Genomic selection (GS) has the potential to improve selection efficiency and shorten the breeding cycle in fruit tree breeding. In this study,we evaluated the effect of prediction methods, marker density and the train...Genomic selection (GS) has the potential to improve selection efficiency and shorten the breeding cycle in fruit tree breeding. In this study,we evaluated the effect of prediction methods, marker density and the training population (TP) size on pear GS for improving its performance and reducing cost. We evaluated GS under two scenarios:(1) five-fold cross-validation in an interspecific pear family;(2) independent validation. Based on the cross-validation scheme, the prediction accuracy (PA) of eight fruit traits varied between 0.33 (fruit core vertical diameter)and 0.65 (stone cell content). Except for single fruit weight, a slightly better prediction accuracy (PA) was observed for the five parametrical methods compared with the two non-parametrical methods. In our TP of 310 individuals, 2 000 single nucleotide polymorphism (SNP) markers were sufficient to make reasonably accurate predictions. PAs for different traits increased by 18.21%-46.98%when the TP size increased from 50to 100, but the increment was smaller (-4.13%-33.91%) when the TP size increased from 200 to 250. For independent validation, the PAs ranged from 0.11 to 0.45 using rrBLUP method. In summary, our results showed that the TP size and SNP numbers had a greater impact on the PA than prediction methods. Furthermore, relatedness among the training and validation sets, and the complexity of traits should be considered when designing a TP to predict the test panel.展开更多
Previously released pear genomes contain a plethora of gaps and unanchored genetic regions.Here,we report a telomere-to-telomere(T2T)gap-free genome for the red-skinned pear,‘Yunhong No.1’(YH1;Pyrus pyrifolia),which...Previously released pear genomes contain a plethora of gaps and unanchored genetic regions.Here,we report a telomere-to-telomere(T2T)gap-free genome for the red-skinned pear,‘Yunhong No.1’(YH1;Pyrus pyrifolia),which is mainly cultivated in Yunnan Province(southwest China),the pear’s primary region of origin.The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb.All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres.The 17 centromeres were predicted and mainly consist of centromeric-specific monomers(CEN198)and long terminal repeat(LTR)Gypsy elements(≥74.73%).By filling all unclosed gaps,the integrity of YH1 is markedly improved over previous P.pyrifolia genomes(‘Cuiguan’and‘Nijisseiki’).A total of 1531 segmental duplication(SD)driven duplicated genes were identified and enriched in stress response pathways.Intrachromosomal SDs drove the expansion of disease resistance genes,suggesting the potential of SDs in adaptive pear evolution.A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization,whichmay affect agronomic traits like stone cell content,sugar content,and fruit skin russet.Furthermore,as core regulators of anthocyanin biosynthesis,we found that MYB10 and MYB114 underwent various gene duplication events.Multiple copies of MYB10 and MYB114 displayed obvious dosage effects,indicating role differentiation in the formation of red-skinned pear fruit.In summary,the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.展开更多
基金supported by the National Key Research and Development Program (Grant No.2022YFD1200503)Jiangsu Agricultural Science and Technology Innovation Fund [Grant No.CX(22)3043]+1 种基金the Earmarked Fund for China Agriculture Research System (Grant No.CARS-28)the Earmarked Fund for Jiangsu Agricultural Industry Technology System (Grant No.JATS [2022]454)。
文摘Genomic selection (GS) has the potential to improve selection efficiency and shorten the breeding cycle in fruit tree breeding. In this study,we evaluated the effect of prediction methods, marker density and the training population (TP) size on pear GS for improving its performance and reducing cost. We evaluated GS under two scenarios:(1) five-fold cross-validation in an interspecific pear family;(2) independent validation. Based on the cross-validation scheme, the prediction accuracy (PA) of eight fruit traits varied between 0.33 (fruit core vertical diameter)and 0.65 (stone cell content). Except for single fruit weight, a slightly better prediction accuracy (PA) was observed for the five parametrical methods compared with the two non-parametrical methods. In our TP of 310 individuals, 2 000 single nucleotide polymorphism (SNP) markers were sufficient to make reasonably accurate predictions. PAs for different traits increased by 18.21%-46.98%when the TP size increased from 50to 100, but the increment was smaller (-4.13%-33.91%) when the TP size increased from 200 to 250. For independent validation, the PAs ranged from 0.11 to 0.45 using rrBLUP method. In summary, our results showed that the TP size and SNP numbers had a greater impact on the PA than prediction methods. Furthermore, relatedness among the training and validation sets, and the complexity of traits should be considered when designing a TP to predict the test panel.
基金supported by the National Science Foundation of China(31820103012)National Key Research and Development Program(2022YFD1200503)+1 种基金Earmarked Fund for China Agriculture Research System(CARS-28)Earmarked Fund for Jiangsu Agricultural Industry Technology System,China(JATS[2022]454).
文摘Previously released pear genomes contain a plethora of gaps and unanchored genetic regions.Here,we report a telomere-to-telomere(T2T)gap-free genome for the red-skinned pear,‘Yunhong No.1’(YH1;Pyrus pyrifolia),which is mainly cultivated in Yunnan Province(southwest China),the pear’s primary region of origin.The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb.All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres.The 17 centromeres were predicted and mainly consist of centromeric-specific monomers(CEN198)and long terminal repeat(LTR)Gypsy elements(≥74.73%).By filling all unclosed gaps,the integrity of YH1 is markedly improved over previous P.pyrifolia genomes(‘Cuiguan’and‘Nijisseiki’).A total of 1531 segmental duplication(SD)driven duplicated genes were identified and enriched in stress response pathways.Intrachromosomal SDs drove the expansion of disease resistance genes,suggesting the potential of SDs in adaptive pear evolution.A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization,whichmay affect agronomic traits like stone cell content,sugar content,and fruit skin russet.Furthermore,as core regulators of anthocyanin biosynthesis,we found that MYB10 and MYB114 underwent various gene duplication events.Multiple copies of MYB10 and MYB114 displayed obvious dosage effects,indicating role differentiation in the formation of red-skinned pear fruit.In summary,the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.
