Stratified sublining: a new option for structuring breeding populations

2000 ◽  
Vol 30 (4) ◽  
pp. 596-604 ◽  
Author(s):  
Seppo Ruotsalainen ◽  
Dag Lindgren
Keyword(s):  
Genetic Gain ◽  
Breeding Population ◽  
Random Allocation ◽  
Genetic Quality ◽  
Seed Orchards ◽  
Breeding Values ◽  
Breeding Populations ◽  
Genetic Value ◽  
Interesting Alternative

When structuring a breeding population into sublines, the conventional approach is to assign parents to sublines randomly, so that each subline has approximately the same genetic value. By using deterministic infinitesimal model we study an alternative, stratified sublining system, where sublines are initially formed by positive assortative grouping of parents according to their breeding values. Stratified and random allocation to sublines are compared by evaluating the genetic quality of the seed orchards that each approach can provide. The seed orchards were established by selecting first the best individual from each subline and then a given best proportion from them. The greater among-subline variance in stratified sublining led to higher genetic gain in resulting seed orchards than did random sublining. For the case studied, stratified sublining gave considerably more genetic gain than random sublining, over 15% more, making it an interesting alternative that deserves further consideration and study.

Effect of controlling future rate of inbreeding on expected genetic gain and genetic variability in small livestock populations

2020 ◽  
Vol 60 (14) ◽  
pp. 1681
Author(s):  
S. I. Mwangi ◽  
T. K. Muasya ◽  
E. D. Ilatsia ◽  
A. K. Kahi
Keyword(s):  
Genetic Variability ◽  
Milk Yield ◽  
Genetic Gain ◽  
Genetic Relationships ◽  
Breeding Population ◽  
Breeding Values ◽  
Sahiwal Cows ◽  
Improvement Programs ◽  
Small Livestock ◽  
Estimated Breeding Values

Context In the present study we assessed the use of average relationship as a means to control future rates of inbreeding in small cattle closed nucleus and its effect on genetic gain for milk yield as a means of managing genetic variability in livestock improvement programs. Aim The aim was to strike an ideal balance between genetic gain and loss of genetic variability for Sahiwal population. Methods A total of 8452 milk yield records of Sahiwal cows from National Sahiwal Stud, Kenya, were used to estimate breeding values and 19315 records used to estimate average relatedness of all individuals. The estimated breeding values and genetic relationships were then used to optimise individual genetic contributions between the best two males and the top 210 females in 2000–2008-year group, as well as between the best four, six and eight males and top, 420, 630 and 840 females based on estimated breeding values for lactation milk yield. Weights on genetic merit and average relationship considered in this study were (1, 0), (1, −300), (1, −500), (1, −1000) and (0, −1). Key results When the best sires were selected and used for mating disregarding average relationship with their mates i.e. (0, –1), genetic gain of up to 213 kg was realised accompanied by a rate of inbreeding per generation of 4%. Restricting average relationship alone i.e. (0, –1), resulted in a future rate of inbreeding of 1.6% and average merit of 154 when top two sires were used for breeding. At the same restriction level but using eight top sires, the rate of inbreeding per generation was 0.9% accompanied by an average merit of 128.2 kg. Controlling average relationship between mates resulted in increased genetic variability i.e. lower rate of inbreeding though average merit declined. Conclusion A rate of inbreeding per generation of <1% is required for a population to maintain its long-term viability. For this level to be attained, the size of the breeding population should be increased from the current two sires vs 210 dams to eight sires vs 840 dams. Implications Practical implications for closed nucleus programs such as the Sahiwal program in Kenya should include expanding the nucleus to comprise other institutional and privately-owned herds.

scholarly journals Optimized breeding strategies to harness Genetic Resources with different performance levels

2019 ◽  
Author(s):  
Antoine Allier ◽  
Simon Teyssèdre ◽  
Christina Lehermeier ◽  
Laurence Moreau ◽  
Alain Charcosset
Keyword(s):  
Genetic Resources ◽  
Genetic Gain ◽  
Breeding Population ◽  
Short Term ◽  
Breeding Programs ◽  
Performance Levels ◽  
Genetic Base ◽  
Base Broadening ◽  
Genetic Value

ABSTRACTThe narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient strategy is required to broaden the genetic base of commercial breeding programs while not compromising short-term variety release. Optimal cross selection aims at identifying the optimal set of crosses that balances the expected genetic value and diversity. We propose to consider genomic selection and optimal cross selection to recurrently improve genetic resources (i.e. pre-breeding), to bridge the improved genetic resources with elites (i.e. bridging), and to manage introductions into the elite breeding population. Optimal cross selection is particularly adapted to jointly identify bridging, introduction and elite crosses to ensure an overall consistency of the genetic base broadening strategy. We compared simulated breeding programs introducing donors with different performance levels, directly or indirectly after bridging. We also evaluated the effect of the training set composition on the success of introductions. We observed that with recurrent introductions of improved donors, it is possible to maintain the genetic diversity and increase mid- and long-term performances with only limited penalty at short-term. Considering a bridging step yielded significantly higher mid- and long-term genetic gain when introducing low performing donors. The results also suggested to consider marker effects estimated with a broad training population including donor by elite and elite by elite progeny to identify bridging, introduction and elite crosses.

scholarly journals Deep scoping: a breeding strategy to preserve, reintroduce and exploit genetic variation

2021 ◽  
Author(s):  
David Vanavermaete ◽  
Jan Fostier ◽  
Steven Maenhout ◽  
Bernard De Baets
Keyword(s):  
Genetic Variation ◽  
Genetic Gain ◽  
Breeding Population ◽  
Breeding Strategy ◽  
Premature Convergence ◽  
Financial Cost ◽  
Truncation Selection ◽  
Trait Locus ◽  
Genetic Value

Abstract Key message The deep scoping method incorporates the use of a gene bank together with different population layers to reintroduce genetic variation into the breeding population, thus maximizing the long-term genetic gain without reducing the short-term genetic gain or increasing the total financial cost. Abstract Genomic prediction is often combined with truncation selection to identify superior parental individuals that can pass on favorable quantitative trait locus (QTL) alleles to their offspring. However, truncation selection reduces genetic variation within the breeding population, causing a premature convergence to a sub-optimal genetic value. In order to also increase genetic gain in the long term, different methods have been proposed that better preserve genetic variation. However, when the genetic variation of the breeding population has already been reduced as a result of prior intensive selection, even those methods will not be able to avert such premature convergence. Pre-breeding provides a solution for this problem by reintroducing genetic variation into the breeding population. Unfortunately, as pre-breeding often relies on a separate breeding population to increase the genetic value of wild specimens before introducing them in the elite population, it comes with an increased financial cost. In this paper, on the basis of a simulation study, we propose a new method that reintroduces genetic variation in the breeding population on a continuous basis without the need for a separate pre-breeding program or a larger population size. This way, we are able to introduce favorable QTL alleles into an elite population and maximize the genetic gain in the short as well as in the long term without increasing the financial cost.

scholarly journals Breeding Values of Parental Trees, Genetic Worth of Seed Orchard Seedlots, and Yields of Improved Stocks in British Columbia

2003 ◽  
Vol 18 (2) ◽  
pp. 88-100 ◽  
Author(s):  
C.Y. Xie ◽  
A.D. Yanchuk
Keyword(s):  
British Columbia ◽  
Linear Prediction ◽  
Growth Potential ◽  
Breeding Value ◽  
Stem Volume ◽  
Genetic Quality ◽  
Breeding Values ◽  
Accuracy And Precision ◽  
Genetically Improved

Abstract This report describes the procedures that are currently used in British Columbia for predicting the breeding values of parents, estimating the genetic worth of orchard seedlots, and projecting the yields of genetically improved stocks. Breeding value is a measure of the genetic quality of an individual as a parent. There are several procedures available for its estimation/prediction. Among those, the best linear prediction (BLP) relaxes most of the assumptions required by the others and minimizes the error variance of prediction. In most situations in British Columbia, it should provide predictions with satisfactory accuracy and precision with greatly reduced computational complexity. In this province, breeding value for growth potential is expressed as percent gain of stem volume over the unimproved population at a designated rotation age.Genetic worth is an important attribute of the genetic quality of a seedlot. It represents the average level of genetic gain expected for the trait of concern at a designated rotation age when a seedlot is used for reforestation. Currently, the genetic worth of a seedlot is estimated by the mean breeding value of all the parents, including those that contribute to pollen contamination and supplemental mass pollination, weighted by their proportional gamete contributionsThe yield of a genetically improved plantation is projected by incorporating the genetic worth of the seedlot into the existing growth model developed based on extensive data from managed unimproved stands. The current approach not only takes account of the stand dynamics determined by site conditions and silvicultural regimes but also the declining nature of expected gain over time because of imperfect age-age genetic correlation.Because of errors from genetic and environmental sampling, measurement, and analysis, as well as possible violation of model assumptions, estimates/predictions may still be subject to errors and/or biases. Various conservative measures have been taken to minimize any possible upwards biases. As more matured data and advanced analytical technologies become available, both the accuracy and precision will be improved. The advancement made in the procedures described in this document should contribute to superior decisions in many aspects of forest management. West. J. Appl. For. 18(2):88–100.

scholarly journals The importance of controlled mating in honeybee breeding

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Manuel Plate ◽  
Richard Bernstein ◽  
Andreas Hoppe ◽  
Kaspar Bienefeld
Keyword(s):  
Maternal Effects ◽  
Genetic Gain ◽  
Positive Impact ◽  
Breeding Population ◽  
Success Rates ◽  
Breeding Populations ◽  
Random Samples ◽  
Breeding Schemes ◽  
Selection For ◽  
Almost All

Abstract Background Controlled mating procedures are widely accepted as a key aspect of successful breeding in almost all animal species. In honeybees, however, controlled mating is hard to achieve. Therefore, there have been several attempts to breed honeybees using free-mated queens. In such breeding schemes, selection occurs only on the maternal path since the drone sires are random samples of the population. The success rates of breeding approaches without controlled mating have so far not been investigated on a theoretical or simulation-based level. Methods Stochastic simulation studies were carried out to examine the chances of success in honeybee breeding with and without controlled mating. We investigated the influence of different sizes of breeding populations (500, 1000, 2000 colonies per year) and unselected passive populations (0, 500, 1000, 2000, infinitely many colonies per year) on selection for a maternally (queen) and directly (worker group) influenced trait with moderate ($$r_{md}=-\,0.53$$rmd=-0.53) or strong ($$r_{md}=-\,0.88$$rmd=-0.88) negative correlation between the two effects. The simulations described 20 years of selection. Results Our simulations showed a reduction of breeding success between 47 and 99% if mating was not controlled. In the most drastic cases, practically no genetic gain could be generated without controlled mating. We observed that in the trade-off between selection for direct or maternal effects, the absence of mating control leads to a shift in favor of maternal effects. Moreover, we describe the implications of different breeding strategies on the unselected passive population that benefits only indirectly via the transfer of queens or drones from the breeding population. We show that genetic gain in the passive population develops parallel to that of the breeding population. However, we found a genetic lag that became significantly smaller as more breeding queens served as dams of queens in the passive population. Conclusions We conclude that even when unwanted admixture of subspecies can be excluded in natural matings, controlled mating is imperative for successful breeding efforts. This is especially highlighted by the strong positive impact that controlled mating in the breeding population has on the unselected passive population.

Genetic gain with desired status number in breeding programs: a study on selection effects

1998 ◽  
Vol 28 (12) ◽  
pp. 1861-1869 ◽  
Author(s):  
R -P Wei ◽  
C R Hansen ◽  
N K Dhir ◽  
F C Yeh
Keyword(s):  
Genetic Gain ◽  
Breeding Population ◽  
Breeding Value ◽  
Index Selection ◽  
Selection Methods ◽  
Family Selection ◽  
Breeding Populations ◽  
High Heritability ◽  
Status Number ◽  
Restricted Selection

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.

scholarly journals Genomics and breeding innovations for enhancing genetic gain for climate resilience and nutrition traits

2021 ◽  
Author(s):  
Pallavi Sinha ◽  
Vikas K. Singh ◽  
Abhishek Bohra ◽  
Arvind Kumar ◽  
Jochen C. Reif ◽  
...  
Keyword(s):  
Statistical Methods ◽  
Genetic Gain ◽  
Crop Improvement ◽  
Breeding Population ◽  
Breeding Cycle ◽  
Climate Resilience ◽  
Heritability Estimation ◽  
Improvement Programs ◽  
Statistical Designs ◽  
Novel Alleles

Abstract Key message Integrating genomics technologies and breeding methods to tweak core parameters of the breeder’s equation could accelerate delivery of climate-resilient and nutrient rich crops for future food security. Abstract Accelerating genetic gain in crop improvement programs with respect to climate resilience and nutrition traits, and the realization of the improved gain in farmers’ fields require integration of several approaches. This article focuses on innovative approaches to address core components of the breeder’s equation. A prerequisite to enhancing genetic variance (σ2g) is the identification or creation of favorable alleles/haplotypes and their deployment for improving key traits. Novel alleles for new and existing target traits need to be accessed and added to the breeding population while maintaining genetic diversity. Selection intensity (i) in the breeding program can be improved by testing a larger population size, enabled by the statistical designs with minimal replications and high-throughput phenotyping. Selection priorities and criteria to select appropriate portion of the population too assume an important role. The most important component of breeder′s equation is heritability (h2). Heritability estimates depend on several factors including the size and the type of population and the statistical methods. The present article starts with a brief discussion on the potential ways to enhance σ2g in the population. We highlight statistical methods and experimental designs that could improve trait heritability estimation. We also offer a perspective on reducing the breeding cycle time (t), which could be achieved through the selection of appropriate parents, optimizing the breeding scheme, rapid fixation of target alleles, and combining speed breeding with breeding programs to optimize trials for release. Finally, we summarize knowledge from multiple disciplines for enhancing genetic gains for climate resilience and nutritional traits.

scholarly journals A survey of recent introduction events, spread and mitigation efforts of mynas (Acridotheres sp.) in Spain and Portugal

2015 ◽  
Vol 38 (1) ◽  
pp. 121-127
Author(s):  
S. Saavedra ◽  
◽  
A. Maraver ◽  
J. D. Anadón ◽  
J. L. Tella ◽  
...  
Keyword(s):  
Field Survey ◽  
Invasive Alien Species ◽  
Breeding Population ◽  
Island Populations ◽  
Common Myna ◽  
Breeding Populations ◽  
Preventive Actions ◽  
Acridotheres Tristis ◽  
The Common ◽  
Exponential Population Growth

The common myna Acridotheres tristis is listed among the world’s 100 worst invasive alien species. We combined previous records with a field survey to update the extent and fate of myna introductions in Spain and Portugal. Results suggest that there have been at least 22 independent accidental introductions of three myna species throughout the Iberian peninsula and three archipelagos since the early 1990s. While bank mynas (A. ginginianus) did not become established elsewhere, common mynas reached breeding populations on four islands. Eradication efforts allowed the extirpation of these breeding island populations, but common mynas continue to breed in the Tagus Estuary (continental Portugal). In this region, there is also a breeding population of crested mynas (A. cristatellus), which was undergone an exponential population growth in the last decade. To avoid further accidental introductions, eradication campaigns should be combined with preventive actions aiming to stop the trade of these species in Europe.

Freshwater pearl culture in China.

2020 ◽  
Author(s):  
Lin Cao
Keyword(s):  
Shell Length ◽  
Culture Period ◽  
Production Cycle ◽  
High Quality ◽  
Host Fish ◽  
Genetic Quality ◽  
Operative Care ◽  
Artificial Breeding

Abstract Artificial breeding of freshwater pearl mussels is widely used to improve the yield of pearl culture. All phases of the production cycle, including collection and culture of the broodstock, release of the glochidia, provision of the host fish for glochidia to attach to, and collection of mussel seeds, can be controlled artificially. The advantages of artificial breeding are that it can help to produce high quality pearls and improve the genetic quality of pearl mussels. Collected mussel seed are transferred from holding jars into small 200 µm mesh baskets (10 cm diameter x 5 cm). Each basket was supplied individually with 0.1-0.2 L of water per minute. When the mussels' shell length reaches over 10 cm, they can be operated to culture pearl. After post-operative care the implanted mussels are stocked in ponds. The mussels are kept in nylon bags (2 mussels per bag) and are hung from bamboo or PVC pipes and placed in ponds at 1 m depth. Periodical checking of mussels, with removal of dead ones and cleaning of bags, is required throughout the culture period of 12-18 months.

scholarly journals Genetic parameters and phenotypic and genetic trends for weight at weaning and visual scores during this phase estimated for Angus-Nellore crossbred young bulls

2010 ◽  
Vol 39 (11) ◽  
pp. 2398-2408 ◽  
Author(s):  
Ronyere Olegário de Araújo ◽  
Paulo Roberto Nogara Rorato ◽  
Tomás Weber ◽  
Dionéia Magda Everling ◽  
Jader Silva Lopes ◽  
...  
Keyword(s):  
Animal Model ◽  
Genetic Gain ◽  
Genetic Parameters ◽  
Southern Brazil ◽  
Linear Effect ◽  
Quadratic Effects ◽  
Genetic Value ◽  
Additive Genetic Effects ◽  
Maternal Heritability ◽  
Genetic Trends

Genetic parameters and genetic and phenotypic trends were estimated for weight at weaning (WW) and visual scores (VS) of conformation (C), precocity (P), musculature (M) and navel (N) for Angus × Nellore crossbred calves. It was used 39,676 records from pre-weaning phase of animals born from 1992 to 2002 in mid-western, southeastern and southern Brazil. The components of covariance were estimated using REML, in animal model, considering as random the maternal and direct additive genetic effects, and as fixed, the effects of contemporaneous group, the genetic group of the animal and of the cow, and as covariates the age of the calf at weaning and the age of the cow at calving, both on days and with linear and quadratic effects, besides direct (DH) and maternal heterosis (MH), both with only the linear effect. Estimates of direct and maternal heritability were 0.30 and 0.19, respectively, for WW, whereas VSs ranged from 0.16 to 0.20 and from 0.09 to 0.16, which indicates the possibility to obtain genetic gain through selection. It is expected answer correlated to C, P and for M when selection is practiced for weight at weaning is expected, as well as for P and M when selection is practiced for C. The direct and maternal genetic trends for WW (g/year) and for C, P, M and N (points/year) were: 221.0 and -312.0; 0.0022 and 0.00003; 0.0010 and 0.0001; 0.0013 and -0.0008; 0.0010 and 0.00009, respectively, while the phenotypic were: -685.2; -0.0102; -0.0219; -0.0256 and -0.0453, which highlights the need to adopt criteria for identifying young bulls of higher genetic value for WW and VSs.

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