., Brouwer, O., Callenbach, P., Covanis, A., … Everett, K. V. (2009). Genome wide high density SNP-based linkage analysis of childhood absence epilepsy identifies a susceptibility locus on chromosome 3p23-p14. Epilepsy Research, 87(2-3), 247-255. doi:10.1016/j.eplepsyres.2009.09.010Ramos, A. M., Crooijmans, R. P. M. A., Affara, N. A., Amaral, A. J., Archibald, A. L., Beever, J. E., … Groenen, M. A. M. (2009). Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS ONE, 4(8), e6524. doi:10.1371/journal.pone.0006524Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., … Sham, P. C. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics, 81(3), 559-575. doi:10.1086/519795Barrett, J. C., Fry, B., Maller, J., & Daly, M. J. (2004). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265. doi:10.1093/bioinformatics/bth457Andersson, L., Haley, C., Ellegren, H., Knott, S., Johansson, M., Andersson, K., … et, al. (1994). Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science, 263(5154), 1771-1774. doi:10.1126/science.8134840Marklund, L., Nyström, P.-E., Stern, S., Andersson-Eklund, L., & Andersson, L. (1999). Confirmed quantitative trait loci for fatness and growth on pig chromosome 4. Heredity, 82(2), 134-141. doi:10.1038/sj.hdy.6884630Fan, B., Onteru, S. K., Du, Z.-Q., Garrick, D. J., Stalder, K. J., & Rothschild, M. F. (2011). Genome-Wide Association Study Identifies Loci for Body Composition and Structural Soundness Traits in Pigs. PLoS ONE, 6(2), e14726. doi:10.1371/journal.pone.0014726Bidanel, J.-P., Milan, D., Iannuccelli, N., Amigues, Y., Boscher, M.-Y., Bourgeois, F., … Chevalet, C. (2001). Detection of quantitative trait loci for growth and fatness in pigs. Genetics Selection Evolution, 33(3). doi:10.1186/1297-9686-33-3-289Geldermann, H., Čepica, S., Stratil, A., Bartenschlager, H., & Preuss, S. (2010). Genome-wide mapping of Quantitative Trait Loci for fatness, fat cell characteristics and fat metabolism in three porcine F2 crosses. Genetics Selection Evolution, 42(1). doi:10.1186/1297-9686-42-31Quintanilla, R., Milan, D., & Bidanel, J.-P. (2002). A further look at quantitative trait loci affecting growth and fatness in a cross between Meishan and Large White pig populations. Genetics Selection Evolution, 34(2), 193. doi:10.1186/1297-9686-34-2-193Sławińska, A., Siwek, M., Knol, E. F., Roelofs-Prins, D. T., van Wijk, H. J., Dibbits, B., & Bednarczyk, M. (2009). Validation of the QTL on SSC4 for meat and carcass quality traits in a commercial crossbred pig population. Journal of Animal Breeding and Genetics, 126(1), 43-51. doi:10.1111/j.1439-0388.2008.00753.xMilan, D., Bidanel, J.-P., Iannuccelli, N., Riquet, J., Amigues, Y., Gruand, J., … Chevalet, C. (2002). Detection of quantitative trait loci for carcass composition traits in pigs. Genetics Selection Evolution, 34(6), 705. doi:10.1186/1297-9686-34-6-705Guo, T., Ren, J., Yang, K., Ma, J., Zhang, Z., & Huang, L. (2009). Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2population. Animal Genetics, 40(2), 185-191. doi:10.1111/j.1365-2052.2008.01819.xLiu, G., Kim, J. J., Jonas, E., Wimmers, K., Ponsuksili, S., Murani, E., … Schellander, K. (2008). Combined line-cross and half-sib QTL analysis in Duroc–Pietrain population. Mammalian Genome, 19(6), 429-438. doi:10.1007/s00335-008-9132-yKIM, C. W., HONG, Y. H., YUN, S.-I., LEE, S.-R., KIM, Y. H., KIM, M.-S., … CHANG, K.-T. (2006). Use of Microsatellite Markers to Detect Quantitative Trait Loci in Yorkshire Pigs. Journal of Reproduction and Development, 52(2), 229-237. doi:10.1262/jrd.17046Liu, G., Jennen, D. G. J., Tholen, E., Juengst, H., Kleinwächter, T., Hölker, M., … Wimmers, K. (2007). A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Animal Genetics, 38(3), 241-252. doi:10.1111/j.1365-2052.2007.01592.xXu, X. L., Xu, X. W., Pan, P. W., Li, K., Jiang, Z. H., Yu, M., … Liu, B. (2009). Porcine skeletal muscle differentially expressed geneCMYA1: isolation, characterization, mapping, expression and association analysis with carcass traits. Animal Genetics, 40(3), 255-261. doi:10.1111/j.1365-2052.2008.01825.xRamos, A. M., Bastiaansen, J. W. M., Plastow, G. S., & Rothschild, M. F. (2009). Genes located on a SSC17 meat quality QTL region are associated with growth in outbred pig populations. Animal Genetics, 40(5), 774-778. doi:10.1111/j.1365-2052.2009.01907.xRusso, V., Fontanesi, L., Scotti, E., Beretti, F., Davoli, R., Nanni Costa, L., … Buttazzoni, L. (2008). Single nucleotide polymorphisms in several porcine cathepsin genes are associated with growth, carcass, and production traits in Italian Large White pigs1. Journal of Animal Science, 86(12), 3300-3314. doi:10.2527/jas.2008-0920Tsai, F.-J., Yang, C.-F., Chen, C.-C., Chuang, L.-M., Lu, C.-H., Chang, C.-T., … Wu, J.-Y. (2010). A Genome-Wide Association Study Identifies Susceptibility Variants for Type 2 Diabetes in Han Chinese. PLoS Genetics, 6(2), e1000847. doi:10.1371/journal.pgen.1000847Silva, K. M., Bastiaansen, J. W. M., Knol, E. F., Merks, J. W. M., Lopes, P. S., Guimarães, S. E. F., & van Arendonk, J. A. M. (2010). Meta-analysis of results from quantitative trait loci mapping studies on pig chromosome 4. Animal Genetics, 42(3), 280-292. doi:10.1111/j.1365-2052.2010.02145.xFontanesi, L., Scotti, E., Buttazzoni, L., Dall’Olio, S., Davoli, R., & Russo, V. (2009). A single nucleotide polymorphism in the porcine cathepsin K (CTSK) gene is associated with back fat thickness and production traits in Italian Duroc pigs. Molecular Biology Reports, 37(1), 491-495. doi:10.1007/s11033-009-9678-0Ojeda, A., Estellé, J., Folch, J. M., & Pérez-Enciso, M. (2008). Nucleotide variability and linkage disequilibrium patterns at the porcineFABP5gene. Animal Genetics, 39(5), 468-473. doi:10.1111/j.1365-2052.2008.01752.xHan, S.-H., Shin, K.-Y., Lee, S.-S., Ko, M.-S., Jeong, D. K., Oh, H.-S., … Cho, I.-C. (2009). SINE indel polymorphism of AGL gene and association with growth and carcass traits in Landrace × Jeju black pig F2 population. Molecular Biology Reports, 37(1), 467-471. doi:10.1007/s11033-009-9644-xYamauchi, T., Kamon, J., Ito, Y., Tsuchida, A., Yokomizo, T., Kita, S., … Kadowaki, T. (2003). Cloning of adiponectin receptors that mediate antidiabetic metabolic effects. Nature, 423(6941), 762-769. doi:10.1038/nature01705Grundberg, E., Brandstrom, H., Ribom, E., Ljunggren, O., Mallmin, H., & Kindmark, A. (2004). Genetic variation in the human vitamin D receptor is associated with muscle strength, fat mass and body weight in Swedish women. European Journal of Endocrinology, 323-328. doi:10.1530/eje.0.1500323Muñoz, G., Alcázar, E., Fernández, A., Barragán, C., Carrasco, A., de Pedro, E., … Rodríguez, M. C. (2011). Effects of porcine MC4R and LEPR polymorphisms, gender and Duroc sire line on economic traits in Duroc×Iberian crossbred pigs. Meat Science, 88(1), 169-173. doi:10.1016/j.meatsci.2010.12.018Krzęcio, E., Koćwin-Podsiadła, M., Kurył, J., Zybert, A., Sieczkowska, H., & Antosik, K. (2008). The effect of interaction between genotype CAST/RsaI (calpastatin) and MYOG/MspI (myogenin) on carcass and meat quality in pigs free of RYR1T allele. Meat Science, 80(4), 1106-1115. doi:10.1016/j.meatsci.2008.05.002Wyszyńska-Koko, J., Pierzchała, M., Flisikowski, K., Kamyczek, M., Różycki, M., & Kurył, J. (2006). Polymorphisms in coding and regulatory regions of the porcineMYF6 andMYOG genes and expression of theMYF6 gene inm. longissimus dorsi versus productive traits in pigs. Journal of Applied Genetics, 47(2), 131-138. doi:10.1007/bf03194612IKEDA, T., KANAZAWA, T., OTSUKA, S., ICHII, O., HASHIMOTO, Y., & KON, Y. (2009). Expression of Caspase Family and Muscle- and Apoptosis-Specific Genes during Skeletal Myogenesis in Mouse Embryo. Journal of Veterinary Medical Science, 71(9), 1161-1168. doi:10.1292/jvms.71.1161Lin, Z., Lou, Y., & Squires, E. J. (2006). Functional polymorphism in porcine CYP2E1 gene: Its association with skatole levels. The Journal of Steroid Biochemistry and Molecular Biology, 99(4-5), 231-237. doi:10.1016/j.jsbmb.2005.07.001Aubert, J., Begriche, K., Knockaert, L., Robin, M. A., & Fromenty, B. (2011). Increased expression of cytochrome P450 2E1 in nonalcoholic fatty liver disease: Mechanisms and pathophysiological role. Clinics and Research in Hepatology and Gastroenterology, 35(10), 630-637. doi:10.1016/j.clinre.2011.04.015Latreille, M., Laberge, M.-K., Bourret, G., Yamani, L., & Larose, L. (2011). Deletion of Nck1 attenuates hepatic ER stress signaling and improves glucose tolerance and insulin signaling in liver of obese mice. American Journal of Physiology-Endocrinology and Metabolism, 300(3), E423-E434. doi:10.1152/ajpendo.00088.2010Akerfeldt, M. C., & Laybutt, D. R. (2011). Inhibition of Id1 Augments Insulin Secretion and Protects Against High-Fat Diet-Induced Glucose Intolerance. Diabetes, 60(10), 2506-2514. doi:10.2337/db11-008

Estudio paleopatológico de la necrópolis mudéjar de la calle Colón, 3 (Novelda, Alicante)

X Congreso Nacional de Paleopatología. Univesidad Autónoma de Madrid, septiembre de 200