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Development of a Gene-based Marker for the non-ripening (nor) Gene in Cultivated Tomato
Thim Thi Nguyen,Sung-Chur Sim 한국원예학회 2017 원예과학기술지 Vol.35 No.5
Long shelf-life is an important trait for providing fresh fruits to consumers in cultivated tomato(Solanum lycopersicum L.) The molecular mechanism of fruit ripening in tomato was previously defined by identifying several genes associated with abnormal ripening. Of these genes, non-ripening (nor) encodes a member of NAC domain family transcription factors that is important for diverse physiological processes, including fruit ripening. In this study, we investigated sequence variations associated with the nor mutation to develop a gene-based marker. Two varieties of S. lycopersicum with representative nor mutants (LA1793 and LA3013) and a wild-type variety (San Marzano) were used for sequence analysis of the nor gene. A total of eight primer sets were designed to sequence the full length of nor gene including a 2.8 kb open reading frame (three exons and two introns) as well as 2.0 kb region upstream from the start codon. Analysis of the 4.8 kb sequence for the nor gene found a 2 bp insertion and deletion (InDel) in the longest exon (725 bp) that results in a frame-shift mutation in the two mutant varieties. This InDel was used to genotype a collection of additional 81 varieties consisting of 30 inbred and 51 commercial F1 hybrid varieties. Of these varieties, two inbred and one F1 hybrid varieties had nor mutations that were in homozygous or heterozygous forms. These results will be useful for marker-assisted selection (MAS) for improving long shelf-life and quality of fruit in tomato breeding programs.
모란과 작약의 구별을 위한 엽록체 기반 InDel 마커의 개발
이미선,정희정,박소현,정 희,정진태,정진태,김문교,김문교,길진수,이재복,김세림,윤기훈,이이 한국약용작물학회 2022 한국약용작물학회지 Vol.30 No.6
Background: Paeonia suffruticosa Andrew and P. lactiflora Pallas are important medicinal plants that are difficult to differentiate due to their similar appearances. The development of molecular markers will aid in the discrimination of these two species. Methods and Results: We found several chloroplast genomic loci that were polymorphic between P. suffruticosa and P. lactiflora. Among them, the insertion/deletion (InDel) marker PsPl-InDel-12 clearly discriminated 25 P. suffruticosa and P. lactiflora samples collected in the Republic of Korea. We were able to discriminate the two species in material of mixed status. Conclusions: The marker developed in this study can be used to ensure P. suffruticosa and P. lactiflora quality and increase consumer confidence when purchasing medicinal products made from these species.
김문교(Moon Kyo Kim),김주혁(Ju Hyeok Kim),이미선(Mi Sun Lee),조남수(Nam Su Jo),박상익(Sang Ik Park),길진수(Jin Su Gil),Enkhtsetseg Yeruult,오하경(Ha Kyung Oh),이경희(Kyeong Hee Lee),김호방(Ho Bang Kim),이문순(Moon Soon Lee),이이(Yi 한국약용작물학회 2021 한국약용작물학회지 Vol.29 No.4
Background: Jujube (Ziziphus jujuba Mill.) friuts are rich in nutrients and an economically and ecologically important medicinal plant in Korea. However, as it is difficult to distinguish jujube cultivars using morphological characters, the development of molecular markers is necessary to protect and distinguish Korean jujube cultivars. Methods and Results: Next-generation sequencing analysis was performed on six major Korean cultivars; Bokjo, Boeun, Chuseok, Mudeung, Geumseong, and Wolchul. Sites with an insertion or deletion (InDel) were identified by comparison from the sequence information of the six Korean cultivars using the CLC Genomics Workbench. Among the identified InDels, we developed Zj-InDel-1 and Zj-InDel-2 markers, which could distinguish Bokjo, Chuseok, and Boeun from the other Korean cultivars. Conclusions: The InDel markers developed in this study could be used for classification of domestic jujube cultivars and protection of the elite ones.
엽록체 유전체 바코딩기술 및 HPLC를 이용한 복분자딸기 식별법
박영상(Young Sang Park),김영준(Young Jun Kim),양태진(Tae Jin Yang),김지연(Ji Yeon Kim) 한국약용작물학회 2021 한국약용작물학회지 Vol.29 No.6
Background: Rubus coreanus and R. occidentalis are commonly sold as, ‘Bokbunja’, in the Korean market. However, according to Korean Pharmacopoeia, ‘Bokbunja’ refers to the unripened fruits of R. coreanus. Therefore, authentication of R. coreanus and its related species is necessary to prevent adulteration and improper use. Methods and Results: Genomic DNA was extracted from leaves, stem and fruits of R. coreanus, fruits of R. occidentalis and leaves of R. longisepalus and R. hirsutus. The anthocyanin profile of R. coreanus and R. occidentalis was identified by high performance liquid chromatography/diode-array detection. We designed four universal barcoding primer sets with optimal restriction enzyme sites to identify polymerase chain reaction-restriction fragment length polymorphisms (PCRRFLPs) between R. coreanus, the newly assembled chloroplast genome of R. occidentalis, and two related species. In addition, two Insertion or Deletion (InDel) markers were also developed. These markers were successfully used to distinguish each species in nine samples. Conclusions: In this study, we sequenced and assembled the complete chloroplast genome of R. occidentalis and developed a DNA barcoding method to differentiate it from other related species. Thus, anthocyanin profiling, PCR-RFLPs, and InDel markers are useful authentication tools to distinguish R. coreanus from R. occidentalis.
오미자과 식물 종 판별을 위한 엽록체 기반 InDel 마커의 개발
정희정(Hee Jeong Jeong),이재복(Jea Bok Lee),길진수(Jin Su Gil),홍창표(Chang Pyo Hong),강상호(Sang Ho Kang),권수진(Soo Jin Kwon),김효진(Hyo Jin Kim),김창국(Chang Kug Kim),이정호(Jung Ho Lee),이이(Yi Lee) 한국약용작물학회 2021 한국약용작물학회지 Vol.29 No.1
Background: The three Schisandracae species, Schisandra chinensis, Schisandra repanda, and Kadsura japonica, which are used as raw materials for the production of herbal medicines, are readily confused. However, of these three species, only S. chinensis is formally registered as a medicinal herb in the Korean Pharmacopeia. In order to facilitate the clear identification of S. chinensis, S. repanda, and K. japonica, we developed insertion or deletion (InDel) markers by comparing the chloroplast sequences of the three species. Methods and Results: Genomic DNA was extracted from the leaves of S. chinensis, S. repanda, and K. japonica, and next generation sequencing (NGS) analysis was performed using the Illumina HiSeq-2500 platform. Chloroplast sequences for the three species were obtained and compared to identify polymorphic loci. Primers were designed for those InDel loci showing polymorphism in all three species, and four InDel markers were accordingly developed and successfully used for species discrimination. Conclusions: In this study, we developed four markers that can be used to discriminate S. chinensis, S. repanda, and K. japonica at the molecular level.