[PA-0047] Newly developing cDNA-SSR markers and genetic diversity in Amaranth

Suyun Moon(Suyun Moon),Hyeran Shin(Hyeran Shin),Jong-Wook Chung(Jong-Wook Chung) 한국육종학회 2022 한국육종학회 공동학술발표집 Vol.2022 No.-

Development of HRM Markers for Discrimination of Pyogo (Lentinula edodes) Cultivars Sanjo 701 and Chamaram

Suyun Moon,Hojin Ryu 한국균학회 2022 韓國菌學會誌 Vol.50 No.3

Pyogo (Shiitake, Lentinula edodes) is one of the most important edible mushrooms because of its outstanding nutritive and medicinal value. In the registration and protection procedure for newly developed mushroom cultivars, the application of molecular markers that can supplement the morphological characteristic-based distinction has been strongly requested. Sanjo 701 and Chamaram, newly developed at the Federation Forest Mushroom Research Center of Korea, have been characterized as innovative cultivars suitable for customer demands because of their high yields and cultivation rates. However, no technical tools can protect the rights to these important cultivars. In this study, using comparative genomic information from 23 commercially available pyogo cultivars, we identified single nucleotide polymorphisms (SNPs) that accurately differentiated Sanjo701 and Chamaram from the other cultivars. We also developed high-resolution melting analysis (HRM)-based SNP markers that discriminate among the tested 23 pyogo cultivars. The developed SNP markers can be utilized for rapid, accurate identification of pyogo cultivars with low genetic diversity and to prevent cultivar contamination caused by illegally distributed inocula. In addition, these markers can serve as a crucial scientific basis for securing the right to conserve new cultivars in international markets.

Characterization of diverse pepper (Capsicum spp.) germplasm based on agro-morphological traits and phytochemical contents

Suyun Moon,Ho-cheol Ko,Nayoung Ro,SuKyeung Lee,Hyeonseok Oh,Bichsaem Kim,Bichsaem Kim,Gi-An Lee 한국육종학회 2023 한국육종학회 공동학술발표집 Vol.2023 No.-

Construction of a CRISPR/Cas9-Mediated Genome Editing System in Lentinula edodes

Moon, Suyun,An, Jee Young,Choi, Yeon-Jae,Oh, Youn-Lee,Ro, Hyeon-Su,Ryu, Hojin The Korean Society of Mycology 2021 韓國菌學會誌 Vol.49 No.6

CRISPR/Cas9 genome editing systems have been established in a broad range of eukaryotic species. Herein, we report the first method for genetic engineering in pyogo (shiitake) mushrooms (Lentinula edodes) using CRISPR/Cas9. For in vivo expression of guide RNAs (gRNAs) targeting the mating-type gene HD1 (LeA1), we identified an endogenous LeU6 promoter in the L. edodes genome. We constructed a plasmid containing the LeU6 and glyceraldehyde-3-phosphate dehydrogenase (LeGPD) promoters to express the Cas9 protein. Among the eight gRNAs we tested, three successfully disrupted the LeA1 locus. Although the CRISPR-Cas9-induced alleles did not affect mating with compatible monokaryotic strains, disruption of the transcription levels of the downstream genes of LeHD1 and LeHD2 was detected. Based on this result, we present the first report of a simple and powerful genetic manipulation tool using the CRISPR/Cas9 toolbox for the scientifically and industrially important edible mushroom, L. edodes.

Construction of a CRISPR/Cas9-Mediated Genome Editing System in Lentinula edodes

( Suyun Moon ),( Jee Young An ),( Yeon-jae Choi ),( Youn-lee Oh ),( Hyeon-su Ro ),( Hojin Ryu ) 한국균학회 2021 Mycobiology Vol.49 No.6

CRISPR/Cas9 genome editing systems have been established in a broad range of eukaryotic species. Herein, we report the first method for genetic engineering in pyogo (shiitake) mushrooms (Lentinula edodes) using CRISPR/Cas9. For in vivo expression of guide RNAs (gRNAs) targeting the mating-type gene HD1 (LeA1), we identified an endogenous LeU6 promoter in the L. edodes genome. We constructed a plasmid containing the LeU6 and glyceraldehyde-3-phosphate dehydrogenase (LeGPD) promoters to express the Cas9 protein. Among the eight gRNAs we tested, three successfully disrupted the LeA1 locus. Although the CRISPRCas9-induced alleles did not affect mating with compatible monokaryotic strains, disruption of the transcription levels of the downstream genes of LeHD1 and LeHD2 was detected. Based on this result, we present the first report of a simple and powerful genetic manipulation tool using the CRISPR/Cas9 toolbox for the scientifically and industrially important edible mushroom, L. edodes.

Development and Molecular Characterization of Novel Polymorphic Genomic DNA SSR Markers in Lentinula edodes

( Suyun Moon ),( Hwa-yong Lee ),( Donghwan Shim ),( Myungkil Kim ),( Kang-hyeon Ka ),( Rhim Ryoo ),( Han-gyu Ko ),( Chang-duck Koo ),( Jong-wook Chung ),( Hojin Ryu ) 한국균학회 2017 Mycobiology Vol.45 No.2

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L.edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering` method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

표고버섯 품종 산마루1호, 천장3호를 구분할 수 있는 CAPS Marker 개발

문수윤 ( Suyun Moon ),이화용 ( Hwa-yong Lee ),김명길 ( Myungkil Kim ),가강현 ( Kang-hyeon Ka ),고한규 ( Han Kyu Ko ),정종욱 ( Jong-wook Chung ),구창덕 ( Chang-duck Koo ),류호진 ( Hojin Ryu ) 한국균학회 2017 韓國菌學會誌 Vol.45 No.2

표고버섯은 주로 아시아 국가에서 재배되는 식용 버섯이다. 표고버섯은 최근 국내에서 신 품종의 개발이 활발히 이루어지고 있으며, 국내외적으로 품종의 보호가 중요해짐에 따라 표고의 품종을 구분할 수 있는 효율적인 마커 개발이 요구되고 있다. 본 연구에서는 산마루1호와 천장3호를 구분할 수 있는 CAPS (cleaved amplified polymorphic sequence) 마커를 개발 하였다. 이 연구에서 개발된 CAPS 마커는 단핵균주인 B17의 표준유전체 정보와 연구에 사용된 10개 균주의 resequencing 정보를 바탕으로 개발되었다. 산마루1호는 scaffold9번, 1630048의 염기서열 G가 T로 변한 SNP를 포함하여 PCR 후 제한효소 TspR I을, 천장3호는 scaffold13번, 920681의 염기서열 G가 A로 변한 single nucleotide polymorphism (SNP)를 포함하여 PCR 후, 제한효소 Xho I을 처리하였을 때 다른 균주들과 구분되었다. 따라서 이를 마커로 개발하였다. Lentinula edodes is an edible mushroom that is mainly cultivated in Asian countries. Recently, new cultivars of this mushroom have been developed in Korea; variety protection is very important, so the development of efficient molecular markers that can distinguish each variety is required. In this study, we developed cleaved amplified polymorphic sequence (CAPS) markers for the identification of L. edodes cultivars (Sanmaru 1ho and Chunjang 3ho). These markers were developed from whole genomic sequencing data from L. edodes monokaryon strain B17 and resequencing data from 10 dikaryon strains. A single nucleotide polymorphism changed in scaffold 9 POS 1630048 in Sanmaru 1ho(G→T), and in scaffold 13 POS 920681 in Chunjang 3ho (G→A). The restriction enzymes TspR I and Xho I distinguished Sanmaru 1ho and Chunjang 3ho, respectively, from other strains. Thus, we developed 2 CAPS markers for the identification of the L. edodes cultivars Sanmaru 1ho and Chunjang 3ho.

표고 품종 산백향과 설백향 구분을 위한 CAPS 마커 개발

문수윤 ( Suyun Moon ),홍창표 ( Chang Pyo Hong ),류호진 ( Hojin Ryu ),이화용 ( Hwa-yong Lee ) 한국균학회 2021 韓國菌學會誌 Vol.49 No.1

본 연구에서는 국내에 유통되고 있는 40개 표고 품종들로부터 산백향과 설백향의 구분이 가능한 CAPS 마커를 개발하였다. 제한효소 HhaⅠ과 HpyCH4Ⅳ를 이용한 밴드 패턴 분석을 통해 각각 산백향과 설백향을 다른 균주들과 구분하여 구별성을 확보할 수 있었다. 본 연구에서 개발된 CAPS 마커는 표고의 품종들 간에 유전적 다양성을 부여함으로써, 품종을 보호할 수 있는 분자생물학적 근거가 될 수 있다. 이로써 향후 유전자원에 대한 국가간 분쟁을 미연에 방지할 수 있을 것이다. Lentinula edodes (Berk.) Pegler, the most produced mushroom in the world, is an edible mushroom with very high nutritional and pharmacological value. Currently, interest in the protection of genetic resources is increasing worldwide, and securing the distinction between new cultivars is very important. Therefore, the development of efficient molecular markers that can discriminate between L. edodes cultivars is required. In this study, we developed cleaved amplified polymorphic sequence (CAPS) markers for the identification of L. edodes cultivars (Sanbaekhyang and Sulbaekhyang). These markers were developed from whole genome sequencing data from L. edodes monokaryon strain B17 and resequencing data from 40 cultivars. A nucleotide deletion existed in scaffold 19 POS 214449 in Sanbaekhyang (GT→G), and a single nucleotide polymorphism changed in scaffold 7 POS 215801 in Sulbaekhyang (G→A). The restriction enzymes HhaⅠ and HpyCH4Ⅳ distinguished Sanbaekhyang and Sulbaekhyang, respectively, from other cultivars. Thus, we developed two CAPS markers for the identification of the L. edodes cultivars Sanbaekhyang and Sulbaekhyang.

Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato

Lee, Jinsu,Shim, Donghwan,Moon, Suyun,Kim, Hyemin,Bae, Wonsil,Kim, Kyunghwan,Kim, Yang-Hoon,Rhee, Sung-Keun,Hong, Chang Pyo,Hong, Suk-Young,Lee, Ye-Jin,Sung, Jwakyung,Ryu, Hojin Elsevier 2018 Plant physiology and biochemistry Vol.127 No.-

<P><B>Abstract</B></P> <P>Brassinosteroids (BRs) are plant steroid hormones that play crucial roles in a range of growth and developmental processes. Although BR signal transduction and biosynthetic pathways have been well characterized in model plants, their biological roles in an important crop, tomato (<I>Solanum lycopersicum</I>), remain unknown. Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using physiological and transcriptomic approaches. The cultivated tomato showed higher tolerance to drought and osmotic stresses than the MT tomato. However, BR-defective phenotypes of MT, including plant growth and stomatal closure defects, were completely recovered by application of exogenous BR or complementation with a <I>SlDWARF</I> gene. Using genome-wide transcriptome analysis, 619 significantly differentially expressed genes (DEGs) were identified between WT and MT plants. Several DEGs were linked to known signaling networks, including those related to biotic/abiotic stress responses, lignification, cell wall development, and hormone responses. Consistent with the higher susceptibility of MT to drought stress, several gene sets involved in responses to drought and osmotic stress were differentially regulated between the WT and MT tomato plants. Our data suggest that BR signaling pathways are involved in mediating the response to abiotic stress via fine-tuning of abiotic stress-related gene networks in tomato plants.</P> <P><B>Highlights</B></P> <P> <UL> <LI> BR-deficient Micro-Tom showed lower drought and osmotic stress tolerance. </LI> <LI> Complementation of BR activity completely restored stress and developmental defects in Micro-Tom. </LI> <LI> BR signaling is tightly connected with gene networks related to abiotic stress and development. </LI> </UL> </P>

Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers in Lentinula edodes

( Hwa-yong Lee ),( Suyun Moon ),( Hyeon-su Ro ),( Jong-wook Chung ),( Hojin Ryu ) 한국균학회 2020 Mycobiology Vol.48 No.2

In this study, the genetic diversity and the population structure of 77 wild strains and 23 cultivars of Lentinula edodes from Korea were analyzed using 20 genomic SSRs, and their genetic relationship was investigated. The tested strains of L. edodes were divided into three sub-groups consisting of only wild strains, mainly wild strains and several cultivars, and mainly cultivars and several wild strains by distance-based analysis. Using model-based analysis, L. edodes strains were divided into two subpopulations; the first one consisting of only wild strains and the second one with mainly cultivars and several wild strains. Moreover, AMOVA analysis revealed that the genetic variation in the cultivars was higher than that in the wild strains. The expected and observed heterozygosity and values indicating the polymorphic information content of L. edodes cultivars from Korea were also higher than that of the wild strains. Based on these results, we presume that the cultivars in Korea have developed by using numerous strains from other countries. In conclusion, the usage of wild strains for the development of new cultivars could improve the adaptability of L. edodes to biotic and abiotic stress.