Variants Within Genes \u3ci\u3eEDIL3\u3c/i\u3e and \u3ci\u3eADGRB3\u3c/i\u3e are Associated With Divergent Fecal Egg Counts in Katahdin Sheep at Weaning

Gastrointestinal nematodes (GIN) pose a severe threat to sheep production worldwide. Anthelmintic drug resistance coupled with growing concern regarding potential environmental effects of drug use have demonstrated the necessity of implementing other methods of GIN control. The aim of this study was to test for genetic variants associated with resistance or susceptibility to GIN in Katahdin sheep to improve the current understanding of the genetic mechanisms responsible for host response to GIN. Linear regression and casecontrol genome-wide association studies were conducted with high-density genotype data and cube-root transformed weaning fecal egg counts (tFEC) of 583 Katahdin sheep. The casecontrol GWAS identified two significant SNPs (P-values 1.49e-08 to 1.01e-08) within introns of the gene adhesion G protein-coupled receptor B3 (ADGRB3) associated with lower fecal egg counts. With linear regression, four significant SNPs (P-values 7.82e-08 to 3.34e-08) were identified within the first intron of the gene EGF-like repeats and discoidin domains 3 (EDIL3). These identified SNPs were in very high linkage disequilibrium (r2 of 0.996–1), and animals with alternate homozygous genotypes had significantly higher median weaning tFEC phenotypes compared to all other genotypes. Significant SNPs were queried through public databases to identify putative transcription factor binding site (TFBS) and potential lncRNA differences between reference and alternate alleles. Changes in TFBS were predicted at two SNPs, and one significant SNPwas found to bewithin a predicted lncRNA sequencewith greater than 90% similarity to a known lncRNA in the bovine genome. The gene EDIL3 has been described in other species for its roles in the inhibition and resolution of inflammation. Potential changes of EDIL3 expression mediated through lncRNA expression and/or transcription factor binding may impact the overall immune response and reduce the ability of Katahdin sheep to control GIN infection. This study lays the foundation for further research of EDIL3 and ADGRB3 towards understanding genetic mechanisms of susceptibility to GIN, and suggests these SNPs may contribute to genetic strategies for improving parasite resistance traits in sheep

Scaling up community-based goat breeding programmes via multi-stakeholder collaboration

Community-based livestock breeding programmes (CBBPs) have emerged as a potential approach to implement sustainable livestock breeding in smallholder systems. In Malawi and Uganda, goat CBBPs were introduced to improve production and productivity of indigenous goats through selective breeding. Scaling up CBBPs have recently received support due to evidence-based results from current implementation and results of CBBPs implemented in other regions of the world. This paper explores strategies for scaling up goat CBBPs in Malawi and Uganda, and documents experiences and lessons learned during implementation of the programme. A number of stakeholders supporting goat-based interventions for improving smallholders’ livelihoods exists. This offers an opportunity for different actors to work together by pooling financial resources and technical expertise for establishment and sustainability of goat CBBPs. Scaling up strategies should be an integral part of the pilot design hence dissemination partners need to be engaged during the design and inception stages of the pilot CBBPs. Creation of self-sustaining CBBPs requires early collaborative programme planning, meaningful investment and long-term concerted and coordinated efforts by collaborating partners. Permanently established actors, like government agencies and research and training institutions, are better placed to coordinate such efforts. The overall goal of the scaling up programme should be creation of a financially sustainable system, in which smallholders are able, on their own, to transact and sustain operations of their local breeding institutions using locally generated revenue/ resources. Since CBBP scaling up is a ‘learning by doing process’, an effective monitoring and evaluation system should be an integral part of the process

Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.)

<p>Abstract</p> <p>Background</p> <p>Cultivated peanut (<it>Arachis hypogaea </it>L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting.</p> <p>Results</p> <p>Here, we report a large set of BAC-end sequences (BES), use them for developing SSR (BES-SSR) markers, and apply them in genetic linkage mapping. The majority of BESs had no detectable homology to known genes (49.5%) followed by sequences with similarity to known genes (44.3%), and miscellaneous sequences (6.2%) such as transposable element, retroelement, and organelle sequences. A total of 1,424 SSRs were identified from 36,435 BESs. Among these identified SSRs, dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant. The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci. A genetic linkage map was constructed, consisting of 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM, with an average distance of 5.3 cM between adjacent loci. Two markers related to resistance gene homologs (RGH) were mapped to two different groups, thus anchoring 1 RGH-BAC contig and 1 singleton.</p> <p>Conclusions</p> <p>The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map. This will aid in the identification of markers linked to genes of interest and map-based cloning.</p

Using Model Test Data to Assess VIV Factor of Safety for SCR and TTR in GOM

This paper presents results obtained as part of the DeepStar Phase 10 program on VIV Factors of Safety. The objective was to develop a general methodology to calibrate Factors of Safety for VIV-induced fatigue and to apply it to partially straked risers. This was achieved using reliability methods, accepted industry VIV prediction software and state-of-the-art model test experiments. Most oil companies use a Factor of Safety of 20 when predicting VIV damage using VIV software tools. There are numerous software tools currently in use in industry to predict VIV damage to straked risers and each of them will have different accuracy, and therefore an intrinsic level of conservatism. Understanding the level of conservatism in different VIV prediction software is therefore critical to determining what Factor of Safety to use. This study benchmarks the latest generation of industry accepted VIV design tools at the time of the study (2011): SHEAR7v4.6, VIVAv6.5 and VIVANAv3.7.24 against high quality VIV data from three separate straked riser experiments. A bias distribution (predicted to measured VIV damage results) is obtained for each software tool as a function of the strake coverage. A novel reliability framework approach is then developed to incorporate all uncertainties associated with VIV fatigue prediction into a limit state function, including variability in met-ocean conditions and variability in the fatigue resistance of the material characterized by a design S-N curve. The limit state function is analyzed using First Order Reliability Methods to develop Factors of Safety for target probabilities of failure. The general method is then applied on two case studies involving an SCR and TTR in Gulf of Mexico loop currents, but it can be easily extended to different locations and riser configurations. The resulting FoS range from about 1 to 15 for most software, and are lower than industry standards for VIV prediction. The FoS do not vary markedly for different riser configurations, indicating the possibility of reducing excess conservatism when predicting VIV damage on straked risers.DeepStar (Consortium)SHEAR7 JI

An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome

BACKGROUND: The domestic sheep (Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Furthermore, a high-quality reference genome allows for precise functional annotation of gene regulatory elements. The rapid advances in genome assembly algorithms and emergence of sequencing technologies with increasingly long reads provide the opportunity for an improved de novo assembly of the sheep reference genome. FINDINGS: Short-read Illumina (55× coverage), long-read Pacific Biosciences (75× coverage), and Hi-C data from this ewe retrieved from public databases were combined with an additional 50× coverage of Oxford Nanopore data and assembled with canu v1.9. The assembled contigs were scaffolded using Hi-C data with Salsa v2.2, gaps filled with PBsuitev15.8.24, and polished with Nanopolish v0.12.5. After duplicate contig removal with PurgeDups v1.0.1, chromosomes were oriented and polished with 2 rounds of a pipeline that consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly is 2.63 Gb in length and has improved continuity (contig NG50 of 43.18 Mb), with a 19- and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. CONCLUSIONS: The ARS-UI_Ramb_v2.0 assembly is a substantial improvement in contiguity that will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits in sheep

PLA Logistics and Sustainment: PLA Conference 2022

The US Army War College People’s Liberation Army Conference (PLA) Conference was held March 31 to April 2, 2022, at Carlisle Barracks, Pennsylvania. The conference focused on PLA logistics and sustainment. As the PLA continues to build and modernize its combat forces, it is important to examine if the capabilities meant to support combat operations are also being developed. Specific topics included: 1) China’s national-level logistics, including how China mobilizes national resources for the military and how it provides joint logistics support to the PLA Theater Commands; 2) the logistics capabilities of the different PLA services, especially the Army, Navy, and Air Forces; 3) PLA logistics in China’s remote regions, such as airpower projection in the Western Theater Command along the Indian border; and, 4) the PLA’s ability to sustain overseas operations at its base in Djibouti. Despite notable potential shortfalls and points of friction, the PLA has successfully sustained counterpiracy maritime operations for many years and conducted noncombatant evacuation operations well-distant from China. It is increasingly able to move forces across the vast distances of China and conduct large training exercises. Far more must be known about PLA sustainment and logistics before the hard questions about PLA operational reach and endurance can be answered.https://press.armywarcollege.edu/monographs/1954/thumbnail.jp

De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is &gt;250× more continuous than the original assembly, with contig N50 &gt;25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

A Distinct Esophageal mRNA Pattern Identifies Eosinophilic Esophagitis Patients With Food Impactions

Eosinophilic esophagitis (EoE), a Th2-type allergic immune disorder characterized by an eosinophil-rich esophageal immune infiltrate, is often associated with food impaction (FI) in pediatric patients but the molecular mechanisms underlying the development of this complication are not well understood. We aim to identify molecular pathways involved in the development of FI. Due to large variations in disease presentation, our analysis was further geared to find markers capable of distinguishing EoE patients that are prone to develop food impactions and thus expand an established medical algorithm for EoE by developing a secondary analysis that allows for the identification of patients with food impactions as a distinct patient population. To this end, mRNA patterns from esophageal biopsies of pediatric EoE patients presenting with and without food impactions were compared and machine learning techniques were employed to establish a diagnostic probability score to identify patients with food impactions (EoE+FI). Our analysis showed that EoE patients with food impaction were indistinguishable from other EoE patients based on their tissue eosinophil count, serum IgE levels, or the mRNA transcriptome-based p(EoE). Irrespectively, an additional analysis loop of the medical algorithm was able to separate EoE+FI patients and a composite FI-score was established that identified such patients with a sensitivity of 93% and a specificity of 100%. The esophageal mRNA pattern of EoE+FI patients was typified by lower expression levels of mast cell markers and Th2 associated transcripts, such as FCERIB, CPA3, CCL2, IL4, and IL5. Furthermore, lower expression levels of regulators of esophageal motility (NOS2 and HIF1A) were detected in EoE+FI. The EoE+FI -specific mRNA pattern indicates that impaired motility may be one underlying factor for the development of food impactions in pediatric patients. The availability of improved diagnostic tools such as a medical algorithm for EoE subpopulations will have a direct impact on clinical practice because such strategies can identify molecular inflammatory characteristics of individual EoE patients, which, in turn, will facilitate the development of individualized therapeutic approaches that target the relevant pathways affected in each patient

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype