scholarly journals How to reach a higher selection plateau with optimal contribution selection and compensatory mating?

2021 ◽  
Author(s):  
Tiret Mathieu ◽  
Pégard Marie ◽  
Sánchez Leopoldo
Keyword(s):  
Genetic Gain ◽  
Random Mating ◽  
Snp Array ◽  
Breeding Strategy ◽  
Genetic Response ◽  
Short Term ◽  
Breeding Programs ◽  
Trade Off ◽  
Study Case

AbstractIn breeding programs, balancing short-term genetic gain and loss of diversity per generation is essential to sustain a long-term genetic response. Depending on the dynamic of the species, the acceptable trade-off will be different. One of the most common and successful tools to achieve this management is the Optimal Contribution Selection (OCS), which readily mathematically formulate the trade-off between genetic gain and coancestry. However, OCS only accounts for the next generation gain and diversity, which can lead to suboptimality given the uncertainties of random mating and segregation. In this paper, we have extended the OCS by conveniently integrating a way to promote certain parental pairs, so that this method can account for the next t+2 generation. In the study case of Populus nigra, fully phenotyped and SNP array genotyped, we have shown that (i) a non negligible part of the long-term success of a breeding strategy depends on the implemented mating strategy, and (ii) favoring a compensatory mating can accelerate the selection without compromising the future diversity.

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 A hybrid optimal contribution approach to drive short-term gains while maintaining long-term sustainability in a modern plant breeding program

2020 ◽  
Author(s):  
Nicholas Santantonio ◽  
Kelly Robbins
Keyword(s):  
Plant Breeding ◽  
Genomic Selection ◽  
Genetic Gain ◽  
Genetic Variance ◽  
Hybrid Approach ◽  
Breeding Program ◽  
Short Term ◽  
Breeding Programs ◽  
Plant Breeding Program

1AbstractPlant breeding programs must adapt genomic selection to an already complex system. Inbred or hybrid plant breeding programs must make crosses, produce inbred individuals, and phenotype inbred lines or their hybrid test-crosses to select and validate superior material for product release. These products are few, and while it is clear that population improvement is necessary for continued genetic gain, it may not be sufficient to generate superior products. Rapid-cycle recurrent truncation genomic selection has been proposed to increase genetic gain by reducing generation time. This strategy has been shown to increase short-term gains, but can quickly lead to loss of genetic variance through inbreeding as relationships drive prediction. The optimal contribution of each individual can be determined to maximize gain in the following generation while limiting inbreeding. While optimal contribution strategies can maintain genetic variance in later generations, they suffer from a lack of short-term gains in doing so. We present a hybrid approach that branches out yearly to push the genetic value of potential varietal materials while maintaining genetic variance in the recurrent population, such that a breeding program can achieve short-term success without exhausting long-term potential. Because branching increases the genetic distance between the phenotyping pipeline and the recurrent population, this method requires sacrificing some trial plots to phenotype materials directly out of the recurrent population. We envision the phenotypic pipeline not only for selection and validation, but as an information generator to build predictive models and develop new products.

scholarly journals Application of marker assisted selection for livestock improvement in Bangladesh

2015 ◽  
Vol 31 (1) ◽  
pp. 1-11 ◽  
Author(s):  
M Moniruzzaman ◽  
R Khatun ◽  
AA Mintoo
Keyword(s):  
Dna Sequences ◽  
Genetic Gain ◽  
Marker Assisted Selection ◽  
Breeding Strategy ◽  
Meat Production ◽  
Economic Traits ◽  
Generation Interval ◽  
Breeding Programmes ◽  
Selection Of

Molecular markers usually do not have any biological effect. They are identifiable DNA sequences, found at specific locations of the genome, and transmitted from one generation to the next. Marker assisted selection (MAS) is a novel technique that can complement traditional breeding methods for rapid genetic gains. Genetic gain through selective breeding is the objective of a breeder to achieve long term improvement in animal and plant genomes; however the pace of improvement is inversely proportional to the Generation Interval. Genetic improvement in livestock, particularly those with long generation intervals, requires decades for tangible results. Successful MAS breeding programmes require gene mapping, marker genotyping, quantitative trait loci (QTL) detection, genetic evaluation and finally MAS. Genomic selection is a form of markerassisted selection. Using markers covering the whole genome could mean potentially that all the genetic variance is explained; and the markers are assumed to be in linkage disequilibrium with the QTL so that the number of effects per QTL to be estimated is small. MAS drastically reduces generation interval and increases selection accuracy. Therefore, a breeding strategy based upon markers making the best use of the two approaches can facilitate rapid genetic gain though selection of markers related to economic traits such as milk and meat production. This review is designed to elaborate the technique of MAS and its application in developing countries. DOI: http://dx.doi.org/10.3329/bvet.v31i1.22837 Bangl. vet. 2014. Vol. 31, No. 1, 1-11

scholarly journals Improving short and long term genetic gain by accounting for within family variance in optimal cross selection

2019 ◽  
Author(s):  
Antoine Allier ◽  
Christina Lehermeier ◽  
Alain Charcosset ◽  
Laurence Moreau ◽  
Simon Teyssèdre
Keyword(s):  
Genetic Diversity ◽  
Genomic Selection ◽  
Genetic Gain ◽  
Family Selection ◽  
Breeding Programs ◽  
Short And Long Term ◽  
Inbreeding Rate ◽  
Genetic Value ◽  
Optimal Set

AbstractThe implementation of genomic selection in recurrent breeding programs raised several concerns, especially that a higher inbreeding rate could compromise the long term genetic gain. An optimized mating strategy that maximizes the performance in progeny and maintains diversity for long term genetic gain on current and yet unknown future targets is essential. The optimal cross selection approach aims at identifying the optimal set of crosses maximizing the expected genetic value in the progeny under a constraint on diversity in the progeny. Usually, optimal cross selection does not account for within family selection, i.e. the fact that only a selected fraction of each family serves as candidate parents of the next generation. In this study, we consider within family variance accounting for linkage disequilibrium between quantitative trait loci to predict the expected mean performance and the expected genetic diversity in the selected progeny of a set of crosses. These predictions rely on the method called usefulness criterion parental contribution (UCPC). We compared UCPC based optimal cross selection and optimal cross selection in a long term simulated recurrent genomic selection breeding program considering overlapping generations. UCPC based optimal cross selection proved to be more efficient to convert the genetic diversity into short and long term genetic gains than optimal cross selection. We also showed that using the UCPC based optimal cross selection, the long term genetic gain can be increased with only limited reduction of the short term commercial genetic gain.

scholarly journals Grapevine Cultivars, Trellis Systems, and Mechanization of the California Raisin Industry

2014 ◽  
Vol 24 (3) ◽  
pp. 285-289 ◽  
Author(s):  
Matthew W. Fidelibus
Keyword(s):  
Production Systems ◽  
The United States ◽  
Medium Term ◽  
Thompson Seedless ◽  
Short Term ◽  
Breeding Programs ◽  
Early Ripening ◽  
Ct System ◽  
Made In

Growers in California’s San Joaquin Valley produced >25% of the world’s raisins in 2012, with a farm-gate value of >$590 million, making the United States the leading global producer of raisins. California’s traditional raisin-making method is a laborious process in which clusters of grapes (Vitis vinifera) are harvested by hand onto paper trays, which are left in the vineyard to dry. The drying fruit may need to be turned or rolled, tasks requiring manual labor, and the trays of dried raisins are also picked up by hand. Most California raisins continue to be made in this way, but in recent years, the declining availability and increasing cost of labor has prompted many growers to implement one of two mechanized production systems, “continuous tray” (CT) or “dry-on-vine” (DOV). In CT systems, machines are used to pick the berries, lay them onto a tray, and pick up the dried raisins. The CT system could be considered a short-term strategy: it is compatible with existing conventional ‘Thompson Seedless’ raisin vineyards and has been widely adopted. The DOV system could be considered a medium-term strategy: it is best suited for vineyards specifically designed for DOV, with early ripening grapevine cultivars on expansive trellis systems, which ensures timely drying, and capitalizes on the fact that sunlit row middles are not needed for fruit drying. Grapevine breeding programs are currently working toward the development of raisin grape cultivars with fruitful basal nodes, with fruit that dry naturally upon ripening. This is a long-term strategy to further reduce labor needs by enabling mechanical pruning in winter and eliminating the need for cane severance in the summer.

scholarly journals A multi-part strategy for introgression of exotic germplasm into elite plant breeding programs using genomic selection

2022 ◽  
Author(s):  
Irene S. Breider ◽  
R. Chris Gaynor ◽  
Gregor Gorjanc ◽  
Steve Thorn ◽  
Manish K. Pandey ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Plant Breeding ◽  
Genomic Selection ◽  
Genetic Gain ◽  
Genetic Improvement ◽  
Breeding Strategy ◽  
Breeding Program ◽  
Breeding Programs ◽  
Polygenic Inheritance ◽  
Polygenic Traits

Abstract Some of the most economically important traits in plant breeding show highly polygenic inheritance. Genetic variation is a key determinant of the rates of genetic improvement in selective breeding programs. Rapid progress in genetic improvement comes at the cost of a rapid loss of genetic variation. Germplasm available through expired Plant Variety Protection (exPVP) lines is a potential resource of variation previously lost in elite breeding programs. Introgression for polygenic traits is challenging, as many genes have a small effect on the trait of interest. Here we propose a way to overcome these challenges with a multi-part pre-breeding program that has feedback pathways to optimise recurrent genomic selection. The multi-part breeding program consists of three components, namely a bridging component, population improvement, and product development. Parameters influencing the multi-part program were optimised with the use of a grid search. Haploblock effect and origin were investigated. Results showed that the introgression of exPVP germplasm using an optimised multi-part breeding strategy resulted in 1.53 times higher genetic gain compared to a two-part breeding program. Higher gain was achieved through reducing the performance gap between exPVP and elite germplasm and breaking down linkage drag. Both first and subsequent introgression events showed to be successful. In conclusion, the multi-part breeding strategy has a potential to improve long-term genetic gain for polygenic traits and therefore, potential to contribute to global food security.

Increasing Southern Pine Timber Production Through Tree Improvement

1977 ◽  
Vol 1 (1) ◽  
pp. 3-10 ◽  
Author(s):  
Bruce Zobel
Keyword(s):  
Rust Resistance ◽  
First Generation ◽  
Tree Improvement ◽  
Breeding Strategy ◽  
Short Term ◽  
Timber Supply ◽  
Major Objective ◽  
Breeding Programs ◽  
Fusiform Rust ◽  
Tree Form

Abstract Increasing pressures on the pine timber supply in the South make it mandatory to find ways to increase the inventory. One effective way is through tree improvement. A major objective is to improve adaptability and maintain a broad genetic base, needed both for short-term development for marginal sites and for long-range breeding programs. Results have been good, with a number of specialty orchards already established. Accomplishments through tree improvement are: (1) volume increases varying from 10 to 30 percent for first-generation orchards, depending on selection intensity, roguing methods, and breeding strategy; (2) improvement in tree form, especially straightness; (3) proof that specific gravity of wood is strongly inherited; and (4) gains in fusiform rust resistance up to 40 percent in heavily infected areas.

scholarly journals Multiple Causes of Dementia as Engineered Senescence

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Mario Dominic Garrett
Keyword(s):  
Antagonistic Pleiotropy ◽  
Misfolded Protein ◽  
Optimal Conditions ◽  
Short Term ◽  
Trade Off ◽  
Age Related ◽  
The Many ◽  
Biology Of Aging ◽  
The Brain

All traumas—cranial, cardiovascular, hormone, viral, bacterial, fungi, parasites, misfolded protein, genetic, behavior, environmental and medication—affect the brain. This paper itemizes studies showing the many different causes of dementia including Alzheimer’s disease. Causes interact with each other, act sequentially by preparing the optimal conditions for its successor, initiate other diseases, allow for other traumas to accumulate and degrade protective features of the brain. Since such age-related cognitive impairment is not exclusively a human attribute there might be support for an evolutionary theory of dementia. Relying on theories of antagonistic pleiotropy and polymorphism, the brain has been designed to sequester trauma. Because of increased longevity, the short-term tactic of sequestering trauma becomes a long-term liability. We are engineered to sequester these insults until a tipping point is reached. Dementia is an evolutionary trade-off for longevity. We cannot cure dementia without understanding the overall biology of aging.

scholarly journals THE FAIR REWARD PROBLEM: THE ILLUSION OF SUCCESS AND HOW TO SOLVE IT

2019 ◽  
Vol 22 (03) ◽  
pp. 1950005 ◽  
Author(s):  
DIDIER SORNETTE ◽  
SPENCER WHEATLEY ◽  
PETER CAUWELS
Keyword(s):  
Risk Taking ◽  
Evolutionary System ◽  
Short Term ◽  
Trade Off ◽  
Politics And Science ◽  
Successful Outcomes ◽  
Exploration Exploitation

Humanity has been fascinated by the pursuit of fortune since time immemorial, and many successful outcomes benefit from strokes of luck. But success is subject to complexity, uncertainty, and change — and at times becoming increasingly unequally distributed. This leads to tension and confusion over to what extent people actually get what they deserve (i.e. fairness/meritocracy). Moreover, in many fields, humans are overconfident and pervasively confuse luck for skill (I win, it is skill; I lose, it is bad luck). In some fields, there is too much risk-taking; in others, not enough. Where success derives in large part from luck — and especially where bailouts skew the incentives (heads, I win; tails, you lose) — it follows that luck is rewarded too much. This incentivizes a culture of gambling, while downplaying the importance of productive effort. And, short-term success is often rewarded, irrespective, and potentially at the detriment, of the long-term system fitness. However, much success is truly meritocratic, and the problem is to discern and reward based on merit. We call this the fair reward problem. To address this, we propose three different measures to assess merit: (i) raw outcome; (ii) risk-adjusted outcome, and (iii) prospective. We emphasize the need, in many cases, for the deductive prospective approach, which considers the potential of a system to adapt and mutate in novel futures. This is formalized within an evolutionary system, comprised of five processes, inter alia handling the exploration–exploitation trade-off. Several human endeavors — including finance, politics, and science — are analyzed through these lenses, and concrete solutions are proposed to support a prosperous and meritocratic society.

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