Texture is a complex trait and a major component of fruit quality in apple. While the major effect of MdPG1, a gene controlling firmness, has already been exploited in elite cultivars, the genetic basis of crispness remains poorly understood. To further improve fruit texture, harnessing loci with minor effects via genomic selection is therefore necessary. In this study, we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture. Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance (0.64). Predictions for biparental families using the entire training set varied from low to high accuracy, depending on the family considered. While adding siblings or half-siblings into the training set did not clearly improve predictions, we performed an optimization of the training set size and composition for each validation set. This allowed us to increase prediction accuracies by 0.17 on average, with a maximal accuracy of 0.81 when predicting firmness in the ‘Gala’ × ‘Pink Lady’ family. Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple. In particular, we advise to rely on a large training population, with high phenotypic variability from which a ‘tailored training population’ can be extracted using a priori information on genetic relatedness, in order to predict a specific target population.

Roth, M.; Muranty, H.; Di Guardo, M.; Guerra, W.; Patocchi, A.; Costa, F. (2020). Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple. HORTICULTURE RESEARCH, 7: 148. doi: 10.1038/s41438-020-00370-5 handle: http://hdl.handle.net/10449/64748

Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple

Di Guardo, M.;Costa, F.
2020-01-01

Abstract

Texture is a complex trait and a major component of fruit quality in apple. While the major effect of MdPG1, a gene controlling firmness, has already been exploited in elite cultivars, the genetic basis of crispness remains poorly understood. To further improve fruit texture, harnessing loci with minor effects via genomic selection is therefore necessary. In this study, we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture. Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance (0.64). Predictions for biparental families using the entire training set varied from low to high accuracy, depending on the family considered. While adding siblings or half-siblings into the training set did not clearly improve predictions, we performed an optimization of the training set size and composition for each validation set. This allowed us to increase prediction accuracies by 0.17 on average, with a maximal accuracy of 0.81 when predicting firmness in the ‘Gala’ × ‘Pink Lady’ family. Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple. In particular, we advise to rely on a large training population, with high phenotypic variability from which a ‘tailored training population’ can be extracted using a priori information on genetic relatedness, in order to predict a specific target population.
Apple
Fruit texture
SNP markers
Genomic selection
Settore AGR/07 - GENETICA AGRARIA
2020
Roth, M.; Muranty, H.; Di Guardo, M.; Guerra, W.; Patocchi, A.; Costa, F. (2020). Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple. HORTICULTURE RESEARCH, 7: 148. doi: 10.1038/s41438-020-00370-5 handle: http://hdl.handle.net/10449/64748
File in questo prodotto:
File Dimensione Formato  
2020 HR Costa.pdf

accesso aperto

Tipologia: Versione editoriale (Publisher’s layout)
Licenza: Creative commons
Dimensione 1.22 MB
Formato Adobe PDF
1.22 MB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/64748
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 31
  • ???jsp.display-item.citation.isi??? 17
social impact