• Molecules and Cells
• /
• 제27권2호
• /
• pp.237-241
• /
• 2009

Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.

• 한국자원식물학회지
• /
• 제10권3호
• /
• pp.241-246
• /
• 1997

Linkage maps based on molecular markers are valuable tools in plant breeding and genetic studies. A population of 76 RI lines from the mating of A3733 and PI437.088 was evaluated with Random Amplified Polymorphic DNA(RAPD) and Simple Sequence Repeats (SSR) markers to create soybean molecular linkage map, 302 RAPD and 21 SSR markers were genetically linked and formed forty linkage groups. These linkage groups spanned a genetic distance of 1,775 cM. The average distance between markers was 5.5 cM.

• Molecules and Cells
• /
• 제24권1호
• /
• pp.60-68
• /
• 2007

Microsatellites, also called simple sequence repeats (SSR), are very useful molecular genetic markers commonly used in crop breeding, species identification and linkage analysis. In the present study, we constructed a microsatellite-enriched genomic library of Panax ginseng, and identified 251 novel microsatellite sequences. Tri-nt repeat units were the most abundant (46.6%), followed by di-nt repeats (35.5%). The $(AG)_n$ motif was most common (23.1%), followed by the $(AAC)_n$ motif (22.3%). From the genotyping of 94 microsatellites using marker-specific primer sets, we identified 11 intraspecific polymorphic markers as well as 14 possible interspecific polymorphic markers differing between P. ginseng and P. quinquefolius. The exact allele structures of the polymorphic markers were determined and the alleles were named. This study represents the first report of the bulk isolation of microsatellites by screening a microsatellite-enriched genomic library in P. ginseng. The microsatellite markers could be useful for linkage analysis, genetic breeding and authentication of Panax species.

• Journal of Plant Biotechnology
• /
• 제46권3호
• /
• pp.158-164
• /
• 2019

Molecular characterization of different genotypes reveals accurate information about the degree of genetic diversity that helps to develop a proper breeding program. In this study, a total of 30 EST-based simple sequence repeat (EST-SSR) markers derived from trumpet lily (Lilium longiflorum) were used across 11 native lily species for their genetic relationship. Among these 30 markers, 24 SSR markers that showed polymorphism were used for evaluation of diversity spectrum. The allelic number at per locus ranged from 1 at SSR2 locus to 34 alleles at SSR15 locus, with an average of 11.25 alleles across 24 loci observed. The polymorphic information content, PIC, values ranged from 0.0523 for SSR9 to 0.9919 for SSR2 in all 24 loci with an average of 0.3827. The allelic frequency at every locus ranged from 0.81% at SSR2 locus to 99.6% at SSR14 locus. The pairwise genetic dissimilarity coefficient revealed the highest genetic distance with a value of 81.7% was in between L. dauricum and L. amabile. A relatively closer genetic distance was found between L. lancifolium and L. dauricum, L. maximowiczii and L. concolor, L. maximowiczii and L. distichum (Jeju), L. tsingtauense and L. callosum, L. cernuum and L. distichum (Jeju ecotype), of which dissimilarity coefficient was 50.0%. The molecular fingerprinting based on microsatellite marker could serve boldly to recognize genetically distant accessions and to sort morphologically close as well as duplicate accessions.

• Plant Breeding and Biotechnology
• /
• 제5권2호
• /
• pp.134-142
• /
• 2017

Resource plants are important and have strong potential for a variety of utilities as crops or pharmaceutical materials. However, most resource plants remain wild and thus their utility for breeding and biotechnology is limited. Molecular markers are useful to initiate genetic study and molecular breeding for these understudied resource plants. We collected various wild collections of Peucedanum japonicum which is indigenous resource plants utilized as oriental medicine and leafy vegetables in Korea. In this study, we produced two independent whole genome sequences (WGSs) from two collections and identified large scale polymorphic simple sequence repeat (pSSR) based on our pipeline to develop SSR markers based on comparison of two WGSs. We identified a total of 452 candidate pSSR contigs. To confirm the accuracy and utility of pSSR, we designed ten SSR primer pairs and successfully applied those to seven collections of P. japonicum. The WGS and pSSR candidates identified in this study will be useful resource for genetic research and breeding purpose for the valuable resource plant, P. japonicum.

• Molecules and Cells
• /
• 제26권3호
• /
• pp.250-257
• /
• 2008

Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species.

• Genomics & Informatics
• /
• 제19권3호
• /
• pp.33.1-33.10
• /
• 2021

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%-62.5%), followed by tri- (23.7%-27.2%), tetra- (5.2%-5.6%), penta- (5.0%-5.3%), and hexa-nucleotide (2.7%-2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.

• 한국환경생태학회:학술대회논문집
• /
• 한국환경생태학회 2006년도 정기총회 및 학술논문발표회
• /
• pp.157-161
• /
• 2006

• 한국균학회지
• /
• 제42권2호
• /
• pp.159-164
• /
• 2014

큰느타리 품종구분을 위한 마커의 개발을 위하여 큰느타리 전체 유전자 염기서열을 바탕으로 제작한 484개의 SSR마커를 사용하여 다형성 분석을 실시하였다. 그 결과 각 275개의 primer에서 다형성이 관찰되었다. 이 중 품종간에 다양한 패턴을 나타내는 5개의 마커를 최종 선발하였다. 이들 마커의 PIC 값은 0.6627에서 0.6848로 나타났고, 평균값은 0.6775였다. 이 결과를 밴드 이미지 인식 방법으로 dendrogram을 작성하였다. UPGMA 집괴분석 결과, 큰느타리 품종은 크게 Cluster 1과 Cluster 2로 구분되었다. SSR primer를 이용한 PCR 결과 나타나는 품종별 고유의 DNA 밴드를 품종특이적 마커로 개발하기 위하여, 선발된 마커중에서 SSR312과 SSR366, SSR178과 SSR 277 마커를 조합하여 초위성체 유래 다중 표지 세트를 개발하였다. Multiplex-SSR 마커의 사용을 통해 두번의 PCR 반응만으로 본 연구에서 사용된 12개의 큰느타리 품종을 구분할 수 있었다.

• Journal of Plant Biotechnology
• /
• 제4권2호
• /
• pp.45-52
• /
• 2002

A lot of SSRs (simple sequence repeats) in peach and pear from enriched genomic libraries and in peach from a cDNA library were developed. These SSRs were applied to other related species, giving phenograms of 52 Prunes and 60 pear accessions. Apple SSRs could also be successfully used in Pyrus spp. Thirteen morphological traits were characterized on the basis of the linkage map obtained from an $F_2$ population of peach. This map was compiled with those morphological markers and 83 DNA markers, including SSR markers used as anchor loci, to compare different peach maps. Molecular markers tightly linked to new root-knot nematode resistance genes were also found. A linkage map including disease related genes, pear scab resistance and black spot susceptibility, in the Japanese pear Kinchaku were constructed using 118 RAPD markers. Another linkage map, of the European pear Bartlett, was also constructed with 226 markers, including 49 SSRs from pear, apple, peach and cherry. Maps of other Japanese pear cultivars, i.e., Kousui and Housui, were also constructed. These maps were the first results of pear species.