scholarly journals Plant breeders should be determining economic weights for a selection index instead of using independent culling for choosing parents in breeding programs with genomic selection

2018 ◽  
Author(s):  
Lorena G. Batista ◽  
R. Chris Gaynor ◽  
Gabriel R. A. Margarido ◽  
Tim Byrne ◽  
Peter Amer ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Genetic Gain ◽  
Recurrent Selection ◽  
Selection Index ◽  
Economic Importance ◽  
Index Selection ◽  
Breeding Programs ◽  
Independent Culling ◽  
Economic Selection ◽  
Selection Of

AbstractIn the context of genomic selection, we evaluated and compared recurrent selection breeding programs using either index selection or independent culling for selection of parents. We simulated a clonally propagated crop breeding program for 20 cycles of selection using either independent culling or an economic selection index with two unfavourably correlated traits under selection. Cycle time from crossing to selection of parents was kept the same for both strategies. Our results demonstrate that accurate knowledge of the economic importance of traits is essential even when performing independent culling. This is because independent culling achieved its optimum genetic gain when the culling threshold for each trait varied accordingly to the economic importance of the traits. When gains from independent culling were maximised, the efficiency of converting genetic diversity into genetic gain of both selection methods were equivalent. When the same proportion selected of 10% for each trait was used instead of optimal culling levels, index selection was 10%, 128% and 310% more efficient than independent culling when T2 had a relative economic importance of 1.0, 2.5 and 5.0, respectively. Given the complexity of estimating optimal culling levels and the fact that the gains achieved with independent culling are, at most, equivalent to index selection, the use of an economic selection index is recommended for multi-trait genomic selection.

scholarly journals Long-term comparison between index selection and optimal independent culling in plant breeding programs with genomic prediction

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0235554
Author(s):  
Lorena G. Batista ◽  
Robert Chris Gaynor ◽  
Gabriel R. A. Margarido ◽  
Tim Byrne ◽  
Peter Amer ◽  
...  
Keyword(s):  
Recurrent Selection ◽  
Genetic Correlations ◽  
Economic Importance ◽  
Index Selection ◽  
Selection Intensity ◽  
Crop Breeding ◽  
Breeding Programs ◽  
Independent Culling ◽  
Selection Of

In the context of genomic selection, we evaluated and compared breeding programs using either index selection or independent culling for recurrent selection of parents. We simulated a clonally propagated crop breeding program for 20 cycles using either independent culling or an economic index with two unfavourably correlated traits under selection. Cycle time from crossing to selection of parents was kept the same for both strategies. Both methods led to increasingly unfavourable genetic correlations between traits and, compared to independent culling, index selection led to larger changes in the genetic correlation between the two traits. When linkage disequilibrium was not considered, the two methods had similar losses of genetic diversity. Two independent culling approaches were evaluated, one using optimal culling levels and one using the same selection intensity for both traits. Optimal culling levels outperformed the same selection intensity even when traits had the same economic importance. Therefore, accurately estimating optimal culling levels is essential for maximizing gains when independent culling is performed. Once optimal culling levels are achieved, independent culling and index selection lead to comparable genetic gains.

scholarly journals GENETIC GAINS AND SELECTION ADVANCES OF THE UENF-14 POPCORN POPULATION

2018 ◽  
Vol 31 (2) ◽  
pp. 271-278 ◽  
Author(s):  
AMANDA GONÇALVES GUIMARÃES ◽  
ANTÔNIO TEIXEIRA DO AMARAL JÚNIOR ◽  
VALTER JÁRIO DE LIMA ◽  
JHEAN TORRES LEITE ◽  
CARLOS ALBERTO SCAPIM ◽  
...  
Keyword(s):  
Grain Yield ◽  
Genetic Gain ◽  
Recurrent Selection ◽  
Selection Index ◽  
Economic Importance ◽  
Average Height ◽  
Breeding Programs ◽  
Genetic Gains ◽  
Full Sibling ◽  
Selection Of

ABSTRACT Recurrent selection can generate successive gains for characters of economic interest without causing genetic narrowing in the population. However, it has rarely been used in breeding programs in popcorn, especially when using full-sibling progenies to generate more expressive gains. The objective of this study was to estimate the genetic gain of the UENF-14 popcorn population through recurrent selection, and verify the evolution of the gains between the selection cycles four and eight. A total of 200 full-sibling progenies were evaluated in randomized blocks arranged in eight sets within three replicates in two environments; each set containing twenty-five progenies and six controls (selection cycles 4, 5, 6 and 7 of the UENF-14, BRS-Angela and IAC-125). The average height, prolificacy, 100-grain weight, ear weight, grain yield, and grain popping expansion of the plants were evaluated. In the selection of the thirty superior progenies for the eighth cycle, the Mulamba and Mock selection index was used, which generated estimated genetic gains of 4.60 for grain yield and 3.61% for popping expansion. The grain yield increased 111.99 kg ha-1 and the popping expansion increased 1.75 mL g-1 per cycle. The evolution of the cycles resulted in an accumulated genetic gain for the main characters of economic importance, allowing the prediction of success in the continuity of the recurrent selection.

scholarly journals Genomic selection strategies for clonally propagated crops

2020 ◽  
Author(s):  
Christian R. Werner ◽  
R. Chris Gaynor ◽  
Daniel J. Sargent ◽  
Alessandra Lillo ◽  
Gregor Gorjanc ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Genetic Gain ◽  
Genomic Prediction ◽  
Breeding Program ◽  
Selection Methods ◽  
Breeding Programs ◽  
Breeding Values ◽  
Parent Selection ◽  
Estimated Breeding Values ◽  
Selection Of

AbstractFor genomic selection in clonal breeding programs to be effective, crossing parents should be selected based on genomic predicted cross performance unless dominance is negligible. Genomic prediction of cross performance enables a balanced exploitation of the additive and dominance value simultaneously. Here, we compared different strategies for the implementation of genomic selection in clonal plant breeding programs. We used stochastic simulations to evaluate six combinations of three breeding programs and two parent selection methods. The three breeding programs included i) a breeding program that introduced genomic selection in the first clonal testing stage, and ii) two variations of a two-part breeding program with one and three crossing cycles per year, respectively. The two parent selection methods were i) selection of parents based on genomic estimated breeding values, and ii) selection of parents based on genomic predicted cross performance. Selection of parents based on genomic predicted cross performance produced faster genetic gain than selection of parents based on genomic estimated breeding values because it substantially reduced inbreeding when the dominance degree increased. The two-part breeding programs with one and three crossing cycles per year using genomic prediction of cross performance always produced the most genetic gain unless dominance was negligible. We conclude that i) in clonal breeding programs with genomic selection, parents should be selected based on genomic predicted cross performance, and ii) a two-part breeding program with parent selection based on genomic predicted cross performance to rapidly drive population improvement has great potential to improve breeding clonally propagated crops.

scholarly journals GENETIC GAINS IN THE POPCORN POPULATION UENF-14: DEVELOPING THE NINTH GENERATION OF INTRAPOPULATION RECURRENT SELECTION

2019 ◽  
Vol 32 (3) ◽  
pp. 625-633
Author(s):  
AMANDA GONÇALVES GUIMARÃES ◽  
ANTÔNIO TEIXEIRA DO AMARAL JÚNIOR ◽  
GUILHERME FERREIRA PENA ◽  
JANEO EUSTÁQUIO DE ALMEIDA FILHO ◽  
MESSIAS GONZAGA PEREIRA ◽  
...  
Keyword(s):  
Grain Yield ◽  
Indirect Effects ◽  
Recurrent Selection ◽  
Selection Process ◽  
Selection Index ◽  
Average Height ◽  
Direct And Indirect Effects ◽  
Genetic Progress ◽  
Breeding Programs ◽  
Selection Of

ABSTRACT The occurrence of negative correlations between grain yield (GY) and popping expansion (PE) in popcorn complicates the selection process. In an attempt to overcome this inconvenience, we proposed the use of the importance characteristic volume per popcorn per hectare (PV). The objectives of this study were to develop the ninth cycle of the UENF-14 popcorn population, to estimate the direct and indirect effects of PV and to verify the genetic progress among all selective cycles. We obtained and evaluated 200 inbred progenies in randomised blocks arranged in replicates within sets, with nine sets consisting of 25 progenies and one set with all previous eight cycles with three replicates. The average height of the plants, prolificacy, 100-grain weight, grain yield, grain popping expansion and volume per popcorn per hectare were evaluated. Track analysis was performed to determine the direct and indirect effects, and the Mulamba and Mock selection index was calculated for the selection of the 40 superior progenies. There was genetic variability among progenies in all evaluated traits, with a cause-and-effect relationship between PV with GY and PE, allowing simultaneous gains with indirect selection. The selection of the best progenies was more effective when using arbitrarily assigned weights, which provided higher predicted gains for PV (20.73%). The means obtained in all cycles indicated increases, demonstrating the efficiency of using continuous recurrent selection in popcorn breeding programs.

scholarly journals Genetic gains under three methods of selection

1962 ◽  
Vol 3 (3) ◽  
pp. 417-423 ◽  
Author(s):  
D. J. Finney
Keyword(s):  
Linear Function ◽  
Genetic Gain ◽  
Index Selection ◽  
Genetic Gains ◽  
Independent Culling

Results obtained by Young for the expectation of genetic gain in an arbitrary linear function of several traits under selection by independent culling levels, under tandem selection, and under index selection have been obtained in slightly more general form and their dependence on basic genetic and phenotypic parameters exhibited. A warning is given about the effects of selection in modifying the distribution of traits; when the distribution has become appreciably non-normal, any calculation of genetic gains from formulae based on normality will tend to overestimation.

scholarly journals Genomic Selection for Any Dairy Breeding Program via Optimized Investment in Phenotyping and Genotyping

2021 ◽  
Vol 12 ◽  
Author(s):  
Jana Obšteter ◽  
Janez Jenko ◽  
Gregor Gorjanc
Keyword(s):  
Genomic Selection ◽  
Genetic Gain ◽  
Breeding Program ◽  
Progeny Testing ◽  
Initial Training ◽  
Training Population ◽  
Breeding Programs ◽  
Use Of Resources ◽  
Dairy Cattle Breeding ◽  
Close Relatives

This paper evaluates the potential of maximizing genetic gain in dairy cattle breeding by optimizing investment into phenotyping and genotyping. Conventional breeding focuses on phenotyping selection candidates or their close relatives to maximize selection accuracy for breeders and quality assurance for producers. Genomic selection decoupled phenotyping and selection and through this increased genetic gain per year compared to the conventional selection. Although genomic selection is established in well-resourced breeding programs, small populations and developing countries still struggle with the implementation. The main issues include the lack of training animals and lack of financial resources. To address this, we simulated a case-study of a small dairy population with a number of scenarios with equal available resources yet varied use of resources for phenotyping and genotyping. The conventional progeny testing scenario collected 11 phenotypic records per lactation. In genomic selection scenarios, we reduced phenotyping to between 10 and 1 phenotypic records per lactation and invested the saved resources into genotyping. We tested these scenarios at different relative prices of phenotyping to genotyping and with or without an initial training population for genomic selection. Reallocating a part of phenotyping resources for repeated milk records to genotyping increased genetic gain compared to the conventional selection scenario regardless of the amount and relative cost of phenotyping, and the availability of an initial training population. Genetic gain increased by increasing genotyping, despite reduced phenotyping. High-genotyping scenarios even saved resources. Genomic selection scenarios expectedly increased accuracy for young non-phenotyped candidate males and females, but also proven females. This study shows that breeding programs should optimize investment into phenotyping and genotyping to maximize return on investment. Our results suggest that any dairy breeding program using conventional progeny testing with repeated milk records can implement genomic selection without increasing the level of investment.

scholarly journals Population Genomics Along With Quantitative Genetics Provides a More Efficient Valorization of Crop Plant Genetic Diversity in Breeding and Pre-breeding Programs

2021 ◽  
Author(s):  
Peter Civan ◽  
Renaud Rincent ◽  
Alice Danguy-Des-Deserts ◽  
Jean-Michel Elsen ◽  
Sophie Bouchet
Keyword(s):  
Genetic Diversity ◽  
Quantitative Genetics ◽  
Genetic Gain ◽  
Recurrent Selection ◽  
Prediction Models ◽  
Population Genomics ◽  
Breeding Program ◽  
Breeding Programs ◽  
Sequencing Technologies ◽  
Genetic Value

AbstractThe breeding efforts of the twentieth century contributed to large increases in yield but selection may have increased vulnerability to environmental perturbations. In that context, there is a growing demand for methodology to re-introduce useful variation into cultivated germplasm. Such efforts can focus on the introduction of specific traits monitored through diagnostic molecular markers identified by QTL/association mapping or selection signature screening. A combined approach is to increase the global diversity of a crop without targeting any particular trait.A considerable portion of the genetic diversity is conserved in genebanks. However, benefits of genetic resources (GRs) in terms of favorable alleles have to be weighed against unfavorable traits being introduced along. In order to facilitate utilization of GR, core collections are being identified and progressively characterized at the phenotypic and genomic levels. High-throughput genotyping and sequencing technologies allow to build prediction models that can estimate the genetic value of an entire genotyped collection. In a pre-breeding program, predictions can accelerate recurrent selection using rapid cycles in greenhouses by skipping some phenotyping steps. In a breeding program, reduced phenotyping characterization allows to increase the number of tested parents and crosses (and global genetic variance) for a fixed budget. Finally, the whole cross design can be optimized using progeny variance predictions to maximize short-term genetic gain or long-term genetic gain by constraining a minimum level of diversity in the germplasm. There is also a potential to further increase the accuracy of genomic predictions by taking into account genotype by environment interactions, integrating additional layers of omics and environmental information.Here, we aim to review some relevant concepts in population genomics together with recent advances in quantitative genetics in order to discuss how the combination of both disciplines can facilitate the use of genetic diversity in plant (pre) breeding programs.

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 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.

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