Estimation of genetic parameters for feed efficiency traits using random regression models in dairy cattle.

Feed efficiency has become an increasingly important research topic in recent years. As feed costs rise and the environmental impacts of agriculture become more apparent, improving the efficiency with which dairy cows convert feed to milk is increasingly important. However, feed intake is expensive to measure accurately on large populations, making the inclusion of this trait in breeding programs difficult. Understanding how the genetic parameters of feed efficiency and traits related to feed efficiency vary throughout the lactation period is valuable to gain understanding into the genetic nature of feed efficiency. This study used 121,226 dry matter intake (DMI) records, 120,500 energy corrected milk (ECM) records, and 98,975 metabolic body weight (MBW) records, collected on 7,440 first lactation Holstein cows from 6 countries (Canada, Denmark, Germany, Spain, Switzerland, and United States of America), from January 2003 to February 2022. Genetic parameters were estimated using a multiple-trait random regression model with a fourth order Legendre polynomial for all traits. Weekly phenotypes for DMI were re-parameterized using linear regressions of DMI on ECM and MBW, creating a measure of feed efficiency that was genetically corrected for ECM and MBW, referred to as genomic residual feed intake (gRFI). Heritability (SE) estimates varied from 0.15 (0.03) to 0.29 (0.02) for DMI, 0.24 (0.01) to 0.29 (0.03) for ECM, 0.55 (0.03) to 0.83 (0.05) for MBW, and 0.12 (0.03) to 0.22 (0.06) for gRFI. In general, heritability estimates were lower in the first stage of lactation compared with the later stages of lactation. Additive genetic correlations between weeks of lactation varied, with stronger correlations between weeks of lactation that were close together. The results of this study contribute to a better understanding of the change in genetic parameters across the first lactation, providing insight into potential selection strategies to include feed efficiency in breeding programs

OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs

<p>Abstract</p> <p>Background</p> <p>The ancestry of mitochondria and chloroplasts traces back to separate endosymbioses of once free-living bacteria. The highly reduced genomes of these two organelles therefore contain very distant homologs that only recently have been shown to recombine inside the mitochondrial genome. Detection of gene conversion between mitochondrial and chloroplast homologs was previously impossible due to the lack of suitable computer programs. Recently, I developed a novel method and have, for the first time, discovered recurrent gene conversion between chloroplast mitochondrial genes. The method will further our understanding of plant organellar genome evolution and help identify and remove gene regions with incongruent phylogenetic signals for several genes widely used in plant systematics. Here, I implement such a method that is available in a user friendly web interface.</p> <p>Results</p> <p><monospace>OrgConv</monospace> (<b>Org</b>anellar <b>Conv</b>ersion) is a computer package developed for detection of gene conversion between mitochondrial and chloroplast homologous genes. <monospace>OrgConv</monospace> is available in two forms; source code can be installed and run on a Linux platform and a web interface is available on multiple operating systems. The input files of the feature program are two multiple sequence alignments from different organellar compartments in FASTA format. The program compares every examined sequence against the consensus sequence of each sequence alignment rather than exhaustively examining every possible combination. Making use of consensus sequences significantly reduces the number of comparisons and therefore reduces overall computational time, which allows for analysis of very large datasets. Most importantly, with the significantly reduced number of comparisons, the statistical power remains high in the face of correction for multiple tests.</p> <p>Conclusions</p> <p>Both the source code and the web interface of <monospace>OrgConv</monospace> are available for free from the <monospace>OrgConv</monospace> website <url>http://www.indiana.edu/~orgconv</url>. Although <monospace>OrgConv</monospace> has been developed with main focus on detection of gene conversion between mitochondrial and chloroplast genes, it may also be used for detection of gene conversion between any two distinct groups of homologous sequences.</p

The Resilient Dairy Genome Project - a general overview of methods and objectives related to feed efficiency and methane emissions.

The Resilient Dairy Genome Project (RDGP) is an international large-scale applied research project that aims to generate genomic tools to breed more resilient dairy cows. In this context, improving feed efficiency and reducing greenhouse gases from dairy is a high priority. The inclusion of traits related to feed efficiency (e.g., dry matter intake [DMI]) or greenhouse gases (e.g., methane emissions [CH4]) relies on available genotypes as well as high quality phenotypes. Currently, 7 countries, i.e., Australia [AUS], Canada [CAN], Denmark [DNK], Germany [DEU], Spain [ESP], Switzerland [CHE], and United States of America [USA] contribute with genotypes and phenotypes including DMI and CH4. However, combining data is challenging due to differences in recording protocols, measurement technology, genotyping, and animal management across sources. In this study, we provide an overview of how the RDGP partners address these issues to advance international collaboration to generate genomic tools for resilient dairy. Specifically, we describe the current state of the RDGP database, data collection protocols in each country, and the strategies used for managing the shared data. As of February 2022, the database contains 1,289,593 DMI records from 12,687 cows and 17,403 CH4 records from 3,093 cows and continues to grow as countries upload new data over the coming years. No strong genomic differentiation between the populations was identified in this study, which may be beneficial for eventual across-country genomic predictions. Moreover, our results reinforce the need to account for the heterogeneity in the DMI and CH4 phenotypes in genomic analysis

Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease

BACKGROUND: Patients with atherosclerotic vascular disease remain at high risk for cardiovascular events despite effective statin-based treatment of low-density lipoprotein (LDL) cholesterol levels. The inhibition of cholesteryl ester transfer protein (CETP) by anacetrapib reduces LDL cholesterol levels and increases high-density lipoprotein (HDL) cholesterol levels. However, trials of other CETP inhibitors have shown neutral or adverse effects on cardiovascular outcomes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial involving 30,449 adults with atherosclerotic vascular disease who were receiving intensive atorvastatin therapy and who had a mean LDL cholesterol level of 61 mg per deciliter (1.58 mmol per liter), a mean non-HDL cholesterol level of 92 mg per deciliter (2.38 mmol per liter), and a mean HDL cholesterol level of 40 mg per deciliter (1.03 mmol per liter). The patients were assigned to receive either 100 mg of anacetrapib once daily (15,225 patients) or matching placebo (15,224 patients). The primary outcome was the first major coronary event, a composite of coronary death, myocardial infarction, or coronary revascularization. RESULTS: During the median follow-up period of 4.1 years, the primary outcome occurred in significantly fewer patients in the anacetrapib group than in the placebo group (1640 of 15,225 patients [10.8%] vs. 1803 of 15,224 patients [11.8%]; rate ratio, 0.91; 95% confidence interval, 0.85 to 0.97; P=0.004). The relative difference in risk was similar across multiple prespecified subgroups. At the trial midpoint, the mean level of HDL cholesterol was higher by 43 mg per deciliter (1.12 mmol per liter) in the anacetrapib group than in the placebo group (a relative difference of 104%), and the mean level of non-HDL cholesterol was lower by 17 mg per deciliter (0.44 mmol per liter), a relative difference of -18%. There were no significant between-group differences in the risk of death, cancer, or other serious adverse events. CONCLUSIONS: Among patients with atherosclerotic vascular disease who were receiving intensive statin therapy, the use of anacetrapib resulted in a lower incidence of major coronary events than the use of placebo. (Funded by Merck and others; Current Controlled Trials number, ISRCTN48678192 ; ClinicalTrials.gov number, NCT01252953 ; and EudraCT number, 2010-023467-18 .)

Electro-driven extraction across a polymer inclusion membrane in a flow-through cell

A flow-through arrangement for electrodriven extraction across a polymer inclusion membrane was developed. Sample introduction into the donor chamber was continuous, while the acceptor solution was stagnant. By adjustment of the total volume of the donor solution pumped through the cell the best compromise between enrichment factor and extraction time can be set. The enriched extract was analyzed by capillary electrophoresis with contactless conductivity detection. Membranes of 20 mu m thickness were employed which consisted of 60% cellulose triacetate as base polymer, 20% o-nitrophenyl octyl ether as plasticizer, and 20% Aliquat 336. By passing through 10 mL of sample at a flow rate of 1 mL/min the model analytes glyphosate (a common herbicide) and its major metabolite aminomethylphosphonic acid could be transported from the aqueous donor solution to the aqueous acceptor solution with efficiencies <87% in 10 min at an applied voltage of 1500 V. Enrichment factors of 87 and 95 and limits of detection down to 43 and 64 pg/mL were obtained for glyphosate and aminomethylphosphonic acid, respectively. The intra- and interday reproducibilities for the extraction of the two compounds from spiked river water were about 6 and 7% respectively when new membranes were used for each experiment. For consecutive extractions of batches of river water with a single piece of membrane a deterioration of recovery by about 16% (after 20 runs) was noted, an effect not observed with purely aqueous standards. (C) 2013 Elsevier B.V. All rights reserved

Genomweite Assoziationsstudien beim Edelschwein

Die Schweizer Edelschweinpopulation wurde im Jahr 2002 aufgespalten in die Edelschwein Mutterlinie (ESM) und die Edelschwein Vaterlinie (ESV). Die Zuchtziele der beiden Populationen unterscheiden sich. So stehen beim ESM die Reproduktionseigenschaften und beim ESV Mastleistung, Schlachtkörperzusammensetzung und Fleischqualität im Vordergrund. Seit ihrer Aufspaltung haben sich die Populationen in unterschiedliche Richtungen entwickelt. Diese Entwicklung konnte basierend auf 60k SNP-Genotypen von 4158 ESM und 2470 ESV Tieren bestätigt werden: bei den beiden Populationen handelt es sich heute um klar getrennte Gruppen. Die mittlere genomische Inzucht für die Tiere mit Geburtsjahr 2018 liegt bei 0.15 (ESM, 214 Tiere) und 0.17 (ESV, 1086 Tiere). Für die zwei Rassen wurden in der Folge getrennte genomweite Assoziationsstudien (GWAS) für die de-regressierten Zuchtwerte der 33 Merkmale des Zuchtprogramms (16 der Produktion, 13 des Exterieurs und 4 der Reproduktion) durchgeführt. Ziel einer GWAS ist es, Hauptgenorte zu identifizieren, die massgeblich an der Ausprägung der untersuchten Merkmale beteiligt sind. Für das Merkmal Schlachtkörperlänge haben wir Hauptgenorte auf den Chromosomen 7 (ESV und ESM) und 17 (ESM) gefunden. Für die Merkmale Anzahl Zitzen links und Anzahl Zitzen rechts haben wir für beide Rassen in der gleichen Region wie für das Merkmal Schlachtkörperlänge ebenfalls einen Hauptgenort auf Chromosom 7 gefunden. Zusätzlich haben wir für die Merkmale Mast-und Lebendtageszunahme Hauptgenorte auf den Chromosomen 1 (ESM) und 7 (ESV) gefunden. Die Ergebnisse der verschiedenen Merkmale stehen und fallen mit der Verfügbarkeit von Tieren mit zuverlässigen Zuchtwerten und Genotypen. Es sind weitere Untersuchungen und zusätzliche Daten nötig, um die genetische Architektur dieser und weiterer Merkmale noch besser beschreiben zu können