Genetic parameters and selection for casein content in Italian Holstein and Brown Swiss.

A total of more than 2,000,000 records on casein contents were collected in Lombardia (Italy) during routine milk recording of Italian Holstein and Brown Swiss dairy cows. Variance components for casein were estimated as well as all the genetic correlations of casein with production and type traits considered in selection. According to the heritabilities estimated (12.4% for Brown and 9.36% for Holstein), breeding values were calculated for bulls and compared to the breeding values for total protein. The results of two different selection scenarios were compared for each breed when including protein or casein as selection criterion. Genetic progress expected for all traits selected were compared after 10 years of selection. The genetic variability of casein allows the use of this trait as selection criterion with the estimation of breeding values and its inclusion in selection indexes. Ranking of breeding values for casein and protein are very similar in both breeds. But some differences in genetic values for casein exist for the same level of breeding value for protein. Nevertheless results in genetic gain differ between breeds depending mainly on genetic correlations with the other traits selected. The positive results in selection response estimated for several traits suggest to the Brown Swiss Association the replacement of protein selection with casein. In contrast the smaller effects estimated for the Italian Holstein suggest to wait for more casein data collected before any change in selection program

investigation of the dgat1 k232a and vntr mutations in dairy and dual purpose cattle breeds

AbstractSeveral studies have reported that the centromeric end of bovine chromosome 14 harbours QTL for milk production and composition traits. The acyl-Coenzyme A:diacylglycerol acyltransferase 1 (DGAT1) gene was indicated to be the quantitative trait gene affecting these traits with a major effect on milk fat content. A two bp mutation in exon 8 causing a nonconservative lysine to alanine amino acid substitution at codon 232 (K232A) showed a confirmed effect across breeds with allele K resulting associated with an increase on fat yield, fat percentage and protein percentage while allele A was associated with higher milk yield. Another mutation in the 5' regulatory region of this gene, a variable number of tandem repeat (VNTR) of 18 bp, was suggested to affect fat percentage. The objective of the present work was to investigate the occurrence of the DGAT1 K232A and VNTR polymorphisms in several Italian dairy and dual purpose cattle breeds as a first step to evaluate their effects on milk production trait..

As sementes tradicionais dos Krahô: uma experiência de integração das estratégias on farm e ex situ de conservação de recursos genéticos.

bitstream/item/115241/1/Caderno-ANA-Sementes-2014-KRAHO.pd

Identification and validation of copy number variants in Italian Brown Swiss dairy cattle using Illumina Bovine SNP50 Beadchip®

The determination of copy number variation (CNV) is very important for the evaluation of genomic traits in several species because they are a major source for the genetic variation, influencing gene expression, phenotypic variation, adaptation and the development of diseases. The aim of this study was to obtain a CNV genome map using the Illumina Bovine SNP50 BeadChip data of 651 bulls of the Italian Brown Swiss breed. PennCNV and SVS7 (Golden Helix) software were used for the detection of the CNVs and Copy Number Variation Regions (CNVRs). A total of 5,099 and 1,289 CNVs were identified with PennCNV and SVS7 software, respectively. These were grouped at the population level into 1101 (220 losses, 774 gains, 107 complex) and 277 (185 losses, 56 gains and 36 complex) CNVR. Ten of the selected CNVR were experimentally validated with a qPCR experiment. The GO and pathway analyses were conducted and they identified genes (false discovery rate corrected) in the CNVR related to biological processes cellular component, molecular function and metabolic pathways. Among those, we found the FCGR2B, PPAR\u3b1, KATNAL1, DNAJC15, PTK2, TG, STAT family, NPM1, GATA2, LMF1, ECHS1 genes, already known in literature because of their association with various traits in cattle. Although there is variability in the CNVRs detection across methods and platforms, this study allowed the identification of CNVRs in Italian Brown Swiss, overlapping those already detected in other breeds and finding additional ones, thus producing new knowledge for association studies with traits of interest in cattle

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

Longer and less overlapping food webs in anthropogenically disturbed marine ecosystems: confirmations from the past

The human exploitation of marine resources is characterised by the preferential removal of the largest species. Although this is expected to modify the structure of food webs, we have a relatively poor understanding of the potential consequences of such alteration. Here, we take advantage of a collection of ancient consumer tissues, using stable isotope analysis and SIBER to assess changes in the structure of coastal marine food webs in the South-western Atlantic through the second half of the Holocene as a result of the sequential exploitation of marine resources by hunter-gatherers, western sealers and modern fishermen. Samples were collected from shell middens and museums. Shells of both modern and archaeological intertidal herbivorous molluscs were used to reconstruct changes in the stable isotopic baseline, while modern and archaeological bones of the South American sea lion Otaria flavescens, South American fur seal Arctocephalus australis and Magellanic penguin Spheniscus magellanicus were used to analyse changes in the structure of the community of top predators. We found that ancient food webs were shorter, more redundant and more overlapping than current ones, both in northern-central Patagonia and southern Patagonia. These surprising results may be best explained by the huge impact of western sealing on pinnipeds during the fur trade period, rather than the impact of fishing on fish populations. As a consequence, the populations of pinnipeds at the end of the sealing period were likely well below the ecosystem's carrying capacity, which resulted in a release of intraspecific competition and a shift towards larger and higher trophic level prey. This in turn led to longer and less overlapping food webs

Pre-launch calibration results of the TROPOMI payload on-board the Sentinel-5 Precursor satellite

The Sentinel-5 Precursor satellite was successfully launched on 13 October 2017, carrying the Tropospheric Monitoring Instrument (TROPOMI) as its single payload. TROPOMI is the next-generation atmospheric sounding instrument, continuing the successes of GOME, SCIAMACHY, OMI, and OMPS, with higher spatial resolution, improved sensitivity, and extended wavelength range. The instrument contains four spectrometers, divided over two modules sharing a common telescope, measuring the ultraviolet, visible, near-infrared, and shortwave infrared reflectance of the Earth. The imaging system enables daily global coverage using a push-broom configuration, with a spatial resolution as low as 7×3.5&thinsp;km2 in nadir from a Sun-synchronous orbit at 824&thinsp;km and an Equator crossing time of 13:30 local solar time. This article reports the pre-launch calibration status of the TROPOMI payload as derived from the on-ground calibration effort. Stringent requirements are imposed on the quality of on-ground calibration in order to match the high sensitivity of the instrument. A new methodology has been employed during the analysis of the obtained calibration measurements to ensure the consistency and validity of the calibration. This was achieved by using the production-grade Level 0 to 1b data processor in a closed-loop validation set-up. Using this approach the consistency between the calibration and the L1b product, as well as confidence in the obtained calibration result, could be established. This article introduces this novel calibration approach and describes all relevant calibrated instrument properties as they were derived before launch of the mission. For most of the relevant properties compliance with the calibration requirements could be established, including the knowledge of the instrument spectral and spatial response functions. Partial compliance was established for the straylight correction; especially the out-of-spectral-band correction for the near-infrared channel needs future validation. The absolute radiometric calibration of the radiance and irradiance responsivity is compliant with the high-level mission requirements, but not with the stricter calibration requirements as the available on-ground validation shows. The relative radiometric calibration of the Sun port was non-compliant. The non-compliant subjects will be addressed during the in-flight commissioning phase in the first 6 months following launch.</p