Genome Resources for Identifying SNPs Associated With Eight Horticultural Traits in Commercial Korean Elite Radish (Raphanus sativus) Lines

Abstract

Radish (Raphanus sativus), which belongs to the family Brassicaceae, has relatively limited genomic resources, especially for elite lines used in commercial breeding and other agricultural applications. Thus, this study aimed to provide a comprehensive catalogue of genome sequences for 100 elite radish lines used in the Korean industry for commercial breeding purposes. These lines were sequenced and mapped to the elite Bakdal genome. A total of 33,919 high‐quality single nucleotide polymorphisms (SNPs) were identified and were found to be associated with eight distinct phenotypic traits. Five diverse machine learning (ML) models revealed that a subset of 198 SNPs had high predictive potential for the eight horticultural traits. Furthermore, the 100 elite lines were grouped into four clusters based on the eight traits, and their predictive potential was evaluated using the ML models trained using both individual and pooled SNPs. The accuracy ranged from 0.83 to 0.96 for the individually trained models and from 0.84 to 0.95 for the pooled models. This study provides a substantial basis for the advancement of digital/precision radish breeding.