Forward selection in a maritime pine polycross progeny trial using pedigree reconstruction

Vidal, Marjorie; Plomion, Christophe; Raffin, Annie; Harvengt, Luc; Bouffier, Laurent

doi:10.1007/s13595-016-0596-8

Cited by 18 publications

(15 citation statements)

References 33 publications

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“…The use of genetic markers to recover paternity identity as a means of improving the accuracy of forward selections' breeding values and to better manage inbreeding was first proposed by Lambeth et al (2001) for tree breeding applications. Following paternity recovery in a maritime pine polycross progeny test, Vidal et al (2017) found slightly higher genetic gains for forward selection than for backward selection with equal constraints on genetic diversity. We propose that the additional level of information provided by the genomic relationship matrix and the potentially enhanced accuracy of offspring's genetic values obtained with GS models may further improve genetic gains in forward selection.…”

Section: Introductionmentioning

confidence: 90%

“…Polycross mating has since been advocated as a cost-effective approach for forward selection (e.g. Doerksen and Herbinger 2010;Vidal et al 2017). The main disadvantage of the polycross was the lack of pedigree tracing and inbreeding control that can nowadays be overcome by using genetic markers for pedigree reconstruction (Bouffier et al 2019) or by using the genomic relationship matrix in GS models.…”

Section: Polycross Mating Integrates Well Into Forward Gsmentioning

confidence: 99%

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Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce

Lenz¹,

Nadeau²,

Azaiez³

et al. 2020

Heredity

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Genomic selection (GS) has a large potential for improving the prediction accuracy of breeding values and significantly reducing the length of breeding cycles. In this context, the choice of mating designs becomes critical to improve the efficiency of breeding operations and to obtain the largest genetic gains per time unit. Polycross mating designs have been traditionally used in tree and plant breeding to perform backward selection of the female parents. The possibility to use genetic markers for paternity identification and for building genomic prediction models should allow for a broader use of polycross tests in forward selection schemes. We compared the accuracies of genomic predictions of offspring's breeding values from a polycross and a full-sib (partial diallel) mating design with similar genetic background in white spruce (Picea glauca). Trees were phenotyped for growth and wood quality traits, and genotyped for 4092 SNPs representing as many gene loci distributed across the 12 spruce chromosomes. For the polycross progeny test, heritability estimates were smaller, but more precise using the genomic BLUP (GBLUP) model as compared with pedigree-based models accounting for the maternal pedigree or for the reconstructed full pedigree. Cross-validations showed that GBLUP predictions were 22-52% more accurate than predictions based on the maternal pedigree, and 5-7% more accurate than predictions using the reconstructed full pedigree. The accuracies of GBLUP predictions were high and in the same range for most traits between the polycross (0.61-0.70) and full-sib progeny tests (0.61-0.74). However, higher genetic gains per time unit were expected from the polycross mating design given the shorter time needed to conduct crosses. Considering the operational advantages of the polycross design in terms of easier handling of crosses and lower associated costs for test establishment, we believe that this mating scheme offers great opportunities for the development and operational application of forward GS.

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Section: Introductionmentioning

confidence: 90%

Section: Polycross Mating Integrates Well Into Forward Gsmentioning

confidence: 99%

Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce

Lenz¹,

Nadeau²,

Azaiez³

et al. 2020

Heredity

View full text Add to dashboard Cite

show abstract

“…It occurs in animal species such as fish and pigs, in which the evaluation of sib performance is largely applied and allows to increase selection accuracy (Sonesson and Meuwissen, 2009;Tribout, 2011;Robledo et al, 2018). A related approach could be interesting for forest trees (Plomion et al, 2016) or forage plants when polycrosses (crosses using a mixture of pollens) are implemented: GS allows the redrawing of pedigrees, on the basis of data from fathers in particular, thus increasing the accuracy of selection (Riday, 2011;Vidal et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience

et al. 2021

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The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.

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“…For example, simulations using the POPSIM software 84 in a Pinus pinaster improvement program, which was designed to maximize both gain and genetic diversity, generated a strategy of performing 150 controlled-crosses to obtain 100 progeny per cross as the most effective approach, but also the most time-consuming approach 18 . As an alternative, the option of using a polycross mating design together with paternity recovery using genotyping, is emerging as the preferred strategy to increase gain, and retain the desired effective population size with only a small decrease in male contributions, thereby allowing tree improvement programs to advance more quickly 17 , 18 , 80 , 85 , 86 . Although our data does not address the advantages of using a polycross directly, understanding the options and impact of different breeding strategies is critical to the rapid advancement of any long-lived tree species program.…”

Section: Discussionmentioning

confidence: 99%

SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

Galeano

Bousquet

Thomas

2021

Sci Rep

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Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7–68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson’s correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.

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Forward selection in a maritime pine polycross progeny trial using pedigree reconstruction

Cited by 18 publications

References 33 publications

Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce

Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce

Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience

SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

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