토마토(Solanum lycopersicum L.) 품종 간 수용성 비타민과 폴리페놀계 성분 함량 변이 분석

Daen Kim,Beunggu Son,Youngwhan Choi,Jumsoon Kang,Yongjae Lee,Beungil Je,Younghoon Park (사)한국식물생명공학회 2020 JOURNAL OF PLANT BIOTECHNOLOGY Vol.47 No.1

Tomato fruit quality is determined by the contents of various functional metabolites in addition to fruit appearance. To develop tomato cultivars with higher amounts of functional compounds, an efficient quantification method is required to identify the natural variations in the compounds in the tomato germplasm. In this study, we investigated tomato varieties, which included 23 inbred lines and 12 commercial F1 cultivars, for their contents of seven watersoluble vitamins (vitamin C, vitamins B1, B2, B3, B5, B6, and B9) and five polyphenolic compounds (quercetin, rutin, kaempferol, myricetin, and naringenin chalcone). The results of high performance liquid chromatography and liquid chromatography- mass spectrometry showed that vitamin C and naringenin chalcone were the major water-soluble vitamins and polyphenolic compounds, respectively, and their abundance was highly variable depending on the cultivar. By contrast, the contents of vitamin B1, quercetin, and kaempferol were lowest among the cultivars. With regard to the relationship between metabolic compounds and fruit characteristics, a significant association was found in fruit size, indicating that cherry tomato varieties contain higher amounts of the compounds compared to large fresh-type varieties. However, no direct association was detected in fruit color, except for naringenin chalcone. The results of this study provide new insights on the quantification of metabolic compounds and the selection of breeding materials, which are prerequisites for the development of functional tomato varieties.

Evaluation of DNA Markers for Fruit-related Traits and Genetic Relationships Based on Simple Sequence Repeat in Watermelon Accessions

Bingkui Jin,Girim Park,Youngmi Choi,Jaejong Nho,Beunggu Son,Younghoon Park(박영훈) 한국원예학회 2018 한국원예학회 학술발표요지 Vol.2018 No.5

조 · 만생종 완전단감의 과실발달 단계별 형질특성 및 유전자 발현 분석

김은경(Eun-Gyeong Kim),안광환(Gwang-Hwan Ahn),박기림(Girim Park),손병구(Beunggu Son),최영환(Youngwhan Choi),강점순(Jumsoon Kang),이용재(Youngjae Lee),제병일(Byeong Il Je),박영훈(Younghoon Park) 한국원예학회 2021 원예과학기술지 Vol.39 No.3

완전단감 품종 중 만생종인 ‘부유’와 조생종인 ‘조추’의 과실 발육 단계 별 주요 형질과 과실 내 발현되는 전사체의 비교 분석을 통해, 만생종과 조생종 간 숙기 조절 관련 유전자를 탐색하였다. 개화 후 6주부터 ‘조추’는 개화 후 18주까지, ‘부유’는 24주까지 과피색과 유리당 함량을 3주 간격으로 조사한 결과 ‘조추’의 과실 성숙이 ‘부유’보다 이른 시기에 시작됨을 보여 주었다. 색도는 ‘부유’에 비해 ‘조추’에서 과피 착색이 빠르게 진행되었고, 개화 후 18주에 두 품종 간 차이가 현저하게 드러났다. 과실내 유리당 함량을 조사한 결과, ‘조추’의 서당 감소 시점이 ‘부유’에 비해 약 9주 빨랐다. 두 품종의 과육 전사체 분석은 개화 후 9주부터 18주까지 3주 간격으로 수행하였다. 전사체의 GO term 분석에서는 세포와 세포소기관에서 대사과정과 발육을 조절하는 촉매작용과 수송 관련 유전자, 그리고 KOG 분석과 KEGG pathway 분석에서는 신호전달과 핵산구조, 전분과 당 대사에 관한 pathway 유전자가 주를 이루었다. DEGs 분석은 각 품종의 개화 후 9주의 과육 샘플을 대조구로 하여 이후 18주까지 3주 간격의 샘플을 처리구로 비교한 DEGs set Ⅰ과 각 단계별로 ‘부유’를 대조구로 하고 ‘조추’를 처리구로 비교한 DEGs set Ⅱ로 분석하였다. DEGs set Ⅰ의 발현량을 분석한 결과, 3가지 비교조합 중에서 ‘부유’는 개화 후 18주에, ‘조추’는 15주에 대조구에 비해 처리구에서 up-regulation된 유전자의 개수가 가장 많았다. DEGs set Ⅱ에서는 ‘부유’에 비해 ‘조추’에서 개화 후 12주에 down-regulation되는 유전자가, 15주에는 up-regulation되는 유전자가 많았다. 과실 형질 관련 후보유전자의 발현량을 형질변화와 비교 분석한 결과, 탄수화물 대사에 관련된 UGPase-1과 AGPase-1, 카로티노이드 생합성 경로의 CRTISO와 PDS는 ‘조추’의 조기 과실 성숙을 유도하는 유전자로 추정되었다. Transcription factor(TF)로는 ethylene responsive gene의 promoter에 결합하는 ERF3와 ACS의 promoter에 결합하는 MADS-box TF인 RIN, AGL, FUL, 그리고 climacteric type의 성숙을 조절하는 NAC가 ‘부유’, ‘조추’ 단감의 성숙 조절에 핵심적 역할을 하는 것으로 추정되었다. We analyzed the major fruit traits and transcriptomes between a late-ripening cultivar ‘Fuyu’ and an early-ripening cultivar ‘Soshu’ of pollination constant non-astringent persimmon (Diospyros kaki Thunb.) at different developmental stages. Sugar concentration and fruit peel color were measured every 3 weeks, until 18 weeks after full bloom (WAB) for ‘Soshu’ and 24 WAB for ‘Fuyu’. For the sugar concentration in fruit, sucrose levels began to decline 9 weeks earlier in ‘Soshu’. Fruit peel coloring progressed faster in ‘Soshu’, and differences in color between the cultivars were most notable at 18 WAB. Transcriptome analysis was carried out for fruit flesh every 3 weeks from 9-18 WAB. Gene ontology term analysis of the transcriptome indicated that catalytic and transport genes involved in metabolism and growth in cells and cellular organelles were mainly expressed, while in KOG and KEGG analysis, the majority of expressed genes were related to signal transduction, nuclear structure, and starch and sucrose metabolism. Differentially expressed genes were analyzed from two sets of samples: set I, in which fruits sampled at 12, 15, and 18 WAB were compared as the treatment group to the sample collected at 9 WAB as the control for each cultivar; and set II, in which fruit samples of ‘Soshu’ were compared as the treatment group to ‘Fuyu’ as the control at each WAB. For the DEGs of set I, containing three comparison combinations, the number of up-regulated genes in the treatment sample was highest at 18 WAB in ‘Fuyu’ and at 15 WAB in ‘Soshu’. For the DEGs of set II, the number of down-regulated genes and the number of up-regulated genes were higher in ‘Soshu’ compared to ‘Fuyu’ at 12 WAB and 15 WAB, respectively. We then compared the expression patterns of fruit trait-related genes with the phenotypic changes in traits. Our results indicated that UGPase-1 and AGPase-1, involved in carbohydrate metabolism, and CRTISO and PDS, involved in carotenoid biosynthesis, may induce early fruit ripening in ‘Soshu’. In addition, the transcription factors (TFs) ERF3, which binds to the promoter of ethylene-responsive genes; the MADS-box TFs RIN, AGL, and FUL; and the NAC TF controlling climacteric-type fruit ripening were considered to play a key role in controlling fruit ripening in ‘Fuyu’ and ‘Soshu’.

Evaluation of DNA Markers for Fruit-related Traits and Genetic Relationships Based on Simple Sequence Repeat in Watermelon Accessions

Bingkui Jin,Girim Park,Youngmi Choi,Jaejong Nho,Beunggu Son,Younghoon Park 한국원예학회 2017 원예과학기술지 Vol.35 No.1

Modern watermelon cultivars (Citrullus lanatus [Thunb.] Matsum.& Nakai var. lanatus ) have fruits with diverse phenotypes, including fruit shape, rind patterns, and flesh color. Molecular markers enable efficient selection of plants harboring desirable phenotypes. In the present study, publicly available DNA markers tightly linked to fruit shape, rind stripe pattern, and flesh color were evaluated using 85 watermelon accessions with diverse fruit phenotypes. For fruit shape, the dCAPS SUN - Cla011257 marker revealed an 81% of marker - trait match for accessions with elongated or round fruits. For rind stripe pattern, the SCAR wsb6-11marker was effective for selecting Jubilee-type rind pattern from other rind patterns. For flesh color, the Clcyb.600 and Lcyb markers derived from a mutation in the Lycopene β - cyclase (Lcyb) gene, were effective at selecting red or yellow flesh. Forty-eight accessions possessing diverse fruit - related traits were selected as a reference array and their genetic relationships assessed using 16 SSR markers. At a coefficient of 0.11, the 48 accessions grouped into two major clades: Clade I and Clade II. Clade I subdivided further into subclades I - 1 and I - 2 at a coefficient of 0.39. All accessions with colored flesh were classified into Clade I, whereas those with white - flesh were classified into Clade II. Differences in fruit traits between subclades I - 1 and I - 2 were observed for rind pattern and fruit color; a majority of the accessions with Crimson-type striped or non-striped rind were grouped together in subclade I - 1, while most accessions in subclade I - 2 had a Jubilee - type rind stripe pattern. These results imply that reference array watermelon accessions possess distinguishable genetic structure based on rind stripe pattern. However, no significant grouping pattern was observed based on other fruit-related traits.

토마토(Solanum lycopersicum L.) 품종 간 수용성 비타민과 폴리페놀계 성분 함량 변이 분석

김다은,손병구,최영환,강점순,이용재,제병일,박영훈,Kim, Daen,Son, Beunggu,Choi, Youngwhan,Kang, Jumsoon,Lee, Yongjae,Je, Beungil,Park, Younghoon 한국식물생명공학회 2020 식물생명공학회지 Vol.47 No.1

기능성 성분이 향상된 토마토 품종 개발을 위해서는 성분 정량분석법과 토마토 유전자원 간 대사성분 변이에 대한 정보의 확보가 필요하다. 본 연구에서는 토마토 유전자원23개 계통과 12개 상용 F₁ 품종을 이용하여 수용성 비타민 7종(vitamin C, B1, B2, B3, B5, B6, B9)과 폴리페놀계 성분 5종(quercetin, rutin, kaempferol, myricetin, and naringenin chalcone)에 대한 함량을 비교 분석 하였다. HPLC와 LC-MS 분석 결과, 수용성 비타민과 폴리페놀계의 주요 성분으로 vitamin C와 naringenin chalcone이 각각 검출되었으며 품종 간 높은 수준의 함량 변이가 존재함을 알 수 있었다. 반면에 vitamin B1, quercetin 과 kaempferol은 전 품종에 있어 함량이 가장 낮았다. 대사성분 함량과 토마토 과실특성 간 상관관계에 있어 서 과크기(과중)와 높은 유의성이 관찰되었는데 대부분의 성분에 있어 방울토마토 품종이 완숙용 토마토 품종보다 높은 함량을 보였다. 하지만 naringenin chalcone을 제외하고 대사성분과 과색 간의 상관관계는 뚜렷하게 나타나지 않았다. 본 결과는 토마토 육종과정에 활용될 수 있는 효율적인 대사성분 정량분석법을 제시할 뿐만 아니라 기능성 성분 고함량 육종소재 선발에 중요한 정보를 제공한다. Tomato fruit quality is determined by the contents of various functional metabolites in addition to fruit appearance. To develop tomato cultivars with higher amounts of functional compounds, an efficient quantification method is required to identify the natural variations in the compounds in the tomato germplasm. In this study, we investigated tomato varieties, which included 23 inbred lines and 12 commercial F₁ cultivars, for their contents of seven watersoluble vitamins (vitamin C, vitamins B1, B2, B3, B5, B6, and B9) and five polyphenolic compounds (quercetin, rutin, kaempferol, myricetin, and naringenin chalcone). The results of high performance liquid chromatography and liquid chromatography-mass spectrometry showed that vitamin C and naringenin chalcone were the major water-soluble vitamins and polyphenolic compounds, respectively, and their abundance was highly variable depending on the cultivar. By contrast, the contents of vitamin B1, quercetin, and kaempferol were lowest among the cultivars. With regard to the relationship between metabolic compounds and fruit characteristics, a significant association was found in fruit size, indicating that cherry tomato varieties contain higher amounts of the compounds compared to large fresh-type varieties. However, no direct association was detected in fruit color, except for naringenin chalcone. The results of this study provide new insights on the quantification of metabolic compounds and the selection of breeding materials, which are prerequisites for the development of functional tomato varieties.

수박 엘리트 계통의 GBS를 통한 마커이용 육종용 SNP 마커 개발

이준우,손병구,최영환,강점순,이용재,제병일,박영훈,Lee, Junewoo,Son, Beunggu,Choi, Youngwhan,Kang, Jumsoon,Lee, Youngjae,Je, Byoung Il,Park, Younghoon 한국식물생명공학회 2018 식물생명공학회지 Vol.45 No.3

본 연구는 국내 육종 회사에서 개발된 수박(Citrullus lanatus L.) 우량 육성계통 20종을 대상으로 Genotyping-by-sequencing(GBS) 분석을 통해 품종식별, 순도검정, 그리고 마커이용여교잡(Marker-assisted backcross, MABC)용 SNP 세트를 개발하고자 수행되었다. GBS 분석 결과 총 1,100,000천개 raw read 중 77%가 수박 유전체에 mapping되었으며 평균 mapping region은 약 4,000 Kb로 2.3%의 genome coverage를 보였다. Filtering을 통해 평균 depth 31.57의 SNP 총 2,670개를 얻었으며, 20개 계통에 대한 이들의 Polymorphic information content(PIC) 값의 범위는 0.1 ~ 0.38 였다. 이 중 PIC 값이0.3이상이며 각 염색체 별로 5개씩 균등히 분포된 SNP 총 55개를 최종 선발하였다. 사용된 20개 계통의 유연관계분석을 위해 선발된 55개 SNP를 기반으로 한 주성분 분석(Principle component analysis, PCA) 결과 주성분 1 (52%)과 주성분 2 (11%)를 기준으로 4개의 그룹으로 분류 되었으며 각 계통 간 유전자형에 따른 뚜렷한 식별이 가능하였다. 계층적 군집화(Hierarchical clustering) 분석에서도PCA에서와 유사한 분류양상을 관찰할 수 있었다. 따라서 본 연구에서 개발된 SNP 세트는 적용 가능성이 검증된 20개 계통뿐 만 아니라 향후 다양한 수박 육종소재 및 품종에 대한 품종식별, F1 순도검정 및 MABC에 활용될 수 있으리라 기대된다. This study was conducted to develop an SNP set that can be useful for marker-assisted breeding (MAB) in watermelon (Citrullus. lanatus L) using Genotyping-by-sequencing (GBS) analysis of 20 commercial elite watermelon inbreds. The result of GBS showed that 77% of approximately 1.1 billion raw reads were mapped on the watermelon genome with an average mapping region of about 4,000 Kb, which indicated genome coverage of 2.3%. After the filtering process, a total of 2,670 SNPs with an average depth of 31.57 and the PIC (Polymorphic Information Content) value of 0.1~0.38 for 20 elite inbreds were obtained. Among those SNPs, 55 SNPs (5 SNPs per chromosome that are equally distributed on each chromosome) were selected. For the understanding genetic relationship of 20 elite inbreds, PCA (Principal Component Analysis) was carried out with 55 SNPs, which resulted in the classification of inbreds into 4 groups based on PC1 (52%) and PC2 (11%), thus causing differentiation between the inbreds. A similar classification pattern for PCA was observed from hierarchical clustering analysis. The SNP set developed in this study has the potential for application to cultivar identification, F1 seed purity test, and marker-assisted backcross (MABC) not only for 20 elite inbreds but also for diverse resources for watermelon breeding.