Quantitative Trait Loci Mapping in <i>Brassica rapa</i> Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of <i>Brassica</i> Species

Li, Xiaonan,Ramchiary, Nirala,Dhandapani, Vignesh,Choi, Su Ryun,Hur, Yoonkang,Nou, Ill-Sup,Yoon, Moo Kyoung,Lim, Yong Pyo Oxford University Press 2013 DNA research Vol.20 No.1

<P><I>Brassica rapa</I> is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in <I>B. rapa</I> and comparative map alignment between <I>B. rapa</I>, <I>B. napus</I>, <I>B. juncea</I>, and <I>Arabidopsis thaliana</I> to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the <I>B. rapa</I> genome. Through synteny analysis with <I>A. thaliana</I>, <I>B. rapa</I> candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of <I>B. rapa</I>, <I>B. juncea</I>, and <I>B. napus</I>. The information of the identified candidate genes could be used for breeding <I>B. rapa</I> and other related <I>Brassica</I> species.</P>

Genome-wide identification of NBS-encoding resistance genes in <i>Brassica rapa</i>

Mun, Jeong-Hwan,Yu, Hee-Ju,Park, Soomin,Park, Beom-Seok Springer-Verlag 2009 Molecular genetics and genomics Vol.282 No.6

<P>Nucleotide-binding site (NBS)-encoding resistance genes are key plant disease-resistance genes and are abundant in plant genomes, comprising up to 2% of all genes. The availability of genome sequences from several plant models enables the identification and cloning of NBS-encoding genes from closely related species based on a comparative genomics approach. In this study, we used the genome sequence of <I>Brassica rapa</I> to identify NBS-encoding genes in the <I>Brassica</I> genome. We identified 92 non-redundant NBS-encoding genes [30 CC-NBS-LRR (CNL) and 62 TIR-NBS-LRR (TNL) genes] in approximately 100 Mbp of <I>B. rapa</I> euchromatic genome sequence. Despite the fact that <I>B. rapa</I> has a significantly larger genome than <I>Arabidopsis thaliana</I> due to a recent whole genome triplication event after speciation, <I>B. rapa</I> contains relatively small number of NBS-encoding genes compared to <I>A. thaliana</I>, presumably because of deletion of redundant genes related to genome diploidization. Phylogenetic and evolutionary analyses suggest that relatively higher relaxation of selective constraints on the TNL group after the old duplication event resulted in greater accumulation of TNLs than CNLs in both <I>Arabidopsis</I> and <I>Brassica</I> genomes. Recent tandem duplication and ectopic deletion are likely to have played a role in the generation of novel <I>Brassica</I> lineage-specific resistance genes.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s00438-009-0492-0) contains supplementary material, which is available to authorized users.</P>

Development and linkage mapping of unigene-derived microsatellite markers in <i>Brassica rapa</i> L.

Ge, Yu,Ramchiary, Nirala,Wang, Tao,Liang, Cui,Wang, Na,Wang, Zhe,Choi, Su-Ryun,Lim, Yong Pyo,Piao, Zhong Yun Japanese Society of Breeding 2011 Breeding science Vol.61 No.2

<P><I>Brassica rapa</I> plants are highly important as vegetables, sources of oilseeds and fodder crop. Here, we developed 450 unigene derived microsatellite (UGMS) markers in <I>B. rapa</I> using unigenes downloaded from the National Center for Biotechnology Information database. Of the 450 UGMS primer pairs, 428 (95.1%) produced repeatable and reliable amplifications of expected size in at least one parental line of <I>B. rapa</I>, and 70 UGMS markers gave 72 polymorphic loci between the two contrasting parental lines. Cross-species transferability analysis of these 70 polymorphic UGMS markers in five other cultivated <I>Brassica</I> species showed varying transferability rates ranging from 82.9% in <I>B. nigra</I> to 97.1% in <I>B. juncea</I> and <I>B. napus</I>, and overall 53 UGMS markers amplified targets in all five species. The <I>B. rapa</I> linkage map was constructed using the 72 UGMS polymorphic loci and 154 previously developed SSRs. The newly developed UGMS markers and linkage map in this study would help in future studies to better understand the organization and evolution of <I>Brassica</I> genomes with respect to unigenes, in addition to mapping, tagging and cloning of economically important trait QTL/gene(s) and marker-assisted breeding in <I>Brassica</I> crops.</P>

속성배추(Rapid-cycling Brassica rapa)를 활용한 초등학생용 자유탐구 프로그램의 개발 및 적용 효과

박미경 ( Park Mi Gyeong ),류진아 ( Ryu Jin A ),김성하 ( Kim Sung Ha ) 서울敎育大學校 初等敎育硏究所 2016 한국초등교육 Vol.27 No.4

이 연구에서 개발된 자유탐구 프로그램은 속성배추(Rapid-cycling Brassica rapa)를 소재로 하여 총 7차시의 학습내용이 들어있는 교사용 지도서 및 학생용 학습지, 속성배추 생장장치, 속성배추의 관찰일지로 구성되어 있으며 학생들의 결과물을 평가할 수 있는 평가틀을 포함하고 있다. 개발된 자유탐구 프로그램은 울산광역시 소재 S 초등학교 4학년 학생들에게 적용하였으며, 효과를 분석하기 위해 과학탐구능력검사와 과학에 관련된 정의적 특성 검사를 실시하였고 학생들의 결과물 평가를 바탕으로 면담을 통하여 정성적 분석을 실시하였다. 개발된 프로그램의 적용 결과, 학생들의 과학탐구능력에 유의미한 향상을 보였고 기초탐구기능의 분류 영역과 통합탐구기능의 변인통제, 가설설정, 일반화 영역이 유의미하게 향상되었다. 과학에 관련된 정의적 특성 검사 결과 유의미한 향상을 보이지 않았으나 과학 수업의 즐거움 영역에서는 낮은 수준의 유의미한 향상을 보였다. 개발된 평가틀에 근거하여 학생 결과물을 평가한 결과 학생들은 탐구 주제선정과 실험 설계에서는 높은 평가를 받았으나 실험 결과를 바탕으로 하여 결론을 도출하는 능력과 자료를 해석하고 변환하는 능력은 부족한 것으로 나타났다. 학생들의 면담 분석 결과, 자기 주도적으로 탐구 활동을 수행하는 학생들의 과학에 관련된 정의적 특성이 긍정적으로 나타났으며, 내용 이해에 어려움이 없는 학생들의 과학탐구능력 향상의 폭이 그렇지 않은 학생들에 비해 크게 나타났으며 수업의 내용을 이해하기 어려웠고 탐구 활동에 어려움을 느낀 학생들의 과학에 관련된 정의적 특성은 크게 향상되지 않았다. This study was intended to develop the open inquiry program and to apply to enhance students` science inquiry skills and the affective characteristics related with science. Developed program was composed of the teacher`s manual containing a total of 7 class hours of teaching contents, student study book, growth chamber for Rapid-cycling Brassica rapa, and the observation log for Rapid-cycling Brassica rapa. It also contained an assessment tool to evaluate students` products. Developed open inquiry program was applied to the fourth grader of S elementary school located in Ulsan. It was found that the students` science inquiry ability was significantly enhanced, and classification domain of basic inquiry skill, and variable control, establishment of hypotheses, generalization domain of integrated inquiry skill were significantly enhanced. Regarding a result of test of affective characteristics related to science, there was no significant enhancement but in the pleasure domain of science class, a low level of significant enhancement was shown. Regarding students` products, it was found that the students were evaluated highly in the selection of inquiry themes and experiment design, but they lacked in the ability to draw a conclusion based on the results of experiments and the ability to interpret and convert the data. Students` responses to the developed open inquiry program were positive. By analyzing the interviews with the students, the attitude towards science of the self-directed students was found to be positive, and the level of enhancement of science inquiry ability of the students who did not have difficulties in understanding the contents in class was found to be greater than that of the students who had difficulties. Affective characteristics related with science of the students who found it difficult to understand the contents in class and had difficulty in inquiry activity were not enhanced much.

Transcriptome Analysis in Brassica rapa under the Abiotic Stresses Using Brassica 24K Oligo Microarray

이상춘,임명호,김진아,이수인,김정선,진미나,권수진,문정환,Yeon-Ki Kim,Hyun Uk Kim,허윤강,박범석 한국분자세포생물학회 2008 Molecules and cells Vol.26 No.6

Genome wide transcription analysis in response to stresses is essential to provide the basis of effective engineering strategies to improve stress tolerance in crop plants. In order to perform transcriptome analysis in Brassica rapa, we constructed a B. rapa oligo microarray, KBGP-24K, using sequence information from approximately 24,000 unigenes and analyzed cold (4˚C), salt (250 mM NaCl), and drought (air-dry) treated B. rapa plants. Among the B. rapa unigenes represented on the microarray, 417 (1.7%), 202 (0.8%), and 738 (3.1%) were identified as responsive genes that were differently expressed 5-fold or more at least once during a 48-h treatment with cold, salt, and drought, respectively. These results were confirmed by RT-PCR analysis. In the abiotic stress responsive genes identified, we found 56 transcription factor genes and 60 commonly responsive genes. It suggests that various transcriptional regulatory mechanisms and common signaling pathway are working together under the abiotic stresses in B. rapa. In conclusion, our new developed 24K oligo microarray will be a useful tool for transcriptome profiling and this work will provide valuable insight in the response to abiotic stress in B. rapa.

국내 배추와 중국 유래 청경채의 영양성분 비교

간치맥(Ganchimeg Gantumar),조만현(Man Hyun Jo),다바잘갈(Davaajargal Igori),함인기(In Ki Ham),이은모(Eun Mo Lee),이왕희(Wang-Hee Lee),임용표(Yongpyo Lim),안길환(Gilhwan An),박종태(Jong-Tae Park) 한국식품영양과학회 2013 한국식품영양과학회지 Vol.42 No.9

본 연구는 중국유래 14 품종 청경채의 영양적 특성을 평가하고자 수행되었다. 14종의 신규 청경채(Brassica rapa L.ssp. chinensis)를 대표적인 국산 배추(Brassica rapa L.ssp. pekinensis) 4 품종과 함께 2008년 충남 예산에서 재배하여 수확한 후 녹색 부위와 백색 부위로 나누어 부위 별 각종 영양 성분 분석을 수행하였다. 청경채의 수분 및 회분함량은 배추에 비교하여 유의적 차이가 없었으나 수분은 백색 부위에서, 회분은 녹색 부위에서 높게 나타났다. 전체적인 무기염류 함량은 배추에 비하여 청경채가 높은 것으로 측정되었는데 특히 녹색 부위의 함유량이 유의적으로 높은 것으로 드러났다. 특히 현대인의 건강에 매우 중요한 Ca과 Mg의 함유량은 청경채(Ca녹색: 2.57, Ca백색: 2.04; Mg녹색: 0.422, Mg백색: 0.301 mg/g 신선물 기준)가 배추(Ca녹색:0.805, Ca백색: 0.477; Mg녹색: 0.244, Mg백색: 0.101 mg/g신선물 기준)에 비하여 매우 높았다. 환원당의 함량은 청경채와 배추가 유사한 값을 나타내었고 색에 따른 유의적 차이도 없었다. 펙틴은 부위에 따른 차이는 있으나 청경채에서 그 함량이 높게 나타났고, 식물 조직의 경도에 영향이 큰 셀룰로오스의 함량은 청경채가 약 4배 이상 배추보다 높았다. 비타민 C와 E 함량은 청경채와 배추가 유사한 것으로 측정되었다. 위와 같이 청경채는 영양적으로 매우 우수하여 소비자들에게 권장할 만한 매일 섭취해야 할 주요 채소작물의 하나로 손색이 없음을 알 수 있었다. 또한 청경채는 국내배추의 품질 향상을 위한 육종 소재로서도 활용가치가 높을 것으로 사료된다. The nutritional components of 14 new cultivars of pak choi (Brassica rapa L. ssp. chinensis) from China were analyzed and compared with 4 cultivars of Chinese cabbage (Brassica rapa L. ssp. pekinensis) popular in Korea. Leaves were separated into green parts (GP) and white parts (WP) for the analyses. The moisture and ash content in the 14 new cultivars of pak choi were not significantly different from the currently popular cultivars of Chinese cabbage. In addition, the levels of vitamin C and E were very similar between the two kinds of Brassica rapa. In contrast, the overall mineral content was higher in the new pak choi cultivars. Specifically, minerals important for human health, calcium and magnesium, were significantly greater in pak choi cultivars (calcium GP 2.57, WP 2.04; magnesium GP 0.422, WP 0.301 mg/g fresh weight) compared to currently popular cultivars (calcium GP 0.805, WP 0.477; magnesium GP 0.244, WP 0.101 mg/g fresh weight). Although the content of reducing sugars was similar, cellulose content (which correlates with the hardness of plant tissue) was four times higher in the new pak choi cultivars compared to currently popular cultivars. These results demonstrate that the new pak choi cultivars have superb nutritional benefits for human health and could be a good food source as a daily staple vegetable.

한국 배추 기능유전체 연구의 현황

유재경,박지현,박영두 한국식물생명공학회 2010 JOURNAL OF PLANT BIOTECHNOLOGY Vol.37 No.2

The purpose of functional genome research is to identify biological function of useful gene and to give an agricultural value in plant biotechnology. Brassica rapa is an economic crop which recorded 1,000 billion won of domestic market and 100 million dollar of exports and it produces 2.5 million ton in 50,000 ha as a major ingredient of representative Korean food, Kimchi. Furthermore, it is very important crop economically and commercially because Korea is major seed exporter. The fact that Multinational Brassica Genome Project (MBGP) was launched and Arabidopsis thaliana, affiliated to same genus with B. rapa, has been fully sequenced activated functional genome research of B. rapa. Besides new technologies related to gene function analysis keep developing, many results are reporting every year by international research including Korea. This review paper introduces development of Chinese cabbage mutants which is a first step in functional genome research, variant phenotypes of mutants, flanking DNA analysis in B. rapa genome, gene identification, gene analysis using microarray,and representative researches. 식물생명공학 분야에 있어 기능유전체 연구는 식물체가 지니고 있는 유용한 유전자의 생물학적 기능을 밝히고, 농업적 유용성을 확보하여 가치를 부여하는 것을 목적으로 한다. 배추는 우리나라 대표 음식 중의 하나인 김치의 주원료이며 식품영양학적으로도 우수성이 인정되었고 약 5만 ha에서 연간 약 250만 톤이 생산되어 1조원의 국내 시장 및 1억 달러의 수출액을 기록하는 경제작물이다. 그리고 우리나라가 주요 종자수출국의 위치를차지하고 있어 재배에 있어서나 경제적, 상업적으로 그 중요성이 매우 높은 작물이다. Multinational Brassica Genome Project (MBGP)가 시작되고 배추와 같은 속에 속하는 애기장대의 전 염기서열 분석이 완료됨으로써 배추의 기능유전체 연구가 더욱 활발해 질 수 있는 환경이 마련되었다. 또한 유전자 기능 분석 연구에 필요한 새로운 기술들이 계속 개발되고 있으며 우리나라를 선두로 하여 국제적으로도 연구가 이루어져 해마다 많은 성과들이 보고되고 있다. 본 총설에서는 기능유전체 연구의 첫 단계인 배추 돌연변이체 유기 방법을 시작으로 다양한 표현형의 돌연변이체를 소개하고 이 돌연변이 배추의 게놈내 flanking DNA 분석 및 유전자 동정, microarray를 이용한 유전자 분석, 대표적인 기능유전체 연구 사례를 제시하고자 하였다.

배추 종간 잡종의 소포자배양에 의한 Double haploid 집단의 플라보노이드 함량 분석

서미숙,원소윤,강상호,김정선 한국식물생명공학회 2017 JOURNAL OF PLANT BIOTECHNOLOGY Vol.44 No.1

One of the most important species, Brassica rapa encompasses a variety of commercial vegetables, such as the Chinese cabbage, pak choi and oilseed crops. The LP08 of yellow sarson (Brassica rapa ssp, tricolaris) have a distinct morphology, with yellow seed color and a unique tetralocular ovary. LP21 of pak choi (Brassica rapa ssp, chinensis) have a dark brown seed color and bilocular ovary. In this study, we generated double haploid plants by crossing the LP08 (maternal variety) and LP21 (paternal variety), using microspore culture. A total of 66 accessions with various morphological characteristics were used for content analysis of flavonoids. The three flavonoids, quercetin, naringenin and kaempferol, showed differing contents in the two crossing parents. The Chinese cabbage type 'Chiifu' was used as the control. The highest accumulation of total flavonoids was observed in LP08. The lowest mean total flavonoids were found in 'Chiifu'. Among the 66 DH accessions, the quercetin contents of 18 accessions showed higher content than LP08. Kaempferol content was also high, and was found to be 79.7% of the total flavonoid content. Naringenin content was low at 2.8%, and was not detected in 22 accessions. Interestingly, the quercetin content positively correlated with the kaempferol content. These results can be used to identify genetic locus and genes related to useful traits. Phenotypic analysis of 66 DH accessions can further be used for natural selection of good breeding materials in B. rapa.

한국 배추 기능유전체 연구의 현황

유재경,박지현,박영두,Yu, Jae-Gyeong,Park, Ji-Hyun,Park, Young-Doo 한국식물생명공학회 2010 식물생명공학회지 Vol.37 No.2

식물생명공학 분야에 있어 기능유전체 연구는 식물체가 지니고 있는 유용한 유전자의 생물학적 기능을 밝히고, 농업적 유용성을 확보하여 가치를 부여하는 것을 목적으로 한다. 배추는 우리나라 대표 음식 중의 하나인 김치의 주원료이며 식품영양학적으로도 우수성이 인정되었고 약 5만 ha에서 연간 약 250만 톤이 생산되어 1조원의 국내 시장 및 1억 달러의 수출액을 기록하는 경제작물이다. 그리고 우리나라가 주요 종자수출국의 위치를 차지하고 있어 재배에 있어서나 경제적, 상업적으로 그 중요성이 매우 높은 작물이다. Multinational Brassica Genome Project (MBGP)가 시작되고 배추와 같은 속에 속하는 애기장대의 전 염기서열 분석이 완료됨으로써 배추의 기능유전체 연구가 더욱 활발해 질 수 있는 환경이 마련되었다. 또한 유전자 기능 분석 연구에 필요한 새로운 기술들이 계속 개발되고 있으며 우리나라를 선두로 하여 국제적으로도 연구가 이루어져 해마다 많은 성과들이 보고되고 있다. 본 총설에서는 기능유전체 연구의 첫 단계인 배추 돌연변이체 유기 방법을 시작으로 다양한 표현형의 돌연변이체를 소개하고 이 돌연변이 배추의 게놈내 flanking DNA 분석 및 유전자 동정, microarray를 이용한 유전자 분석, 대표적인 기능유전체 연구 사례를 제시하고자 하였다. The purpose of functional genome research is to identify biological function of useful gene and to give an agricultural value in plant biotechnology. Brassica rapa is an economic crop which recorded 1,000 billion won of domestic market and 100 million dollar of exports and it produces 2.5 million ton in 50,000 ha as a major ingredient of representative Korean food, Kimchi. Furthermore, it is very important crop economically and commercially because Korea is major seed exporter. The fact that Multinational Brassica Genome Project (MBGP) was launched and Arabidopsis thaliana, affiliated to same genus with B. rapa, has been fully sequenced activated functional genome research of B. rapa. Besides new technologies related to gene function analysis keep developing, many results are reporting every year by international research including Korea. This review paper introduces development of Chinese cabbage mutants which is a first step in functional genome research, variant phenotypes of mutants, flanking DNA analysis in B. rapa genome, gene identification, gene analysis using microarray, and representative researches.

국내 재배포장에서 수집한 뿌리혹병균(Plasmodiophora brassicae) 균주들에 대한 배추 품종들의 저항성 반응

조수정(Su-Jung Jo),심선아(Sun-Ah Shim),장경수(Kyoung Soo Jang),최용호(Yong Ho Choi),김진철(Jin-Cheol Kim),최경자(Gyung Ja Choi) 한국원예학회 2011 원예과학기술지 Vol.29 No.6

Plasmodiphora brassicae에 의해 발생하는 뿌리혹병은 전세계 십자화과 작물에 많은 피해를 주고 있다. 본 연구에서는 우리나라 여러 지역으로부터 10개의 뿌리혹병균을 채집하여 Williams 판별품종을 이용하여 레이스를 검정하고, 이들 균주에 대한 뿌리혹병 저항성(CR) 배추 품종 25개의 저항성 정도를 조사하였다. 실험한 뿌리혹병균 중 HS와 YC균주는 레이스 2, HN1과 HN2는 레이스 4, DJ와 SS 균주는 레이스 5 그리고 GS, GN, JS 및 PC 균주는 레이스 9로 동정되었다. 시판 중인 25개 CR 배추 품종의 이들 균주에 대한 저항성을 조사한 결과, 각 균주에 대하여 25개 CR 품종은 거의 동일하게 반응하였으며, 뿌리혹병균의 레이스와 관계 없이 두 종류의 반응을 나타냈다. DJ, GS, GN, HS 및 JS 등의 5개 균주에는 저항성 반응을 나타내었으며, SS, HN1,HM2, PC 및 YC 균주에 의해서는 감수성 품종과 동일한 정도의 뿌리혹병 발생을 보였다. 이상의 결과로부터 우리나라 포장에는 CR 배추를 감염하는 뿌리혹병균이 이미 존재하고 있으며, 실험한 CR 품종들의 저항성 유전자원은 매우 단순하다고 생각되었다. 또 동일한 레이스의 뿌리혹병균도 CR 품종에 다른 반응을 나타내므로 CR 배추 품종의 저항성 유전자는 Williams 판별 기주의 저항성 유전자와 다르다고 추정된다. Clubroot disease caused by Plasmodiophora brassicae, induces damage to cruciferous vegetables worldwide. For control of the disease, many CR (clubroot resistant) F1 hybrid cultivars of Chinese cabbage have been bred and released in Korea. In this study, we determined the race of 10 field isolates of P. brassicae collected from ten regions in Korea using Williams" differential varieties and investigated the degree of resistance of 25 commercial CR cultivars of Chinese cabbage to the isolates. The clubroot pathogens were assigned into two (HS and YC), two (HN1 and HN2), two (DJ and SS) and four (GS, GN, JS, and PC) isolates for race 2, race 4, race 5, race 9, respectively. All CR cultivars showed similar response, resistant or susceptible, to each isolate and the P. brassicae isolates were divided into two groups. Among them, the DJ, GS, GN, HS, and JS isolates could not infect the CR cultivars. In contrast, the SS, HN1, HN2, PC, and YC isolates caused severe clubroot disease on the CR cultivars li ke susceptible cultivars. Even though they belong to the same race, the CR cultivars showed a different response to the pathogens. The results suggest that the breakdown of CR in Chinese cabbage has already occurred in cultivation areas of Korea and resistance source introduced in CR cultivars may be very limited. In addition, it is likely that resistance genes of Williams"differential varieties to P. brassicae are different from the gene of CR cultivars of Chinese cabbage used in the study.