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Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches

‘Chinese Cling’ is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this s...

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Autores principales: Li, Xiongwei, Wang, Jiabo, Su, Mingshen, Zhang, Minghao, Hu, Yang, Du, Jihong, Zhou, Huijuan, Yang, Xiaofeng, Zhang, Xianan, Jia, Huijuan, Gao, Zhongshan, Ye, Zhengwen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10419450/
https://www.ncbi.nlm.nih.gov/pubmed/37577398
http://dx.doi.org/10.1093/hr/uhad117
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author Li, Xiongwei
Wang, Jiabo
Su, Mingshen
Zhang, Minghao
Hu, Yang
Du, Jihong
Zhou, Huijuan
Yang, Xiaofeng
Zhang, Xianan
Jia, Huijuan
Gao, Zhongshan
Ye, Zhengwen
author_facet Li, Xiongwei
Wang, Jiabo
Su, Mingshen
Zhang, Minghao
Hu, Yang
Du, Jihong
Zhou, Huijuan
Yang, Xiaofeng
Zhang, Xianan
Jia, Huijuan
Gao, Zhongshan
Ye, Zhengwen
author_sort Li, Xiongwei
collection PubMed
description ‘Chinese Cling’ is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the ‘Shanghai Shuimi’ landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.
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spelling pubmed-104194502023-08-12 Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches Li, Xiongwei Wang, Jiabo Su, Mingshen Zhang, Minghao Hu, Yang Du, Jihong Zhou, Huijuan Yang, Xiaofeng Zhang, Xianan Jia, Huijuan Gao, Zhongshan Ye, Zhengwen Hortic Res Article ‘Chinese Cling’ is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the ‘Shanghai Shuimi’ landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars. Oxford University Press 2023-05-31 /pmc/articles/PMC10419450/ /pubmed/37577398 http://dx.doi.org/10.1093/hr/uhad117 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nanjing Agricultural University. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Li, Xiongwei
Wang, Jiabo
Su, Mingshen
Zhang, Minghao
Hu, Yang
Du, Jihong
Zhou, Huijuan
Yang, Xiaofeng
Zhang, Xianan
Jia, Huijuan
Gao, Zhongshan
Ye, Zhengwen
Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches
title Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches
title_full Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches
title_fullStr Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches
title_full_unstemmed Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches
title_short Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches
title_sort multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10419450/
https://www.ncbi.nlm.nih.gov/pubmed/37577398
http://dx.doi.org/10.1093/hr/uhad117
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