Exploring Genetic Variation Between Hallabong and Suneat, Clade by Whole Genome Re-sequencing

Kiwoung Yang,Senthil Kumar Thamilarasan,Sathishkumar Natarajan,Hoyteak Kim,Mi-Young Chung,Ill-Sup Nou 한국원예학회 2016 한국원예학회 학술발표요지 Vol.2016 No.5

Genetic mapping of anthocyanin biosynthetic genes in soybean seed coat.

Kiwoung Yang,Jung-Kyung Moon,Soon-Chun Jeong 한국작물학회 2007 한국작물학회 학술발표대회 논문집 Vol.2007 No.11

Proanthocyanidins and anthocyanins derived from the phenylpropanoid pathway most likely play a protective function from pathogens and UV light exposure within the plant and, in addition, act as signal molecules in plant-microbe interactions. The metabolites are now attracting attention because of the medicinal and nutritional values due to their antioxidant properties and flavors. Three independent loci (I, R, and T) control pigmentation of the seed coats determined by proanthocyanidins and anthocyanins in soybean (Glycine max). The I locus controls distribution of anthocyanin and proanthocyanidin pigments, which in its dominant form exhibits homology-dependent gene silencing leading to a yellowish seed coat. The R and T genes determine the anthocyanin and proanthocyanidin products and specific seed coat color such as black, imperfect black, brown, or buff. The I and T loci have been cloned. The objectives of this study were to develop PCR-based molecular markers cosegregating with the genetic loci controlling the biosynthesis of these interesting metabolites using public soybean EST and genomic sequence data and is to develop molecular markers to establish a marker-assisted selection scheme for these natural products-related traits. A population of 112 F11 recombinant inbred lines generated by an interspecific cross between a Glycine max line 'Hwangkeumkong' and a G. soja Siebold & Zucc. line ‘IT182932' was used to construct a frame map consisting of 20 soybean linkage groups. The frame map contains over 300 SSR, RAPD and transposon markers. PCR-based molecular markers cosegregating with the I and T loci that control pigmentation of the seed coats determined by secondary metabolites derived from the flavonoid pathway including anthocyanins and proanthocyanidins in soybean have been developed. We have developed three SSR cosegregating with the I locus and one codominant STS and one SNP markers cosegregating with the T locus. So far, we have developed SSR, SNP, and STS markers cosegregating with the I locus and with the T locus. Work is in progress to develop markers cosegregating with other genetic loci. The markers will facilitate markers-assisted selection of seed coat colors in molecular breeding programs.

Identification of various complete circle form of mitochondrial genome sequences using WGS in Brassica oleracea

Kiwoung Yang,Nasar Uddin Ahmed,Jonghoon Lee,Junki Lee,Ill-Sup Nou,Tae-Jin Yang 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

Mitochondria are essential organelles of eukaryotic cells and plant cells contain varying numbers of mitochondrial genome sequences. Sizes and shapes of mitochondria differ within a tissue or in the same cells. Previously sequenced complete mitochondrial genome (NC_016118) of Brassica oleracea size was 360,271 bp, where segmental duplication (repeat block) was 141,800 bp. In this study, we resequenced this whole mitochondrial genome by using WGS (whole genome sequencing) and assembled organelles genome method (unpublished). Newly sequenced mitochondrial genome length was 219,975 bp and circle form. A new sequence segment of approximately 4,800 bp was obtained compared to the previous genome sequence without any large repeat block. Newly obtained mitochondria genome sequence was compared with recently reported mitochondria genome sequences of various species (B. oleracea, B. juncea, B. rapa, B. napus and B. carinata) and subspecies (cabbage, cauliflower, brussels sprouts, kohlrabi, broccoli and kale) by PCR using primers specifying different region of genome sequences. PCR analysis results have also confirmed the variation between previous and newly sequenced mitochondrial genome circles form. Thus, the results suggest new B. oleracea mitotype, including evolutionary events such as inheritance, rearrangement, genome compaction, and diversity

Specific DNA Markers Selection Using Miniature Inverted-Repeat Transposable Element (MITE)Families in Brassica Juncea

Kiwoung Yang,Go-eun Yi,Arif Hasan Khan Robin,Jongin Park,Ill-Sup Nou 한국원예학회 2015 한국원예학회 학술발표요지 Vol.2015 No.5

Development of Molecular Markers for Low Raffinose and Stachyose in Korean Soybean Cultivars

( Kiwoung Yang ),( Jong Min Ko ),( Tae Joung Ha ),( Yeong Hoon Lee ),( In Youl Baek ),( Tae Jin Yang ),( Ill Sup Nou ) 한국육종학회 2014 Plant Breeding and Biotechnology Vol.2 No.2

A novel allele of the putative soybean raffinose synthase gene, RS2, was discovered in PI200508 that is associated with the low raffinose and stachyose content. Soybean line PI200508 was identified as expressing reduced levels of raffinose and stachyose as well as elevated levels of sucrose. The RS2 mutant gene shows three base pairs InDel with the normal gene. Based on InDel region we developed novel co-dominant and dominant marker. The aim of this study was to develop Korean soybean cultivars, Daewon, Cheongja, and Danmiput, containing low levels of raffinose and stachyose. A specific markers assay for the PI200508 RS2 allele was developed to allow direct selection of the low raffinose and stachyose phenotype. Our findings highlight the efficiency of allele-specific markers in selection, which is evident in the matching genotype and results of the HPLC in the F2 generations of Daewon×PI200508 population.

Identification of Turnip Mosaic Virus Resistant Gene in Chinese Cabbage (Brassica rapa L.)

Kiwoung Yang,Go-Eun Yi,Arif Hasan Khan Robin,Mi-Young Chung,Ill-Sup Nou 한국원예학회 2015 한국원예학회 학술발표요지 Vol.2015 No.10

갓 (Brassica juncea) 품종구분을 위한 ITS 영역 및 MITE Family 정보를 이용한 분자표지 개발

양기웅(Kiwoung Yang),이고은(Go-eun Yi),아리프 하산 칸 로빈(Arif Hasan Khan Robin),정남희(Namhee Jeong),이용혁(Yong-Hyuk Lee),박종인(Jongin Park),김회택(Hoyteak Kim),정미영(Mi-Young Chung),노일섭(Ill-Sup Nou) 한국원예학회 2016 원예과학기술지 Vol.34 No.2

갓(Brassica juncea; 2n = 4x = 36, AABB genome, 1,068Mb)은 U’s triangle의 배추와 흑겨자 사이의 복이배체 작물로 구분한다. 본 연구는 갓 15 품종의 ribosomal DNA ITS 영역과 MITE를 이용하여 갓의 유연관계 및 품종구분 분자표지를 확인하였다. Ribosomal DNA ITS 영역은 종 및 품종의 유연관계를 알아보는 연구로 많이 사용되고 있어서, 이를 이용하여 갓 15 품종의 유연관계를 알아보았다. 또한, MITE는 매우 많은 copy 수를 가지고 있고, 유전적으로 안정적이기 때문에 유전체 및 진화연구에 매우 적합한 재료이다. MITE를 이용한 갓의 품종구분 분자표지를 확인하기 위해 MITE super-families 중 Stowaway(BraSto) 관련 70점, Tourist(BraTo) 관련 79점, hAT(BrahAT) 관련 6점, Mutator(BraMu) 관련 5점으로 품종구분 표지를 알아보았다. 총 160점의 분자표지 중 32점이 갓 15 품종에서 뚜렷한 다형성을 보였다. 특히, 흑갓은 표현형뿐만 아니라 유전자형도 매우 다르게 나타났다. 또한 8점의 MITE 분자표지를 활용하여 47점의 유전자원에서 다형성 및 품종구분 표지로의 활용 가능성을 확인하였다. 이러한 다형성 표지들은 갓의 품종구분 및 품종 보호에 매우 유용하게 사용할 수 있을 것이라 기대한다. Brassica juncea (2n = 4x = 36, AABB genome, 1,068 Mb) is a U’s triangle species and an amphidiploid derivative of B. rapa and B. nigra. Fifteen varieties were used to study the ITS (internal transcribed spacer) regions of ribosomal DNA and MITEs (miniature inverted-repeat transposable elements) with a view of developing specific molecular markers. ITSs and MITEs are an excellent resource for developing DNA markers for genomics and evolutionary studies because most of them are stably inherited and present in high copy numbers. The ITS (ITS1 and ITS2) sequence was compared with the consensus sequence of B. rapa and B. nigra. Variation in ITS1 created two separate groups among 15 varieties, with 10 varieties in one group and 5 in the other. Phylogenetic analysis revealed two major clusters for those 10 and 5 varieties. Among the 160 different MITE primers used to evaluate the selected 15 varieties of B. juncea, 70 were related to the Stowaway, 79 to the Tourist, 6 to the hAT, and 5 to the Mutator super-families of MITEs. Of 160 markers examined, 32 were found to be polymorphic when fifteen different varieties of B. juncea were evaluated. The variety ‘Blackgat’ was different from the other mustard varieties with respect to both phenotype and genotype. The diversity of 47 additional accessions could be verified using eight selected molecular markers derived from MITE family sequences. The polymorphic markers identified in this study can be used for varietal classification, variety protection, and other breeding purposes.

콩 불마름병 저항성 및 감수성 품종을 이용한 rxp 유전자 근접 분자표지 개발

양기웅(Kiwoung Yang),이영훈(Yeong Hoon Lee),고종민(Jong Min Ko),전명기(Myeong Gi Jeon),이병원(Byong Won Lee),김현태(Hyun Tae Kim),윤홍태(Hong Tae Yun),정찬식(Chan Sik Jung),백인열(In Youl Baek) 한국육종학회 2011 한국육종학회지 Vol.43 No.4

본 연구는 최근 콩 재배에서 심각한 병으로 대두된 콩 불마름병에 대한 저항성 유전자인 rxp 근접분자표지를 개발하고 자수행하였다. 콩 불마름병은 국내에서 전국적으로 발생하는 심각한 세균병으로 이에 관련하여 세균병 접종을 이용한 저 항성 품종과 감수성 품종에 대한 연구가 많이 진행되고 있지 만 정확한 유전자의 염기서열이 밝혀져 있지 않고 있다. 본 연구는 콩 불마름병에 저항성 품종 8개체와 감수성 품종 8개체를 이용하여 rxp 유전자 근접분자표지를 확인하기 위하여 수행하였다. 콩 불마름병 저항성 유전자로 알려진 rxp 유전자는 chromosome 17의 Satt486과 Satt372 사이에 있다고 알려져 있으며, 최근 연구결과로 chromosome 17의 7.27-7.30 Mbp 사이에 있다. 연구진은 chromosome 17의 6.6-7.3 Mbp 사이 에 random으로 분자표지를 제작하여 저항성과 감수성 품종 에서 다형성을 알아보았다. 실험결과로 콩 불마름병관련 근접 분자표지 3점을 개발하였고, Rxp17-700 분자표지는 흥미로운 rxp 근접분자표지임을 확인하였다. 이러한 콩 불마름병 저항성관련 근접분자표지는 앞으로 저항성 품종을 선발하는데 도움이 될 것이다. Bacterial pustule (BP) is a leaf disease of soybean that is most common in Korea. Inoculation of 8ra, pathogen strain, to resistant and susceptible cultivars for finding the BP resistance gene (rxp) was much tried but the sequence of the exact gene is not found. This research performed in order to confirm the rxp gene near molecular marker by using the resistant and susceptible cultivars. Soybean BP resistance gene which related to region of near molecular marker could select the resistant cultivar. For the near molecular marker of rxp, reference genomics data available at sequenced Phytozome was used for designing molecular markers. The rxp was mapped between Satt372 and Satt486 on chromosome 17. According to previous study, rxp released in find mapping 7.2 Mbp to 7.3 Mbp on chromosome 17. In this study, we developed 3 random markers near from 6.6 Mbp to 7.3 Mbp on chromosome 17 identified to increase the genetic resolution of the rxp gene region using resistant and susceptible cultivars. Particularly, Rxp17-700 marker was mostly coincided resistance and susceptible genotype to rxp. This result suggests that Rxp17-700 marker will be more tightly linked to rxp gene.

Modifying <i>Myxococcus xanthus</i> protoporphyrinogen oxidase to plant codon usage and high level of oxyfluorfen resistance in transgenic rice

Yang, Kiwoung,Jung, Sunyo,Lee, Yonghyuk,Back, Kyoungwhan Academic Press 2006 Pesticide biochemistry and physiology Vol.86 No.3

<P><B>Abstract</B></P><P>Protoporphyrinogen oxidase (Protox) of <I>Myxococcus xanthus</I> (<I>Mx</I> Protox) is a 49-kDa membrane protein that catalyzes conversion of protoporphyrinogen IX (Protogen IX) into protoporphyrin IX (Proto IX). Upon heterologous expression in transgenic rice plants, <I>Mx</I> Protox is dually targeted into plastids and mitochondria, increasing resistance against the herbicidal Protox inhibitor oxyfluorfen. Here, we describe the chemical synthesis of the <I>Mx</I> Protox gene by assembling several small synthetic DNA fragments derived by ligation-PCR. Codon usage in the resulting 1416-bp gene was modified to correspond to that of the <I>Arabidopsis</I> Protox gene, a change that resulted in a decrease in G+C content from 71 to 49%. The modified <I>Mx</I> Protox gene was used to generate transgenic rice plants <I>via Agrobacterium</I>-mediated transformation. Integration, expression, and inheritance of the transgenes were demonstrated by Southern, Northern, and Western blot analyses. In plants transformed with the modified, low G+C-content <I>Mx</I> Protox gene, levels of Protox expression and enzyme activity were low compared to the levels observed for plants transformed with the native <I>Mx</I> Protox gene. Nonetheless, like the native gene, the modified gene conferred a high level of resistance to the herbicide oxyfluorfen in a seedling growth test.</P>

Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of <i>Brassica oleracea</i> L. var. <i>capitata</i>

Yang, Kiwoung,Robin, Arif Hasan Khan,Yi, Go-Eun,Lee, Jonghoon,Chung, Mi-Young,Yang, Tae-Jin,Nou, Ill-Sup MDPI 2015 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.16 No.12

<P>Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in <I>B. oleracea</I> var. <I>alboglabra</I>. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were quite similar in length. The 45S IGSs were found to follow Mendelian inheritance in a population of 15 F<SUB>1</SUB>s and their 30 inbred parental lines, which suggests that these sequences could be useful for development of new breeding tools. In addition, this study represents the first report of intra-specific (within subspecies) variation of the 45S IGS in <I>B. oleracea.</I></P>