Authors: Forneris, Natalia Soledad; Steibel, J. P.; Legarra, Andres; Vitezica, Zulma G.; Bates, R. O.; Ernst, C. W.; Basso Abraham, Alicia Leonor Rufina; Cantet, Rodolfo Juan Carlos
Publication Date: 2016.
Language: English.
Abstract:
Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR -O) or the base population (GVR -B) allele frequencies and (ii) identity by descent using linkage analysis (GIBD -L). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. GIBD -L displayed the lowest sampling error and the highest correlation with true genome-shared values. GVR -B approximated GIBD -L's correlation and had lower error than GVR -O. Accuracy of GEBV for selection candidates was significantly higher when GIBD -L was used and identical between GVR -O and GVR -B. In real data, GIBD -L's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV.
Author affiliation: Forneris, Natalia Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina
Author affiliation: Steibel, J. P.. Michigan State University; Estados Unidos
Author affiliation: Legarra, Andres. Institut National de la Recherche Agronomique; Francia
Author affiliation: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia
Author affiliation: Bates, R. O.. Michigan State University; Estados Unidos
Author affiliation: Ernst, C. W.. Michigan State University; Estados Unidos
Author affiliation: Basso Abraham, Alicia Leonor Rufina. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Biología Aplicada y Alimentos; Argentina
Author affiliation: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas
Authors: Cavagnaro, Pablo; Iorizzo, Massimo; Yildiz, Mehtap; Senalik, Douglas A.; Parsons, Joshua; Ellison, Shelby L.; Simon, Philipp W.
Publication Date: 2014.
Language: English.
Abstract:
Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations.
EEA La Consulta
Author affiliation: Cavagnaro, Pablo. INTA. Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina. University of Wisconsin. Department of Horticulture; Estados Unidos
Author affiliation: Iorizzo, Massimo. University of Wisconsin. Department of Horticulture; Estados Unidos.
Author affiliation: Yildiz, Mehtap. Yuzuncu Yil University. Faculty of Agriculture. Department of Agricultural Biotechnology; Turquía
Author affiliation: Senalik, Douglas. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Author affiliation: Parsons, Joshua. University of Wisconsin. Department of Horticulture; Estados Unidos
Author affiliation: Ellison, Shelby. University of Wisconsin. Department of Horticulture; Estados Unidos
Author affiliation: Simon, Philipp. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Repository: INTA Digital (INTA). Instituto Nacional de Tecnología Agropecuaria
Authors: Adhikari, Kaustubh; Fuentes Guajardo, Macarena; Quinto Sanchez, Mirsha Emmanuel; Mendoza Revilla, Javier; Chacon Duque, Juan Camilo; Acuña Alonzo, Víctor; Jaramillo, Claudia; Arias, William; Barquera Lozano, Rodrigo; Macín Pérez, Gastón; Gómez Valdés, Jorge; Villamil Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio Cesar; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria Catira; Canizales Quinteros, Samuel; Cheeseman, Michael; Rosique, Javier; Bedoya Berrío, Gabriel; Rothhammer, Francisco; Headon, Denis; González José, Rolando; Balding, David; Ruiz Linares, Andrés
Publication Date: 2016.
Language: English.
Abstract:
We report a genome-wide association scan for facial features in â 1/46,000 Latin Americans. We evaluated 14 traits on an ordinal scale and found significant association (P values<5 × 10 â '8) at single-nucleotide polymorphisms (SNPs) in four genomic regions for three nose-related traits: columella inclination (4q31), nose bridge breadth (6p21) and nose wing breadth (7p13 and 20p11). In a subsample of â 1/43,000 individuals we obtained quantitative traits related to 9 of the ordinal phenotypes and, also, a measure of nasion position. Quantitative analyses confirmed the ordinal-based associations, identified SNPs in 2q12 associated to chin protrusion, and replicated the reported association of nasion position with SNPs in PAX3. Strongest association in 2q12, 4q31, 6p21 and 7p13 was observed for SNPs in the EDAR, DCHS2, RUNX2 and GLI3 genes, respectively. Associated SNPs in 20p11 extend to PAX1. Consistent with the effect of EDAR on chin protrusion, we documented alterations of mandible length in mice with modified Edar funtion.
Author affiliation: Adhikari, Kaustubh. University College London; Estados Unidos
Author affiliation: Fuentes Guajardo, Macarena. University College London; Estados Unidos. Universidad de Tarapacá; Chile
Author affiliation: Quinto Sanchez, Mirsha Emmanuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina
Author affiliation: Mendoza Revilla, Javier. University College London; Estados Unidos. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Chacon Duque, Juan Camilo. University College London; Estados Unidos
Author affiliation: Acuña Alonzo, Víctor. University College London; Estados Unidos. Escuela Nacional de Antropología e Historia; México
Author affiliation: Jaramillo, Claudia. Universidad de Antioquia; Colombia
Author affiliation: Arias, William. Universidad de Antioquia; Colombia
Author affiliation: Barquera Lozano, Rodrigo. Escuela Nacional de Antropología e Historia; México. Universidad Nacional Autónoma de México; México
Author affiliation: Macín Pérez, Gastón. Escuela Nacional de Antropología e Historia; México. Universidad Nacional Autónoma de México; México
Author affiliation: Gómez Valdés, Jorge. Universidad Nacional Autónoma de México; México
Author affiliation: Villamil Ramírez, Hugo. Universidad Nacional Autónoma de México; México
Author affiliation: Hunemeier, Tábita. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Silva de Cerqueira, Caio Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Hurtado, Malena. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Villegas, Valeria. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Granja, Vanessa. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Gallo, Carla. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Poletti, Giovanni. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Schuler Faccini, Lavinia. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Salzano, Francisco M.. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Bortolini, Maria Catira. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Canizales Quinteros, Samuel. Universidad Nacional Autónoma de México; México
Author affiliation: Cheeseman, Michael. University of Edinburgh; Reino Unido
Author affiliation: Rosique, Javier. Universidad de Antioquia; Colombia
Author affiliation: Bedoya Berrío, Gabriel. Universidad de Antioquia; Colombia
Author affiliation: Rothhammer, Francisco. Universidad de Tarapacá; Chile
Author affiliation: Headon, Denis. University of Edinburgh; Reino Unido
Author affiliation: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina
Author affiliation: Balding, David. University College London; Estados Unidos. University of Melbourne; Australia
Author affiliation: Ruiz Linares, Andrés. University College London; Estados Unidos
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas
Authors: Adhikari, Kaustubh; Fontanil, Tania; Cal, Santiago; Mendoza Revilla, Javier; Fuentes Guajardo, Macarena; Chacón Duque, Juan Camilo; Al Saadi, Farah; Johansson, Jeanette A.; Quinto Sanchez, Mirsha Emmanuel; Acuña Alonzo, Victor; Jaramillo, Claudia; Arias, William; Barquera Lozano, Rodrigo; Macín Pérez, Gastón; Gómez Valdés, Jorge; Villamil Ramírez, Hugo; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio Cesar; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria Catira; Canizales Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; González José, Rolando; Headon, Denis; López Otín, Carlos; Tobin, Desmond J.; Balding, David; Ruiz Linares, Andrés
Publication Date: 2016.
Language: English.
Abstract:
We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10-8 to 3 × 10-119), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair.
Author affiliation: Adhikari, Kaustubh. University College London; Reino Unido
Author affiliation: Fontanil, Tania. Universidad de Oviedo; España
Author affiliation: Cal, Santiago. Universidad de Oviedo; España
Author affiliation: Mendoza Revilla, Javier. University College London; Reino Unido. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Fuentes Guajardo, Macarena. University College London; Reino Unido. Universidad de Tarapacá; Chile
Author affiliation: Chacón Duque, Juan Camilo. University College London; Reino Unido
Author affiliation: Al Saadi, Farah. University College London; Reino Unido
Author affiliation: Johansson, Jeanette A.. University of Edinburgh; Reino Unido
Author affiliation: Quinto Sanchez, Mirsha Emmanuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina
Author affiliation: Acuña Alonzo, Victor. University College London; Reino Unido. Instituto Nacional de Antropología E Historia; México
Author affiliation: Jaramillo, Claudia. Universidad de Antioquia; Colombia
Author affiliation: Arias, William. Universidad de Antioquia; Colombia
Author affiliation: Barquera Lozano, Rodrigo. Instituto Nacional de Antropología E Historia; México. Universidad Nacional Autónoma de México; México
Author affiliation: Macín Pérez, Gastón. Instituto Nacional de Antropología E Historia; México. Universidad Nacional Autónoma de México; México
Author affiliation: Gómez Valdés, Jorge. Universidad Nacional Autónoma de México; México
Author affiliation: Villamil Ramírez, Hugo. Universidad Nacional Autónoma de México; México
Author affiliation: Hunemeier, Tábita. Universidade Federal do Rio Grande do Sul; Brasil. Universidade de Sao Paulo; Brasil
Author affiliation: Ramallo, Virginia. Universidade Federal do Rio Grande do Sul; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina
Author affiliation: Silva de Cerqueira, Caio Cesar. Universidade Federal do Rio Grande do Sul; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina
Author affiliation: Hurtado, Malena. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Villegas, Valeria. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Granja, Vanessa. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Gallo, Carla. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Poletti, Giovanni. Universidad Peruana Cayetano Heredia; Perú
Author affiliation: Schuler Faccini, Lavinia. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Salzano, Francisco M.. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Bortolini, Maria Catira. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Canizales Quinteros, Samuel. Universidad Nacional Autónoma de México; México
Author affiliation: Rothhammer, Francisco. Universidad de Tarapacá; Chile
Author affiliation: Bedoya, Gabriel. Universidad de Antioquia; Colombia
Author affiliation: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina
Author affiliation: Headon, Denis. University of Edinburgh; Reino Unido
Author affiliation: López Otín, Carlos. Universidad de Oviedo; España
Author affiliation: Tobin, Desmond J.. University of Bradford; Reino Unido
Author affiliation: Balding, David. University College London; Reino Unido. University of Melbourne; Australia
Author affiliation: Ruiz Linares, Andrés. University College London; Reino Unido
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas
Authors: Adhikari, Kaustubh; Reales, Guillermo; Smith, Andrew J. P.; Konka, Esra; Palmen, Jutta; Quinto Sanchez, Mirsha Emmanuel; Acuña Alonzo, Victor; Jaramillo, Claudia; Arias, Williams; Fuentes, Macarena; Pizarro, María; Barquera Lozano, Rodrigo; Macín Peréz, Gastón; Gómez-Valdés, Jorge; Vilamil-Ramirez, Hugo; Hünemeier, Tábita; Ramallo, Virginia; Cerqueira, Caio C. Silva de; Hurtado, Malena; Villegas, Valeria; Granja, Vanessa; Gallo, Carla; Poletti, Giovanni; Schuler Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria Cátira; Canizales Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Calderón, Rosario; Rosique, Javier; Cheeseman, Michael; Bhutta, Mahmood F.; Humphries, Steve E.; Gonzalez Jose, Rolando; Headon, Denis; Balding, David; Ruiz Linares, Andres
Publication Date: 2015.
Language: English.
Abstract:
Here we report a genome-wide association study for non-pathological pinna morphology in over 5,000 Latin Americans. We find genome-wide significant association at seven genomic regions affecting: lobe size and attachment, folding of antihelix, helix rolling, ear protrusion and antitragus size (linear regression P values 2108 to 31014). Four traits are associated with a functional variant in the Ectodysplasin A receptor (EDAR) gene, a key regulator of embryonic skin appendage development. We confirm expression of Edar in the developing mouse ear and that Edar-deficient mice have an abnormally shaped pinna. Two traits are associated with SNPs in a region overlapping the T-Box Protein 15 (TBX15) gene, a major determinant of mouse skeletal development. Strongest association in this region is observed for SNP rs17023457 located in an evolutionarily conserved binding site for the transcription factor Cartilage paired-class homeoprotein 1 (CART1), and we confirm that rs17023457 alters in vitro binding of CART1.
Author affiliation: Adhikari, Kaustubh. University College London. UCL Genetics Institute. Department of Genetics, Evolution and Environment; Reino Unido
Author affiliation: Reales, Guillermo. University College London. UCL Genetics Institute. Department of Genetics, Evolution and Environment; Reino Unido
Author affiliation: Smith, Andrew J. P.. University College London. Institute Cardiovascular Sciences. BHF Laboratories; Reino Unido
Author affiliation: Konka, Esra. University College London. UCL Genetics Institute. Department of Genetics, Evolution and Environment; Reino Unido
Author affiliation: Palmen, Jutta. University College London. Institute Cardiovascular Sciences. BHF Laboratories; Reino Unido
Author affiliation: Quinto Sanchez, Mirsha Emmanuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina
Author affiliation: Acuña Alonzo, Victor. University College London. UCL Genetics Institute. Department of Genetics, Evolution and Environment.; Reino Unido. National Institute of Anthropology and History; México
Author affiliation: Jaramillo, Claudia. Universidad de Antioquia; Colombia
Author affiliation: Arias, Williams. Universidad de Antioquia; Colombia
Author affiliation: Fuentes, Macarena. Universidad de Tarapacá. Facultad de Medicina Universidad de Chile y Centro de Investigaciones del Hombre en el Desierto. Instituto de Alta Investigación.; Chile
Author affiliation: Pizarro, María. Universidad de Tarapacá. Facultad de Medicina Universidad de Chile y Centro de Investigaciones del Hombre en el Desierto. Instituto de Alta Investigación; Chile
Author affiliation: Barquera Lozano, Rodrigo. National Institute of Anthropology and History; México. UNAM-Instituto Nacional de Medicina Genómica. Facultad de Química. Unidad de Genómica de Poblaciones Aplicada a la Salud; México
Author affiliation: Macín Peréz, Gastón. National Institute of Anthropology and History; México. Universidad Nacional Autónoma de México; México
Author affiliation: Gómez-Valdés, Jorge. Universidad Nacional Autónoma de México; México
Author affiliation: Vilamil-Ramirez, Hugo. Universidad Nacional Autónoma de México; México
Author affiliation: Hünemeier, Tábita. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Cerqueira, Caio C. Silva de. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Hurtado, Malena. Universidad Peruana Cayetano Heredia. Facultad de Ciencias y Filosofía. Laboratorios de Investigación y Desarrollo; Perú
Author affiliation: Villegas, Valeria. Universidad Peruana Cayetano Heredia. Facultad de Ciencias y Filosofía. Laboratorios de Investigación y Desarrollo; Perú
Author affiliation: Granja, Vanessa. Universidad Peruana Cayetano Heredia. Facultad de Ciencias y Filosofía. Laboratorios de Investigación y Desarrollo; Perú
Author affiliation: Gallo, Carla. Universidad Peruana Cayetano Heredia. Facultad de Ciencias y Filosofía. Laboratorios de Investigación y Desarrollo; Perú
Author affiliation: Poletti, Giovanni. Universidad Peruana Cayetano Heredia. Facultad de Ciencias y Filosofía. Laboratorios de Investigación y Desarrollo; Perú
Author affiliation: Schuler Faccini, Lavinia. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Salzano, Francisco M.. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Bortolini, Maria Cátira. Universidade Federal do Rio Grande do Sul; Brasil
Author affiliation: Canizales Quinteros, Samuel. Universidad Nacional Autónoma de México; México
Author affiliation: Rothhammer, Francisco. Universidad de Tarapacá. Facultad de Medicina Universidad de Chile y Centro de Investigaciones del Hombre en el Desierto. Instituto de Alta Investigación; Chile
Author affiliation: Bedoya, Gabriel. Universidad de Antioquia; Colombia
Author affiliation: Calderón, Rosario. Universidad Complutense de Madrid. Departamento de Zoología y Antropología Física; España
Author affiliation: Rosique, Javier. Universidad de Antioquia. Facultad de Ciencias Sociales y Humanas. Departamento de Antropología; Colombia
Author affiliation: Cheeseman, Michael. University of Edinburgh. The Roslin Institute and Royal (Dick) School of Veterinary Studies; Reino Unido
Author affiliation: Bhutta, Mahmood F.. University College London. UCL Ear Institute; Reino Unido. Royal National Throat Nose and Ear Hospital; Reino Unido
Author affiliation: Humphries, Steve E.. University College London. UCL Genetics Institute. Department of Genetics, Evolution and Environment; Reino Unido. University College London. Institute Cardiovascular Sciences. BHF Laboratories.; Reino Unido
Author affiliation: Gonzalez Jose, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina
Author affiliation: Headon, Denis. University of Edinburgh. The Roslin Institute and Royal (Dick) School of Veterinary Studies; Reino Unido
Author affiliation: Balding, David. University College London. UCL Genetics Institute. Department of Genetics, Evolution and Environment; Reino Unido. The University Of Melbourne; Australia
Author affiliation: Ruiz Linares, Andres. University College London. UCL Genetics Institute. Department of Genetics, Evolution and Environment; Reino Unido
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas
Authors: Iorizzo, Massimo; Ellison, Shelby L.; Senalik, Douglas A.; Peng, Zeng; Satapoomin, Pimchanok; Jiaying, Huang; Bowman, Megan; Iovene, Marina; Sanseverino, Walter; Cavagnaro, Pablo; Yildiz, Mehtap; Macko-Podgórni, Alicja; Moranska, Emilia; Grzebelus, Ewa; Grzebelus, Dariusz; Ashrafi, Hamid; Zhijun, Zheng; Shifeng, Cheng; Spooner, David M.; Deynze, Allen Van; Simon, Philipp W.
Publication Date: 2016.
Language: English.
Abstract:
We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.
EEA La Consulta
Author affiliation: Iorizzo, Massimo. University of Wisconsin. Department of Horticulture; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados Unidos
Author affiliation: Ellison, Shelby L. University of Wisconsin. Department of Horticulture; Estados Unidos
Author affiliation: Senalik, Douglas A. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Author affiliation: Peng, Zeng. Beijing Genomics Institute–Shenzhen; China
Author affiliation: Satapoomin, Pimchanok. University of Wisconsin. Department of Horticulture; Estados Unidos
Author affiliation: Jiaying, Huang. Beijing Genomics Institute–Shenzhen; China
Author affiliation: Bowman, Megan. Michigan State University. Department of Plant Biology; Estados Unidos
Author affiliation: Iovene, Marina. Consiglio Nazionale delle Ricerche. Istituto di Bioscienze e Biorisorse; Italia
Author affiliation: Sanseverino, Walter. Sequentia Biotech; España
Author affiliation: Cavagnaro, Pablo Federico. . INTA. Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Author affiliation: Yildiz, Mehtap. Yuzuncu Yil University. Faculty of Agriculture. Department of Agricultural Biotechnology; Turquía
Author affiliation: Macko-Podgórni, Alicja. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Author affiliation: Moranska, Emilia. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Author affiliation: Grzebelus, Ewa. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Author affiliation: Grzebelus, Dariusz. University of Agriculture in Krakow. Institute of Plant Biology and Biotechnology; Polonia
Author affiliation: Ashrafi, Hamid. University of California. Seed Biotechnology Center; Estados Unidos. North Carolina State University. Plants for Human Health Institute, Department of Horticultural Science; Estados Unidos
Author affiliation: Zhijun, Zheng. Beijing Genomics Institute–Shenzhen; China
Author affiliation: Shifeng, Cheng. Beijing Genomics Institute–Shenzhen; China
Author affiliation: Spooner, David M. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Author affiliation: Deynze, Allen Van. University of California. Seed Biotechnology Center; Estados Unidos
Author affiliation: Simon, Philipp W. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department of Agriculture–Agricultural Research Service. Vegetable Crops Research Unit; Estados Unidos
Keywords: Zanahoria; Genomas; Carotenoides; Carrots; Genomes; Carotenoids.
Repository: INTA Digital (INTA). Instituto Nacional de Tecnología Agropecuaria
Authors: Iorizzo, Massimo; Ellison, Shelby; Senalik, Douglas A.; Zeng, Peng; Satapoomin, Pimchanok; Huang, Jiaying; Bowman, Megan; Iovene, Marina; Sanseverino, Walter; Cavagnaro, Pablo Federico; Yildiz, Mehtap; Macko Podgórni, Alicja; Moranska, Emilia; Grzebelus, Ewa; Grzebelus, Dariusz; Ashrafi, Hamid; Zheng, Zhijun; Cheng, Shifeng; Spooner, David; Van Deynze, Allen; Simon, Philipp
Publication Date: 2016.
Language: English.
Abstract:
We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR-032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR-032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.
Author affiliation: Iorizzo, Massimo. North Carolina State University; Estados Unidos. University Of Wisconsin Madison; Estados Unidos
Author affiliation: Ellison, Shelby. University Of Wisconsin Madison; Estados Unidos
Author affiliation: Senalik, Douglas A.. University Of Wisconsin Madison; . US Department of Agriculture; Estados Unidos
Author affiliation: Zeng, Peng. Beijing Genomics Institute–Shenzhen; China
Author affiliation: Satapoomin, Pimchanok. University Of Wisconsin Madison; Estados Unidos
Author affiliation: Huang, Jiaying. Beijing Genomics Institute–Shenzhen; China
Author affiliation: Bowman, Megan. Michigan State University; Estados Unidos
Author affiliation: Iovene, Marina. Consiglio Nazionale delle Ricerche; Italia
Author affiliation: Sanseverino, Walter. Sequentia Biotech; España
Author affiliation: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Cuyo; Argentina. Instituto Nacional de Tecnología Agropecuaria; Argentina
Author affiliation: Yildiz, Mehtap. Yuzuncu Yil Universitesi; Turquía
Author affiliation: Macko Podgórni, Alicja. niversity of Agriculture in Krakow; Polonia
Author affiliation: Moranska, Emilia. niversity of Agriculture in Krakow; Polonia
Author affiliation: Grzebelus, Ewa. niversity of Agriculture in Krakow; Polonia
Author affiliation: Grzebelus, Dariusz. niversity of Agriculture in Krakow; Polonia
Author affiliation: Ashrafi, Hamid. North Carolina State University; Estados Unidos. University of California at Davis; Estados Unidos
Author affiliation: Zheng, Zhijun. Beijing Genomics Institute–Shenzhen; China
Author affiliation: Cheng, Shifeng. Beijing Genomics Institute–Shenzhen; China
Author affiliation: Spooner, David. University Of Wisconsin Madison; Estados Unidos. US Department of Agriculture; Estados Unidos
Author affiliation: Van Deynze, Allen. University of California at Davis; Estados Unidos
Author affiliation: Simon, Philipp. University Of Wisconsin Madison; Estados Unidos. US Department of Agriculture; Estados Unidos
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas
Authors: Westbury, Michael; Baleka, Sina; Barlow, Axel; Hartmann, Stefanie; Paijmans, Johanna L.A.; Kramarz, Alejandro Gustavo; Forasiepi, Analia Marta; Bond, Mariano; Gelfo, Javier Nicolás; Reguero, Marcelo Alfredo; López Mendoza, Patricio Gonzalo; Taglioretti, Matias Luciano; Scaglia, Fernando; Rinderknecht, Andrés; Jones, Washington; Mena, Francisco; Billet, Guillaume; de Muizon, Christian; Aguilar, José Luis; Macphee, Ross Douglas Earle; Hofreiter, Michael
Publication Date: 2017.
Language: English.
Abstract:
The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of -1/466 Ma (95% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.
Author affiliation: Westbury, Michael. Universitat Potsdam; Alemania
Author affiliation: Baleka, Sina. Universitat Potsdam; Alemania
Author affiliation: Barlow, Axel. Universitat Potsdam; Alemania
Author affiliation: Hartmann, Stefanie. Universitat Potsdam; Alemania
Author affiliation: Paijmans, Johanna L.A.. Universitat Potsdam; Alemania
Author affiliation: Kramarz, Alejandro Gustavo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; Argentina
Author affiliation: Forasiepi, Analia Marta. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; Argentina
Author affiliation: Bond, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentina
Author affiliation: Gelfo, Javier Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentina
Author affiliation: Reguero, Marcelo Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentina
Author affiliation: López Mendoza, Patricio Gonzalo. Center for Maritime Archeology Research of the South Eastern Pacific; Chile
Author affiliation: Taglioretti, Matias Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata; Argentina. Provincia de Buenos Aires. Municipalidad de General Pueyrredon. Secretaría de Cultura. Museo Municipal de Ciencias Naturales Lorenzo Scaglia; Argentina
Author affiliation: Scaglia, Fernando. Provincia de Buenos Aires. Municipalidad de General Pueyrredon. Secretaría de Cultura. Museo Municipal de Ciencias Naturales Lorenzo Scaglia; Argentina
Author affiliation: Rinderknecht, Andrés. Museo Nacional de Historia Natural; Uruguay
Author affiliation: Jones, Washington. Museo Nacional de Historia Natural; Uruguay
Author affiliation: Mena, Francisco. Centro de Investigacinn En Ecosistemas de la Patagonia; Chile
Author affiliation: Billet, Guillaume. Museum National d'Histoire Naturelle; Francia
Author affiliation: de Muizon, Christian. Museum National d'Histoire Naturelle; Francia
Author affiliation: Aguilar, José Luis. Museo Paleontologico San Pedro; Argentina
Author affiliation: Macphee, Ross Douglas Earle. American Museum of Natural History; Estados Unidos
Author affiliation: Hofreiter, Michael. Universitat Potsdam; Alemania
Keywords: DNA; Mitochondrial genome; Macrauchenia; Panperissodactyla; Litopterna; Notoungulata; Darwin; Otras Ciencias Biológicas; Ciencias Biológicas; CIENCIAS NATURALES Y EXACTAS; Paleontología; Ciencias de la Tierra y relacionadas con el Medio Ambiente; CIENCIAS NATURALES Y EXACTAS; Meteorología y Ciencias Atmosféricas; Ciencias de la Tierra y relacionadas con el Medio Ambiente; CIENCIAS NATURALES Y EXACTAS.
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas
Authors: Polat, Meripet; Takeshima, Shin-nosuke; Hosomichi, Kazuyoshi; Kim, Jiyun; Miyasaka, Taku; Yamada, Kazunori; Arainga, Mariluz; Murakami, Tomoyuki; Matsumoto, Yuki; de la Barra Diaz, Verónica; Panei, Carlos Javier; Gonzalez, Ester Teresa; Kanemaki, Misao; Onuma, Misao; Giovambattista, Guillermo; Aida, Yoko
Publication Date: 2016.
Language: English.
Abstract:
Background: Bovine leukemia virus (BLV) is a member of retroviridae family, together with human T cell leukemia virus types 1 and 2 (HTLV-1 and -2) belonging to the genes deltaretrovirus, and infects cattle worldwide. Previous studies have classified the env sequences of BLV provirus from different geographic locations into eight genetic groups. To investigate the genetic variability of BLV in South America, we performed phylogenetic analyses of whole genome and partial env gp51 sequences of BLV strains isolated from Peru, Paraguay and Bolivia, for which no the molecular characteristics of BLV have previously been published, and discovered a novel BLV genotype, genotype-9, in Bolivia. Results: In Peru and Paraguay, 42.3 % (139/328) and over 50 % (76/139) of samples, respectively, were BLV positive. In Bolivia, the BLV infection rate was up to 30 % (156/507) at the individual level. In Argentina, 325/420 samples were BLV positive, with a BLV prevalence of 77.4 % at the individual level and up to 90.9 % at herd level. By contrast, relatively few BLV positive samples were detected in Chile, with a maximum of 29.1 % BLV infection at the individual level. We performed phylogenetic analyses using two different approaches, maximum likelihood (ML) tree and Bayesian inference, using 35 distinct partial env gp51 sequences from BLV strains isolated from Peru, Paraguay, and Bolivia, and 74 known BLV strains, representing eight different BLV genotypes from various geographical locations worldwide. The results indicated that Peruvian and Paraguayan BLV strains were grouped into genotypes-1, -2, and -6, while those from Bolivia were clustered into genotypes-1, -2, and -6, and a new genotype, genotype-9. Interestingly, these results were confirmed using ML phylogenetic analysis of whole genome sequences obtained by next generation sequencing of 25 BLV strains, assigned to four different genotypes (genotypes-1, -2, -6, and -9) from Peru, Paraguay, and Bolivia. Comparative analyses of complete genome sequences clearly showed some specific substitutions, in both structural and non-structural BLV genes, distinguishing the novel genotype-9 from known genotypes. Conclusions: Our results demonstrate widespread BLV infection in South American cattle and the existence of a new BLV genotype-9 in Bolivia. We conclude that at least seven BLV genotypes (genotypes-1, -2, -4, -5, -6, -7, and -9) are circulating in South America.
Author affiliation: Polat, Meripet. University of Tokyo; Japón. RIKEN; Japón
Author affiliation: Takeshima, Shin-nosuke. University of Tokyo; Japón. RIKEN; Japón
Author affiliation: Hosomichi, Kazuyoshi. Kanazawa University; Japón
Author affiliation: Kim, Jiyun. RIKEN; Japón
Author affiliation: Miyasaka, Taku. RIKEN; Japón
Author affiliation: Yamada, Kazunori. RIKEN; Japón
Author affiliation: Arainga, Mariluz. RIKEN; Japón
Author affiliation: Murakami, Tomoyuki. RIKEN; Japón
Author affiliation: Matsumoto, Yuki. RIKEN; Japón
Author affiliation: de la Barra Diaz, Verónica. Laboratorio Veterinario Lavet; Chile
Author affiliation: Panei, Carlos Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - La Plata. Instituto de Genética Veterinaria Ing. Fernando Noel Dulout; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Microbiología. Cátedra de Virología; Argentina
Author affiliation: Gonzalez, Ester Teresa. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Microbiología. Cátedra de Virología; Argentina
Author affiliation: Kanemaki, Misao. Institute for Animal Science; Japón
Author affiliation: Onuma, Misao. RIKEN; Japón
Author affiliation: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - CONICET - La Plata. Instituto de Genética Veterinaria Ing. Fernando Noel Dulout; Argentina
Author affiliation: Aida, Yoko. University of Tokyo; Japón. RIKEN; Japón
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas
Publication Date: 2017.
Language: English.
Abstract:
The tribe Leucocoryneae is taxonomically andcytogenetically complex, mainly due to its extraordinarymorphological and karyological variation. Robertsoniantranslocations had long been recognized as a central factorcontributing to karyotype diversity within the Leucocoryneae,but so far no major tendency prevailing on theobserved complexity of karyotype formula among specieshas been identified. The assessment of nuclear DNAcontents by flow cytometry using propidium iodide in 23species, representing all genera within the tribe, showed amonoploid genome size variation of 1Cx = 9.07?30.46 pgdenoting a threefolds fluctuation. A highly significant linearassociation between the average DNA content per chromosomearm (2C/FN) and the monoploid genome size (1Cx)is reported for the first time and identified as a novel indicatorof a trend governing karyotype diversity within Leucocoryneae.This trend shows that a reduction in DNA contentper chromosome arm is influencing and has shaped karyotypeevolution of different monophyletic groups within thetribe despite the complex karyotype diversity and apparentlycontrasting patterns of genome sizes.
Author affiliation: Sassone, Agostina Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentina
Author affiliation: López, Alicia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentina
Author affiliation: Hojsgaard, Diego Hernan. Goethe Universitat Frankfurt; Alemania
Author affiliation: Giussani, Liliana Mónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentina
Repository: CONICET Digital (CONICET). Consejo Nacional de Investigaciones Científicas y Técnicas