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

Vanavermaete, David; Fostier, Jan; Maenhout, Steven; Baets, Bernard De

doi:10.1007/s00122-021-03932-w

Cited by 9 publications

(10 citation statements)

References 32 publications

(86 reference statements)

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“…This appears as mandatory for the successful use of low-performance genetic resources, as they otherwise get introduced in the elite pool to sustain diversity, but with no chance of entering the pedigree of released elite varieties. This was recently confirmed by Vanavermaete et al ( 38 ) and Breider et al ( 39 ), who extended this idea by introducing a multicycle bridging component between the genetic resource component and the elite program. These studies showed a large long-term benefit of introducing genetic diversity, even from low-performing genetic resource collections, over closed elite schemes with an optimized diversity trajectory management.…”

mentioning

confidence: 73%

Improving the use of plant genetic resources to sustain breeding programs’ efficiency

Sanchez

Sadoun

Mary‐Huard

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Genetic progress of crop plants is required to face human population growth and guarantee production stability in increasingly unstable environmental conditions. Breeding is accompanied by a loss in genetic diversity, which hinders sustainable genetic gain. Methodologies based on molecular marker information have been developed to manage diversity and proved effective in increasing long-term genetic gain. However, with realistic plant breeding population sizes, diversity depletion in closed programs appears ineluctable, calling for the introduction of relevant diversity donors. Although maintained with significant efforts, genetic resource collections remain underutilized, due to a large performance gap with elite germplasm. Bridging populations created by crossing genetic resources to elite lines prior to introduction into elite programs can manage this gap efficiently. To improve this strategy, we explored with simulations different genomic prediction and genetic diversity management options for a global program involving a bridging and an elite component. We analyzed the dynamics of quantitative trait loci fixation and followed the fate of allele donors after their introduction into the breeding program. Allocating 25% of total experimental resources to create a bridging component appears highly beneficial. We showed that potential diversity donors should be selected based on their phenotype rather than genomic predictions calibrated with the ongoing breeding program. We recommend incorporating improved donors into the elite program using a global calibration of the genomic prediction model and optimal cross selection maintaining a constant diversity. These approaches use efficiently genetic resources to sustain genetic gain and maintain neutral diversity, improving the flexibility to address future breeding objectives.

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mentioning

confidence: 73%

Improving the use of plant genetic resources to sustain breeding programs’ efficiency

Sanchez

Sadoun

Mary‐Huard

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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“…Experts' opinions still differ on the best way to exploit PGR in breeding. Most emphasize the need for clear trait prioritization and the use of well-characterized PGR for germplasm enhancement [51][52][53][54], while others advocate the use of PGR without prior information [11,45,55].…”

Section: Introductionmentioning

confidence: 99%

“…Vanavermaete et al [55] addressed these issues and proposed a multi-layer approach called "deep scoping" that keeps PGR and modern germplasm separate when modeling their relative contribution to GEBV, including specific factors to assess genetic diversity. A simpler approach would be to develop two training populations; one consisting of the PGR of interest together with other entries of the same species; and the other consisting only of modern germplasm.…”

Section: Introgression Of Quantitative Traits From Pgrmentioning

confidence: 99%

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm

Sharma¹,

Schulthess

Bassi³

et al. 2021

Biology

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Wheat (Triticum sp.) is one of the world’s most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade.

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“…They suggest the use of optimal cross-selection (Allier et al 2019a) as a complementary strategy to increase genetic gain in the long-term. Vanavermaete et al (2021) proposed the use of deep scoping to reintroduce genetic variation and maximise genetic gain both in the short-and long-term. Deep scoping enables introgression of favourable alleles by creating selection layers through which favourable alleles can ow, due to selection of one parent based on genomic EBV (GEBV) and the other parent selected to maximise genetic variation in the offspring.…”

Section: Introductionmentioning

confidence: 99%

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

Breider

Gaynor

Thorn

et al. 2022

Preprint

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

Cited by 9 publications

References 32 publications

Improving the use of plant genetic resources to sustain breeding programs’ efficiency

Improving the use of plant genetic resources to sustain breeding programs’ efficiency

Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm

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

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