Abstract
Poplar (Populus spp.) breeding programs increasingly prioritize the development of male varieties due to the environmental issues caused by female catkins. Therefore, there is an urgent need for a reliable technique for early sex identification in Populus. Genomic selection (GS), as an efficient predictive method, offers a promising solution for early sex identification in poplar. In this study, we conducted genomic prediction for sex in Populus deltoides. Using five full-sib families of P. deltoides as the reference population, we identified 801 sex-associated loci through GWAS and precisely localized the sex determination region at the telomeric end of chromosome 19. We evaluated 14 GS statistical models using fivefold cross-validation under six marker densities. The results showed significant differences in prediction accuracy (PA) among different statistical models, ranging from 0.19 to 0.79, with the gradient boosting decision tree exhibiting the highest accuracy and stability. Notably, single nucleotide polymorphisms selected through GWAS significantly improved PA compared to random markers, achieving a corrected accuracy of 0.999. Using the optimal model and markers, we predicted the sex of 505 progenies from 27 full-sib families, with over 90% of the predictions being accurate. Overall, this study achieved high-accuracy sex prediction in P. deltoides through genome prediction, providing a novel and efficient method for poplar sex identification.
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Claims 6
Claim · model-written summary
GWAS identified 801 sex associated loci.
- Taxon
- Populus deltoides
Populus deltoidest0 - Outcome
- sex-associated locie0
- Value
- 801e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we identified 801 sex-associated loci through GWAS”
t0“Populus deltoides”
Claim · model-written summary
The sex determination region was localized at the telomeric end of chromosome 19.
- Taxon
- Populus deltoidesPopulus deltoidest0
- Outcome
- sex determination region at the telomeric end of chromosome 19e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“precisely localized the sex determination region at the telomeric end of chromosome 19”
t0“Populus deltoides”
Claim · model-written summary
Prediction accuracy differed significantly among models and ranged from 0.19 to 0.79.
- Taxon
- Populus deltoidesPopulus deltoidest0
- Outcome
- prediction accuracy (PA)e0
- Value
- 0.19 to 0.79e0
- Comparator
- different statistical modelse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“significant differences in prediction accuracy (PA) among different statistical models, ranging from 0.19 to 0.79”
t0“Populus deltoides”
Claim · model-written summary
Gradient boosting decision tree had the highest accuracy and stability.
- Taxon
- Populus deltoidesPopulus deltoidest0
- Outcome
- accuracy and stabilitye0
- Direction
- higheste0
- Value
- higheste0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the gradient boosting decision tree exhibiting the highest accuracy and stability”
t0“Populus deltoides”
Claim · model-written summary
GWAS selected SNPs significantly improved prediction accuracy over random markers, reaching 0.999 corrected accuracy.
- Taxon
- Populus deltoidesPopulus deltoidest0
- Outcome
- corrected accuracye0
- Direction
- improvede0
- Value
- 0.999e0
- Comparator
- random markerse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“single nucleotide polymorphisms selected through GWAS significantly improved PA compared to random markers, achieving a corrected accuracy of 0.999”
t0“Populus deltoides”
Claim · model-written summary
The optimal model and markers predicted sex for 505 progenies with over 90% accuracy.
- Taxon
- Populus deltoidesPopulus deltoidest0
- Outcome
- predictions being accuratee0
- Value
- over 90%e0
- Qualifier
- 505 progenies from 27 full-sib familiese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Using the optimal model and markers, we predicted the sex of 505 progenies from 27 full-sib families, with over 90% of the predictions being accurate.”
t0“Populus deltoides”