Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits
Abstract Novel genomics-based approaches such as genome-wide association studies (GWAS) and genomic selection (GS) are expected to be useful in fruit tree breeding, which requires much time from the cross to the release of a cultivar because of the long generation time. In this study, a citrus paren...
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2017
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oai:doaj.org-article:80c6378caffc4c3d9910cc1f5eb627922021-12-02T16:06:20ZGenome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits10.1038/s41598-017-05100-x2045-2322https://doaj.org/article/80c6378caffc4c3d9910cc1f5eb627922017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05100-xhttps://doaj.org/toc/2045-2322Abstract Novel genomics-based approaches such as genome-wide association studies (GWAS) and genomic selection (GS) are expected to be useful in fruit tree breeding, which requires much time from the cross to the release of a cultivar because of the long generation time. In this study, a citrus parental population (111 varieties) and a breeding population (676 individuals from 35 full-sib families) were genotyped for 1,841 single nucleotide polymorphisms (SNPs) and phenotyped for 17 fruit quality traits. GWAS power and prediction accuracy were increased by combining the parental and breeding populations. A multi-kernel model considering both additive and dominance effects improved prediction accuracy for acidity and juiciness, implying that the effects of both types are important for these traits. Genomic best linear unbiased prediction (GBLUP) with linear ridge kernel regression (RR) was more robust and accurate than GBLUP with non-linear Gaussian kernel regression (GAUSS) in the tails of the phenotypic distribution. The results of this study suggest that both GWAS and GS are effective for genetic improvement of citrus fruit traits. Furthermore, the data collected from breeding populations are beneficial for increasing the detection power of GWAS and the prediction accuracy of GS.Mai F. MinamikawaKeisuke NonakaEli KaminumaHiromi Kajiya-KanegaeAkio OnogiShingo GotoTerutaka YoshiokaAtsushi ImaiHiroko HamadaTakeshi HayashiSatomi MatsumotoYuichi KatayoseAtsushi ToyodaAsao FujiyamaYasukazu NakamuraTokurou ShimizuHiroyoshi IwataNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-13 (2017) |
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Medicine R Science Q Mai F. Minamikawa Keisuke Nonaka Eli Kaminuma Hiromi Kajiya-Kanegae Akio Onogi Shingo Goto Terutaka Yoshioka Atsushi Imai Hiroko Hamada Takeshi Hayashi Satomi Matsumoto Yuichi Katayose Atsushi Toyoda Asao Fujiyama Yasukazu Nakamura Tokurou Shimizu Hiroyoshi Iwata Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits |
| description |
Abstract Novel genomics-based approaches such as genome-wide association studies (GWAS) and genomic selection (GS) are expected to be useful in fruit tree breeding, which requires much time from the cross to the release of a cultivar because of the long generation time. In this study, a citrus parental population (111 varieties) and a breeding population (676 individuals from 35 full-sib families) were genotyped for 1,841 single nucleotide polymorphisms (SNPs) and phenotyped for 17 fruit quality traits. GWAS power and prediction accuracy were increased by combining the parental and breeding populations. A multi-kernel model considering both additive and dominance effects improved prediction accuracy for acidity and juiciness, implying that the effects of both types are important for these traits. Genomic best linear unbiased prediction (GBLUP) with linear ridge kernel regression (RR) was more robust and accurate than GBLUP with non-linear Gaussian kernel regression (GAUSS) in the tails of the phenotypic distribution. The results of this study suggest that both GWAS and GS are effective for genetic improvement of citrus fruit traits. Furthermore, the data collected from breeding populations are beneficial for increasing the detection power of GWAS and the prediction accuracy of GS. |
| format |
article |
| author |
Mai F. Minamikawa Keisuke Nonaka Eli Kaminuma Hiromi Kajiya-Kanegae Akio Onogi Shingo Goto Terutaka Yoshioka Atsushi Imai Hiroko Hamada Takeshi Hayashi Satomi Matsumoto Yuichi Katayose Atsushi Toyoda Asao Fujiyama Yasukazu Nakamura Tokurou Shimizu Hiroyoshi Iwata |
| author_facet |
Mai F. Minamikawa Keisuke Nonaka Eli Kaminuma Hiromi Kajiya-Kanegae Akio Onogi Shingo Goto Terutaka Yoshioka Atsushi Imai Hiroko Hamada Takeshi Hayashi Satomi Matsumoto Yuichi Katayose Atsushi Toyoda Asao Fujiyama Yasukazu Nakamura Tokurou Shimizu Hiroyoshi Iwata |
| author_sort |
Mai F. Minamikawa |
| title |
Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits |
| title_short |
Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits |
| title_full |
Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits |
| title_fullStr |
Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits |
| title_full_unstemmed |
Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits |
| title_sort |
genome-wide association study and genomic prediction in citrus: potential of genomics-assisted breeding for fruit quality traits |
| publisher |
Nature Portfolio |
| publishDate |
2017 |
| url |
https://doaj.org/article/80c6378caffc4c3d9910cc1f5eb62792 |
| work_keys_str_mv |
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| _version_ |
1718385035121262592 |