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

Abstract

‘Chinese Cling’ is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection (GS) 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 solid content, along with fourteen key volatile odor compounds (VOCs) were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified to be 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 solid content and cis-3-hexenyl acetate. The multiple-traits genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-traits 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 “Shanghai Shuimi” landrace. Overall, our findings will be helpful to determine the peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve the accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between QTLs and marker assisted selection (MAS) for developing strong-aroma cultivars.

Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics

“…GS via genomic prediction (GP) has been employed in both animal and plant breeding ( Daetwyler et al., 2013 ), including numerous crops of economic relevance such as Solanaceae ( Tong et al., 2022 ), cereals, legumes ( Krishnappa et al., 2021 ; Kaler et al., 2022 ) and other horticultural crops ( Hernandez et al., 2020 ; Liu et al., 2021 ). GP was also applied to fruit crops ( Table 2 ) including apple ( Roth et al., 2020 ; Minamikawa et al., 2021 ), apricot ( Nsibi et al., 2020 ); passion fruit ( Viana et al., 2017 ), pear ( Minamikawa et al., 2018 ), peach ( Li et al., 2023 ), banana ( Nyine et al., 2018 ), blueberry ( de Bem Oliveira et al., 2020 ), strawberry ( Yamamoto et al., 2021 ), cranberry ( Covarrubias-Pazaran et al., 2018 ), oil palm ( Cros et al., 2015 ) and Citrus spp. ( Minamikawa et al., 2017 ).…”