• Plant Breeding and Biotechnology
• /
• v.6 no.4
• /
• pp.391-403
• /
• 2018

Genome resequencing by next-generation sequencing technology can reveal numerous single nucleotide polymorphisms (SNPs) within a closely-related cultivar group, which would enable the development of sufficient SNP markers for mapping and the identification of useful genes present in the cultivar group. We analyzed genome sequence data from 13 Korean japonica rice varieties and discovered 740,566 SNPs. The SNPs were distributed at 100-kbp intervals throughout the rice genome, although the SNP density was uneven among the chromosomes. Of the 740,566 SNPs, 1,014 SNP sites were selected on the basis of polymorphism information content (PIC) value higher than 0.4 per 200-kbp interval, and 506 of these SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers. The 506 KASP markers were tested for genotyping with the 13 sequenced Korean japonica rice varieties, and polymorphisms were detected in 400 KASP markers (79.1%) which would be suitable for genetic analysis and molecular breeding. Additionally, a genetic map comprising 205 KASP markers was successfully constructed with 188 $F_2$ progenies derived from a cross between the varieties, Junam and Nampyeong. In a phylogenetic analysis with 81 KASP markers, 13 Korean japonica varieties showed close genetic relationships and were divided into three groups. More KASP markers are being developed and these markers will be utilized in gene mapping, quantitative trait locus (QTL) analysis, marker-assisted selection and other strategies relevant to crop improvement.

• BMB Reports
• /
• v.36 no.6
• /
• pp.533-537
• /
• 2003

The nonsyndromic cleft lip and palate (NSCL/P) is a congenital deformity of multifactorial origin with a relatively high incidence in the oriental population. Various etiologic candidate genes have been reported with conflicting results, according to race and analysis methods. Recently, the ablation of the TGF-${\beta}3$ gene function induced cleft palates in experimental animals. Also, polymorphisms in the TGF-${\beta}3$ gene have been studied in different races; however, they have not been studied in Koreans. A novel A $\rightarrow$ G single nucleotide polymorphism (defined by the endonuclease SfaN1) was identified in intron 5 of TGF-${\beta}3$ (IVS5+104 A > G). It resulted in different genotypes, AA, AG, and GG. The objective of this study was to investigate the relationship between the SfaN1 polymorphism in TGF-${\beta}3$ and the risk of NSCL/P in the Korean population. The population of this study consisted of 28 NSCL/P patients and 41 healthy controls. The distribution of the SfaN1 genotypes was different between the cases and controls. The frequency of the G allele was significantly associated with the increased risk of NSCL/P [odds ratio (OR) = 15.92, 95% confidence interval (CI) = 6.3-41.0]. The risk for the disease increased as the G allele numbers increased (GA genotype: OR = 2.11, 95% CI = 0.38-11.68; GG genotype: OR = 110.2, 95% CI = 10.67 - 2783.29) in NSCL/P. A stratified study in patients revealed that the SfaN1 site IVS5+104A > G substitution was strongly associated with an increased risk of NSCL/P in males (p < 0.001), but not in females. In conclusion, the polymorphism of the SfaN1 site in TGF-${\beta}3$ was significantly different between the NSCL/P patients and the control. This may be a good screening marker for NSCL/P patients among Koreans.

• Journal of Animal Science and Technology
• /
• v.47 no.2
• /
• pp.159-166
• /
• 2005

Porcine myostatin(MS1N) gene plays a key role in the differentiation of myoblast and muscle development. Genetic polymorphism was screened by single stranded conformation polymorphism(SSCP) analysis and subsequent DNA sequencing detected a nucleotide substitution(C2150T) in exon 3 of MSIN gene. Phenotypic association of the polymorphism was tested in a Landrace population and positive effects of the allele T for lean growth traits were found in the population. Even though it is not significant, the pigs have IT and TC genotypes were heavier for the body weight at birth and at twenty weeks of age than those containing genotype. Cc. However, the allele T was significantly associated with higher eye muscle area(P < 0.05). As a result of this study, we suggested that the allele T in exon 3 of MSTN gene comes a significant effect for increasing the eye muscle area without decreasing backfat thickness. This polymorphism did not change the amino acid but Taq I -RFLP matched to SSCP band patterns in exon 3 of MSTN gene, which will be an useful molecular marker for breeding of Landrace pigs.

• Asian-Australasian Journal of Animal Sciences
• /
• v.32 no.1
• /
• pp.58-62
• /
• 2019

Objective: The oxidized low density lipoprotein receptor 1 (OLR1) gene plays an important role in the degradation of oxidized low-density lipoprotein and adipocyte proliferation in mammals. For this reason, we aimed at investigating the association of OLR1 gene polymorphisms with carcass quality traits in Chinese Qinchuan cattle. Methods: The single nucleotide polymorphism (SNP) was identified in the 3' untranslated region of bovine OLR1 gene by DNA sequencing. In addition, the haplotype frequency and linkage disequilibrium estimates of three SNPs were evaluated in 520 individuals. Results: Results indicated that the studied three SNPs were within the range of moderate genetic diversity (0.25< polymorphism information content<0.5). Haplotype analysis of three SNPs showed that ten different haplotypes were identified, but only five haplotypes were listed as those with a frequency of <0.05 were excluded. The Hap3 ($-G_1T_2C_3-$) had the highest haplotype frequency (42.10%). Linkage disequilibrium analysis showed that the three SNPs had a low linkage ($r^2<0.001$). The T10588C and C10647T were significantly associated with backfat thickness and intramuscular fat content in Qinchuan cattle. Conclusion: Based on our results, we believe that the OLR1 gene could be a strong candidate gene for influencing carcass quality traits in Qinchuan cattle.

• Genomics & Informatics
• /
• v.12 no.4
• /
• pp.254-260
• /
• 2014

Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.

• Horticultural Science & Technology
• /
• v.31 no.1
• /
• pp.72-79
• /
• 2013

Inactivation of the gene coding for dihydroflavonol 4-reductase (DFR) is responsible for the color difference between red and yellow onions (Allium cepa L.). Two inactive DFR-A alleles, DFR-$A^{PS}$ and DFR-$A^{DEL}$, were identified in our previous study. A functional marker was developed on the basis of the premature stop codon that inactivated the DFR-$A^{PS}$ allele. A derived cleaved amplified polymorphic sequences (dCAPS) primer was designed to detect the single nucleotide polymorphism, an A/T transition, which produced the premature stop codon. Digested PCR products clearly distinguished the homozygous and heterozygous red $F_2$ individuals. Meanwhile, to develop a molecular marker for detection of the DFR-$A^{DEL}$ allele in which entire DFR-A gene was deleted, genome walking was performed and approximately 3 kb 5' and 3' flanking sequences of the DFR-$A^R$ coding region were obtained. PCR amplification using multiple primers binding to the extended flanking regions showed that more of the extended region of the DFR-A gene was deleted in the DFR-$A^{DEL}$ allele. A dominant simple PCR marker was developed to identify the DFR-$A^{DEL}$ allele using the dissimilar 3' flanking sequences of the DFR-A gene and homologous DFR-B pseudogene. Distribution of the DFR-$A^{PS}$ and DFR-$A^{DEL}$ alleles in yellow onion cultivars bred in Korea and Japan was surveyed using molecular makers developed in this study. Results showed predominant existence of the DFR-$A^{PS}$ allele in yellow onion cultivars.

• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.10
• /
• pp.1535-1541
• /
• 2018

Objective: In birds, three types of melatonin receptors (MTNR1A, MTNR1B, and MTNR1C) have been cloned. Previous researches have showed that three melatonin receptors played an essential role in reproduction and ovarian physiology. However, the association of polymorphisms of the three receptors with duck reproduction traits and egg quality traits is still unknown. In this test, we chose MTNR1A, MTNR1B, and MTNR1C as candidate genes to detect novel sequence polymorphism and analyze their association with egg production traits in Shaoxing duck, and detected their mRNA expression level in ovaries. Methods: In this study, a total of 785 duck blood samples were collected to investigate the association of melatonin receptor genes with egg production traits and egg quality traits using a direct sequencing method. And 6 ducks representing two groups (3 of each) according to the age at first eggs (at 128 days of age or after 150 days of age) were carefully selected for quantitative real-time polymerase chain reaction. Results: Seven novel polymorphisms (MTNR1A: g. 268C>T, MTNR1B: g. 41C>T, and g. 161T>C, MTNR1C: g. 10C>T, g. 24A>G, g. 108C>T, g. 363 T>C) were detected. The single nucleotide polymorphism (SNP) of MTNR1A (g. 268C>T) was significantly linked with the age at first egg (p<0.05). And a statistically significant association (p<0.05) was found between MTNR1C g.108 C>T and egg production traits: total egg numbers at 34 weeks old of age and age at first egg. In addition, the mRNA expression level of MTNR1A in ovary was significantly higher in late-mature group than in early-mature group, while MTNR1C showed a contrary tendency (p<0.05). Conclusion: These results suggest that identified SNPs in MTNR1A and MTNR1C may influence the age at first egg and could be considered as the candidate molecular marker for identify early maturely traits in duck selection and improvement.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.8
• /
• pp.1084-1089
• /
• 2015

Chemerin, highly expressed in adipose and liver tissues, regulates glucose and lipid metabolism and immunity in these tissues in ruminants and mice. Our previous reports showed that chemerin is involved in adipogenesis and lipid metabolism in adipose tissue as an adipokine. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in the coding region of the chemerin gene and to analyze their effects on carcass traits and intramuscular fatty acid compositions in Japanese Black cattle. The SNPs in the bovine chemerin gene were detected in 232 Japanese Black steers (n = 161) and heifers (n = 71) using DNA sequencing. The results revealed five novel silent mutations: NM_001046020: c.12A>G (4aa), c.165GT (92aa), c.321 A>G (107aa), and c.396C>T (132aa). There was no association between 4 of the SNPs (c.12A>G [4aa], c.165GG [107aa], and c.396C>T) and carcass traits or intramuscular fatty acid compositions. Regarding the remaining SNP, c.276C>T, we found that cattle with genotype CC had a higher beef marbling score than that of cattle with genotype CT, whereas cattle with genotype CT had a higher body condition score (p<0.10). Further, cattle with genotype CC had significantly higher C18:0 content in their intramuscular fat tissue than that of cattle with genotype CT (p<0.05). On the other hand, cattle with genotype CT had significantly higher C14:0 and C16:0 content in their intramuscular fat tissue (p<0.05). Moreover, the number of individuals carrying the minor allele of c.276C>T SNP is small. It is suggested that the c.276C>T SNP of the chemerin gene has potential in cattle breeding using modern methods, such as marker assisted selection. So, further functional and physiological research elucidating the impact of the chemerin gene on bovine lipid metabolism including fatty acid synthesis will help in understanding these results.

• Journal of Life Science
• /
• v.26 no.1
• /
• pp.1-7
• /
• 2016

Fatness is one of the most important economic traits in pigs. The leptin receptor (LEPR) gene may be a potential candidate for the fatness quantitative trait locus (QTL) on porcine chromosome 6, due to its position and physiological role. Thus, this study was carried out to evaluate the associations between structural variants in the LEPR gene and economic traits in pigs. We obtained an approximately 114-kb sequence containing the complete genomic DNA of the porcine LEPR gene, using shotgun sequencing of a bacterial artificial chromosome clone. We report the complete genomic structure of the porcine LEPR gene. Dozens of transcription factor-binding sites were found in the 1.2 kb upstream region from the transcription start point. An association study was performed with 550 Duroc pigs for 24 single-nucleotide polymorphisms (SNPs), including 6 SNPs within exons and 18 SNPs within the putative 5‘ regulatory region of the porcine LEPR gene. Among them, one SNP (−790C/G) was significantly associated with backfat thickness and lean meat percentage, whereas the others, including two SNPs with missense polymorphisms, had no effect on any phenotype. These results suggest that SNP −790C/G may be a useful marker for genetic improvements of fatness and leanness in Duroc pigs.

• Radiation Oncology Journal
• /
• v.36 no.3
• /
• pp.218-226
• /
• 2018

Purpose: Standard treatment for locally advanced rectal cancer consists of neoadjuvant radiochemotherapy with concomitant fluoropyrimidine or oxaliplatin and surgery with curative intent. Pathological complete response has shown to be predictive for better outcome and survival; nevertheless there are no biological or genetic factors predictive for response to treatment. We explored the correlation between the single nucleotide polymorphisms (SNPs) GSTP1 (A313G) and XRCC1 (G28152A), and the pathological complete response and survival after neoadjuvant radiochemotherapy in locally advanced rectal cancer patients. Materials and Methods: Genotypes GSTP1 (A313G) and XRCC1 (G28152A) were determined by pyrosequencing technology in 80 patients affected by locally advanced rectal cancer. Results: The overall rate of pathological complete response in our study population was 18.75%. Patients homozygous AA for GSTP1 (A313G) presented a rate of pathological complete response of 26.6% as compared to 8.5% of the AG+GG population (p = 0.04). The heterozygous comparison (AA vs. AG) showed a significant difference in the rate of pathological complete response (26.6% vs. 6.8%; p = 0.034). GSTP1 AA+AG patients presented a 5- and 8-year cancer-specific survival longer than GSTP1 GG patients (87.7% and 83.3% vs. 44.4% and 44.4%, respectively) (p = 0.014). Overall survival showed only a trend toward significance in favor of the haplotypes GSTP1 AA+AG. No significant correlations were found for XRCC1 (G28152A). Conclusion: Our results suggest that GSTP1 (A313G) may predict a higher rate of pathological complete response after neoadjuvant radiochemotherapy and a better outcome, and should be considered in a more extensive analysis with the aim of personalization of radiation treatment.