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

• Animal Bioscience
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• v.35 no.12
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• pp.1827-1838
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• 2022

Objective: The semen quality of stallions including sperm motility is an important target of selection as it has a high level of individual variability. However, effects of the molecular architecture of the genome on the mechanisms of sperm formation and their preservation after thawing have been poorly investigated. Here, we conducted a genome-wide association study (GWAS) for the sperm motility of cryopreserved semen in stallions of various breeds. Methods: Semen samples were collected from the stallions of 23 horse breeds. The following semen characteristics were examined: progressive motility (PM), progressive motility after freezing (FPM), and the difference between PM and FPM. The respective DNA samples from these stallions were genotyped using Axiom Equine Genotyping Array. Results: We performed a GWAS search for single nucleotide polymorphism (SNP) markers and potential genes related to motility properties of frozen-thawed semen in the stallions of various breeds. As a result of the GWAS analysis, two SNP markers, rs1141327473 and rs1149048772, were identified that were associated with preservation of the frozen-thawed stallion sperm motility, the relevant putative candidate genes being NME/NM23 family member 8 (NME8), olfactory receptor family 2 subfamily AP member 1 (OR2AP1), and olfactory receptor family 6 subfamily C member 4 (OR6C4). Potential implications of effects of these genes on sperm motility are herein discussed. Conclusion: The GWAS results enabled us to localize novel SNPs and candidate genes for sperm motility in stallions. Implications of the study for horse breeding and genetics are a better understanding of genomic regions and candidate genes underlying stallion sperm quality, and improvement in horse reproduction and breeding techniques. The identified markers and genes for sperm cryotolerance and the respective genomic regions are promising candidates for further studying the biological processes in the formation and function of the stallion reproductive system.

• Animal Bioscience
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• v.37 no.7
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• pp.1168-1176
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• 2024

Objective: As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future. Methods: Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations. Results: Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations. Conclusion: The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.

• Journal of Animal Science and Technology
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• v.66 no.4
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• pp.717-725
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• 2024

The Hanwoo traceability system currently utilizes 11 dinucleotide repeat microsatellite (MS) markers. However, dinucleotide repeat markers are known to have a high incidence of polymerase chain reaction (PCR) artifacts, such as stutter bands, which can complicate the accurate reading of alleles. In this study, we examined the polymorphisms of the 11 dinucleotide repeat MS markers currently employed in traceability systems. Additionally, we explored four trinucleotide repeat MS markers and one tetranucleotide repeat MS marker in a sample of 1,106 Hanwoo cattle. We also assessed the potential utility of the tri- and tetranucleotide repeat MS markers. The polymorphic information content (PIC) of the five tri- and tetranucleotide repeat markers ranged from 0.663 to 0.767 (mean: 0.722), sufficiently polymorphic and slightly higher than the mean (0.716) of the current 11 dinucleotide repeat markers. Using all 16 markers, the mean PIC was 0.718. The estimated probability of identity (PI) was 3.13 × 10^-12 using the 11 dinucleotide repeat markers, 7.03 × 10^-6 using the five tri- and tetranucleotide repeat markers, and 2.39 × 10^-17 using all 16 markers; the respective PI_half-sibs values were 2.69 × 10^-9, 1.29 × 10^-4, and 3.42 × 10^-13; and the respective PIsibs values were 3.89 × 10^-5, 9.6 × 10^-3, and 3.69 × 10^-7. The probability of exclusion1 (PE₁) was 0.999864 for the 11 dinucleotide repeat markers, 0.981141 for five of the tri- and tetranucleotide repeat markers, and > 0.99 for all 16 markers; the respective PE₂ values were 0.994632, 0.901369, and > 0.99; and the respective PE₃ values were 0.998702, > 0.99, and > 0.99. The five investigated triand tetranucleotide repeat MS markers can be used in combination with the 11 existing MS markers to improve the accuracy of individual identification and paternity testing in Hanwoo.

• Journal of Life Science
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• v.28 no.3
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• pp.314-319
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• 2018

We analyzed QTLs for alkali-related digestion by using 120 population crossed Cheongcheong and Nagdong derived from anther culture (CNDH). The DNA markers located in the QTLs gene were selected and applied to existing cultivars. As a result of the investigation of the alkali decay degree, brown rice of Cheongcheong and Nagdong was 1.9 and 1.6, respectively, and the CNDH was $3.79{\pm}2.01$, and the distribution of variance was distributed to 7.0-1.0. The milled rice of Cheongcheong and Nagdong was 5.6 and 4.1, respectively. The mean of the CNDH was $4.86{\pm}1.55$, and the distribution of variance was distributed to 7.0-2.0. Variation distribution curves showed continuous variation that was close to non-normal distribution. In the QTLs analysis, qBRA2, qBRA6, and qBRA11 were mapped in 1-2 replications of brown rice. QHRA2-1, qHRA2-2, qHRA2-3, qHRA3, and qHRA8 were mapped in the first replication. QHRA2-1, qHRA2-2, qHRA2-3 and qHRA3 were mapped in the second replicates. And mapped to qHRA5 in 4 replicates. These were found on chromosome 2, 3, 6, 8 and 11, respectively. The phenotypic variations of qBRA2, qBRA6, and qBRA11 on the chromosomes of brown and milled rice were 1-9%. The polymorphism was analyzed for 12 types of the japonica type and six types of the indica type, based on the nine markers found in the QTLs analysis of alkali digestion. Chromosome 11, RM27258, was selected to determine the segregation ratio, which shows the difference in size by the band pattern. The results of this study will be used as basic data for the development of high-quality rice cultivars.

• Journal of Life Science
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• v.28 no.7
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• pp.795-801
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• 2018

This study was conducted to investigate the association of single nucleotide polymorphism (SNP) markers on equine chromosomes (ECA) 3 and 9 with body weight in Jeju horses. We used DNA samples and body weight data of 320 horses provided by the Livestock Promotion Agency, Jeju Special Self-Governing Province, and the Korean Racing Association, respectively. We genotyped all the experimental animals using nine SNP markers located on ECA 3 (BIEC2-808466, BIEC2-808543, BIEC2-808967, and BIEC2-809370) and ECA 9 (BIEC2-1105370, BIEC2-1105372, BIEC2-1105377, BIEC21105505, and BIEC2-1105840). These markers were selected due to their effects on body conformation traits in horses. The joint effect of the genotypes of the two SNP markers (BIEC2-808467 and BIEC2-1105377) regarding body weight were also evaluated. The estimated breeding value (EBV) of body weight was obtained as the dependent variable for association analyses using a linear mixed model. Significant associations were detected between SNP markers (BIEC2-808543, BIEC2-808967, BIEC2-809370, BIEC2-1105370, BIEC2-1105372, and BIEC2-1105377) and the body weight EBV. In addition, the joint genotype effect of the BIEC2-808467 and BIEC2-1105377 on the body weight EBV was significant. These results indicate that the SNP markers, which showed their significant effects on body conformation, can be used as genetic markers to improve the efficiency of the selective breeding program for the body weight traits in Jeju horses.

• Tuberculosis and Respiratory Diseases
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• v.49 no.4
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• pp.453-465
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• 2000

Background : Lung carcinogenesis is a multistage process involving alterations in multiple genes and diverse pathway. Mutational activation of oncogenes and inactivation of tumor suppressor genes, and subsequent increased genetic instability are the major genetic events. The p53 gene and FHIT gene as tumor suppressor genes contribute to the pathogenesis of lung cancer, evidenced by mutation, microsatellite instability(MI) and loss of heterozygosity(LOH). Methods : We analysed genetic mutations of p53 and FHIT gene in 29 surgical specimens of nonsmall cell lung cancer using PCR-single strand conformation polymorphism, DNA sequencing and RT-PCR. MI and LOH were analyzed in loci of D3S1285, D9S171, and TP53. Results : In 2 cases, point mutation of p53 gene was observed on exon 5. MI of 3 times and LOH of 14 times were observed in at least one locus. In terms of the location of microsatellite, D3S1285 as a marker of FH1T was observed in 5 cases out of 26 specimens; D9S171 as a marker of p16 in 5 out of 17; and TP53 as a marker of p53 in 7 out of 27. In view of histologic type, squamous cell carcinoma presented higher frequency of microsatellite alteration, compared to others. Mutation of FHIT gene was observed in 11 cases and 6 cases of those were point mutation as a silent substitution on exon 8. FHIT mRNA expression exhibited deletion on exon 6 to 9 in 4 cases among 15 specimens, presenting beta-actin normally. Conclusion : Our results show comparable frequency of genetic alteration in nonsmall cell lung cancer to previous studies of Western countries. Microsatellite analysis might have a role as a tumor marker especially in squamous cell carcinoma. Understanding molecular abnormalities involved in the pathogenesis could potentially lead to prevention, earlier diagnosis and the development of novel investigational approaches to the treatment of lung cancer.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.7
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• pp.925-937
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• 2016

In the last few decades, transgenic animal technology has witnessed an increasingly wide application in animal breeding. Reproductive traits are economically important to the pig industry. It has been shown that the bone morphogenetic protein receptor type IB (BMPR1B) A746G polymorphism is responsible for the fertility in sheep. However, this causal mutation exits exclusively in sheep and goat. In this study, we attempted to create transgenic pigs by introducing this mutation with the aim to improve reproductive traits in pigs. We successfully constructed a vector containing porcine BMPR1B coding sequence (CDS) with the mutant G allele of A746G mutation. In total, we obtained 24 cloned male piglets using handmade cloning (HMC) technique, and 12 individuals survived till maturation. A set of polymerase chain reactions indicated that 11 of 12 matured boars were transgene-positive individuals, and that the transgenic vector was most likely disrupted during cloning. Of 11 positive pigs, one (No. 11) lost a part of the terminator region but had the intact promoter and the CDS regions. cDNA sequencing showed that the introduced allele (746G) was expressed in multiple tissues of transgene-positive offspring of No.11. Western blot analysis revealed that BMPR1B protein expression in multiple tissues of transgene-positive $F_1$ piglets was 0.5 to 2-fold higher than that in the transgene-negative siblings. The No. 11 boar showed normal litter size performance as normal pigs from the same breed. Transgene-positive $F_1$ boars produced by No. 11 had higher semen volume, sperm concentration and total sperm per ejaculate than the negative siblings, although the differences did not reached statistical significance. Transgene-positive $F_1$ sows had similar litter size performance to the negative siblings, and more data are needed to adequately assess the litter size performance. In conclusion, we obtained 24 cloned transgenic pigs with the modified porcine BMPR1B CDS using HMC. cDNA sequencing and western blot indicated that the exogenous BMPR1B CDS was successfully expressed in host pigs. The transgenic pigs showed normal litter size performance. However, no significant differences in litter size were found between transgene-positive and negative sows. Our study provides new insight into producing cloned transgenic livestock related to reproductive traits.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.4 no.1
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• pp.28-33
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• 2001

Purpose: H. pylori infection is thought to contribute to iron-deficiency anemia, especially during puberty. The ferritin protein Pfr of H. pylori is homologous to eukaryotic and prokaryotic ferritins. The purpose of this study was to analyze the H. pylori pfr status in gastric biopsy specimens according to clinical data, including antral gastritis with or without iron-deficiency anemia. Methods: A total of 26 H. pylori-positive patients aged from ten to 18 years were categorized into subgroups based on the presence or absence of iron-deficiency anemia. All of them had antral gastritis. Sixteen patients were proved to have iron-deficiency anemia by hematological study, two of which had a duodenal ulcer. The other ten patients showed normal hematological findings. DNA isolation was performed from each of the gastric biopsy specimens. PCR amplification of the pfr gene coding was done using two sets of primers. The pfr region, 501 bp, was generated by linking the sequences of the two PCR products. The nucleotide and protein sequences were compared between the pfr regions from Korean H. pylori strains and the NCTC 11638, 26695, and J99 strain, which were obtained from the Genbank. Sequence comparisons were also performed for the pfr regions between the iron-deficiency anemia (+) and (-) groups. Results: Analysis of the complete coding region of pfr gene revealed three sites of mutation. The Ser39Ala mutation was found in 100% (26/26), Gly111Asn in 26.9% (7/26), and Gly82Ser in 11.5% (3/26). There were no significant differences in the mutations of the pfr regions between the iron deficiency anemia (+) and (-) groups. Conclusion: The mutation in the pfr gene did not relate with the clinical phenotype, iron deficiency anemia. Further studies are needed on the aspects of host side or other complex factors to elucidate anemia. Further studies are needed on the aspects of host side or other complex factors to elucidate the mechanisms by which the H. pylori infection might lead to iron deficiency anemia.

• Development and Reproduction
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• v.10 no.4
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• pp.227-238
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• 2006

Genomic DNAs(gDNAs) were isolated from the venus clam(Gomphina aequilatera) from Samcheok(venus clam from Samcheok; VCS) and Wonsan(venus clam from Wonsan; VCW) located in the East Sea of the Korean Peninsula. The amplified products were generated by agarose gel electrophoresis(AGE) with oligonucleotides primer, detected by staining with ethidium bromide and viewed by ultraviolet ray. The seven arbitrarily selected primers BION-21, BION-23, BION-25, BION-27, BION-29, BION-31 and BION-33 generated the shared loci, polymorphic, and specific loci, with the molecular sizes ranging from 150 bp to 2,400 bp. In this study, 147 polymorphic loci(147/954 loci, 15.41%) in VCS population and 274(274/996 loci, 27.51%) in VCW population were generated with seven primers. These results suggest the genetic variation in VCW population is higher than in VCS population. Especially, the 700 bp bands generated by the primer BION-21 were identified commonly in two Gomphina populations, which identified populations and/or species. This specific primer was found to be useful in the identification of individuals and/or population, resulting from the different DNA polymorphism among individuals/species/population. Two Gomphina populations between the individual SAMCHEOK no. 03 and WONSAN no. 22 showed the longest genetic distance(0.696) in comparison with other individuals used. The complete linkage cluster analysis indicating three genetic groupings and dendrogram revealed close relationships among individual identities within two geographical populations of venus clam(G. aequilatera) from the Samcheok and Wonsan. The intra-species classification and clustering analyses inferred from molecular markers supported the traditional taxonomy of the species based on morphological characters such as shell size, shape and color. Accordingly, as mentioned above, RAPD analysis showed that VCS population was more or less separated from VCW population.