Mixed-species allometric equations and estimation of aboveground biomass and carbon stocks in restoring degraded landscape in northern Ethiopia

Accurate biomass estimation is critical to quantify the changes in biomass and carbon stocks following the restoration of degraded landscapes. However, there is lack of site-specific allometric equations for the estimation of aboveground biomass (AGB), which consequently limits our understanding of the contributions of restoration efforts in mitigating climate change. This study was conducted in northwestern Ethiopia to develop a multi-species allometric equation and investigate the spatial and temporal variation of C-stocks following the restoration of degraded landscapes. We harvested and weighed 84 trees from eleven dominant species from six grazing exclosures and adjacent communal grazing land. We observed that AGB correlates significantly with diameter at stump height D 30 (R 2 = 0.78; P < 0.01), and tree height H (R 2 = 0.41, P < 0.05). Our best model, which includes D 30 and H as predictors explained 82% of the variations in AGB. This model produced the lowest bias with narrow ranges of errors across different diameter classes. Estimated C-stock showed a significant positive correlation with stem density (R 2 = 0.80, P < 0.01) and basal area (R 2 = 0.84, P < 0.01). At the watershed level, the mean C-stock was 3.8 (±0.5) Mg C ha−1. Plot-level C-stocks varied between 0.1 and 13.7 Mg C ha−1. Estimated C-stocks in three- and seven-year-old exclosures exceeded estimated C-stock in the communal grazing land by 50%. The species that contribute most to C-stocks were Leucaena sp. (28%), Calpurnia aurea (21%), Euclea racemosa (20.9%), and Dodonaea angustifolia (15.8%). The equations developed in this study allow monitoring changes in C-stocks and C-sequestration following the implementation of restoration practices in northern Ethiopia over space and time. The estimated C-stocks can be used as a reference against which future changes in C-stocks can be compared

Electron Loss from 1.4-MeV / u U\u3csup\u3e4,6,10+\u3c/sup\u3e Ions Colliding with Ne, N₂, and Ar Targets

Absolute, total, single- and multiple-electron-loss cross sections are measured for 1.4-MeV / u U4,6,10+ ions colliding with neon and argon atoms and nitrogen molecules. It is found that the cross sections all have the same dependence on the number of electrons lost and that multiplying the cross sections by the initial number of electrons in the 6s, 6p, and 5f shells yields good agreement between the different projectiles. By combining the present data with previous measurements made at the same velocity, it is shown that the scaled cross sections slowly decrease in magnitude for incoming charge states between 1 and 10, whereas the cross sections for higher-charge-state ions fall off much more rapidly

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species

Published: 10 April 2015In recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements in terms of genotyping cost, manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species: ranging from one for goats to more than ten for cattle, and the number of arrays available is increasing rapidly. However, there is limited or no effort to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. past and current assemblies) SNP information.Here we present SNPchiMp v.3, a solution to these issues for the six major livestock species (cow, pig, horse, sheep, goat and chicken). Original data was collected directly from SNP array producers and specific international genome consortia, and stored in a MySQL database. The database was then linked to an open-access web tool and to public databases. SNPchiMp v.3 ensures fast access to the database (retrieving within/across SNP array data) and the possibility of annotating SNP array data in a user-friendly fashion.This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines. In recognition of the open-access use of Ensembl resources, SNPchiMp v.3 was officially credited as an Ensembl E!mpowered tool. Availability at http://bioinformatics.tecnoparco.org/SNPchimp.Ezequiel L Nicolazzi, Andrea Caprera, Nelson Nazzicari, Paolo Cozzi, Francesco Strozzi, Cindy Lawley, Ali Pirani, Chandrasen Soans, Fiona Brew, Hossein Jorjani, Gary Evans, Barry Simpson, Gwenola Tosser-Klopp, Rudiger Brauning, John L Williams and Alessandra Stell

Sheep Genome Functional Annotation Reveals Proximal Regulatory Elements Contributed to The Evolution of Modern Breeds

Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species

Resolving the evolution of extant and extinct ruminants with hith-throughput phylogenomics.

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Genome-wide association study revealed putative SNPs and candidate genes associated with growth and meat traits in Japanese quail

The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F 2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement

Genotyping-by-sequencing strategy for integrating genomic structure, diversity and performance of various Japanese quail (Coturnix japonica) breeds

Simple Summary: Artificial selection has been applied to domesticated birds for many decades. More recently, this selection has made use of so-called single-nucleotide polymorphism (SNP) markers—simple variants in a DNA sequence. These SNPs can be used for whole-genome screening to detect the unique traces of areas of the genome that are subject to selection. Doing this may help to shed light on the evolutionary and family history (phylogeny) of domestic Japanese quails of different breeds and utility types (e.g., egg, meat or dual-purpose breeds). In this study, 99 birds were used, representing eight breeds (11% of the world’s quail gene pool) and various purposes of use to gather genetic (whole-genome) data in the first-ever analysis of its kind performed on domestic quails. We thereby uncovered evolutionary relationships and points of divergence of individual quail breeds, gleaning important insights into the genetic diversity of domestic quail breeds and their future breeding potential. Abstract: Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies