• Title/Summary/Keyword: SSR Marker

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Genetic diversity and population structure of European button mushroom (Agaricus bisporus) using SSR markers (SSR 마커를 이용한 유럽 양송이 자원의 유전적 다양성 및 집단구조분석)

  • Shin, Hye-Ran;An, Hyejin;Bang, Jun Hyoung;Kim, Jun Je;Han, Seahee;Lee, Hwa-Yong;Chung, Jong-Wook
    • Journal of Mushroom
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    • v.18 no.4
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    • pp.323-330
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    • 2020
  • Agaricus bisporus is an important edible mushroom that is used as a functional food. In this study, European A. bisporus strains were analyzed for genetic diversity, population structure, and genetic differentiation using simple sequence repeat (SSR) markers. European A. bisporus strains were divided into four groups by distance-based analysis and two subpopulations by model-based analysis. The SSR markers used in this study did not group European A. bisporus strains by geographical region or pileus color. Genetic diversity was high in Group 4 based on distance-based analysis and Pop. 2 based on model-based analysis. A. bisporus strains showed very low genetic differentiation. The results of this study can be used for breeding A. bisporus in the future.

Development of RAPD Marker Related to Brown Planthopper Resistance Gene Derived from Rice Cultivar, Cheongcheongbyeo (청청벼에서 유래한 벼멸구 저항성관련 RAPD Marker의 개발)

  • Seo Ji-Hun;Kim Kyung-Min;Kim Suk-Man;Sohn Jea-Keun
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.50 no.6
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    • pp.453-456
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    • 2005
  • This study was carried out to select DNA markers closely linked to brown planthopper (BPH) resistance gene originated from a rice cultivar 'Cheongcheong­byeo'. For the mapping of resistant gene to BPH, a doubled-haploid (DH) population was developed by anther culture of $F_1$ plants from a cross 'Cheongcheong­byeo/Nagdongbyeo'. In BPH bioassay and marker screen­ing for the DH population, the segregation of resistant and susceptible plants to BPH fitted to a 1:1 ratio. A total of 310 RAPDs of 520 markers showed polymorphism in parental survey using 'Cheongcheongbyeo' and 'Nag­dongbyeo'. In the analysis of relationship between BPH resistance and marker pattern for 40 DH lines, the OPE16 produced a specific dominant fragment, 700 bp, which was closely linked with BPH resistance gene of 'Cheong­cheongbyeo'. Based on the linkage analysis using 7 markers, BPH resistance of 'Cheongcheongbyeo' was mapped on chromosome 12, which was closely linked with $OPE16_{700}$ at a distance of 4.6 cM.

Construction of an Integrated Pepper Map Using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC End Sequences

  • Lee, Heung-Ryul;Bae, Ik-Hyun;Park, Soung-Woo;Kim, Hyoun-Joung;Min, Woong-Ki;Han, Jung-Heon;Kim, Ki-Taek;Kim, Byung-Dong
    • Molecules and Cells
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    • v.27 no.1
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    • pp.21-37
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    • 2009
  • Map-based cloning to find genes of interest, marker-assisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

Identification of Lettuce Germplasms and Commercial Cultivars Using SSR Markers Developed from EST (EST로부터 개발된 SSR 마커를 이용한 상추 유전자원 및 유통품종의 식별)

  • Hong, Jee-Hwa;Kwon, Yong-Sham;Choi, Keun-Jin;Mishra, Raghvendra Kumar;Kim, Doo Hwan
    • Horticultural Science & Technology
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    • v.31 no.6
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    • pp.772-781
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    • 2013
  • The objective of this study was to develop simple sequence repeat (SSR) markers from expressed sequence tags (EST) of lettuce (Lactuca sativa) and identify 9 germplasms from 3 wild species of lettuce and 61 commercial cultivars using the developed EST-SSR markers. A total of 81,330 lettuce ESTs from NCBI databases were used to search for SSR and 4,229 SSR loci were identified. The highest proportion (59.12%, 2500) was represented by trinucleotide, followed by dinucleotide (29.70%, 1256) and hexanucleotide (6.62%, 280) among SSR repeat motifs. Totally 474 EST-SSR primers were developed from EST and a random set of 267 primers was used to assess the genetic diversity among 9 germplasms and 61 cultivars. Out of 267 primers, 47 EST-SSR markers showed polymorphism between 7 cultivars. Twenty-six EST-SSR markers among 47 EST-SSR markers showed high polymorphism, reproducibility, and band clearance. The relationship between 26 markers genotypes and 70 accessions was analyzed. Totally 127 polymorphic amplified fragments were obtained by 26 EST-SSR markers and two to nine SSR alleles were detected for each locus with an average of 4.88 alleles per locus. Average polymorphism information content was 0.542, ranging from 0.269 to 0.768. Genetic distance of clusters ranged from 0.05 to 0.94 between 70 accessions and dendrogram at a similarity of 0.34 gave 7 main clusters. Analysis of genetic diversity revealed by these 26 EST-SSR markers showed that the 9 germplasms and 61 commercial cultivars were discriminated by marker genotypes. These newly developed EST-SSR markers will be useful for cultivar identification and distinctness, uniformity and stability test of lettuce.

Evaluation of Germplasm and Development of SSR Markers for Marker-assisted Backcross in Tomato (분자마커 이용 여교잡 육종을 위한 토마토 유전자원 평가 및 SSR 마커 개발)

  • Hwang, Ji-Hyun;Kim, Hyuk-Jun;Chae, Young;Choi, Hak-Soon;Kim, Myung-Kwon;Park, Young-Hoon
    • Horticultural Science & Technology
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    • v.30 no.5
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    • pp.557-567
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    • 2012
  • This study was conducted to achieve basal information for the development of tomato cultivars with disease resistances through marker-assisted backcross (MAB). Ten inbred lines with TYLCV, late blight, bacterial wilt, or powdery mildew resistance and four adapted inbred lines with superior horticultural traits were collected, which can be useful as the donor parents and recurrent parents in MAB, respectively. Inbred lines collected were evaluated by molecular markers and bioassay for confirming their disease resistances. To develop DNA markers for selecting recurrent parent genome (background selection) in MAB, a total of 108 simple sequence repeat (SSR) primer sets (nine per chromosome at average) were selected from the tomato reference genetic maps posted on SOL Genomics Network. Genetic similarity and relationships among the inbred lines were assessed using a total of 303 polymorphic SSR markers. Similarity coefficient ranged from 0.33 to 0.80; the highest similarity coefficient (0.80) was found between bacterial wilt-resistant donor lines '10BA333' and '10BA424', and the lowest (0.33) between a late blight resistant-wild species L3708 (S. pimpinelliforium L.) and '10BA424'. UPGMA analysis grouped the inbred lines into three clusters based on the similarity coefficient 0.58. Most of the donor lines of the same resistance were closely related, indicating the possibility that these lines were developed using a common resistance source. Parent combinations (donor parent ${\times}$ recurrent parent) showing appropriate levels of genetic distance and SSR marker polymorphism for MAB were selected based on the dendrogram. These combinations included 'TYR1' ${\times}$ 'RPL1' for TYLCV, '10BA333' or '10BA424' ${\times}$ 'RPL2' for bacterial wilt, and 'KNU12' ${\times}$ 'AV107-4' or 'RPL2' for powdery mildew. For late blight, the wild species resistant line 'L3708' was distantly related to all recurrent parental lines, and a suitable parent combination for MAB was 'L3708' ${\times}$ 'AV107-4', which showed a similarity coefficient of 0.41 and 45 polymorphic SSR markers.

Determination and Application of Combined Genotype of Simple Sequence Repeats (SSR) DNA Marker for Cultivars of Cymbidium goeringii (춘란(Cymbidium goeringii) 품종에 대한 Simple Sequence Repeats (SSR) DNA 마커의 복합 유전자형 결정과 적용)

  • Lee, Dae-Gun;Koh, Jae-Chul;Chung, Ki-Wha
    • Horticultural Science & Technology
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    • v.30 no.3
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    • pp.278-285
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    • 2012
  • Cymbidium goeringii is one of the most important and popular species in the orchid family in north-east Asia. In the present study, we prepared multiplex PCR system, and used it for the genotyping of eight simple sequence repeats (SSR) markers (CG409, CG415, CG709, CG722, CG787, CG1023, CG1210, and CG1281) in subject with 40 samples of cultivated varieties. All the analyzed samples showed different combined genotypes. The average combined power of discrimination was very high value of $7.14{\times}10^{-10}$, and observed heterozygosity (Ho = 0.466) was similar with two wild populations of C. goeringii, which may indicate no or little occurrence of genetic change after collection from wild habitats. The present study also developed a two-dimensional barcode to express information of genotype results of eight SSR markers (SSR DNA ID). The discrimination power of DNA ID between two individuals will be statistically more than 99.999999%. The SSR DNA ID and two-dimensional barcode may be very usefully applied for the discrimination and maintence of cultivars of C. goeringii.

Phenotypic and Marker Assisted Evaluation of Korean Wheat Cultivars

  • Jung, Yeonju;Park, Chul Soo;Jeung, Ji-Ung;Kang, Chon-Sik;Lee, Gi-An;Choi, Yu-Mi;Lee, Jung-Ro;Lee, Myung-Chul;Kim, Chung-Kon;Seo, Yong Weon
    • Korean Journal of Breeding Science
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    • v.43 no.4
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    • pp.273-281
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    • 2011
  • Fusarium head blight (FHB), also known as scab, caused mainly by Fusarium graminearum is a devastating disease of wheat in regions that are warm and humid during flowering. In addition to significant yield and quality losses, the mycotoxin deoxynivalenol produced by the pathogen in infected wheat kernels is a serious problem for food and feed safety. Twenty- three Korean cultivars and "Sumai 3", which is a FHB-resistant Chinese cultivar were tested for Type I, Type II resistances of FHB. Three cultivars were identified as resistant in Type I assessment, and two cultivars were resistant in Type II assessment. Genetic variation and relationship among the cultivars were evaluated on the basis of 11 Simple Sequence Repeat (SSR) and 29 Sequence Tagged Site (STS) markers that were linked to FHB resistance Quantitative Trait Loci (QTL) on chromosome 3BS. One SSR and 7 STS markers detected polymorphisms. Especially, using a STS marker (XSTS3B-57), 32.4% of the variation for Type II FHB resistance could be explained. Genetic relationship among Korean wheat cultivars was generally consistent with their released year. These markers on chromosome 3BS have the potential for accelerating the development of Korean wheat cultivars with improved Fusarium head blight resistance through the use of marker-assisted selection.

Development of Multiplex Microsatellite Marker Set for Identification of Korean Potato Cultivars (국내 감자 품종 판별을 위한 다중 초위성체 마커 세트 개발)

  • Cho, Kwang-Soo;Won, Hong-Sik;Jeong, Hee-Jin;Cho, Ji-Hong;Park, Young-Eun;Hong, Su-Young
    • Horticultural Science & Technology
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    • v.29 no.4
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    • pp.366-373
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    • 2011
  • To analyze the genetic relationships among Korean potato cultivars and to develop cultivar identification method using DNA markers, we carried out genotyping using simple sequence repeats (SSR) analysis and developed multiplex-SSR set. Initially, we designed 92 SSR primer combinations reported previously and applied them to twenty four Korean potato cultivars. Among the 92 SSR markers, we selected 14 SSR markers based on polymorphism information contents (PIC) values. PIC values of the selected 14 markers ranged from 0.48 to 0.89 with an average of 0.76. PIC value of PSSR-29 was the lowest with 0.48 and PSSR-191 was the highest with 0.89. UPGMA clustering analysis based on genetic distances using 14 SSR markers classified 21 potato cultivars into 2 clusters. Cluster I and II included 16 and 5 cultivars, respectively. And 3 cultivars were not classified into major cluster group I and II. These 14 SSR markers generated a total of 121 alleles and the average number of alleles per SSR marker was 10.8 with a range from 3 to 34. Among the selected markers, we combined three SSR markers, PSSR-17, PSSR-24 and PSSR-24, as a multiplex-SSR set. This multiplex-SSR set used in the study can distinguish all the cultivars with one time PCR and PAGE (Polyacrylamide gel electrophoresis) analysis and PIC value of multiplex-SSR set was 0.95.

Analysis of Genetic Polymorphism and Relationship of Korean Ginseng Cultivars and Breeding Lines using EST-SSR Marker (EST-SSR 마커를 이용한 인삼 품종과 육성계통의 유전적 다형성 및 유연관계 분석)

  • Bang, Kyong-Hwan;Seo, A-Yeon;Chung, Jong-Wook;Kim, Young-Chang;Jo, Ick-Hyun;Kim, Jang-Uk;Kim, Dong-Hwi;Cha, Seon-Woo;Cho, Yong-Gu;Kim, Hong-Sig
    • Korean Journal of Medicinal Crop Science
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    • v.20 no.4
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    • pp.277-285
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    • 2012
  • In this study, Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) analyses were used to clarify the genetic polymorphisms among Korean ginseng cultivars and breeding lines and to classify them into distinct genetic groups. Polymorphic and reproducible bands were produced by 14 primers out of total 30 primers used in this study. Fourteen EST-SSR loci generated a total of 123 bands. Amplified PCR products showed the highly reproducible banding patterns at 110~920 bp. The number of amplified bands for each EST-SSR primers ranged from 2 to 19 with a mean of 8.8 bands. P26 and P35 primers showed 13 and 12 banding patterns, respectively. The number of alleles for each EST-SSR locus ranged from 1.67 to 2.00 with a mean of 1.878 alleles. P34 and P60 primers showed the highest and the lowest genetic polymorphism, respectively. Cluster analysis based on genetic similarity estimated by EST-SSR markers classified Korean cultivars and breeding lines into 4 groups. Group included Gopoong and Chunpoong and 9 breeding lines (55%), group included 2 breeding lines (10%), group included 3 breeding lines (15%), group included Gumpoong and 3 breeding lines (20%). Consequently, the EST-SSR marker developed in this study may prove useful for the evaluation of genetic diversity and differentiation of Korean ginseng cultivars and breeding lines.

Studies on the Hereditary Properties of SSR Marker in Silkworm (Bombyx mori L.)

  • Li Muwang;Li Minghui;Miao Xuexia;Lu Cheng;Huang Yongping
    • International Journal of Industrial Entomology and Biomaterials
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    • v.11 no.1
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    • pp.49-55
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    • 2005
  • Two BC1 group, c108 $\times$ (p50 $\times$ c108) and p50 $\times$ (p50 $\times$ c108), one group of F$_{2}$ progeny, (p50 $\times$ c108) F$_{2}$ ,and 3 SSR markers, F10539, FlO626 and FlO618 were used to test the hereditary properties of SSR markers in silkworm. FI0539, FlO626 were proved to be linkage, and FlO618 was proved to be independent to those two markers. According to Mendel's law, the recombinant value between F10539, FlO626 was calculated in all of these groups, and they were 8.55$\%$ (c108BC1), 8.02$\%$ (p50BC1) and 7.81 $\%$ (F$_{2}$) respectively. There was dominant difference among the crossing-over value using paired-samples tests by SPSS 10.0 software. This research proved that SSR markers were co-dominant in B. mori too, and F 2 progeny could be used to construct SSR linkage map although B. mori lacked of crossing over in females.