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Paternity recovery in two maritime pine polycross mating designs and consequences for breeding


Polycross mating systems are widely used in forest tree breeding for genetic testing. Backward selection based on polycross testing assumes equal male reproductive success and true half-sib progeny. The main objectives of this study were, firstly, to investigate the departure from these assumptions in a maritime pine polycross trial and, secondly, to evaluate the consequences for heritability and breeding values estimations. A total of 984 offspring from 98 half-sib families was genotyped with single nucleotide polymorphism markers to recover the full pedigree. Paternity was assigned successfully for 89 % of the offspring at a 99 % confidence level. We thus concluded there was an 11 % pollen contamination rate, assuming contamination when no genotype from the polymix composition could be identified as a father. The paternal contribution to the offspring varied among the males, but the departure from half-sib assumption was moderate since the average genetic correlation within the family was 0.26. Heritability and breeding values for girth at breast height and stem sweep were estimated using individual-tree mixed models with either partial or full pedigree information. The results highlighted a minor bias in heritability estimation due to unknown paternity, as well as a high correlation for estimated breeding values between the partial and full pedigree models, suggesting that the genetic merit of the parental generation for backward selection was adequately predicted using the partial pedigree model. Finally, pedigree recovery was also discussed in a perspective of forward selection.

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This study was funded by INRA (EFPA division projet innovant), the European-Union (ProCoGen project: n° 289841), and Conseil Regional d’Aquitaine (IMAF project co-funded by FCBA: n° 120009468–052). Marjorie Vidal received a CIFRE PhD fellowship (public/private research partnerships between FCBA and the French Ministry of Higher Education and Research). This study would not have been possible without the support of the maritime Pine Breeding Cooperative (GIS Pin Maritime du Futur). We gratefully acknowledge all its members. The authors also thank the INRA Experimental Unit (UE0570) for field measurements, Sophie Gerber (INRA) for helpful discussions on paternity recovery, Adline Delcamp (INRA) for the genotyping stage, Jean-Mathieu De Boisseson (FCBA) for needle sampling, Maël Ruby for his preliminary study on paternity recovery, and Fikret Isik (NCSU, USA) for his advice in shaping the content of the paper and his help in ASReml analysis.

The genotyping was performed at the Genomic Facility of Bordeaux (grants from the Conseil Regional d’Aquitaine: n°20030304002FA and 20040305003FA, the European Union: FEDER n°2003227 and ANR: n°ANR-10-EQPX-16 Xyloforest).

Data archiving statement

All SNPs used in this study were deposited in dbSNP (NCBI database), available on

The supplemental data “Supplemental_data_SNP_description.txt” contains the dbSNP accession ID for each SNP (#ss) and some useful information (SNP ID, set identity, contig name, linkage group LG, position on the LG, SNP type, and sequence surrounding the SNP).

The genotypes of G2 trees and their potential parents (G1 trees) are available in the supplemental data file “Subset_A_genotypes_56SNPs.csv” for Subset A and “Subset_B_genotypes_63SNPs.csv” for subset B. The first column contains the individual IDs, and the first line contains the SNP IDs. Blank cells are missing data.

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Correspondence to Laurent Bouffier.

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This article is part of the Topical Collection on Breeding

Communicated by: J. Beaulieu

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Vidal, M., Plomion, C., Harvengt, L. et al. Paternity recovery in two maritime pine polycross mating designs and consequences for breeding. Tree Genetics & Genomes 11, 105 (2015).

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  • Pedigree reconstruction
  • SNP markers
  • Paternal reproductive success
  • Pollen contamination
  • Breeding strategies
  • Pinus pinaster Ait.