Distribution of MITE Transposons in a Rice Genetic Map

박경철,이주경,권순재,신지현,이점호,양찬인,김남수 한국육종학회 2004 한국육종학회지 Vol.36 No.2

Molecular genetic markers have wide applicability for a various genetic analyses, and genetic mapping with PCR-based markers has identified many loci in the rice genome. This study was conducted to develop a genetic map of rice based on SSR and MITE-AFLP markers. The F2 mapping population was established from a cross between Oryza sativa var. Ilpoombyeo (Japonica type variety) and O. rufipogon W259. A total of 334 markers, including 54 SSR and 280 MITE-AFLP markers, were mapped on rice chromosomes using an F2 population. Of these, 280 markers, including 226 MITE-AFLP and 54 SSR markers were found to be genetically linked to form 12 linkage groups. The size of framework map spanned 2899.7 cM of the 12 linkage groups. The average linkage distance between markers among all linkage groups was 10.4 cM. The number of markers per linkage group ranged from 15 to 37. Most of MITE-AFLP markers were well distributed through the twelve rice chromosomes. In this study, we have exploited the MITE-AFLP markers to develop a new class of molecular markers for rice genome study. These new markers are expected to provide valuable resources for map-based studies, such as marker-assisted selection, gene tagging, and the analysis of quantitative trait loci (QTLs) in rice genome research program.

Genetic localization of the SPC gene controlling pod coiling direction in Medicago truncatula

Xiaocheng Yu,Qiulin Qin,Xia Wu,Dandan Li,Shengming Yang 한국유전학회 2020 Genes & Genomics Vol.42 No.7

Background Handedness in plants introduced by helical growth of organs is frequently observed, and it has fascinated plant scientists for decades. However, the genetic control of natural handedness has not been revealed. In the model legume Medicago truncatula, pods can be coiled in a clockwise or anti-clockwise manner, providing a model for genetic analysis of plant handedness. Objective We aimed to localize the Sense of Pod Coiling (SPC) gene controlling pod coiling direction in M. truncatula. Methods Linkage analysis was used with a biparental population for fine mapping of the SPC gene. The genome sequence of M. truncatula Mt4.0 was used for marker identification and physical mapping. Single nucleotide polymorphisms (SNPs) between the parental lines were converted to CAPS (cleaved amplified polymorphic sequences) markers. Genetic map was constructed using the software JoinMap version 3.0. Gene predication and annotation provided by the M. truncatula genome database (http://www.medic agoge nome.org) was confirmed with the programs of FGENESH and Pfam 32.0, respectively. Quantitative reverse transcription PCR (qRT-PCR) was used to analyze the relative expression levels of candidate genes. Results The genetic analysis indicated that the anti-clockwise coiling is dominant to clockwise and is controlled by the single gene, SPC. The SPC gene was delimited to a 250 kb-region on Chromosome 7. Total of 15 protein-coding genes were identified in the SPC locus through gene annotation and sequence analysis. Of those, two genes, potentially encoding a receptor-like kinase and a vacuolar cation/proton exchanger respectively, were selected as candidates for the SPC gene. Conclusions The result presented here lay a foundation for gene cloning of SPC, which will help us to understand the molecular mechanisms underlying helical growth in plant organs.

박테리오파지 E3의 Major Capsid Protein을 만드는 유전자의 Mapping 및 염기서열 분석

배수진,명희준,Bae, Soo-Jin,Myung, Hee-Joon 한국미생물학회 1999 미생물학회지 Vol.35 No.4

박테리오파지 E3가 만드는 plaque은 그 지름이 약 1㎝정도이고 대단히 빠르게 성장한다. 구조 단백질 중 가장 많은 copy를 가지는 major capsid 단백질을 발현하는 유전자를 조절하는 promoter가 가장 효율적일 것이라 생각되며, 이 promoter를 찾기 위하여 먼저 이 유전자를 mapping하였다. 정제한 파지 입자로부터 major capsid 단백질을 분리하여 그 N-terminal amino acid 서열을 확인하였고, 그에 해당하는 degenerate oligonucleotide probe를 이용하여 E3의 genomic library로부터 major capsid 단백질을 발현하는 유전자를 함유하는 clone을 찾았다. 이 clone의 DNA 서열 분석을 통하여 major capsid 단백질을 발현하는 유전자를 확인하였으며, 이는 E3 genome에서 약 72%에 mapping 되었다. 이 gene을 조절하는 promoter의 성질을 고찰하기 위하여 E3의 성장이 rifampicin에 의하여 영향을 받는지 확인한 결과 E3는 자기 고유의 RNA polymerase를 가지고 있음을 알 수 있었다. Bacteriophage E3 grows very rapidly and forms a large size plaque with a diameter of 1 cm. The promoter controlling the expression of the gene encoding the major capsid protein is thought to be most efficient. To find out this promoter, this gene was mapped in the genome according to the following procedure. The major capsid protein was purified from phage particle and the N-terminal amino acid sequence was revealed. Based on this sequence,a degernerate oligonucleotide probe was designed and used for screening of the genomic DNA fragments. From the DNA sequence of the selected clone, the gene encoding the major capsid protein was mapped at 70% of E3 genome. The expression of this gene was not sensitive to rifampicin which indicated the presence of E3's own RNA polymerase.

Genetic Analysis and Molecular Mapping of Dull Gene in Low Amylose Rice Cultivar, Milyang262

Gilang Kiswara,Jong-Hee Lee,Yeon-Jae Hur,Jun-Hyun Cho,Ji-Yoon Lee,Sang-Yeol Kim,Yeong-Bo Sohn,Choon-Woo Lee,You-Chun Song,Kyung-Min Kim,Min-Hee Nam 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

Amylose content of rice endosperm is one of the determinants of rice eating quality. This study was conducted to elucidate the mode of inheritance of dull gene in Milyang262, tentatively designated as du7(t), and to identify the molecular marker for du7(t) to be employed in marker-assisted breeding and gene pyramiding. Genetic analysis was carried out on F2 population derived from a cross between Junam and Milyang262. The low amylose content of Milyang262 was indicated to be under single recessive control. Allelism tests were as well conducted by crossing Milyang262 with Baegjinju and Baegokchal, which harbor du1 and wx gene, respectively. du7(t) was demonstrated to be inherited independently to du1 and wx. F2 population of Baegokchal/Milyang262 was used for molecular mapping. Linkage analysis was conducted on a population consisted of 120 individuals by several SSR markers. Initial mapping indicated that du7(t) is located on the end of long arm of chromosome 6 between SSR marker RM20590 and RM3509. To fine map the gene, a bigger population and several additional markers were employed. du7(t) was further mapped to a 1.74 Mb region between two SSR markers (RM6926 and RM412). Furthermore, we indentified three SSR markers that co-segregated with du(t) i.e. RM6811, RM3765, and RM176.

Genetic linkage map construction and quantitative trait loci mapping of agronomic traits in Gloeostereum incarnatum

Jiang Wan-Zhu,Yao Fang-Jie,Lu Li-Xin,Fang Ming,Wang Peng,Zhang You-Min,Meng Jing-Jing,Lu Jia,Ma Xiao-Xu,He Qi,Shao Kai-Sheng 한국미생물학회 2021 The journal of microbiology Vol.59 No.1

Gloeostereum incarnatum is an edible medicinal mushroom widely grown in China. Using the whole genome of G. incarnatum, simple sequence repeat (SSR) markers were developed and synthetic primers were designed to construct its first genetic linkage map. The 1,048.6 cm map is composed of 10 linkage groups and contains 183 SSR markers. In total, 112 genome assembly sequences were anchored, representing 16.43 Mb and covering 46.41% of the genome. Selfing populations were used for quantitative trait loci (QTL) targeting, and the composite interval mapping method was used to co-localize the mycelium growth rate (potato dextrose agar and sawdust), growth period, yield and fruiting body length, and width and thickness. The 14 QTLs of agronomic traits had LOD values of 3.20–6.51 and contribution rates of 2.22– 13.18%. No linkage relationship was found between the mycelium growth rate and the growth period, but a linkage relationship was observed among the length, width and thickness of the fruiting bodies. Using NCBI’s BLAST alignment, the genomic sequences corresponding to the QTL regions were compared, and a TPR-like protein candidate gene was selected. Using whole-genome data, 138 candidate genes were found in four sequence fragments of two SSR markers located in the same scaffold. The genetic map and QTLs established in this study will aid in developing selective markers for agronomic traits and identifying corresponding genes, thereby providing a scientific basis for the further gene mapping of quantitative traits and the marker-assisted selection of functional genes in G. incarnatum breeding programs.

SNP Discovery and Mapping of a Major Gene Rhg4 Conferring Resistance to Soybean Cyst Nematode

장수연,반규정,김문영,곽재균,장현주,이석하 한국육종학회 2004 한국육종학회지 Vol.36 No.2

Two important loci, designated Rhg1 and Rhg4, are responsible for most resistance to soybean cyst nematode (SCN). The objective of this study was to survey single nucleotide polymorphism (SNP) and to map the SCN-resistant gene, Rhg4, on soybean genetic map. Direct sequencing with two primer sets Rhg4 gene revealed that three SNPs and seven indels were detected among six different soybean genotypes. The designed oligonucleotide complementary to the 5 region from the T(A)/C(G) SNP out of 10 SNPs detected was used in SNaPshot reactions, confirming polymorphism between PI 96188 and Jinju 1. Using a total of 90 recombinant inbred lines (RILs) derived from a cross between PI 96188?´?Jinju 1, the genetic population was mapped with 32 SSR markers, in which thirteen markers were placed into 5 linkage groups, covering 78.6 cM, and average distance between markers was 6.1 cM. Even though the genetic map was not completely saturated with SSR markers, linkage study revealed that Rhg4 was tightly linked to Satt187 on LG A2 with a distance of 6.8 cM. The location of Rhg4 on the genetic map is a good agreement with the previous report in the USDA map. From this study, it was concluded that sequence data availability of the responsible gene for the SCN resistance and sequence polymorphism between two parents map the gene successfully without phenotypic evaluation. In addition, SNP marker for SCN resistance map may be used in a marker-assisted selection for development of SCN-resistant soybean varieties in a breeding program.

Construction of Genetic Linkage Map for Korean Soybean Genotypes using Molecular Markers

Myung Sik Kim,Ye Jin Cho,Dae Jin Park,Sung Jin Han,Ju Ho Oh,Jung Gyu Hwang,Mi Suk Ko,Jong Il Chung 韓國作物學會 2003 Korean journal of crop science Vol.48 No.4

Genetic linkage maps serve the plant geneticist in a number of ways, from marker assisted selection in plant improvement to map-based cloning in molecular genetic research. Genetic map based upon DNA polymorphism is a powerful tool for the study of qualitative and quantitative traits in crops. The objective of this study was to develop genetic linkage map of soybean using the population derived from the cross of Korean soybean cultivar 'Kwangkyo, and wild accession 'IT182305'. Total 1,000 Operon random primers for RAPD marker, 49 combinations of primer for AFLP marker, and 100 Satt primers for SSR marker were used to screen parental polymorphism. Total 341 markers (242 RAPD, 83 AFLP, and 16 SSR markers) was segregated in 85 ~textrmF2 population. Forty two markers that shown significantly distorted segregation ratio (1:2:1 for codominant or 3:1 for domimant marker) were not used in mapping procedure. A linkage map was constructed by applying the computer program MAPMAKER/EXP 3.0 to the 299 marker data with LOD 4.0 and maximum distance 50 cM. 176 markers were found to be genetically linked and formed 25 linkage groups. Linkage map spanned 2,292.7 cM across all 25 linkage groups. The average linkage distance between pair of markers among all linkage groups was 13.0 cM. The number of markers per linkage group ranged from 2 to 55. The longest linkage group 3 spanned 967.4 cM with 55 makers. This map requires further saturation with more markers and agronomically important traits will be joined over it.

A Genetic Linkage Map of Soybean with RFLP, RAPD, SSR and Morphological Markers

Kim, Hong-Sik,Lee, Suk-Ha,Lee, Yeong-Ho The Korean Society of Crop Science 2000 Korean journal of crop science Vol.45 No.2

The objective of this study was to develop a linkage map of soybean under the genetic background of Korean soybean. A set of 89 F/sub 5/ lines was developed from a cross between 'Pureunkong', which was released for soy-bean sprout, and 'Jinpumkong 2', which had no beany taste in seed due to lack of lipoxygenase 1, 2, and 3. A linkage map was constructed for this population with a set of 113 genetic markers including 7 restriction fragment length polymorphism (RFLP) markers, 79 randomly amplified polymorphic DNA (RAPD) markers, 24 simple sequence repeat(SSR) markers, and 3 morphological markers. The map defined approximately 807.4 cM of the soybean genome comprising 25 linkage groups with 98 polymorphic markers. Fifteen markers remained unlinked. Seventeen linkage groups identified here could be assigned to the respective 13 linkage groups in the USDA soybean genetic map. RFLP and SSR markers segregated at only single genetic loci. Fourteen of the 25 linkage groups contained at least one SSR marker locus. Map positions of most of the SSR loci and their linkages with RFLP markers were consistent with previous reports of the USDA soybean linkage groups. For RAPD, banding patterns of 13 decamer primers showed independent segregations at two or more marker loci for each primer. Only the segregation at op Y07 locus was expressed with codominant manner among all RAPD loci. As the soybean genetic map in our study is more updated, molecular approaches of agronomically important genes would be useful to improve Korean soybean improvement.

Comparative Mapping of Consensus SSR Markers in an Intraspecific F₈ Recombinant Inbred Line Population in Capsicum

Hai Thi Hong Truong,Ki-Taek Kim,Su Kim,Young Chae,Jeong-Hyun Park,Dae-Geun Oh,Myoung-Cheol Cho 한국원예학회 2010 Horticulture, Environment, and Biotechnology Vol.51 No.3

A saturated intraspecific genetic map is critical for studying QTLs associated with Phytophthora root rot resistance in pepper. The map was constructed using a population of 126 F8 recombinant inbred lines derived from a cross between YCM334 (resistant to Phytophthora root rot) and the susceptible local variety, Tean. To identify a set of consensus markers for mapping, 67 anchor SSR markers were selected from the reference map Pepper-FAO3 and 130 from SNU3. Polymorphic rates were low: 43 out of 197 were polymorphic. In addition, 1,667 EST-SSR primers were used. Given 11% of polymorphism rate was enough to frame, but not to saturate the map. To saturate the map, 66 AFLP primer combinations were also used. Among the 454 markers used, 281 AFLPs, 101 EST-SSRs, 37 consensus SSRs and 1 CAPS marker were mapped and distributed in 19 linkage groups (LGs). Based on distribution of the consensus markers, 14 linkage groups were assigned into 12 chromosomes of pepper. The map covered 2177.5 cM with an average of 5.2 cM. Distribution and order of consensus markers in the present linkage map were consistent with the previously developed maps. The map will become a useful tool for analyzing QTLs of the mapping population.

Brassica A genome의 최근 연구 동향

최수련,권수진 한국식물생명공학회 2012 식물생명공학회지 Vol.39 No.1

As a scientific curiosity to understand the structure and the function of crops and experimental efforts to apply it to plant breeding, genetic maps have been constructed in various crops. Especially, in the case of Brassica crop, genetic mapping has been accelerated since genetic information of model plant Arabidopsis was available. As a result, the whole B. rapa genome (A genome) sequencing has recently been done. The genome sequences offer opportunities to develop molecular markers for genetic analysis in Brassica crops. RFLP markers are widely used as the basis for genetic map construction, but detection system is inefficiency. The technical efficiency and analysis speed of the PCR-based markers become more preferable for many form of Brassica genome study. The massive sequence informative markers such as SSR, SNP and InDels are also available to increase the density of markers for highresolution genetic analysis. The high density maps are invaluable resources for QTLs analysis, marker assisted selection (MAS), map-based cloning and comparative analysis within Brassica as well as related crop species. Additionally, the advents of new technology, next-generation technique, have served as a momentum for molecular breeding. Here we summarize genetic and genomic resources and suggest their applications for the molecular breeding in Brassica crop.