• Fisheries and Aquatic Sciences
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• v.11 no.2
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• pp.82-87
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• 2008

Marine fisheries are important natural resources and must be maintained, especially fish species that are important sources of food. Despite the increase in stocking programs to maintain fisheries with artificially raised fish, the genetic impact stocking has on the wild fry population has not been addressed. Genetic variation in rock bream, Oplegnathus fasciatus, within and between wild-caught parents and the $F_1$ generation produced by them in 1 day was assayed using nine highly variable micro satellite markers. The nine micro satellite loci used in this study displayed diverse polymorphisms, and in total, 98 different alleles were observed over all loci. Differences in genetic variability of the $F_1$ offspring compared to their wild-caught parents (brood stock) were observed in terms of allele frequency, gene diversity, and heterozygosity. Although the $F_1$ generation of rock bream was missing 16% of the micro satellite alleles, no significant reduction was found in mean heterozygosity of the $F_1$ population compared to the brood stock. Eight of nine loci showed significant Hardy-Weinberg equilibrium (HWE) deviations in the $F_1$ population, while the brood stock deviated from HWE at three micro satellite loci (KOF85, KOF360 and KOF374). These deviations showed mostly a deficit of heterozygotes. Our results provide evidence for genetic differences in the $F_1$ hatchery offspring compared to their wild-caught parents and reinforce the need for a series of consecutive egg collections to avoid the loss of genetic variability. This also further underscores the importance of monitoring genetic variability of hatchery populations for the conservation of natural rock bream resources.

• Korean Journal of Breeding Science
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• v.41 no.4
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• pp.429-436
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• 2009

We conducted a QTL analysis of grain quality traits using 117 $BC_3F_4$ and $BC_3F_5$ lines developed from a cross between Ilpumbyeo and Moroberekan. Genotypes of 117 $BC_3F_5$ lines were determined using 134 simple sequence repeat (SSR) markers. A linkage map constructed using 134 SSR markers was employed to characterize quantitative trait loci (QTL). The 117 $BC_3F_4$ and $BC_3F_5$ lines were evaluated for eleven grain quality traits in 2005 and 2006. A total of 18 QTLs were identified for eleven traits, and the phenotypic variance explained by each QTL ranged from 9.9% to 35.2%. Moroberekan alleles contributed positive effects in the Ilpumbyeo background at two QTL loci for 1,000 grain weight. Four QTLs, two for chalky rice and one each for 1,000 grain weight and head rice were consistently detected in two consecutive years indicating that these QTLs are stable. Clusters of QTLs were observed in three chromosome regions. One cluster harboring five QTLs including head rice and brown rice ratio near SSR markers RM190 and RM314 was detected on chromosome 6. Another cluster harboring grain weight and white belly was detected on chromosome 2. Increase in white belly at this locus might be due to the increase in grain weight due to the presence of the Moroberekan allele. The Moroberekan alleles at two QTL loci, gw3 and gw4 associated with increased grain weight might be useful in breeding programs to develop high-yielding cultivars.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.1
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• pp.1-6
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• 2009

Genetic variability is an important component in the ability of populations to adapt in the face of environmental change. Severe human impacts reduced Muzzafarnagri sheep of India from 500,000 in 1972 to 10,989 in 1973-74. Here we report for the first time the effect of this population decline on levels of genetic variability at 13 FAO recommended ovine microsatellite loci and contrast levels of variability to that in a breed from the same geographical region, which differed in numbers, by an order of magnitude (Marwari sheep). Of the 13 loci, 100% were polymorphic in both breeds. A high degree of genetic variation was observed within populations in terms of both allele diversity (number of alleles per locus, >4) and gene diversity (expected heterozygosity, >0.5), which implied that there is still a substantial amount of genetic diversity at the nuclear loci in a declining population. Nevertheless, overall low number of alleles per locus and relatively less abundance of low frequency alleles in Muzzafarnagri sheep suggested that genetic variability has been comparatively reduced in this population. Bottleneck analysis indicated that a genetic bottleneck did not occur during the most recent decline. In addition, we found that the differentiation among populations was moderate ($F_{ST}$= 11.8%). This study on assessment of genetic effects of the population declines in ovines is a step towards identification of genetically impoverished or healthy populations, which could prove to be a useful tool to facilitate conservation planning in this important species of small ruminants.

• Parasites, Hosts and Diseases
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• v.45 no.1 s.141
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• pp.59-63
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• 2007

Merozoite surface protein-1(MSP-1) and merozoite surface protein-2(MSP-2) were used to develop vaccines and to investigate the genetic diversity in Plasmodium falciparum malaria in Iran. Nested polymerase chain reaction amplification was used to determine polymorph isms of block 2 of the MSP-1 and the central domain of MSP-2 genes. A total of 67 microscopically positive P. falciparum infected individuals from a major endemic region, southeast Iran, were included in this trial. Nine alleles of MSP-1 and 11 alleles of MSP-2 were identified. The results showed that amplified product from these surface antigen genes varied in size and there was specific pattern for each isolate. Besides, regarding this pattern, 23 multiple infections with at least 2 alleles were observed. While the endemic regions of malaria in Iran is classified in low to moderate group, but extensive polymorphism was observed for each marker and the MSP-2 central repeat was the most diverse that could be considered in designing malaria vaccine.

• Animal cells and systems
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• v.16 no.3
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• pp.224-229
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• 2012

The Korean shiner (Coreoleuciscus splendidus, Gobioninae), a small freshwater fish native to Korea Peninsula, widely inhabits in most of the major drainages in South Korea. Here we describe the development of 14 novel and polymorphic microsatellites for this species and its effective utilization in estimation of genetic diversity using 72 individuals from three sampling sites in different drainages. Loci were isolated from a microsatellite enrichment procedure using probe-labeled magnetic beads. A total of 242 alleles were detected across all loci with an average of 17.3 alleles per locus ranging 4 32. The loci varied levels of polymorphism as evident from its expecte heterozygosity ranging from 0.111 to 0.957. The average pairwise $F_{ST}$ between two populations examined shows significant differentiation ($F_{ST}$ = 0.215, p<0.05). The 14 microsatellite loci developed here will also be useful to explain for the genetic structures among geographically isolated populations and gene flow dynamics within drainages in this species as well as the closely related species.

• Journal of Crop Science and Biotechnology
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• v.11 no.2
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• pp.83-90
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• 2008

Two hundred and sixty Korean soybean landrace accessions were analyzed for polymorphism at 92 simple sequence repeat(SSR) loci. The 995 identified alleles served as raw data for estimating genetic diversity and population structure. The number of alleles at a locus ranged from three to 27 with a mean of 10.4 alleles per locus. $F_{ST}$ values estimated by analysis of molecular variance(AMOVA) using SSR data set were 0.018, 0.027, and 0.016 for usage, collection site and maturity groups, respectively, indicating little genetic differentiation. The model-based clustering analysis placed the accessions into three clusters(K=3) with 0.0503 of $F_{ST}$, indicating moderate genetic differentiation. Duncan's Multiple Range Test at K = 3 on the basis of 18 quantitative traits revealed that one cluster was mainly differentiated from the other two clusters by seed related traits and the other two clusters were differentiated from each other by biochemical traits. Genetic structure of Korean soybean landraces was differentiated by model-based clustering and supported by their phenotypic traits in part. This preliminary study could be the first step towards more efficient germplasm management and utilization of soybean landraces and helpful in association studies between genotypic and phenotypic traits in Korean soybean landraces.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.6
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• pp.776-783
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• 2008

In this study, we investigated the genetic diversity and phylogenetic relationship of six duck populations by employing the genetic polymorphisms of 20 microsatellites. The parameters used in this study included number of alleles, average effective numbers of alleles (E) and average rates of heterozygosity of each population. The results showed that all the microsatellite loci were highly polymorphic except that the locus AJ515896 in Muscovy duck was 0. The average PIC (0.762), average h (0.7843) and average E (5.261) of the six duck populations were all high, indicating that the gene polymorphisms and genetic diversity were high. The test of Hardy-Weinberg equilibrium showed that the six populations in this study were all in Hardy-Weinberg disequilibrium. The F-statistic analysis results showed the range of FST was from 0.0205 (AJ515895) to 0.2558 (AJ515896). The mean FST was 0.0936. Phylogenetic study revealed that Peking duck (Z1 and Z4), Shaoxing duck, Cherry Valley duck and Aobaixing duck were clustered in one group, while the Muscovy duck was clustered in one group alone. The phylogenetic relationships among different populations were in accordance with their breeding history and distribution. Our data suggested that the 20 microsatellite loci were effective markers for analysis of genetic relationships among duck populations.

• IMMUNE NETWORK
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• v.20 no.5
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• pp.43.1-43.11
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• 2020

Capicua (CIC) is a transcriptional repressor that regulates several developmental processes. CIC deficiency results in lymphoproliferative autoimmunity accompanied by expansion of CD44^hiCD62L^lo effector/memory and follicular Th cell populations. Deletion of Cic alleles in hematopoietic stem cells (Vav1-Cre-mediated knockout of Cic) causes more severe autoimmunity than that caused by the knockout of Cic in CD4⁺CD8⁺ double positive thymocytes (Cd4-Cre-mediated knockout of Cic). In this study, we compared splenic CD4⁺ T cell activation and proliferation between whole immune cell-specific Cic-null (Cic^f/f;Vav1-Cre) and T cell-specific Cic-null (Cic^f/f;Cd4-Cre) mice. Hyperactivation and hyperproliferation of CD4⁺ T cells were more apparent in Cic^f/f;Vav1-Cre mice than in Cic^f/f;Cd4-Cre mice. Cic^f/f;Vav1-Cre CD4⁺ T cells more rapidly proliferated and secreted larger amounts of IL-2 upon TCR stimulation than did Cic^f/f;Cd4-Cre CD4⁺ T cells, while the TCR stimulation-induced activation of the TCR signaling cascade and calcium flux were comparable between them. Mixed wild-type and Cic^f/f;Vav1-Cre bone marrow chimeras also exhibited more apparent hyperactivation and hyperproliferation of Cic-deficient CD4⁺ T cells than did mixed wild-type and Cic^f/f;Cd4-Cre bone marrow chimeras. Taken together, our data demonstrate that CIC deficiency at the beginning of T cell development endows peripheral CD4⁺ T cells with enhanced T cell activation and proliferative capability.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.95-95
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• 2017

Lodging is a serious issue in rice production, because it drastically decreases the biomass production and grain yield. Since the Green Revolution, the lodging resistance has been increased by lowering the moment of above-ground parts due to the short culm by the semi-dwarf gene sd1. However, it has been pointed out that sd1 alone has suppressive effects for biomass production and yield. To increase rice yield, the long-culm and large panicle type varieties with a superior lodging resistance need to be developed. To improve the lodging resistance and yield of these type varieties, it would be effective to identify novel alleles for these traits underlying natural variations in rice and to pyramid these alleles to a single rice variety. In order to perform this strategy, we have developed new rice lines derived from crosses among varieties with superior alleles. At first, TULT-gh-5-5 was selected from a cross between strong culm and high biomass variety Leaf Star and high-yielding variety Takanari, and TUAT-32HB was selected from a cross between high-yielding variety Akenohoshi and Takanari. Then, we developed the super thick-culm and super grain-bearing line, LTAT-29 derived from a cross between TULT-gh-5-5 and TUAT-32HB. In the current study, to identify the QTLs and genes relating to the strong culm and the high yield of LTAT-29, we performed QTL analysis using SNPs markers with $F_2$ population derived from a cross between LTAT-29 and Takanari. LTAT-29 has never lodged throughout the growth period despite it had long culms and heavy panicles. LTAT-29 had a larger outer diameter of the culm and twice the size of the section modulus than Takanari. As a result, the bending moment at breaking of LTAT-29 was significantly larger than that of Takanari. Brown rice yield of LTAT-29 was $9.2t\;ha^{-1}$ about 10% higher than that of Takanari due to the larger number of spikelets per panicle. LTAT-29 had a greater number of secondary branches per panicle. In the $F_2$ population between LTAT-29 and Takanari, we found continuous frequency distributions in the section modulus and the spikelet number per panicle. Two QTLs increased the section modulus by the alleles of LTAT-29 were detected on Chr.1L and Chr.2L. One QTL increased the spikelet number per panicle of Takanari by the allele of LTAT-29 was detected on Chr.1L, and two QTLs increased the number of secondary branches per panicle by the alleles of LTAT-29 were detected on Chr.1L and Chr.4L. It was found that the alleles of these QTLs were the japonica type originated from Leaf Star or Akenohoshi. The novel QTLs for the traits related to super thick-culm and super grain-bearing and their combinations could be utilized for improving the lodging resistance and yield in rice varieties.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.33-33
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• 2015

Clubroot disease is the major threat to the production of Chinese cabbage (Brassica rapa L.) in Japan. Although the breeding of the clubtoot resistant (CR) cultivars is one of the most efficient ways to control this disease, the CR cultivars do not always have effects due to the breakdown of resistance. Therefore, it is necessary to develop the breeding strategy to accumulate multiple CR genes in a single cultivar effectively. We have identified two incomplete dominant CR loci, Crr1 and Crr2, which are originated from the European CR turnip Siloga. To investigate the effectiveness of marker-assisted selection (MAS) for CR breeding, the inbred line with Crr1 and Crr2 was crossed with parental lines of the existing CR $F_1$ cultivar of Chinese cabbage, followed by 5 times of MAS and backcrossing. The $F_1$ derived from a cross between the resulting parental lines improved the clubroot resistance as expected and had the same morphological characters as the original $F_1$ cultivar. We have shown that the Crr1 locus comprised two loci: Crr1a, which by itself conferred resistance to the mild isolate; and Crr1b, which had a minor effect, but was not required for Crr1a-mediated resistance. Further genetic analysis suggested that Crr1b was necessary to acquire resistance to the more virulent isolate in combination with Crr2. Molecular characterization of Crr1a encoding TIR-NB-LRR class of R protein revealed that there were at least 4 alleles in Japanese CR cultivars of Chinese cabbage. PCR analysis with Crr1a-specific markers demonstrated that the functional alleles were predicted to be present in European CR turnips, Debra and 77b besides Siloga, whereas rarely in Japanese CR cultivars, indicating that Crr1a is an useful source to improve the resistance of Chinese cabbage cultivars.