scholarly journals Estimation of Pool Construction and Technical Error

Agriculture ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1091
Author(s):  
John Keele ◽  
Tara McDaneld ◽  
Ty Lawrence ◽  
Jenny Jennings ◽  
Larry Kuehn
Keyword(s):  
Low Cost ◽  
Genetic Evaluation ◽  
Technical Error ◽  
Pedigree Data ◽  
Phenotypic Data ◽  
Tissue Mass ◽  
Novel Traits ◽  
Extreme Phenotypes ◽  
Processing Plants ◽  
Average Contribution

Pooling animals with extreme phenotypes can improve the accuracy of genetic evaluation or provide genetic evaluation for novel traits at relatively low cost by exploiting large amounts of low-cost phenotypic data from animals in the commercial sector without pedigree (data from commercial ranches, feedlots, stocker grazing or processing plants). The average contribution of each animal to a pool is inversely proportional to the number of animals in the pool or pool size. We constructed pools with variable planned contributions from each animal to approximate errors with different numbers of animals per pool. We estimate pool construction error based on combining liver tissue, from pulverized frozen tissue mass from multiple animals, into eight sub-pools containing four animals with planned proportionality (1:2:3:4) by mass. Sub-pools were then extracted for DNA and genotyped using a commercial array. The extracted DNA from the sub-pools was used to form super pools based on DNA concentration as measured by spectrophotometry with planned contribution of sub-pools of 1:2:3:4. We estimate technical error by comparing estimated animal contribution using sub-samples of single nucleotide polymorphism (SNP). Overall, pool construction error increased with planned contribution of individual animals. Technical error in estimating animal contributions decreased with the number of SNP used.

scholarly journals Exploring Two Honey Bee Traits for Improving Resistance Against Varroa destructor: Development and Genetic Evaluation

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 216
Author(s):  
Matthieu Guichard ◽  
Benoît Droz ◽  
Evert W. Brascamp ◽  
Adrien von Virag ◽  
Markus Neuditschko ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Varroa Destructor ◽  
Field Trial ◽  
Genetic Evaluation ◽  
Phenotypic Correlation ◽  
Apis Mellifera Mellifera ◽  
Novel Traits ◽  
Resistance Traits

For the development of novel selection traits in honey bees, applicability under field conditions is crucial. We thus evaluated two novel traits intended to provide resistance against the ectoparasitic mite Varroa destructor and to allow for their straightforward implementation in honey bee selection. These traits are new field estimates of already-described colony traits: brood recapping rate (‘Recapping’) and solidness (‘Solidness’). ‘Recapping’ refers to a specific worker characteristic wherein they reseal a capped and partly opened cell containing a pupa, whilst ‘Solidness’ assesses the percentage of capped brood in a predefined area. According to the literature and beekeepers’ experiences, a higher recapping rate and higher solidness could be related to resistance to V. destructor. During a four-year field trial in Switzerland, the two resistance traits were assessed in a total of 121 colonies of Apis mellifera mellifera. We estimated the repeatability and the heritability of the two traits and determined their phenotypic correlations with commonly applied selection traits, including other putative resistance traits. Both traits showed low repeatability between different measurements within each year. ‘Recapping’ had a low heritability (h2 = 0.04 to 0.05, depending on the selected model) and a negative phenotypic correlation to non-removal of pin-killed brood (r = −0.23). The heritability of ‘Solidness’ was moderate (h2 = 0.24 to 0.25) and did not significantly correlate with resistance traits. The two traits did not show an association with V. destructor infestation levels. Further research is needed to confirm the results, as only a small number of colonies was evaluated.

scholarly journals New Male Specific Markers for Hop and Application in Breeding Program

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Andreja Čerenak ◽  
Zala Kolenc ◽  
Petra Sehur ◽  
Simon P. Whittock ◽  
Anthony Koutoulis ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Dna Sequences ◽  
Low Cost ◽  
Pcr Amplification ◽  
Breeding Program ◽  
Phenotypic Data ◽  
World Collection ◽  
Crude Sample ◽  
Male Sex ◽  
Male Specific

Abstract Male specific DNA sequences were selected from a Diversity Arrays Technology (DArT) mapping study to evaluate their suitability for determination of the sex phenotype among young seedlings in a hop (Humulus lupulus L.) breeding program. Ten male specific DArT markers showed complete linkage with male sex phenotype in three crossing families. Following optimization, four were successfully converted into PCR markers and a multiplex PCR approach for their use was developed. Among 197 plants (97 from the world collection; 100 from three segregating families), 94–100% positive correlation with sex phenotypic data was achieved for the single PCR amplification, whereas the multiplex approach showed 100% correlation. To develop a fast and low-cost method, crude sample multiplex PCR was evaluated in 253 progenies from 14 segregating populations without losing accuracy. The study describes, for the first time, the routine application of molecular markers linked to male sex in an intensive Slovenian hop breeding program. The methods described could be employed for screening of sex at the seedling stage in other hop programs worldwide, thereby saving resources for desirable female plants.

Adsorption of Crude Oil Using Meshed Groundnut Husk

2010 ◽  
Vol 5 (1) ◽  
Author(s):  
Darlington Bon Nwokoma ◽  
Uchenna Anene
Keyword(s):  
Crude Oil ◽  
Urban Areas ◽  
Low Cost ◽  
Sorption Process ◽  
Experimental Conditions ◽  
Oil Processing ◽  
High Affinity ◽  
Processing Plants ◽  
Groundnut Shell ◽  
The Impact

There is an increasing awareness of the impact of spilled crude oil and its refined products on human health and environment. The potential of using groundnut husk, agro-based waste, which is not only ubiquitous but indiscriminately littered around Nigerian urban areas, as an adsorbent in removal of oil spilled on water was investigated. Groundnut shell, a waste generated in local vegetable oil processing plants, has been converted into a low cost adsorbent. The groundnut husk was treated and meshed to adsorb crude oil from water at various experimental conditions. Investigations include the effects of sorbent dosage, particle size, contact time and temperature on the adsorption of crude oil. Meshed groundnut shell, especially less than 150 µm, exhibited high affinity for oil adsorption with time. The optimum adsorption temperature range lies between 25 – 45°C. The adsorption data indicates that a pseudo-second-order equation could be used to study the adsorption kinetics and the correlation coefficient of 0.9985 indicates that the sorption process is dominated by adsorption process. The results demonstrate that crude oil removal by adsorption onto this abundantly available low cost and readily biodegradable material is feasible. With high affinity for oil and low water pick up, meshed groundnut shell adsorbent could be said to be oleophilic or hydrophobic.

scholarly journals Using recent versus complete pedigree data in genetic evaluation of a closed nucleus broiler line

1999 ◽  
Vol 78 (7) ◽  
pp. 937-941 ◽  
Author(s):  
H Mehrabani-Yeganeh ◽  
JP Gibson ◽  
LR Schaeffer
Keyword(s):  
Genetic Evaluation ◽  
Pedigree Data

Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data

Genome ◽  
2007 ◽  
Vol 50 (4) ◽  
pp. 373-384 ◽  
Author(s):  
M. Maccaferri ◽  
S. Stefanelli ◽  
F. Rotondo ◽  
R. Tuberosa ◽  
M.C. Sanguineti
Keyword(s):  
Durum Wheat ◽  
Genetic Relatedness ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Phenotypic Traits ◽  
Pedigree Data ◽  
Crop Species ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Triticum Durum Desf

The determination of genetic relatedness among elite materials of crop species allows for more efficient management of breeding programs and for the protection of breeders’ rights. Seventy simple sequence repeats (SSRs) and 234 amplified fragment length polymorphisms (AFLPs) were used to profile a collection of 58 durum wheat ( Triticum durum Desf.) accessions, representing the most important extant breeding programs. In addition, 42 phenotypic traits, including the morphological characteristics recommended for the official distinctness, uniformity, and stability tests, were recorded. The correlation between the genetic similarities obtained with the 2 marker classes was high (r = 0.81), whereas lower values were observed between molecular and phenotypic data (r = 0.46 and 0.56 for AFLPs and SSRs, respectively). Morphological data, even if sampled in high numbers, largely failed to describe the pattern of genetic similarity, according to known pedigree data and the indications provided by molecular markers.

scholarly journals Computationally Repurposing Drugs for Breast Cancer Subtypes Using a Network-Based Approach

2021 ◽  
Author(s):  
Forough Firoozbakht ◽  
Iman Rezaeian ◽  
Luis Rueda ◽  
Alioune Ngom
Keyword(s):  
Breast Cancer ◽  
Large Scale ◽  
De Novo ◽  
Low Cost ◽  
Drug Repurposing ◽  
Breast Cancer Subtypes ◽  
Therapeutic Effects ◽  
Phenotypic Data ◽  
Cancer Subtypes ◽  
Experimental Drugs

Abstract 'De novo' drug discovery is costly, slow, and with high risk. Repurposing known drugs for treatment of other diseases offers a fast, low-cost/risk and highly-efficient method toward development of efficacious treatments. The emergence of large-scale heterogeneous biomolecular networks, molecular, chemical and bioactivity data, and genomic and phenotypic data of pharmacological compounds is enabling the development of new area of drug repurposing called 'in silico' drug repurposing, i.e., computational drug repurposing (CDR). The aim of CDR is to discover new indications for an existing drug (drug-centric) or to identify effective drugs for a disease (disease-centric). Both drug-centric and disease-centric approaches have the common challenge of either assessing the similarity or connections between drugs and diseases. However, traditional CDR is fraught with many challenges due to the underlying complex pharmacology and biology of diseases, genes, and drugs, as well as the complexity of their associations. As such, capturing highly non-linear associations among drugs, genes, diseases by most existing CDR methods has been challenging.We propose a network-based integration approach that can best capture knowledge (and complex relationships) contained within and between drugs, genes and disease data. A network-based machine learning approach is applied thereafter by using the extracted knowledge and relationships in order to identify single and pair of approved or experimental drugs with potential therapeutic effects on different breast cancer subtypes.

scholarly journals Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Pascal M. Frey ◽  
Julian Baer ◽  
Judith Bergada-Pijuan ◽  
Conor Lawless ◽  
Philipp K. Bühler ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
High Throughput ◽  
Low Cost ◽  
Reproductive Fitness ◽  
Computational Approach ◽  
Phenotypic Data ◽  
Resistance Analysis ◽  
High Throughput Method ◽  
Severe Infections

Reproductive fitness of bacteria is a major factor in the evolution and persistence of antimicrobial resistance and may play an important role as a pathogen factor in severe infections. With a computational approach to quantify fitness in bacteria growing competitively on agar plates, our high-throughput method has been designed to obtain additional phenotypic data for antimicrobial resistance analysis at a low cost.

scholarly journals Genetic Parameters of Workability Traits in the Population of Polish Holstein-Friesian Cows Based on Conventional and Genomic Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2443
Author(s):  
Bartosz Szymik ◽  
Piotr Topolski ◽  
Wojciech Jagusiak
Keyword(s):  
Fixed Effects ◽  
Genetic Parameters ◽  
Genetic Parameter ◽  
Correlation Coefficients ◽  
Genomic Data ◽  
Phenotypic Correlation ◽  
Pedigree Data ◽  
Effective Population ◽  
Phenotypic Data ◽  
Holstein Friesian

Heritabilities of workability (WT) traits—milking speed (MS) and temperament (MT)—as well as genetic and phenotypic correlations between these traits in the population of Polish Holstein-Friesian (PHF) cows were estimated. The estimation of genetic parameters was performed twice: first with the use of pedigree data; and second with the use of pedigree and genomic data. Phenotypic data from routinely conducted MS and MT evaluations for 1,045,511 cows born from 2004 to 2013 were available; the cows were evaluated from 2011 to 2015. The main dataset was reduced based on imposed restrictions (e.g., on age of calving, stage of lactation and day of first trial milking). The dataset prepared in this manner comprised 391,615 cows. It was then reduced to daughters of 10% randomly selected sires for computational reasons. Finally, for genetic parameter estimation, 13,280 records of cows were used. The linear observation model included additive random effects of animal, fixed effects of herd-year-season of calving subclass (HYS) and lactation phase, fixed regressions on cow age at calving and the percent of HF breed genes in the cow genotype. Heritabilities estimated based on pedigree data were 0.12 (±0.0067) for MS and 0.08 (±0.0063) for MT, the genetic correlation between MS and MT was estimated at 0.05 (±0.0002) and the phenotypic correlation coefficient was estimated at 0.14 (±0.0004). The inclusion of genomic information of sire bulls had no clear effect on the size of the estimated WT genetic parameters. The heritabilities of MS and MT were 0.11 (±0.0065) and 0.09 (±0.0012), respectively. The genetic and phenotypic correlation coefficients were 0.07 (±0.0003) and 0.12 (±0.0005), respectively. The sizes of the obtained heritabilities of WT and of the genetic and phenotypic correlation between these traits indicate the possibility of effective population improvement for both WT traits.

scholarly journals Molecular characterization of soybean cultivars by microsatellite markers with universal tail sequence

2013 ◽  
Vol 48 (3) ◽  
pp. 270-279 ◽  
Author(s):  
Carlos Alexandre Gomes Ribeiro ◽  
Janaína Paula Marques Tanure ◽  
Talles Eduardo Ferreira Maciel ◽  
Everaldo Gonçalves de Barros
Keyword(s):  
Polymorphic Information Content ◽  
Low Cost ◽  
High Accuracy ◽  
Genetic Purity ◽  
Phenotypic Data ◽  
Soybean Cultivars ◽  
Highly Correlated ◽  
Semiautomated Method

The objective of this work was to standardize a semiautomated method for genotyping soybean, based on universal tail sequence primers (UTSP), and to compare it with the conventional genotyping method that uses electrophoresis in polyacrylamide gels. Thirty soybean cultivars were genotypically characterized by both methods, using 13 microsatellite loci. For the UTSP method, the number of alleles (NA) was 50 (2-7 per marker) and the polymorphic information content (PIC) ranged from 0.40 to 0.74. For the conventional method, the NA was 38 (2-5 per marker) and the PIC varied from 0.39 to 0.67. The genetic dissimilarity matrices obtained by the two methods were highly correlated with each other (0.8026), and the formed groups were coherent with the phenotypic data used for varietal registration. The 13 markers allowed the distinction of all analyzed cultivars. The low cost of the UTSP method, associated with its high accuracy, makes it ideal for the characterization of soybean cultivars and for the determination of genetic purity.

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