Rates of inbreeding using DNA fingerprinting in aquaculture breeding programs at various broodstock fitness levels — a simulation study

2005 ◽  
Vol 45 (8) ◽  
pp. 893 ◽  
Author(s):  
M. Macbeth
Keyword(s):  
Dna Fingerprinting ◽  
Simulation Study ◽  
Intraclass Correlation ◽  
Genetic Selection ◽  
Selection Response ◽  
Phenotypic Variance ◽  
Selection Intensity ◽  
Breeding Programs ◽  
Inbreeding Rate ◽  
Number Of Individuals

A simulation study was used to examine the potential use of DNA fingerprinting (DNA tagging) as a tool to avoid excessive inbreeding by identifying suitable candidate breeders in genetic selection programs. ‘Broodstock fitness’ (the ability of broodstock to survive from harvest and reproduce) needs to be considered in designing breeding programs using DNA tagging. In this study, reduced broodstock fitness increased inbreeding exponentially. The level of inbreeding was also dependent on the intraclass correlation (t), selection intensity, number of individuals DNA tagged (NDNA), number of families maintained (Nf) and the number of candidate breeders retained per sex/family at harvest (C). With a broodstock fitness of 0.90, DNA tagging could theoretically achieve a selection intensity, in terms of the total phenotypic variance, of 2.90 standard deviations with 800 000 graded at harvest, while maintaining an inbreeding rate of 1.0% per generation (NDNA = 800, Nf = 30, C = 4, t = 0.3). In practice, the numbers required could be achieved by growing families in individual facilities (e.g. sea cages for barramundi or ponds for prawns). When mechanical grading is not possible, the selection pool may be limited to a level where physical tagging is feasible. In this case, there was no advantage in selection response using DNA tagging compared with physical tags. DNA tagging as a selection tool may be more feasible when broodstock fitness is above 0.6, and may fill a niche where industry infrastructure is not large enough to support separate rearing of families or where physical tagging is not economically viable or suitable. DNA tagging may also be useful as a means of recovering families in backup facilities where families have been pooled to reduce infrastructure costs. Due to the random nature of DNA sampling, not all families may be recovered and a reduction in selection pressure may facilitate family recovery.

ESTIMASI NILAI HERITABILITAS BOBOT IKAN MAS VARIETAS PUNTEN DALAM PROGRAM SELEKSI INDIVIDU

2016 ◽  
Vol 11 (3) ◽  
pp. 217
Author(s):  
Estu Nugroho ◽  
Budi Setyono ◽  
Mochammad Su’eb ◽  
Tri Heru Prihadi
Keyword(s):  
Body Weight ◽  
Selection Response ◽  
Base Population ◽  
Breeding Programs ◽  
Male And Female ◽  
Body Weight Trait ◽  
Population Selection ◽  
Selection For ◽  
Weight Trait ◽  
Selection Of

Program pemuliaan ikan mas varietas Punten dilakukan dengan seleksi individu terhadap karakter bobot ikan. Pembentukan populasi dasar untuk kegiatan seleksi dilakukan dengan memijahkan secara massal induk ikan mas yang terdiri atas 20 induk betina dan 21 induk jantan yang dikoleksi dari daerah Punten, Kepanjen (delapan betina dan enam jantan), Kediri (tujuh betina dan 12 jantan), Sragen (27 betina dan 10 jantan), dan Blitar (15 betina dan 11 jantan). Larva umur 10 hari dipelihara selama empat bulan. Selanjutnya dilakukan penjarangan sebesar 50% dan benih dipelihara selama 14 bulan untuk dilakukan seleksi dengan panduan hasil sampling 250 ekor individu setiap populasi. Seleksi terhadap calon induk dilakukan saat umur 18 bulan pada populasi jantan dan betina secara terpisah dengan memilih berdasarkan 10% bobot ikan yang terbaik. Calon induk yang terseleksi kemudian dipelihara hingga matang gonad, kemudian dipilih sebanyak 150 pasang dan dipijahkan secara massal. Didapatkan respons positif dari hasil seleksi berdasarkan bobot ikan, yaitu 49,89 g atau 3,66% (populasi ikan jantan) dan 168,47 g atau 11,43% (populasi ikan betina). Nilai heritabilitas untuk bobot ikan adalah 0,238 (jantan) dan 0,505 (betina).Punten carp breeding programs were carried out by individual selection for body weight trait. The base population for selection activities were conducted by mass breeding of parent consisted of 20 female and 21 male collected from area Punten, eight female and six male (Kepanjen), seven female and 12 male (Kediri), 27 female and 10 male (Sragen), 15 female and 11 male (Blitar). Larvae 10 days old reared for four moths. Then after spacing out 50% of total harvest, the offspring reared for 14 months for selection activity based on the sampling of 250 individual each population. Selection of broodstock candidates performed since 18 months age on male and female populations separately by selecting based on 10% of fish with best body weight. Candidates selected broodstocks were then maintained until mature. In oder to produce the next generation 150 pairs were sets and held for mass spawning. The results revealed that selection response were positive, 49.89 g (3.66%) for male and 168.47 (11.43%) for female. Heritability for body weight is 0.238 (male) and 0.505 (female).

A cutting edge approach to assessing physical activities occurring on sidewalks/streets (Preprint)

2018 ◽  
Author(s):  
Richard Robert Suminski Jr ◽  
Gregory Dominick ◽  
Philip Sapanaro
Keyword(s):  
Physical Activity ◽  
Environmental Conditions ◽  
Intraclass Correlation ◽  
Physical Activity Behavior ◽  
Physical Activities ◽  
Video Data ◽  
Considerable Proportion ◽  
High Definition ◽  
Deep Convolutional Neural Networks ◽  
Number Of Individuals

BACKGROUND A considerable proportion of outdoor physical activity is done on sidewalk/streets. For example, we found that ~70% of adults who walked during the previous week used the sidewalks/streets around their homes. Interventions conducted at geographical levels (e.g., community) and studies examining relationships between environmental conditions (e.g., traffic) and walking/biking, necessitate a reliable measure of physical activities performed on sidewalks/streets. The Block Walk Method (BWM) is one of the more common approaches available for this purpose. Although it utilizes reliable observation techniques and displays criterion validity, it remains relatively unchanged since its introduction in 2006. It is a non-technical, labor-intensive, first generation method. Advancing the BWM would contribute significantly to our understanding of physical activity behavior. OBJECTIVE Therefore, the objective of the proposed study is to develop and test a new BWM that utilizes a wearable video device (WVD) and computer video analysis to assess physical activities performed on sidewalks/streets. The following aims will be completed to accomplish this objective. Aim 1: Improve the BWM by incorporating a WVD into the methodology. The WVD is a pair of eyeglasses with a high definition video camera embedded into the frames. We expect the WVD to be a viable option for improving the acquisition and accuracy of data collected using the BWM. Aim 2: Advance the WVD-enhanced BWM by applying machine learning and recognition software to automatically extract information on physical activities occurring on the sidewalks/streets from the videos. METHODS Trained observers (one wearing and one not wearing the WVD) will walk together at a set pace along predetermined, 1000 ft. sidewalk/street observation routes representing low, medium, and high walkable areas. During the walks, the non-WVD observer will use the traditional BWM to record the number of individuals standing/sitting, walking, biking, and running along the routes. The WVD observer will only record a video while walking. Later, two investigators will view the videos to determine the numbers of individuals performing physical activities along the routes. For aim 2, the video data will be analyzed automatically using multiple deep convolutional neural networks (CNNs) to determine the number of humans along an observation route as well as the type of physical activities being performed. Bland Altman methods and intraclass correlation coefficients will be used to assess agreement. Potential sources of error such as occlusions (e.g., trees) will be assessed using moderator analyses. RESULTS Outcomes from this study are pending; however, preliminary studies supporting the research protocol indicate that the BWM is reliable and the number of individuals were seen walking along routes are correlated with several environmental characteristics (e.g., traffic, sidewalk defects). Further, we have used CNNs to detect cars, bikes, and pedestrians as well as individuals using park facilities. CONCLUSIONS We expect the new approach will enhance measurement accuracy while reducing the burden of data collection. In the future, the capabilities of the WVD-CNNs system will be expanded to allow for the determination of other characteristics captured by the videos such as caloric expenditure and environmental conditions.

scholarly journals QTL Mapping of Seedling and Adult Plant Resistance to Septoria Tritici Blotch in Winter Wheat cv. Mandub (Triticum aestivum L.)

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1108
Author(s):  
Dominika Piaskowska ◽  
Urszula Piechota ◽  
Magdalena Radecka-Janusik ◽  
Paweł Czembor
Keyword(s):  
Mapping Population ◽  
Triticum Aestivum L ◽  
Seedling Stage ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Adult Plant ◽  
Resistance Locus ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Plant Stage

Septoria tritici blotch (STB) is one of the most devastating foliar diseases of wheat worldwide. Host resistance is the most economical and safest method of controlling the disease, and information on resistance loci is crucial for effective breeding for resistance programs. In this study we used a mapping population consisting of 126 doubled-haploid lines developed from a cross between the resistant cultivar Mandub and the susceptible cultivar Begra. Three monopycnidiospore isolates of Z. tritici with diverse pathogenicity were used to test the mapping population and parents’ STB resistance at the seedling stage (under a controlled environment) and adult plant stage (polytunnel). For both types of environments, the percentage leaf area covered by necrosis (NEC) and pycnidia (PYC) was determined. A linkage map comprising 5899 DArTSNP and silicoDArT markers was used for the quantitative trait loci (QTL) analysis. The analysis showed five resistance loci on chromosomes 1B, 2B and 5B, four of which were derived from cv. Mandub. The location of QTL detected in our study on chromosomes 1B and 5B may suggest a possible identity or close linkage with Stb2/Stb11/StbWW and Stb1 loci, respectively. QStb.ihar-2B.4 and QStb.ihar-2B.5 detected on chromosome 2B do not co-localize with any known Stb genes. QStb.ihar-2B.4 seems to be a new resistance locus with a moderate effect (explaining 29.3% of NEC and 31.4% of PYC), conferring resistance at the seedling stage. The phenotypic variance explained by QTL detected in cv. Mandub ranged from 11.9% to 70.0%, thus proving that it is a good STB resistance source and can potentially be utilized in breeding programs.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 513-530
Author(s):  
J P Hanrahan ◽  
E J Eisen ◽  
J E Legates
Keyword(s):  
Population Size ◽  
Selection Response ◽  
Selection Intensity ◽  
Realized Heritability ◽  
Family Selection ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For ◽  
Selection Intensities ◽  
Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

scholarly journals Corrigendum to: Consequences of genetic selection for environmental impact traits on economically important traits in dairy cows

2018 ◽  
Vol 58 (10) ◽  
pp. 1966
Author(s):  
Purna Kandel ◽  
Sylvie Vanderick ◽  
Marie-Laure Vanrobays ◽  
Hélène Soyeurt ◽  
Nicolas Gengler
Keyword(s):  
Dairy Cows ◽  
Body Condition Score ◽  
Genetic Correlations ◽  
Genetic Selection ◽  
Selection Response ◽  
Direct Selection ◽  
Correlated Response ◽  
Production Traits ◽  
Ch4 Emissions ◽  
Natural Logarithm

Methane (CH4) emission is an important environmental trait in dairy cows. Breeding aiming to mitigate CH4 emissions require the estimation of genetic correlations with other economically important traits and the prediction of their selection response. In this study, test-day CH4 emissions were predicted from milk mid-infrared spectra of Holstein cows. Predicted CH4 emissions (PME) and log-transformed CH4 intensity (LMI) computed as the natural logarithm of PME divided by milk yield (MY). Genetic correlations of PME and LMI with traits used currently were approximated from correlations between estimated breeding values of sires. Values were for PME with MY 0.06, fat yield (FY) 0.09, protein yield (PY) 0.13, fertility 0.17; body condition score (BCS) –0.02; udder health (UDH) 0.22; and longevity 0.22. As expected by its definition, values were negative for LMI with production traits (MY –0.61; FY –0.15 and PY –0.40) and positive with fertility (0.36); BCS (0.20); UDH (0.08) and longevity (0.06). The genetic correlations of 33 type traits with PME ranged from –0.12 to 0.25 and for LMI ranged from –0.22 to 0.18. Without selecting PME and LMI (status quo) the relative genetic change through correlated responses of other traits were in PME by 2% and in LMI by –15%, but only due to the correlated response to MY. Results showed for PME that direct selection of this environmental trait would reduce milk carbon foot print but would also affect negatively fertility. Therefore, more profound changes in current indexes will be required than simply adding environmental traits as these traits also affect the expected progress of other traits.

scholarly journals Mapping and Characterization QTLs for Phenological Traits in Seven Pedigree-connected Peach Families

2020 ◽  
Author(s):  
Zena Rawandoozi ◽  
Timothy Hartmann ◽  
Silvia Carpenedo ◽  
Ksenija Gasic ◽  
Cassia da Silva Linge ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Large Tree ◽  
Early Seedling ◽  
Sib Families ◽  
Functional Alleles ◽  
Genomic Regions ◽  
Marker Identification

Abstract BackgroundEnvironmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.ResultsPhenotypic data of seven F1 low to medium chill full-sib families were collected over two years at two locations and genotyped using the 9K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172 – 182 cM), LG4 (48 – 54 cM), and LG7 (62 – 70 cM), explaining 17-54%, 11-55%, and 11-18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40 - 46 cM) and explained between 40-75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.ConclusionsA multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL for the creation of predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

Resistance to the tick Rhipicephalus microplus and Babesia bovis infection levels in beef heifers raised in an endemic area of Sao Paulo state, Brazil

2019 ◽  
Vol 59 (5) ◽  
pp. 938 ◽  
Author(s):  
A. M. Maiorano ◽  
R. Giglioti ◽  
M. C. S. Oliveira ◽  
H. N. Oliveira ◽  
J. N. S. G. Cyrillo ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Intraclass Correlation ◽  
Rhipicephalus Microplus ◽  
Babesia Bovis ◽  
Phenotypic Variance ◽  
Beef Heifers ◽  
Animal Blood ◽  
Blood Samples ◽  
Bos Taurus Indicus ◽  
Tick Resistance

Repeatability coefficients (r) for tick resistance and Babesia bovis infection levels and the correlation (ρ) between these traits were estimated in beef heifers, using artificial infestations and short intervals between measurements. Forty heifers, including 20 Bos taurus taurus (Caracu) and 20 Bos taurus indicus (Nelore) animals, were submitted to three artificial infestations with Rhipicephalus microplus larvae at intervals of 14 days. The number of standard female was counted from the 19th through the 23rd day after each infestation, considering only the left side of each animal. Blood samples were collected on Days 0, 6, 20, 34 and 48 after the first infestation. The number of copies of B. bovis DNA (CN) was estimated from blood samples through the quantitative PCR technique to evaluate the level of infection in the animals. Total tick count (TTC), the percentage of return (PRij) and CN were analysed using the MIXED procedure of the SAS program. The r of the variables were estimated by intraclass correlation between measures of the same animal, with the variance component of the animal being divided by the phenotypic variance (residual + animal), using models with a CS structure matrix. Additionally, ρ among variables were estimated using the CORR procedure. The following results were obtained for Caracu and Nelore animals, respectively: 1.83 ± 0.37 and 0.63 ± 0.40 for TTC, 1.10 ± 0.23 and 0.47 ± 0.23 for PRij, and 2.29 ± 0.64 and 2.32 ± 0.58 for CN. The r was moderate for TTC (0.62) and PRij (0.53) and low for CN (0.10). The ρ between TTC and CN obtained in the same measurement day was not significant in either breed (P > 0.05; –0.07 for Caracu and 0.19 for Nelore). Results showed both breeds were able to develop resistance against B. bovis; however, Nelore exhibited higher tick resistance. The r obtained for CN and the weak association with tick resistance indicate that it is not possible to recommend the use of CN as a trait to predict tick resistance in these two breeds.

scholarly journals A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea

2020 ◽  
Author(s):  
Rachit K. Saxena ◽  
Anil Hake ◽  
Abhishek Bohra ◽  
Aamir W. Khan ◽  
Anupama Hingane ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Diagnostic Marker ◽  
Development Program ◽  
Cost Effective ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Specific Pcr ◽  
Novel Approach ◽  
Resistant Varieties ◽  
Pathogen Variability

Abstract Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker–trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the diversity of these loci has shown the role of different alleles in different resistant genotypes. Two genes (C.cajan_03691 and C.cajan_18888) for FW resistance and four genes (C.cajan_07858, C.cajan_20995, C.cajan_21801 and C.cajan_17341) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.

Validation of an Instrument for Real-Time Assessment of Neonatal Intubation Skills: A Randomized Controlled Simulation Study

2020 ◽  
Author(s):  
Lindie J.M.K. Kuijpers ◽  
Mathijs Binkhorst ◽  
Nicole K. Yamada ◽  
Romy N. Bouwmeester ◽  
Arno F.J. van Heijst ◽  
...  
Keyword(s):  
Construct Validity ◽  
Real Time ◽  
Simulation Study ◽  
Intraclass Correlation ◽  
Intervention Group ◽  
Control Group ◽  
Validity And Reliability ◽  
Patient Simulator ◽  
Randomized Controlled ◽  
Time Assessment

Objective This study aimed to evaluate the construct validity and reliability of real-time assessment of a previously developed neonatal intubation scoring instrument (NISI). Study Design We performed a randomized controlled simulation study at a simulation-based research and training facility. Twenty-four clinicians experienced in neonatal intubation (“experts”) and 11 medical students (“novices”) performed two identical elective intubations on a neonatal patient simulator. Subjects were randomly assigned to either the intervention group, receiving predefined feedback between the two intubations, or the control group, receiving no feedback. Using the previously developed NISI, all intubations were assessed, both in real time and remotely on video. Construct validity was evaluated by (1) comparing the intubation performances, expressed as percentage scores, with and without feedback, and (2) correlating the intubation performances with the subjects' level of experience. The intrarater reliability, expressed as intraclass correlation coefficient (ICC), of real-time assessment compared with video-based assessment was determined. Results The intervention group contained 18 subjects, the control group 17. Background characteristics and baseline intubation scores were comparable in both groups. The median (IQR) change in percentage scores between the first and second intubation was significantly different between the intervention and control group (11.6% [4.7–22.8%] vs. 1.4% [0.0–5.7%], respectively; p = 0.013). The 95% CI for this 10.2% difference was 2.2 to 21.4%. The subjects' experience level correlated significantly with their percentage scores (Spearman's R = 0.70; p <0.01). ICC's were 0.95 (95% CI: 0.89–0.97) and 0.94 (95% CI: 0.89–0.97) for the first and second intubation, respectively. Conclusion Our NISI has construct validity and is reliable for real-time assessment. Key Points

Sign in / Sign up

Export Citation Format

Share Document