• Korean Journal of Breeding Science
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• v.43 no.5
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• pp.405-412
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• 2011

Knowledge of genetic diversity and genetic relationships among inbred lines gives a significant impact on the selection of parental lines for hybrid maize varieties. Genetic diversity and genetic relationships among 86 popcorn inbred lines were analyzed using 50 SSR markers distributed over the whole genome. A total of 256 alleles were identified at all the SSR loci with an average of 5.1 and a range between two and sixteen per locus. The gene diversity values varied from 0.21 to 0.831 with an average of 0.579. The cluster tree generated using the described SSR markers recognized three major groups at 35.8% genetic similarity. Groups I, II, III respectively included 40, 39 and 7 inbred lines. The present study indicates that the SSR markers chosen for this analysis are effective for the assessment of genetic diversity and genetic relationships among 86 popcorn inbred lines in Korea.

• Journal of Life Science
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• v.33 no.11
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• pp.897-904
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• 2023

This study was done to develope genetic markers with the unique characteristics of genes according to the genomic information of Bacillus velezensis K10. B. velezensis K10 maintained a total of 4,159,835 bps, which was found to encode 5,136 open reading frames (orfs). B. velezensis K10 was found to have much more gene migration due to external factors overall compared to standard strain B. velezensis JS25R. In order to discover genetic selection markers, orfs on the genome to be easily induced to gene mutation were surveyed such as recombinase, integrase, transposase, and phage-related genes. As a result of the investigation, 9 candidate markers were isolated with high possibility as genetic selection markers. Although a part in the various origin's areas showed specificities in comparison with homology, the selected markers were all existed in phage-related areas because they were relatively lower homologies in phage-related genes. PCR analysis was done on B. licheniformis K12, B. velezensis K10, B. subtilis, and B. cereus to establish them as inter-species candidate selection markers. As a result, it was confirmed that B. velezensis K10-specific PCR products were formed in a total of 6 primer sets such as BV3 and BV5 to 9. On the other hand, analysis at the subspecies level observed the formation of B. velezensis K10-specific PCR products in 4 primer sets such as BV3, 5, 8, and 9. Among them, since BV5 and BV8 were detected by very specific results, we suggest that BV5 and 8 can be used as B. velezensis K10 gene selection markers at the species and sub-species level.

• Molecules and Cells
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• v.25 no.4
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• pp.467-478
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• 2008

Simple sequence repeats (SSRs) and interSSR (ISSR) marker systems were used in this study to reveal genetic changes induced by artificial selection for short/long larval duration in the tropical strain Nistari of the silkworm Bombyx mori. Artificial selection separated longer larval duration (LLD) ($29.428{\pm}0.723days$) and shorter larval duration (SLD) ($22.573{\pm}0.839days$) lines from a base, inbred population of Nistari (larval span of $23.143{\pm}0.35days$). SSR polymorphism was observed between the LLD and SLD lines at one microsatellite locus, Bmsat106 ($CA_7$) and at two loci of 1074 bp and 823 bp generated with the ISSR primer UBC873. Each of these loci was present only in the LLD line. The loci segregated in the third generation of selection and were fixed in opposite directions. In the $F_2$ generation of the $LLD{\times}SLD$ lines, the alleles of Bmsat106 and $UBC873_{1074bp}$ segregated in a 1:1 ratio and the loci were present only in the LLD individuals. $UBC873_{823bp}$ was homozygous. Single factor ANOVA showed a significant association between the segregating loci and longer larval duration. Together, the two alleles contributed to an 18% increase in larval duration. The nucleotide sequences of the $UBC873_{1074bp}$ and $UBC873_{823bp}$ loci had 67% A/T content and consisted of direct, reverse, complementary and palindromic repeats. The repeats appeared to be "nested" (59%) in larger repeats or as clustered elements adjacent to other repeats. Of 203 microsatellites identified, dinucleotides (67.8%) predominated and were rich in A/T and T/A motifs. The sequences of the $UBC873_{1074bp}$ and $UBC873_{823bp}$ loci showed similarity (E = 0.0) to contigs located in Scaffold 010774 and Scaffold 000139, respectively, of the B. mori genome. BLASTN analysis of the $UBC873_{1074bp}$ sequence showed significant homology of (nt.) 45-122 with upstream region of three exons from Bombyx. The complete sequence of this locus showed ~49% nucleotide conservation with transposon 412 of Drosophila melanogaster and the Ikirara insertions of Anopheles gambiae. The A + T richness and lack of coding potential of these small loci, and their absence in the SLD line, reflect the active process of genetic change associated with the switch to short larval duration as an adaptation to the tropics.

• Horticultural Science & Technology
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• v.29 no.4
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• pp.336-344
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• 2011

Using the abundant available information about the tomato genome, we developed DNA markers that are linked to disease resistant loci and performed marker-assisted selection (MAS) to construct multi-disease resistant lines and varieties. Resistance markers of Ty-1, T2, and I2, which are linked to disease resistance to Tomato yellow leaf curl virus (TYLCV), Tomato mosaic virus (ToMV), and Fusarium wilt, respectively, were developed in a co-dominant fashion. DNA sequences near the resistance loci of TYLCV, ToMV, and Fusarium wilt were used for primer design. Reported candidate markers for powdery mildew-resistance were screened and the 32.5Cla marker was selected. All four markers (Ty-1, T2, I2, and 32.5Cla) were converted to cleavage amplification polymorphisms (CAPS) markers. Then, the CAPS markers were applied to 96 tomato lines to determine the phenetic relationships among the lines. This information yielded clusters of breeding lines illustrating the distribution of resistant and susceptible characters among lines. These data were utilized further in a MAS program for several generations, and a total of ten varieties and ten inbred lines were constructed. Among four traits, three were introduced to develop varieties and breeding lines through the MAS program; several cultivars possessed up to seven disease resistant traits. These resistant trait-related markers that were developed for the tomato MAS program could be used to select early stage seedlings, saving time and cost, and to construct multi-disease resistant lines and varieties.

• Journal of the Korean Chemical Society
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• v.46 no.2
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• pp.157-163
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• 2002

To identify RNA motifs interacting with $tRNA^{Val}$, a SELEX(Systematic Evolution of Ligands by Exponential Enrichment) was applied. Random DNA library which contains a region of ran-domized 48-mer oligonucleotide flanked by conserved sequ ence primers was transcribed into RNA pool using T7 RNA polymerase and RNA aptamers were selected with $tRNA^{Val}$ -immobilized affinity column through 14 rounds of SELEX. Some of the resulting aptamers contained a consensus sequence similar to the sequence in the loop regions of three rRNAs; C43GAAC47 sequence of 5S rRNA, G1491AAGU1495, G1379UUCC1383 sequence of 16S rRNA and C1064UUAG1068, G2110UGUA2114, C2480GACGG2485, A2600CAGU2604 sequence of 23S rRNA. These results suggest that $tRNA^{Val}$ can interact with 5S rRNA, 16S rRNA and 23S rRNA with variety in ribosome.

• Journal of Life Science
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• v.21 no.1
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• pp.15-21
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• 2011

Cultivated tomato, Lycopersicum esculentum, is a very important crop. We selected 36 cultivars and studied them for identification and polymorphism by employing random amplified DNA (RAPD) analysis with 80 oligonucleotide primers. Of the 80 primers, 36 primers (45.0%) were polymorphic. Detection of polymorphism in cultivated tomato opens up the possibility of development of its molecular map by judicious selection of genotypes. Molecular markers can also be used for cultivar identification and protection of the plant breeder's intellectual property rights (plant breeders' rights, PBRs). As an example, DNA polymorphism using OPC-13 primer that did not produce the OPC-13-01 band was only found in Junk Pink and Ailsa Craighp cultivars. OPA-12-03 and OPB-15-07 were fragments specific to the TK-70 cultivar and were absent in other cultivars. DNA polymorphism in cultivated tomato in this study was correlated with a type of inflorescence, although some cultivars had exceptions. These approaches will be useful for developing marker-assisted selection tools for genetic enhancement of the tomato plant for desirable traits.

• BMB Reports
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• v.36 no.5
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• pp.427-432
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• 2003

Jute is the principal coarse fiber for commercial production and use in Bangladesh. Therefore, the development of a high-yielding and environmental-stress tolerant jute variety would be beneficial for the agro economy of Bangladesh. Two molecular fingerprinting techniques, random-amplified polymorphic DNA (RAPD) and amplified-fragment length polymorphism (AFLP) were applied on six jute samples. Two of them were cold-sensitive varieties and the remaining four were cold-tolerant accessions. RAPD and AFLP fingerprints were employed to generate polymorphism between the cold-sensitive varieties and cold-tolerant accessions because of their simplicity, and also because there is no available sequence information on jute. RAPD data were obtained by using 30 arbitrary oligonucleotide primers. Five primers were found to give polymorphism between the varieties that were tested. AFLP fingerprints were generated using 25 combinations of selective-amplification primers. Eight primer combinations gave the best results with 93 polymorphic fragments, and they were able to discriminate the two cold-sensitive and four cold-tolerant jute populations. A cluster analysis, based on the RAPD and AFLP fingerprint data, showed the population-specific grouping of individuals. This information could be useful later in marker-aided selection between the cold-sensitive varieties and cold-tolerant jute accessions.

• Molecules and Cells
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• v.20 no.2
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• pp.201-209
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• 2005

We have constructed an AFLP-based linkage map of Japanese red pine (Pinus densiflora Siebold et Zucc.) using haploid DNA samples of 96 megagametophytes from a single maternal tree, selection clone Kyungbuk 4. Twenty-eight primer pairs generated a total of 5,780 AFLP fragments. Five hundreds and thirteen fragments were verified as genetic markers with two alleles by their Mendelian segregation. At the linkage criteria LOD 4.0 and maximum recombination fraction 0.25(${\theta}$), a total of 152 markers constituted 25 framework maps for 19 major linkage groups. The maps spanned a total length of 2,341 cM with an average framework marker spacing of 18.4 cM. The estimated genome size was 2,662 cM. With an assumption of equal marker density, 82.2% of the estimated genome would be within 10 cM of one of the 230 linked markers, and 68.1% would be within 10 cM of one of the 152 framework markers. We evaluated map completeness in terms of LOD value, marker density, genome length, and map coverage. The resulting map will provide crucial information for future genomic studies of the Japanese red pine, in particular for QTL mapping of economically important breeding target traits.

• Journal of agriculture & life science
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• v.45 no.5
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• pp.1-8
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• 2011

In this study, 160 tea tree (Camellia sinensis L.) lines were classified by caffeine content using colorimetric methods. Among them, caffeine-rich lines (HR-78, HR-137, HR-82 and HR-123) and poor lines (HP-85, HP-88, HP-19, and HP-131) were selected. To know the difference in morphological and genetic characters between caffeine-rich and poor lines, we used leaf/shoot growth and RAPD methods. Cluster pattern of morphological characters (leaf width, leaf length, leaf area and shoot length) showed that shoot length was longer in caffein-rich lines than in -poor lines. In genetic analysis, amplified DNA bands having various sizes were detected in RAPD analysis where 30 random primers were used. However, the discriminated primer set that distinguish caffein-rich tree line from -poor lines was not found. These results can be used as the basic data to determine the morphological and genetic differences among caffein-rich and -poor lines.

• Korean Journal of Breeding Science
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• v.42 no.2
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• pp.139-143
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• 2010

Late blight caused by Phytophthora infestans is historically a serious epidemic disease in potato and tomato cultivations. Accession L3708 (Solanum pimpinellifolium), a new source for late blight resistance was identified in AVRDC, and carries the resistance gene, Ph-3, incompatible to P. infestans race 3. The AFLP markers linked to Ph-3 were previously developed from the L3708 accession (Chunwongse et al. 2002). To facilitate tomato breeding with the Ph-3 gene, an attempt was made to convert AFLP markers to sequence-characterized amplified region (SCAR) markers. Among 6 AFLP markers, only one AFLP marker, L87, was successfully converted to SCAR marker. The resistance-specific 230 bp AFLP fragment was cloned and sequenced, and the PCR primer amplifying a 123 bp fragment was designed. This SCAR marker could discriminate resistant and susceptible individuals with high stringency. The developed SCAR marker could be used for the marker assisted-selection in tomato breeding programs.