Copy number variation in cattle breeds

Detecting all classes of genetic variation in livestock species, such as cattle, is a pre-requisite to studying their association to traits of interest. Copy Number Variations (CNVs) are classes of polymorphic DNA regions including deletions, duplications and insertions of DNA fragments of at least 0.5 kb to several Mb, that are copy number variable when compared to a reference genome. CNVs can be identified using various approaches, among those the SNP array data are low cost, dense coverage, and high throughput. The aim of this study was to obtain a consensus genome map of Copy Number Variable Regions (CNVRs) in the Brown Swiss (dataset of 192 bulls), Red Pied Valdostana (dataset of 143 bulls) and Finnish Ayrshire (dataset of 243 bulls) cattle breeds all genotyped on the Illumina Bovine HD BeadChip, and two SNP based CNV calling algorithms. Brown Swiss cattle originated in the Swiss Alps, kept as a triple purpose breed. Once imported in the US, it was mainly selected for increased milk production. The Valdostana Red Pied cattle is the most common autochthonous dual purpose breed in the region Valle d\u2019Aosta in Italy (13,000 animals in 2013, almost all of them registered in the Herd Book). The Finnish Ayrshire is the most common cattle in Finland. CNVs were called with the PennCNV and SVS7 software and were summarized to CNVRs at the population level as overlapping CNV calls within breed. PennCNV identified 2,377, 1,723 and 1,689 for the Italian Brown Swiss, the Red Pied Valdostana and the Finnish Ayrshire, respectively. SVS7 detected 370, 235 and 2,063 for the three cattle breeds. These regions were annotated with Ensembl v78 Bos taurus gene set (UMD3.1) and genomic regions harboring QTL for production and functional traits. The comparison among CNVRs here identified provided common regions in the breeds. The results of this study are a comprehensive genomic analysis of cattle CNVs derived from SNP data, which will be a valuable genomic variation resource and will enrich the bovine CNV map in the cattle genome, providing new information for association studies with traits included in the selection programs

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Morphological and physiological behaviour of sweet cherry 'somaclone' HS plants in field

The somaclonal variant HS (HS), regenerated from Prunus avium `Hedelfinger\u2019 (H) leaf explants, had previously been molecularly and physiologically characterized both in vitro and in early ex vitro condition showing reduced apical dominance. Somaclone HS, here assessed for several morphological and physiological field performances showed reduced vegetative vigour as determined by trunk circumference and tree height nevertheless natural architecture of the tree was preserved. HS canopy was less crowded compared to H as leaves were shorter with a shorter petiole, they were better spaced out as indicated by internodes length and they had a significantly thinner cuticle and wax layer compared to that found on H leaves surface. Leaf histological analysis also evidenced that HS had thicker mesophyll and palisade the latter composed of more than one layer which, together with increased stomatal density, are distinguishing signs of extensively sun exposed leaves. HS showed a reduction in leaf chlorophyll b and \u3b2-carotene content. On the other hands no significant differences were found between the two genotypes in terms of net photosynthesis, intercellular CO2 concentration, leaf transpiration and water use efficiency. HS flowered one year later than H and fertility parameters such as floral buds and number of flowers per bud were reduced. In consideration of the fact that the large size of trees has contributed to make P. avium commercial cultivars unpopular with modern orchardists, HS could be used as either germplasm in breeding programs aiming to reduce tree vigour or a rootstock

Variation of milk components in the Italian Brown cattle

The aim of this study was to evaluate the variations of protein, casein, saturated (SFA), unsaturated (UFA), monounsaturated (MUFA), polyunsaturated (PUFA) fatty acids contents and cheese yield in the milk of two groups of Italian Brown cows conventionally reared in indoor period of housing or consuming pasture during the summer months in 2008 and 2013. Milk components were obtained from samples collected during the national routine (conventionally reared) and 'extraordinary' (pasture period) milk recording scheme in herds located near Sondrio (Lombardia, Italy). Milk samples were processed with the MilkoScanTM FT6000 for the identification of milk casein, SFA, UFA, MUFA and PUFA composition. The groups were analysed separately per year and the environmental factors affecting milk protein, casein, and fatty acids contents (pasture/indoor, parity, data of sampling, days in milk, days from collection to analysis) were included in the MIXED procedure of SAS 9.3. A total of 778 milk samples were available, including 234 records from indoor and 544 observations from pasture feeding. Pasture intake affected the content of casein (%) and the proportion of fat in milk (g/100 g), enhancing milk casein levels (from 2.90 to 3) and reducing the concentration of milk SFA in milk from grazing cows (from 2.29 to 1.92). Additionally, the cheese yield was calculated as 'kg of cheese per 100 kg of milk' and resulted to be 10.4 and 12 in 2008 from milk of cows reared indoor and with pasture based diet, respectively. The dairy industry should take advantage of the milk production during grazing periods from which high quality products may be obtained

Níveis de treonina digestível para suínos machos castrados, de alto potencial genético para deposição de carne, na fase de terminação Digestible threonine levels for high genetic potential lean deposition finishing barrows

Avaliou-se o efeito de níveis de treonina digestível em rações sobre o desempenho e características de cacaça de suínos machos castrados, selecionados geneticamente, para deposição de carne na carcaça, na fase de terminação. Foram utilizados 70 animais, com peso inicial de 59,00+1,25kg, distribuídos em delineamento experimental de blocos ao acaso, com cinco tratamentos, sete repetições e dois animais por unidade experimental, sendo que na distribuição dos animais, foi adotado como critério o peso inicial. Os tratamentos foram níveis de treonina na ração (0,480; 0,504; 0,528; 0,554 e 0,572% de treonina digestível). Não houve efeito (P>0,05) dos tratamentos sobre o ganho de peso, consumo de ração e conversão alimentar. Os níveis de treonina digestível não influenciaram (P>0,05) a porcentagem de carne e a espessura de toucinho na carcaça. Conclui-se que o nível de 0,480% de treonina digestível, correspondente a relação de treonina digestível:lisina digestível de 60%, atendeu as exigências de suínos machos castrados de alto potencial para deposição de carne na carcaça dos 60 aos 95kg.<br>An experiment was carried out to determine the effects of digestible threonine levels in ration on the performance and carcass traits of hogs genetically selected for lean deposition at finishing. Seventy barrows averaging an initial weight of 59.00+1.25kg were distributed in a randomized experimental block design with five treatments and seven replicates, being two animals per experimental unit. Initial weight was adopted as a criterion for animal distribution in the treatments, which were the levels of digestible treonine in the diet (0.480; 0.504; 0.528; 0.554; and 0.572%). No effect (P>0.05) was observed among the treatments on daily weight gain, daily feed intake, and feed conversion. Digestible threonine levels did not influence (P>0.05) lean and backfat thickness percentage. It can be concluded that the level of 0.480% of digestible treonine, corresponding to the rate digestible treonine:lysine 60%, supplied the requirments of high potential lean deposition barows from 60 to 95kg