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

• Korean Journal of Breeding Science
• /
• v.43 no.4
• /
• pp.304-310
• /
• 2011

In previous studies, we reported QTLs for grain weight (GW), qGW3 and for spikelets per panicle (SPP), qSPP3 linked to RM60 on chromosome 3 using advanced backcross lines derived from a cross between Oryza sativa ssp. Indica cv. Milyang 23 and O. glaberrima. The O. glaberrima alleles at this locus increased GW and spikelets per panicle in the Milyang 23 background. To further confirm and narrow down the position of the QTLs on chromosome 3, substitution mapping was performed using five lines containing the target O. glaberrima segment on chromosome 3. The size and position of the O. glaberrima segment on chromosome 3 were different in each line. These lines possessed 3-10 non-target O. glaberrima introgressions in the Milyang 23 background. These five lines were evaluated for seven agronomic traits including 1,000 grain weight and spikelets per panicle and also genotyped with seven SSR markers. Four lines were informative in delimiting the position of QTLs, qGW3 and qSPP3. Two lines with the O. glaberrima segment flanked by SSR markers, RM60 and RM523 displayed significantly higher values than Milyang 23 in GW and SPP whereas two lines without that O. glaberrima segment displayed no difference in GW and SPP compared to Milyang 23. The result indicates that two QTL, qGW3 and qSPP3 are located in the interval between RM60 and RM523 which are 1.2-Mb apart. Introgression lines having QTLs, qGW3 and qSPP3 would be useful materials not only to indentify the relationship between these two yield QTLs, but also to develop high yielding variety via marker-aided selection technology.

• Journal of Life Science
• /
• v.29 no.2
• /
• pp.152-157
• /
• 2019

Porphyra yezoensis is a red algal species in the genus Porphyra. The phenetics and genetic diversity of four populations of P. yezoensis in Korea were reconstructed using random amplified polymorphic DNA (RAPD) markers. Overall, 55 fragments were generated among the tested P. yezoensis array with 20 OPERON primers. A total of 30(54.5%) of these bands were polymorphic. The OPA-18-02 band was amplified in the samples of Nakdong population and absent in them of other three populations. The OPA-20-02 band was only amplified in the Seocheon population. Both bands exhibited distinctive patterns in specific populations. The effective number of alleles per locus (Ae) ranged from 1.161 to 1.293 with a mean of 1.366. The Seocheon population had a high expected diversity (0.163). The Nakdong population was an isolated endemic and intertidal zone. Thus the narrow distributed Nakdong population had a low expected diversity (0.092). Shannon's index of phenotypic diversity (I) of the Seocheon population (0.238) was the highest among all populations. Total genetic diversity ($H_T$) varied between 0.132 for OPA-02 and 0.420 for OPA-19. The interlocus variation of genetic diversity ($H_S$) was 0.059 for OPA-18 and 0.339 for OPA-19. On a per locus basis, the proportion of total genetic variation due to differences among populations ($G_{ST}$) ranged from 0.012 for OPA-11 to 0.762 for OPA-18 with a mean of 0.415, indicating that 42% of the total variation was found among these populations. In an assessment of the proportion of diversity present within this species, 58.5% (100%-41.5%) of genetic variation resided within the populations studied. The Nm was estimated to be low (0.705).

• Korean Journal of Plant Resources
• /
• v.34 no.5
• /
• pp.478-490
• /
• 2021

We aimed to generate basic breeding data for melon (Cucumis melo L.). A total of 219 melon accessions conserved at the National Agrobiodiversity Center (NAC) in Rural Development Administration (RDA) were used in this study, of which 72 (33%) were collected from India. The majority of accessions showed orange (42%) and white (36%) flesh color. In addition to phenotypic evaluations, the accessions were genotyped using a molecular marker for the carotenoid biosynthesis gene CmOr. DNA fragments of the expected size were amplified in 205 out of 219 accessions. Digestion of the PCR products with HinfI restriction endonuclease showed 100% concordance between phenotype and genotype in green-fleshed accessions, but 98%, 97%, and 80% concordance in orange-, white-, and creamy-fleshed accessions, respectively. Sequence analysis revealed single nucleotide changes in the three positions of SNP1, SNP2 and SNP1int in the CmOr gene among accessions. These newly found alleles suggest that there are multiple mechanisms in determining fruit flesh color in melon. Also, the phenotype data of diverse accessions obtained in this study will be a valuable source for melon breeding.

• Korean Journal of Clinical Laboratory Science
• /
• v.53 no.3
• /
• pp.249-256
• /
• 2021

Asthma is a chronic inflammatory airway disease. There are many factors including genetic and environmental factors that influence asthma. The mitogen-activated protein kinase (MAPK) pathway is involved in maintaining the T helper cells 1 and 2 (Th1/Th2) balance and plays an important role in the development of asthma. In this study, the correlation between the NDFIP2 gene that regulates the MAPK pathway and asthma was analyzed. The genetic polymorphism of the NDFIP2 gene was analyzed between 193 asthma patients and 3,228 healthy controls in Korea. As a result, 4 single nucleotide polymorphisms (SNPs) showed a significant correlation (P<0.05) and high relative risk with asthma. Among them, rs2783122 of NDFIP2 showed a statistically significant association with asthma (P-value=9.76×10^-6, odds ratio (OR)=1.67, 95% confidence interval (CI)=1.33~2.10). In the SNP imputation on the NDFIP2, 16 SNPs were discovered, and all of them showed significant correlation with asthma and high odds ratio. The genotype-based mRNA expression analysis revealed that the group of minor alleles of rs1408049 showed increased mRNA expression. Increased NDFIP2 expression causes the activation of the MAPK pathway, and this may influence the development of asthma. In conclusion, the polymorphisms of NDFIP2 are associated with asthma development and this can provide the basis for new guidelines for the management of asthma in the Korean population.

• Animal Bioscience
• /
• v.34 no.1
• /
• pp.2-11
• /
• 2021

Objective: The aim of the study was to evaluate the influence of polymorphic loci and other factors on milk performance and the technological properties of milk. Methods: The analysis was performed on Simmental and Holstein cows in field conditions (n = 748). Milk yield in kg, fat and protein percentage and yield were evaluated. Technological properties were evaluated by milk fermentation ability, renneting, and an alcohol test. Polymorphisms in the acyl-CoA diacylgycerol transferase 1 (DGAT1), leptin (LEP), fatty acid synthase (FASN), stearoyl CoA desaturase 1 (SCD1), casein beta (CSN2), casein kappa (CSN3), and lactoglobulin beta genes were genotyped, and association analysis was performed. Results: The DGAT1 AA genotype was associated with higher milk, protein and fat yields (p<0.05). The MM genotype in the LEP gene was associated with a lower protein percentage and the W allele with a higher protein percentage (p<0.05). In cows with the FASN GG genotype, the protein percentage was higher, but the A allele was associated with higher milk, protein and fat yields than the G allele. The TT genotype in SCD1 was associated with the lowest milk, protein and fat yields and with the highest milk protein percentage (p<0.01). The T allele had higher values than the C allele (p<0.05) except for fat percentage. The genotype CSN3 AA was associated with a significantly heightened milk yield; BB was associated with a high protein percentage. The effect of the alleles on the technological properties was not significant. The CSN2 BB genotype was associated with the best alcohol test (p<0.01), and the renneting order was inverse. Milk from cows with the CSN2 A1A1 genotype was best in the milk fermentation ability. CSN3 significantly affected the technological properties. Conclusion: The findings revealed the potential of some polymorphic loci for use in dairy cattle breeding and for the management of milk quality. In field research, the pivotal role of farms in milk yield, composition and technological properties was confirmed.

• Animal Bioscience
• /
• v.34 no.7
• /
• pp.1116-1122
• /
• 2021

Objective: The aim was to characterize the genetic diversity evolution of the registered Mexican Charolais cattle population by pedigree analysis. Methods: Data consisted of 331,390 pedigree records of animals born from 1934 to 2018. Average complete generation equivalent, generation interval, effective population size (N_e), and effective numbers of founders (f_e), ancestors (f_a), and founder genomes (N_g) were calculated for seven five-year periods. The inbreeding coefficient was calculated per year of birth, from 1984 to 2018, whereas the gene contribution of the most influential ancestors was calculated for the latter period. Results: Average complete generation equivalent consistently increased across periods, from 4.76, for the first period (1984 through 1988), to 7.86, for the last period (2014 through 2018). The inbreeding coefficient showed a relative steadiness across the last seventeen years, oscillating from 0.0110 to 0.0145. During the last period, the average generation interval for the father-offspring pathways was nearly 1 yr. longer than that of the mother-offspring pathways. The effective population size increased steadily since 1984 (105.0) and until 2013 (237.1), but showed a minor decline from 2013 to 2018 (233.2). The population displayed an increase in the f_a since 1984 and until 2008; however, showed a small decrease during the last decade. The effective number of founder genomes increased from 1984 to 2003, but revealed loss of genetic variability during the last fifteen years (from 136.4 to 127.7). The f_a:f_e ratio suggests that the genetic diversity loss was partially caused by formation of genetic bottlenecks in the pedigree; in addition, the N_g:f_a ratio indicates loss of founder alleles due to genetic drift. The most influential ancestor explained 1.8% of the total genetic variability in the progeny born from 2014 to 2018. Conclusion: Inbreeding, N_e, f_a, and N_g are rather beyond critical levels; therefore, the current genetic status of the population is not at risk.

• Animal Bioscience
• /
• v.35 no.5
• /
• pp.639-647
• /
• 2022

Objective: This study was conducted to clone and compare the molecular characteristics of the deiodinase 2 (DIO2) gene between Sichuan White geese and Landes geese, and to analyze the association between polymorphisms of the DIO2 gene and head dimensions in Tianfu meat geese. Methods: The coding sequence of the DIO2 gene was cloned by polymerase chain reaction and vector ligation and aligned by DNAMAN software. A total of 350 Tianfu meat geese were used to genotype the polymorphisms of the DIO2 gene and measure the head dimensions. Association analysis between the polymorphisms of the DIO2 gene and head dimensions was carried out. Results: An 840-bp coding sequence of the DIO2 gene was obtained and comparison analysis identified four polymorphic loci between Sichuan White geese and Landes geese. Further analysis showed that the dominant alleles for the four polymorphic loci were G, G, A, and T and the frequency of the heterozygous genotype was higher than that of the homozygous genotype in Tianfu meat geese. Compared to that in the population of non-knob geese of Tianfu meat geese, the head dimensions in the population of knob geese were significantly higher except for nostril height. However, in the non-knob geese, beak width 1, beak width 2, nostril length, cranial width 1, and maxillary length had significant differences among different genotypes or haplotypes/diplotypes. Conclusion: These results suggested that polymorphisms of the DIO2 gene could be considered molecular markers to select larger heads of geese in the population of non-knob geese.

• Journal of Life Science
• /
• v.33 no.8
• /
• pp.623-631
• /
• 2023

This study was conducted to develop microsatellite markers in Parapristipoma trilineatum using next-generation sequencing. A total of 402,244,934 reads were generated on the Illumina Hiseq X Ten System, yielding 60,738,985,034 bp of sequences. The de novo assembly resulted in 1,320,995 contigs. A total of 952,326 contigs (0.016%) including 151 microsatellite loci were derived from the 1,320,995 contigs longer than 640 bp. A total of 34 primer sets were designed from the 151 microsatellite loci. As a result, 15 microsatellite loci were chosen and used for assuming population genetic parameters in the wild and farmed populations. The mean number of effective alleles was 12, ranging from 6 to 25. The observed heterozygosity (H_O) and the expected heterozygosity (H_E) ranged between 0.530 and 0.873, with an average of 0.750, and from 0.647 to 0.895, with an average of 0.793, respectively. According to these results, the developed set of 15 microsatellite markers is expected to be useful for the analysis of genetic characteristics in the population of P. trilineatum in Korea. There are requirements now for further genetic information, fishery resource management, breeding guidelines, support with the selection of breeds and studies on the effects of release, all of which will improve species conservation, and through future research, we aim to offer genetic foundational data with that goal.

• Clinical and Experimental Pediatrics
• /
• v.48 no.4
• /
• pp.376-379
• /
• 2005

Purpose : Mycoplasama pneumoniae is a leading cause of pneumonia and exacerbates other respiratory conditions such as asthma. Surfactant protein A(SP-A) is involved in surfactant physiology and surfactant structure, and plays a major role in innate host defense and inflammatory processes in the lung. In this study, SP-A mediated mycoplasma cidal activity. The candidate-gene approach was used to study the association between the SP-A gene locus and Mycoplasama pneumoniae pneumonia in the genetically homogeneous Korean population. Methods : PCR-cRFLP-based methodology was used to detect SP-A genotype. The forty nine children with Mycoplasama pneumoniae pneumonia were matched to 50 nomal neonates. Results : The specific frequencies for the alleles of the SP-A1 and SP-A2 gene in the study population were : $6A^2=21$ percent, $6A^3=45$ percent, $6A^4=11$ percent, $6A^8=9$ percent, $6A^{14}=8$ percent, 1A=11.3 percent, $1A^0=38$ percent, $1A^1=12.7$ percent, $1A^2=9.2$ percent, $1A^5=15.5$ percent, $1A^7=2.9$ percent, $1A^8=4.9$ percent, $1A^9=2.2$ percent, others=3.3 percent. The frequencies of specific genotypes such as $1A^2$ was higher than control group, significantly. Conclusion : $1A^2$ are susceptible factors for Mycoplasama pneumoniae pneumonia. We conclude that the SP-A gene locus($1A^2$) is an important determinant for predisposition to Mycoplasama pneumoniae pneumonia in children.