• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.2
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• pp.303-308
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• 2002

Genetic markers engendered by genome projects drew enormous interest in quantitative genetics, but knowledge on genetic architecture of complex traits is limited. Complexities in genetics will not allow us to easily clarify relationship between genotypes and phenotypes for quantitative traits. Quantitative genetics guides an important way in facing such challenges. It is our exciting task to find genes that affect complex traits. In this paper, landmark research and future prospects are discussed on genetic parameter estimation and quantitative trait locus (QTL) mapping as major subjects of interest.

• Proceedings of the Korean Society of Fisheries Technology Conference
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• 2003.05a
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• pp.279-280
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• 2003

Although it has been known though many morphological and physiological studies, its genetic diversity and population structure have not yet been investigated in this species. Therefore, detailed studies, in particular at the DNA level, on genetic diversity of natural populations of wild sea lettuce, and genetic relationships between natural sea lettuce and cultivated sea lettuce are necessary from the viewpoint of plant evolution. (omitted)

• The Plant Pathology Journal
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• v.35 no.3
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• pp.189-199
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• 2019

In this research, the relationships among the 31 microsatellite markers with charcoal rot disease resistance related indices in 130 different soybean cultivars and lines were evaluated using association analysis based on the general linear model (GLM) and the mixed linear model (MLM) by the Structure and Tassel software. The results of microsatellite markers showed that the genetic structure of the studied population has three subpopulations (K=3) which the results of bar plat also confirmed it. In association analysis based on GLM and MLM models, 31 and 35 loci showed significant relationships with the evaluated traits, respectively, and confirmed considerable variation of the studied traits. The identified markers related to some of the studied traits were the same which can probably be due to pleiotropic effects or tight linkage among the genomic regions controlling these traits. Some of these relationships were including, the relationship between Sat_252 marker with amount of charcoal rot disease, Satt359, Satt190 and Sat_169 markers with number of microsclerota in stem, amount of charcoal rot disease and severity of charcoal rot disease, Sat_416 marker with number of microsclerota in stem and amount of charcoal rot disease and the Satt460 marker with number of microsclerota in stem and severity of charcoal rot disease. The results of this research and the linked microsatellite markers with the charcoal rot disease-related characteristics can be used to identify the suitable parents and to improve the soybean population in future breeding programs.

• International Journal of Industrial Entomology and Biomaterials
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• v.37 no.1
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• pp.1-8
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• 2018

The nerippe fritillary butterfly, Argynnis nerippe, is listed as an endangered species in Korea. Establishment of effective conservation strategies can be aided by the development and application of molecular markers that can be used to investigate the population genetics of the butterfly. Therefore, in this study, we identified ten microsatellite markers specific to A. nerippe using the Next-Seq 500 platform, and applied these markers to investigate the characteristics of five South Korean butterfly populations. Genotyping of 48 A. nerippe individuals from five localities showed that at each locus the number of alleles ranged from 4 to 14, and that the observed and expected heterozygosities were 0.324-0.863 and 0.138-0.985, respectively. Significant deviation from the Hardy-Weinberg equilibrium was not observed at any locus. Population structure analysis indicated that there are two genetic groups in Korea, but no population-based gene pool assignments were found. Analysis of $F_{ST}$, $R_{ST}$, and a principal coordinates analysis suggested that the Gureopdo and Yaecheon populations were isolated from other populations. Genetic isolation of the Gureopdo population may be a consequence of unequal population change between Gureopdo and inland populations and to the offshore habitat of Gureopdo. Genetic isolation of the Yaecheon population may be a consequence either of the southernmost location of the population or of the limited sample size available. Further studies with increased sample sizes will be necessary to draw robust conclusions on population isolation and to devise conservation strategies.

• Horticultural Science & Technology
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• v.29 no.6
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• pp.600-609
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• 2011

One hundred twenty two accessions of 6 species in genus Allium were collected throughout 5 regions of Korea. Their genetic relationship was investigated by using inter simple sequence repeat (ISSR) markers. The morphological analysis was measured for 6 quantitative and quantified for 1 qualitative trait. ISSR analysis obtained a total of 370 polymorphic bands by using seventeen primers. The cluster analysis of genus Allium based on morphological data could identify three groups. The accessions of Allium belonged to the Allium monanthum clustered into five groups at genetic distance ranging from 0.94 on the base of ISSR analysis. Correlation analysis between morphological and ISSR analysis showed low coefficient(r = 0.036). These markers are thought to be used in research of molecular markers for classification and cross breeding of Allium monanthum and A. grai.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1703-1709
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• 2008

As genetic markers, single nucleotide polymorphisms (SNP) are very appropriate for the development of genetic tests for economic traits in livestock. Several microsatellite markers have been identified as useful markers for the genetic improvement of Hanwoo. Among those markers, ILSTS035 was recently mapped at a similar position with four SNPs (AH1_11, AH1_9, 31465_446, and 12273_165) in a linkage map of EST-based SNP in BAT6. Among the four SNPs, two SNPs (31465_446 and 12273_165) were analyzed using BLAST at the NCBI web site. The sequences including the 12273_165 SNP were identified at the intron region within the LOC534614 gene on the gene sequence map (Bos taurus NCBI Map view, build 3.1). The LOC534614 gene represents a protein similar to myosin heavy chain, fat skeletal muscle, embryonic isoform 1 in the dog, and myosin_1 (Myosin heavy chain D) in Macaca mulatta. In cattle, the myosin heavy chain was associated with muscle development. The phenotypic data for growth and carcass traits in the 415 animals were analyzed by the mixed ANCOVA (analysis of covariance) linear model using PROC GLM module in SAS v9.1. By the genotyping of Hanwoo individuals (n = 415) to evaluate the association of SNP with growth and carcass traits, it was shown that the 12273_165 SNP region within LOC534614 may be a candidate marker for growth. The results of the statistical analyses suggested that the genotype of the 12273_165 SNP significantly affected birth weight, weight of the cattle at 24 months of age, average daily gain and carcass cold weight (p<0.05). Consequently, the 12273_165 SNP polymorphisms at the LOC534614 gene may be associated with growth in Hanwoo, and functional validation of polymorphisms in LOC534614 should be performed in the future.

• Korean Journal of Veterinary Research
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• v.44 no.2
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• pp.287-292
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• 2004

The objective of present study was to ascertain genetic diversity for cattle parentage testing. A total of 59 random cattle samples(29 Korean native cattle and 30 dairy cows) were genotyped by using 11 microsatellite loci(BM1824, BM2113, ETH10, ETH225, EH3, INRA23, SPS115, TGLA122, TGLA227, TGLA53, and TGLA126). This method consisted of multiplexing PCR procedure and showed reasonable amplification of all PCR products. Genotyping was performed with an ABI 310 genetic analyzer. The number of alleles per locus varied from 5 to 11 with a mean value of 6.73 in the Korean native cattle(KNC), 4 to 9 with a mean of 5.91 in dairy cows(DC). Expected heterozygosity was ranged 0.534~0.855(mean 0.732), 0.370~0.866(mean 0.692) in the KNC and DC, respectively. PIC value was ranged 0.485~0.821(mean 0.684), 0.336~0.834(mean 0.640) in the KNC and DC, respectively. Of the 11 markers, 7 markers(ETH10, EH3, INRA23, SPS115, TGLA122, TGLA227, TGLA53) and 3 markers(INRA23, TGLA227, TGLA53) have relatively high PIC value (>0.7) in the KNC and DC, respectively. The total exclusion probability of 11 microsatellite loci was 0.9997 and 0.9991 in the KNC and DC, respectively. These results present basic information for developing a system for parentage verification and individual identification in the KNC and DC.

• Korean Journal of Weed Science
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• v.18 no.1
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• pp.76-83
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• 1998

Echinochloa species maintained by selling for more than 10 years were classified using random amplified polymorphic DNAs(RAPDs) analysis. Seventy-four decamer of randomly sequence markers were used to classify intraspecific variation irt Echinochloa species. The number of amplification products increased with increasing GC content of the primer in the range between 60% and 70% GC. Single-base substitutions of a primer altered amplification, providing new polymorphisms. The size of amplified DNA was mostly between 0.40kbp and 1.4kbp with the most common bands at 1.1kbp. Echinochloa species were detected with 6 primers which generated 26 polymorphic amplified DNAs. By hierarchical cluster analysis, Echinochloa species collected in Korea were divided into three groups. These results revealed that RAPD markers are useful tools for the determination of genetic variations in Echinochloa species.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.321-336
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• 2018

Sesame (Sesamum indicum L.) is an important oilseed crop grown in tropical and subtropical areas. The objective of this study was to investigate the genetic relationships among 129 sesame landraces and cultivars using simple sequence repeat (SSR) markers. Out of 70 SSRs, 23 were found to be informative and produced 157 alleles. The number of alleles per locus ranged from 3 - 14, whereas polymorphic information content ranged from 0.33 - 0.86. A distance-based phylogenetic analysis revealed two major and six minor clusters. The population structure analysis using a Bayesian model-based program in STRUCTURE 2.3.4 divided 129 sesame accessions into three major populations (K = 3). Based on pairwise comparison estimates, Pop1 was observed to be genetically close to Pop2 with $F_{ST}$ value of 0.15, while Pop2 and Pop3 were genetically closest with $F_{ST}$ value of 0.08. Analysis of molecular variance revealed a high percentage of variability among individuals within populations (85.84%) than among the populations (14.16%). Similarly, a high variance was observed among the individuals within the country of origins (90.45%) than between the countries of origins. The grouping of genotypes in clusters was not related to their geographic origin indicating considerable gene flow among sesame genotypes across the selected geographic regions. The SSR markers used in the present study were able to distinguish closely linked sesame genotypes, thereby showing their usefulness in assessing the potentially important source of genetic variation. These markers can be used for future sesame varietal classification, conservation, and other breeding purposes.