scholarly journals Stepwise Penalty Index Selection from Populations with a Hierarchical Structure

2006 ◽  
Vol 55 (1-6) ◽  
pp. 62-70 ◽  
Author(s):  
Run-Peng Wei ◽  
D. Lindgren

Abstract By adding a penalty to a candidate’s breeding value for its relationship with the selected individuals, two indexes were constructed as criteria for stepwise selection of superior individuals from populations with a hierarchical structure. The relationship was expressed in terms of either family contribution or group coancestry. One of the indexes was derived from an optimal selection model. A stepwise procedure that screened superior individuals one by one was introduced to make selection based on these indexes possible. Two penalty selection methods exclusively maximized gain at given coancestry. Both methods produced all identical solutions in most of the populations simulated, and were nearly equivalent in the remaining populations, particularly when heritability was high and the population structure was simple. A better balance between gain and coancestry following penalty index selection can be obtained by avoiding the two extreme solutions: combined- index and within-family selection, and using simple mating designs rather than complex ones.

1998 ◽  
Vol 28 (12) ◽  
pp. 1861-1869 ◽  
Author(s):  
R -P Wei ◽  
C R Hansen ◽  
N K Dhir ◽  
F C Yeh

Genetic gain and average coancestry or status number was investigated for five selection methods: penalty index selection (PIS), family index selection (FIS), combined between-family and within-family selection (CBW), restricted individual selection (RIS), and combined index selection (RCS). PIS was a function of an individual's breeding value and family contributions, modelled as a stepwise procedure to select superior individuals one by one. A penalty would indicate the need to have low average coancestry or large status number. Breeding populations of unrelated families were investigated by Monte Carlo simulation to examine the genetic response of the five selection methods at a restricted selection intensity and average coancestry. PIS attained the greatest genetic gain, except at the selection limits of maximum genetic gain and minimum average coancestry where PIS might be identical to the other selection methods. FIS and RCS well approximated PIS at high average coancestry. RIS was similar to RCS when the heritability was high, particularly at low average coancestry. CBW attained the least genetic gain among the selection methods. For all selections, high heritability would contribute to a greater genetic gain and status number or low average coancestry. PIS was applied to a practical breeding program in Alberta that included several subpopulations. The results suggested that the selection efficiency for balancing genetic gain and average coancestry would increase when deploying a subpopulation strategy for breeding population management.


PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244064
Author(s):  
Anne Ricard ◽  
Bernard Dumont Saint Priest ◽  
Marjorie Chassier ◽  
Margot Sabbagh ◽  
Sophie Danvy

The aim was to assess the efficiency of gaits characteristics in improving jumping performance of sport horses and confront accelerometers and judge scores for this purpose. A sample of 1,477 young jumping horses were measured using accelerometers for walk, trot, and canter. Of these, 702 were genotyped with 541,175 SNPs after quality control. Dataset of 26,914 horses scored by judges in breeding shows for gaits and dataset of 142,682 horses that performed in jumping competitions were used. Analysis of accelerometric data defined three principal components from 64% to 89% of variability explained for each gait. Animal mixed models were used to estimate genetic parameters with the inclusion to up 308,105 ancestors for the relationship matrix. Fixed effects for the accelerometric variables included velocity, gender, age, and event. A GWAS was performed on residuals with the fixed effect of each SNP. The GWAS did not reveal other QTLs for gait traits than the one related to the height at withers. The accelerometric principal components were highly heritable for the one linked to stride frequency and dorsoventral displacement at trot (0.53) and canter (0.41) and moderately for the one linked to longitudinal activities (0.33 for trot, 0.19 for canter). Low heritabilities were found for the walk traits. The genetic correlations of the accelerometric principal components with the jumping competition were essentially nil, except for a negative correlation with longitudinal activity at canter (-0.19). The genetic correlation between the judges’ scores and the jumping competition reached 0.45 for canter (0.31 for trot and 0.17 for walk). But these correlations turned negative when the scores were corrected for the known parental breeding value for competition at the time of the judging. In conclusion, gait traits were not helpful to select for jumping performances. Different gaits may be suitable for a good jumping horse.


Author(s):  
А. I. Grabovets ◽  
V. P. Kadushkina ◽  
S. А. Kovalenko

With the growing aridity of the climate on the Don, it became necessary to improve the methodology for conducting the  breeding of spring durum wheat. The main method of obtaining the source material remains intraspecific step hybridization. Crossings were performed between genetically distant forms, differing in origin and required traits and properties. The use of chemical mutagenesis was a productive way to change the heredity of genotypes in terms of drought tolerance. When breeding for productivity, both in dry years of research and in favorable years, the most objective markers were identified — the size of the aerial mass, the mass of grain per plant, spike, and harvest index. The magnitude of the correlation coefficients between the yield per unit area and the elements of its structure is established. It was most closely associated with them in dry years, while in wet years it decreased. Power the correlation of the characteristics of the pair - the grain yield per square meter - the aboveground biomass averaged r = 0.73, and in dry years it was higher (0.91) than in favorable ones (0.61 - 0.70) , between the harvest and the harvest index - r = 0.81 (on average). In dry years, the correlation coefficient increased to 0.92. Research data confirms the greatest importance of the mass of grain from one ear and the plant in the formation of grain yield per unit area in both dry and wet years. In dry years, the correlation coefficient between yield and grain mass per plant was on average r = 0.80; in favorable years, r = 0.69. The relationship between yield and grain mass from the ear was greater — r = 0.84 and r = 0.82, respectively. Consequently, the breeding significance of the aboveground mass and the productivity of the ear, as a criterion for the selection of the crop, especially increases in the dry years. They were basic in the selection.


Author(s):  
N.V. SIVKIN ◽  
N.V. STREKOZOV ◽  
V.I. CHINAROV

В симментальской породе предусматривается разведение скота, сбалансировано сочетающего молочную и мясную продуктивность. Однако в практике совершенствования племенных стад в подборах быков доминируют улучшатели удоя, что во многом предопределяет результаты селекции и продуктивный тип животных. Объектом нашего исследования стало стадо чистопородного симментальского скота в условиях стойловой системы беспривязного и привязного содержания коров. Для изучения эффективности использования быков-производителей разного племенного достоинства сформировали 2 опытные группы: I состояла из бычков, полученных от отцов с племенной ценностью (ПЦ) по удою 100 кг и более, а во II с ПЦ от 0 до 100 кг молока. Симментальские бычки, отобранные для контрольного убоя, достигали весовых кондиций 500 кг и более в 17,5 мес при среднесуточном приросте 911 г. При использовании на маточном поголовье быков-производителей с улучшающим эффектом по удою 100 кг и более, их сыновья (I группа), на фоне более высоких суточных приростов (на 30 г) и раннем возрасте достижения живой массы 500 кг (на 18 дней) имели массу и выход туши на 21,4 кг и 2,7 ниже, чем у бычков II группы. При формировании молочно-мясного типа быки-производители с умеренной племенной ценностью по удою обеспечивали получение потомства, сочетающего молочную и мясную продуктивность в экономически значимых пропорциях.The Simmental breed provides for the breeding of cattle that combines milk and meat productivity in a balanced proportion. However, in the practice of improving breeding herds, the selection of bulls is dominated by milk yield improvers, which largely determines the results of selection and the productive type of animals. The object of our research was a breeding herd of purebred Simmental cattle in variety feeding and housing practices. To study the effectiveness of using bulls-producers of different breeding values, 2 experimental groups were formed: I consisted of bulls received from fathers with a breeding value (BV) of milk yield 100 kg or more, and II with a BV from 0 to 100 kg of milk. Simmental bulls selected for control slaughter reached weight standards of 500 kg or more in 17.5 months with an average daily increase of 911 g. When used on breeding of bulls with an improving effect on the yield of 100 kg or more, their sons (group I), against the background of higher daily gains (30 g) and an early age of reaching a live weight of 500 kg (18 days), had a mass and carcass yield of 21.4 kg and 2.7 lower than that of group II bulls. When forming a dairy-meat type, producing bulls with a moderate breeding value for milk yield provided for the production of offspring that combined dairy and meat productivity in economically significant proportions.


2018 ◽  
Vol 2 (2) ◽  
pp. 137
Author(s):  
Muhammad Abi Berkah Nadi

Radin Inten II Airport is a national flight in Lampung Province. In this study using the technical analysis stated preference which is the approach by conveying the choice statement in the form of hypotheses to be assessed by the respondent. By using these techniques the researcher can fully control the hypothesized factors. To determine utility function for model forecasting in fulfilling request of traveler is used regression analysis with SPSS program. The analysis results obtained that the passengers of the dominant airport in the selection of modes of cost attributes than on other attributes. From the result of regression analysis, the influence of independent variable to the highest dependent variable is when the five attributes are used together with the R square value of 8.8%. The relationship between cost, time, headway, time acces and service with the selection of modes, the provision that states whether or not there is a decision. The significance of α = 0.05 with chi-square. And the result of Crame's V test average of 0.298 is around the middle, then the relationship is moderate enough.


2018 ◽  
Vol 15 (5) ◽  
pp. 429-442 ◽  
Author(s):  
Nishant Verma ◽  
S. Natasha Beretvas ◽  
Belen Pascual ◽  
Joseph C. Masdeu ◽  
Mia K. Markey ◽  
...  

Background: Combining optimized cognitive (Alzheimer's Disease Assessment Scale- Cognitive subscale, ADAS-Cog) and atrophy markers of Alzheimer's disease for tracking progression in clinical trials may provide greater sensitivity than currently used methods, which have yielded negative results in multiple recent trials. Furthermore, it is critical to clarify the relationship among the subcomponents yielded by cognitive and imaging testing, to address the symptomatic and anatomical variability of Alzheimer's disease. Method: Using latent variable analysis, we thoroughly investigated the relationship between cognitive impairment, as assessed on the ADAS-Cog, and cerebral atrophy. A biomarker was developed for Alzheimer's clinical trials that combines cognitive and atrophy markers. Results: Atrophy within specific brain regions was found to be closely related with impairment in cognitive domains of memory, language, and praxis. The proposed biomarker showed significantly better sensitivity in tracking progression of cognitive impairment than the ADAS-Cog in simulated trials and a real world problem. The biomarker also improved the selection of MCI patients (78.8±4.9% specificity at 80% sensitivity) that will evolve to Alzheimer's disease for clinical trials. Conclusion: The proposed biomarker provides a boost to the efficacy of clinical trials focused in the mild cognitive impairment (MCI) stage by significantly improving the sensitivity to detect treatment effects and improving the selection of MCI patients that will evolve to Alzheimer’s disease.


Author(s):  
A. A. Sheptulin ◽  
O. A. Storonova

Aim of review. Interpretation of published evidence on the relationship between the excessive belching syndrome and functional dyspepsia (FD) and their management in patient care.Key points. According to the Rome IV criteria of functional gastrointestinal disorders (FGID), excessive belching in the absence of other dyspeptic symptoms is to be considered a manifestation of the excessive belching syndrome, which can be of gastric or supragastric nature. Combination of high-resolution manometry and impedancemetry allows an accurate diagnosis of belching and selection of optimal treatment strategy. Belching complicated by other symptoms of dyspepsia is to be considered yet another FD symptom according to the Rome IV criteria of FGID. Prokinetics are recommended to relieve belching in such cases.Conclusion. Understanding the relationship between the excessive belching syndrome and FD requires further research.


Toxins ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 158
Author(s):  
Colin Eady

For 30 years, forage ryegrass breeding has known that the germplasm may contain a maternally inherited symbiotic Epichloë endophyte. These endophytes produce a suite of secondary alkaloid compounds, dependent upon strain. Many produce ergot and other alkaloids, which are associated with both insect deterrence and livestock health issues. The levels of alkaloids and other endophyte characteristics are influenced by strain, host germplasm, and environmental conditions. Some strains in the right host germplasm can confer an advantage over biotic and abiotic stressors, thus acting as a maternally inherited desirable ‘trait’. Through seed production, these mutualistic endophytes do not transmit into 100% of the crop seed and are less vigorous than the grass seed itself. This causes stability and longevity issues for seed production and storage should the ‘trait’ be desired in the germplasm. This makes understanding the precise nature of the relationship vitally important to the plant breeder. These Epichloë endophytes cannot be ‘bred’ in the conventional sense, as they are asexual. Instead, the breeder may modulate endophyte characteristics through selection of host germplasm, a sort of breeding by proxy. This article explores, from a forage seed company perspective, the issues that endophyte characteristics and breeding them by proxy have on ryegrass breeding, and outlines the methods used to assess the ‘trait’, and the application of these through the breeding, production, and deployment processes. Finally, this article investigates opportunities for enhancing the utilisation of alkaloid-producing endophytes within pastures, with a focus on balancing alkaloid levels to further enhance pest deterrence and improving livestock outcomes.


2003 ◽  
Vol 785 ◽  
Author(s):  
Seth S. Kessler ◽  
S. Mark Spearing

ABSTRACTEmbedded structural health monitoring systems are envisioned to be an important component of future transportation systems. One of the key challenges in designing an SHM system is the choice of sensors, and a sensor layout, which can detect unambiguously relevant structural damage. This paper focuses on the relationship between sensors, the materials of which they are made, and their ability to detect structural damage. Sensor selection maps have been produced which plot the capabilities of the full range of available sensor types vs. the key performance metrics (power consumption, resolution, range, sensor size, coverage). This exercise resulted in the identification of piezoceramic Lamb wave transducers as the sensor of choice. Experimental results are presented for the detailed selection of piezoceramic materials to be used as Lamb wave transducers.


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