Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.Abstract Background Natural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data. Results We generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism. Conclusions Results revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs

Pengaruh Kualitas Produk, Harga, Dan Saluran Distribusi Terhadap Loyalitas Pelanggan Majalah Swa Melalui Variabel Kepuasan Pelanggan (Studi Kasus Pada Pelanggan Majalah Swa Di DKI Jakarta)

Customer loyalty is a goal that has to be achieved by a company. To be able to get loyal customers, SWA magazine needs to pay attention on the factors that influence customers\u27 loyalty. Moreover, business and economy themed magazines are mushrooming, leading to the opportunity for the readers to move from one magazine to another.This research aimed to ascertain the effect of product quality, price, and distribution channel on customer loyalty of SWA magazine in Jakarta through customer satisfaction variable both simultaneously and partially. The hypothesis was there was an effect of product quality, price, and distribution channel on customer loyalty of SWA magazine in Jakarta through customer satisfaction variable both simultaneously and partially. The type of this research was explanatory research with 97 respondents with multi stage sampling technique through questionnaire and interview. The data was analyzed using linear regression method with the assistance of SPSS 16.0.The result of this research showed that product quality, price and distribution channel variables had significant and positive effect partially on customer satisfaction. Product quality variable did not have partially significant effect on customer loyalty. Price and distribution channel variables had partially significant and positive effect on customer loyalty. Product quality and price variables had simultaneously positive and significant effect on customer satisfaction while distribution channel had simultaneously negative effect on customer satisfaction. Simultaneously, product quality, price, and distribution channel variables had positive effect and not significant effect on customer loyalty. Partially, customer satisfaction had positive and significant effect on customer loyalty.Based on the result of this research, a conclusion was drawn that customers\u27 perception on product quality, price, and distribution channel was good. Customers\u27 satisfaction and loyalty of SWA magazine were also good. The company was suggested to improving the product quality, adjusting the price and boosting the distribution channel of SWA magazine in accordance with customers\u27 needs and expectation, so that, customers can feel the satisfaction and decided to be loyal customers

The genome landscape of indigenous African cattle

Background: The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems. Results: We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/ or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds. Conclusions: Our findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent

Modulating Energetic Characteristics of Multicomponent 1D Coordination Polymers: Interplay of Metal-Ligand Coordination Modes

The energetic properties of multicomponent explosive materials can be altered for high detonation capabilities and minimized safety risk by changing their building components. We synthesized energetic coordination polymers (ECPs) using a 5,5'-bis(tetrazole)-1,1'-diolate linker and a N,N-dimethylacetamide (DMA) solvent, together with Cu and Mn metal cations. The new compounds, ECP-1 and ECP-2, contain two different types of 1D chain structures, straight and helical. We have conducted comprehensive studies on these ECP structures, energetic properties, and sensitivity and found excellent insensitivity owing to the long chain-to-chain distances created by the DMA solvent molecules. The results indicate that the metals as well as solvents used are crucial components influencing both the structure and energetic properties

Genome-wide Association Study (GWAS) and Its Application for Improving the Genomic Estimated Breeding Values (GEBV) of the Berkshire Pork Quality Traits

The missing heritability has been a major problem in the analysis of best linear unbiased prediction (BLUP). We introduced the traditional genome-wide association study (GWAS) into the BLUP to improve the heritability estimation. We analyzed eight pork quality traits of the Berkshire breeds using GWAS and BLUP. GWAS detects the putative quantitative trait loci regions given traits. The single nucleotide polymorphisms (SNPs) were obtained using GWAS results with p value <0.01. BLUP analyzed with significant SNPs was much more accurate than that with total genotyped SNPs in terms of narrow-sense heritability. It implies that genomic estimated breeding values (GEBVs) of pork quality traits can be calculated by BLUP via GWAS. The GWAS model was the linear regression using PLINK and BLUP model was the G-BLUP and SNP-GBLUP. The SNP-GBLUP uses SNP-SNP relationship matrix. The BLUP analysis using preprocessing of GWAS can be one of the possible alternatives of solving the missing heritability problem and it can provide alternative BLUP method which can find more accurate GEBVs

Tetrazole-Based Energetic Metal-Organic Frameworks: Impacts of Metals and Ligands on Explosive Properties

New energetic materials are required to compensate for the shortcomings of the current ones. Especially secondary explosives are the ones with low-sensitivity, while maintaining energetic performance similar to those of primary ones, and particularly useful when safety must be ensured. Herein, we report two energetic metal-organic frameworks (eMOFs), eMOF-1, [Mn-5(mtz)(6.1)(atz)(2.9)(NO3)] (mtz=5-methyltetrazole, atz=5-aminotetrazole) and eMOF-2, [Cu(mtz)(2)], both of which have unique detonation and sensitivity properties. In particular, eMOF-1, firstly reported here, shows better energetic performance when compared with the previously reported material, Cd-based mtz MOF, an isostructural series. In addition, eMOF-2 synthesized in water shows a great detonation performance, whereas isotopological Zn-based mtz MOF did not show a meaningful performance as an explosive. Therefore, such reticular approach, i. e. replacing metal ions or ligands in isostructural frameworks, can be quite effective for the development of a new breed of energetic materials

Origamic metal-organic framework toward mechanical metamaterial

Abstract Origami, known as paper folding has become a fascinating research topic recently. Origami-inspired materials often establish mechanical properties that are difficult to achieve in conventional materials. However, the materials based on origami tessellation at the molecular level have been significantly underexplored. Herein, we report a two-dimensional (2D) porphyrinic metal-organic framework (MOF), self-assembled from Zn nodes and flexible porphyrin linkers, displaying folding motions based on origami tessellation. A combined experimental and theoretical investigation demonstrated the origami mechanism of the 2D porphyrinic MOF, whereby the flexible linker acts as a pivoting point. The discovery of the 2D tessellation hidden in the 2D MOF unveils origami mechanics at the molecular level

Additional file 2: Figure S1. of Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

The distributions of novel SNV and known SNP in each chromosome. Figure S2. A statistical enrichment test (Fisher’s exact test) for detecting enriched non-synonymous SNP site on targeted genes. Figure S3. A statistical enrichment test (Fisher’s exact test) for detecting enriched Indel site on targeted genes. Figure S4. The overall reads mapping rate of assembled contigs for each breed and reference genome by aligning the total sequence reads of each Berkshire sample. (DOCX 3433 kb