Analysis of genetic diversity of yuzu ( Citrus junos Sieb. Ex Tanaka) using single nucleotide polymorphisms identified through RNA-seq and whole-genome resequencing analyses

Abstract

ABSTRACTYuzu (Citrus junos Sieb. Ex Tanaka) is widely cultivated in Asia. However, a system for variety identification has not been developed yet. RNA-seq analysis was performed to identify variants among five yuzu samples including a seedless variety. However, only four variants were found, suggesting that the seedless trait might originate from bud mutations. To identify more variants, whole-genome resequencing was performed. A total of 140 reliable variants were screened. Based on these variants, 30 high-resolution melting (HRM) markers were developed. After genotyping 265 yuzu samples using the HRM markers, the yuzu samples were classified into 18 types. Three yuzu-like samples (B-37-1, B-UK2, and B-MD6-8) showing different fruit morphologies and off-type HRM peak patterns were assumed to originate from interspecific hybridisation. To identify the parent species of these yuzu-like samples, nucleotide sequences of a hypervariable chloroplast genomic region and a nuclear CitRWP gene responsible for nucellar embryony were obtained. Chloroplast genome sequence analysis indicated that the maternal parents of B-37-1 and B-MD6-8 were yuzu, whereas the B-UK2 sequence was identical to that of sweet orange. Moreover, the CitRWP sequences indicated that the male parents of B-37-1, B-UK2, and B-MD6-8 were mandarin, yuzu, and pummelo, respectively.KEYWORDS: YuzuCitrus junosvariety identificationmolecular markerhigh-resolution meltingnucellar embryony AcknowledgementsThe authors thank Ji-hwa Heo, Jeong-An Yoo, and Su-jeong Kim for their dedicated technical assistance. This study was supported by the “Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ016161)” funded by the Rural Development Administration, Republic of Korea, and the BK21 FOUR grant funded by the Ministry of Education of Korea and National Research Foundation of Korea.Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementTranscriptome and whole genome resequencing data obtained in this study are accessible at NCBI SRA database.Supplementary materialSupplemental data for this article can be accessed online at https://doi.org/10.1080/14620316.2023.2265360.Additional informationFundingThe work was supported by the Rural Development Administration [PJ016161].