Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits

Mai F Minamikawa,Keisuke Nonaka,Hiroyoshi Iwata,Akio Onogi,Satomi Matsumoto,Yuichi Katayose,Asao Fujiyama,Hiromi Kajiya-Kanegae,Yasukazu Nakamura,Atsushi Imai,Hiroko Hamada,Takeshi Hayashi,Terutaka Yoshioka,Atsushi Toyoda,Shingo Goto,Eli Kaminuma,Tokurou Shimizu

doi:10.1038/s41598-017-05100-x

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.

Highlights

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
The r2 values were plotted against the physical distance for the parental population and the combined population; curves fitted for the relationships between r2 and physical map distance indicated that linkage disequilibrium (LD) extended over 1 Mb (r2 > 0.25) and decayed to relatively low levels (r2 < 0.10) within 20 Mb in both populations (Fig. 1)
Whereas part of the parental population belonged to the clusters of large- or small-fruit varieties, most varieties showed no clear separation in hierarchical clustering, ADMIXTURE clustering, or principal component analysis (PCA)

Summary

Introduction

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. 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. The data collected from breeding populations are beneficial for increasing the detection power of GWAS and the prediction accuracy of GS. Large plant size limits the number of fruit trees in orchards, and their long juvenile period lengthens the time required for breeding, increasing the www.nature.com/scientificreports/.

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