首页|Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems:application to apple fruit quality traits

Genomic prediction and genome-wide association study using combined genotypic data from different genotyping systems:application to apple fruit quality traits

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With advances in next-generation sequencing technologies,various marker genotyping systems have been developed for genomics-based approaches such as genomic selection(GS)and genome-wide association study(GWAS).As new genotyping platforms are developed,data from different genotyping platforms must be combined.However,the potential use of combined data for GS and GWAS has not yet been clarified.In this study,the accuracy of genomic prediction(GP)and the detection power of GWAS increased for most fruit quality traits of apples when using combined data from different genotyping systems,Illumina Infinium single-nucleotide polymorphism array and genotyping by random amplicon sequencing-direct(GRAS-Di)systems.In addition,the GP model,which considered the inbreeding effect,further improved the accuracy of the seven fruit traits.Runs of homozygosity(ROH)islands overlapped with the significantly associated regions detected by the GWAS for several fruit traits.Breeders may have exploited these regions to select promising apples by breeders,increasing homozygosity.These results suggest that combining genotypic data from different genotyping platforms benefits the GS and GWAS of fruit quality traits in apples.Information on inbreeding could be beneficial for improving the accuracy of GS for fruit traits of apples;however,further analysis is required to elucidate the relationship between the fruit traits and inbreeding depression(e.g.decreased vigor).

Mai F.Minamikawa、Miyuki Kunihisa、Shigeki Moriya、Tokurou Shimizu、Minoru Inamori、Hiroyoshi Iwata

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Institute for Advanced Academic Research(IAAR),Chiba University,1-33 Yayoi,Inage,Chiba,Chiba 263-8522,Japan

Laboratory of Biometry and Bioinformatics,Department of Agricultural and Environmental Biology,Graduate School of Agricultural and Life Sciences,The University of Tokyo,1-1-1 Yayoi,Bunkyo,Tokyo 113-8657,Japan

Institute of Fruit Tree and Tea Science,National Agriculture and Food Research Organization(NARO),2-1 Fujimoto,Tsukuba,Ibaraki 305-8605,Japan

Institute of Fruit Tree and Tea Science,NARO,92-24 Shimokuriyagawa Nabeyashiki,Morioka,Iwate 020-0123,Japan

Institute of Fruit Tree and Tea Science,NARO,Okitsu Nakacho,Shimizu,Shizuoka 424-0292,Japan

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2024

10.1093/hr/uhae131

园艺研究(英文)

园艺研究(英文)

CSTPCD
ISSN：
年,卷(期)：2024.11(7)