Genetic diversity in the modern horse illustrated from genome-wide SNP data

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection

Refining the evolutionary tree of the horse Y chromosome

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Peer reviewe

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Peer reviewe

Transformação de embriões somáticos de Vitis sp. (videira) com diferentes produtos, contendo sequências nucleotídicas de genes de proteína da cápsula de nepovirus

O melhoramento de videiras, uma das plantas mais cultivadas no mundo, tal como muitas outras plantas lenhosas, é dificultado devido à sua elevada heterozigocidade genética e longo ciclo vegetativo. Assim a engenharia genética torna-se um instrumento importante num programa de melhoramento de videiras. Os nepovirus são os vírus da videira com maior importância económica devido à sua distribuição pelo mundo inteiro e aos graves danos que provocam. Um sistema de transformação genética através de Agrobacterium baseado na embriogénese somática repetitiva, foi utilizado para regenerar vinhas transgénicas. Culturas embriogénicas de Vitis vinifera (Russalka - auto-polinizada) e Richter 110 (Vitis rupestris x Vitis berlandieri) foram transformadas com Agrobacterium tumefaciens estirpe LBA 4404, contendo vários plasmídeos binários. pBinGUSint, transportando diferentes marcadores genéticos, ß-glucuronidase (GUS), e sete construções diferentes contendo quimeras do gene da proteína da cápsula do vírus do urticado da videira (GFLV) e do vírus mosaico-arábico (ArMV), incluindo formas não transcríveis e incompletas, respectivamente. Os embriões transformados foram selecionados através da sua contínua proliferação em meios contendo kanamicina. A expressão do gene marcador foi demonstrada através de análises histoquímicas do produto do gene GUS.ABSTRACT: Breeding of grapevines, one of the world's most widely-grown fruit crop, as in the case with many woody crops, is hampered by genetic heterozygozity and long generation time. Transformation offers new alternatives in the genetic improvement of grapevine. Nepoviruses are the grapevine viruses of greatest economic importance because of their worldwide occurrence and the severe damages they cause. An Agrobacterium-mediated gene transfer system relying on repetitive embryogenesis has been used to regenerate transgenic grapevines. Embryogenic cultures of Vitis vinifera (Russalka - selfpollinated) and 1 10 Richter (Vitis rupestris x Vitis berlandieri) were transformed with Agrobacterium tumefaciens strain LBA 4404 containing various binary plasmids, pBinCUSint, carrying the marker gene P-glucuronidase (GUS), and seven different constructs containing chimeric coat protein (CP) genes of grapevine fanleaf virus (CFLV), including nontranslatable and truncated forms of the CP gene, and arabis mosaic virus (ArMV), respectively. Putative transformed embryos were selected by continued proliferation on kanamycin containing medium. Embryos transformed with the plasmid pBinCUSint were shown to express the GUS gene by histochemical analyses

Investigating the past to foresee the future: a bibliometric analysis on Azorean research in SCI Journals during 1974-2012

Jornadas "Ciência nos Açores – que futuro? Tema Ciências Naturais e Ambiente", Ponta Delgada, 7-8 de Junho de 2013.A sociedade de conhecimento solicita a todas as regiões, a participação na construção de um futuro mais sustentável, na linha da estratégia Europeia para o Horizonte 2020. Que contributos tem dado a investigação produzida nos Açores com vista à "Inovação para a Especialização Inteligente"? Neste estudo apresentamos uma análise bibliométrica referente às publicações de autores residentes nos Açores disponíveis na Science Citation Index (SCI), entre 1974-2012, explorando vários indicadores: "média de autores por estudo" e "factor de impacto" ao longo do tempo e por disciplina, "rede de colaborações" com o continente português e outros países, "áreas de investigação", "palavras chave" e "categorias do Web of Science" além do "número total de citaç.es" e do "número de páginas". A produção científica nos Açores tem vindo a crescer, destacando-se os últimos seis anos (154%), seguindo uma tendência análoga à de Portugal continental. Os principais temas de publicação situam-se no âmbito das Ciências Naturais. Verifica-se que o factor de impacto das publicações cresceu, passando de 2.0 em 1999 para 2.6 em 2012. A relevância internacional das publicações também tem vindo a aumentar, sendo que em 2002 se registou o valor mais baixo, 1.78 vezes em média, enquanto que em 2009 uma publicação foi citada, em média, 3,52 vezes. Três quartos das publicações possuem pelo menos um co-autor de outra regi.o, sendo as colaborações mais importantes com instituições nacionais (22%), mas também com o Reino Unido (13%), Espanha (11%) e USA (9%). Cerca de metade 60 das 100 publicações mais citadas foram publicadas entre 2006 e 2010.ABSTRACT: The knowledge society requires all regions to participate in building a more sustainable future, in line with the European strategy for Horizon 2020. What contributions has the Azorean research given to support "Innovation for Smart Specialization"? A bibliometric analysis is made for all the published research in the Azores for the period 1974-2012. Based on the Science Citation Index database (SCI), we explore several indicators: "mean number of authors" and "journals impact factor" across time and discipline, "network of collaborations", "Research Areas", "Keywords" and "Web of Science Categories" as well as "total citation" and "page" counts. Just like in mainland Portugal, the number of publications has increased in the last six years (154%). Natural sciences dominate the Web of Science categories. The impact factor of the publications has also increased, with a mean value of 2.6 in 2012 compared to 2.0 in 1999. Publications have also increased their global relevance, with a paper being cited 3.52 times (in average) for the 2009 publications compared to a minimum of 1.78, observed in 2002. Three quarters of the publications have at least one co-author of another region, mainly coming from other Portuguese regions (22%), but also UK (13%), Spain (11%) and USA (9%). From the 100 most cited publications, about 60 were published between 2006 and 2010.Governo dos Açores; Fundo Regional para a Ciência

Morphological and genetic characterization of the Graciosa donkey breed

ABSTRACTThe Graciosa donkey has been associated with husbandry and social activities in Graciosa Island for decades. Although donkeys played an essential role in the development of the island, their numbers are severely reduced. The Graciosa donkey is characterised by its small stature, strong bony constitution and strong hooves. They are extremely gentle, patient and submissive fully integrated into the island's ecosystem. As so they must be considered as elements of an environmentally sustainable ecosystem. This study aimed to define the morphotype of the Graciosa donkey and to access its genetic diversity using microsatellite markers. Biometric data consisted of 15 morphological traits from 39 individuals. The Graciosa donkey is dolichocephalic, hypermetric according to the dactilothoracic index, hypometric regarding the approximate live weight and far from ground. Twenty-four individuals, which showed no kinship, based on results of 13 markers were considered as founders and were genotyped for two additional markers and further analysed in this study. All microsatellites used were polymorphic, but low levels of genetic diversity were identified. As the Graciosa donkey gains popularity, the information obtained from this study will be very useful for conservation and management purposes by safeguarding its genetic diversity