• Asian-Australasian Journal of Animal Sciences
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• v.20 no.4
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• pp.466-470
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• 2007

CCAAT/enhancer binding protein ${\alpha}$($C/EBP{\alpha}$) plays an important role in lipid deposition and adipocyte differentiation. In order to find genetic markers to improve the meat quality of Korean cattle, the bovine $C/EBP{\alpha}$ gene was chosen as a candidate gene to investigate its association with carcass and meat quality traits in Korean cattle. A single nucleotide polymorphism (SNP) was identified at position 271 (A/C substitution) of coding region in the $C/EBP{\alpha}$ gene. A PCR-RFLP procedure with restriction enzyme SmaI was developed for determining the marker genotypes. The frequencies of alleles C and A and were 0.374 and 0.626, respectively. The genotype frequencies for CC, AC and AA were 12.9, 49.0 and 38.1%, respectively, in Korean cattle population. The frequencies of genotype were in agreement with Hardy-Weinberg equilibrium. Association analysis indicated that the gene-specific SNP marker of $C/EBP{\alpha}$ showed a significant association with marbling score (p<0.05). The animals with AA genotype had higher marbling score than those with the AC or CC genotype. Although further studies are needed to validate our results, the $C/EBP{\alpha}$ gene could be useful as a genetic marker for carcass and meat quality traits in Korean cattle.

• Korean Journal of Agricultural Science
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• v.45 no.2
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• pp.238-247
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• 2018

The overall consumption of meat is increasing as the level of national income increases. The end weight is a trait closely associated with dressed meat. Genome-wide association study (GWAS) is an effective method of analyzing genetic variation and gene identification associated with a number of natural alternative traits because it can detect variations. So this paper did a GWAS analysis to identity the location on the genome related to the end weight in purebred landrace pigs and to explore the relevant candidate gene. This study identified a significant single nucleotide poly morphism (SNP) marker in chromosome 6 (ASGA0029422, $p=1.22{\times}10^{-6}$). Adhesion G protein-coupled receptor L2 (ADGRL2) was found to be the candidate gene at the identified SNP marker location. ADGRL2 genes have been found to be associated with cell development in relation to the external and internal environment of a cell. In addition, genotype and statistical analyses were done on nine variations on the exon of ADGRL2. The results show that the SNP marker (ASGA0029422, $p=1.32{\times}10^{-6}$) was significant, but the significance of the nine variations on the ADGRL2 exon was not verified. However, by performing further experiments and functional studies on other SNPs showing possible genetic ADGRL-Exon mutations, objects with high associations of high-end weights can be selected.

• Korean Journal of Poultry Science
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• v.36 no.3
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• pp.207-213
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• 2009

Adenylosuccinate lyase (ADSL) deficiency is a disease of purine metabolism which affects patients both biochemicall and behaviorally. An obstacle of this purine nucleotide cycle(PNC) can be caused brain functional disorder and growth disorder. So ADSL deficiency, which is associated with sever mental retardation, autistic features and energy metabolism. This study was performed to identify SNP on ADSL gene in chicken. The nucleotides were observed as T to C ($7724^{th}$ nucleotide), C to T ($7732^{nd}$ nucleotide), G to T ($10108^{th}$ nucleotide), A to T ($10356^{th}$ nucleotide), G to A($10375^{th}$ nucleotide), A to C ($10402^{nd}$ nucleotide), A to T ($12716^{th}$ nucleotide), T to A ($12717^{th}$ nucleotide), C to T ($15491^{st}$ nucleotide), C to T ($15542^{nd}$ nucleotide) and C to T ($15550^{th}$ nucleotide). The nucleotide substitutions at $15542^{nd}$ and $15550^{th}$ (GeneBank accession no. AY665559) were found as missense mutation (alanine$\rightarrow$valine, proline$\rightarrow$serine, respectively). This study will be useful for farther researches for identifying association between these SNPs and energy metabolism in chicken. The C15550T SNP showed three genotypes, CC, CT, TT by digestion with the genotype TT had significantly faster the first lay day (150.0) than CT (162.0, P<0.05) and genotype TT (150.0, P<0.05) had significantly higher the egg production rate than CT (172.4, P<0.05). According to result of this study, a C15550T was found to have a significantly effect first lay day and mean egg production. It will be possible to use SNP marker on selecting chicken to improve important economic traits, which is the first lay day and mean egg production.

• Horticultural Science & Technology
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• v.35 no.2
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• pp.232-242
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• 2017

The goal of marker-assisted backcrossing (MAB) is to significantly reduce the number of breeding generations required by using genome-based molecular markers to select for a particular trait; however, MAB systems have only been developed for a few vegetable crops to date. Among the types of molecular markers, SNPs (single-nucleotide polymorphisms) are primarily used in the analysis of genetic diversity due to their abundance throughout most genomes. To develop a MAB system in Chinese cabbage, a high-throughput (HT) marker system was used, based on a previously developed set of 468 SNP probes (BraMAB1, Brassica Marker Assisted Backcrossing SNP 1). We selected a broad-spectrum TuMV (Turnip mosaic virus) resistance (trs) Chinese cabbage line (SB22) as a donor plant, constructing a $BC_1F_1$ population by crossing it with the TuMV-susceptible 12mo-682-1 elite line. Foreground selection was performed using the previously developed trsSCAR marker. Background selection was performed using 119 SNP markers that showed clear polymorphism between donor and recipient plants. The background genome recovery rate (% recurrent parent genome recovery; RPG) was good, with three of 75 $BC_1F_1$ plants showing a high RPG rate of over 80%. The background genotyping result and the phenotypic similarity between the recurrent parent and $BC_1F_1$ showed a correlation. The plant with the highest RPG recovery rate was backcrossed to construct the $BC_2F_1$ population. Foreground selection and background selection were performed using 169 $BC_2F_1$ plants. This study shows that, using MAB, we can recover over 90% of the background genome in only two generations, highlighting the MAB system using HT markers as a highly efficient Brassica rapa backcross breeding system. This is the first report of the application of a SNP marker set to the background selection of Chinese cabbage using HT SNP genotyping technology.

• Journal of Life Science
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• v.19 no.1
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• pp.152-155
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• 2009

The old-gold-crimson ($og^c$) fruit color mutation produces deep red tomato fruit with high lycopene content. age is a null mutation allele of lycopene-${\beta}$-cyclase (Crt-b) gene (B locus) that converts lycopene to ${\beta}$-carotene in the cartenoid biosynthesis pathway in tomato. Breeding of high lycopene tomato cultivars can be accelerated by marker-assisted selection (MAS) for introgression of $og^c$ allele by using a gene-based DNA marker. In order to develop a marker, single nucleotide deletion of adenine(A) with. in a poly-A repeat that has been known to be responsible for frame-shift mutation of $og^c$ was confirmed by resequencing mutant allele and wild-type allele at B locus of several tomato lines. For allele discrimination and detection of $og^c$, derived CAPS (dCAPS) approach was used by designing a primer that artificially introduced restriction enzyme recognition site of Hin fI in PCR products from $og^c$ allele. This dCAPS marker is co-dominant gene-based PCR marker that can be efficiently used for MAS breeding program aiming the development of high lycopene tomato.

• Horticultural Science & Technology
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• v.34 no.6
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• pp.912-923
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• 2016

Watermelon production is often limited by powdery mildew in areas with a large daily temperature range. Development of resistant watermelon cultivars can protect against powdery mildew; however, little is known about the characteristics of its causal agents. Here, we identified the genus and race of a causal pathogen of powdery mildew in Ansung province of South Korea, and developed molecular markers for the generation of resistant watermelon cultivars. The causal pathogen was determined to be Podosphaera xanthii based on multiple sequence alignments of internal transcribed spacers (ITS) of rDNA. The physiological race was identified as 1W, and the Ansung isolate was named P. xanthii 1W-AN. Following inoculation with the identified P. xanthii 1W-AN, we found inheritance of the resistant gene fitting a single dominant Mendelian model in a segregated population ('SBA' ${\times}$ PI 254744). To develop molecular markers linked to fungus-resistant loci, random amplified polymorphic DNA (RAPD) was accomplished between DNA pooled from eight near-isogenic lines (NILs; $BC_4F_6$), originated from PI 254744 and susceptible 'SBB' watermelon. After sequencing bands from RAPD were identified in all eight NILs and PI254744, 42 sequence-characterized amplifiedregion (SCAR) markers were developed. Overall, 107 $F_2$ plants derived from $BC_4F_6$ NIL-1 ${\times}$ 'SBB' were tested, and one SCAR marker was selected. Sequence comparison between the SCAR marker and the reference watermelon genome identified three Nco I restriction enzyme sites harboring a single nucleotide polymorphism, and codominant cleavage-amplified polymorphic site markers were subsequently developed. A CAPS marker was converted to a high-resolution melt (HRM) marker, which can discriminate C/T SNP (254PMR-HRM3). The 254PMR-HRM3 marker was evaluated in 138 $F_{2:3}$ plants of a segregating population ('SBA' ${\times}$ PI254744) and was presumed to be 4.3 cM from the resistance locus. These results could ensure P. xanthii 1W-AN resistance in watermelon germplasm and aid watermelon cultivar development in marker-assist breeding programs.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.722-729
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• 2015

Powdery mildew (PM) caused by Podosphaera aphanis is a major disease that can result in significant yield losses in strawberry (Fragaria ${\times}$ ananassa Duchesne). For preventing PM, pesticides are usually applied in strawberry. In this study, molecular markers were developed to increase breeding efficiency of PM-resistance cultivars by marker-assisted selection (MAS). An $F_2$ population derived from a cross between PM-resistance 'Seolhyang' and PM-susceptibility 'Akihime' was evaluated for disease resistance to PM and RAPD (random amplification of polymorphic DNA)-BSA (bulked segregant analysis). Among 200 RAPD primers tested, OPE10 primer amplified a 311bp-band present in with 331bp. Sequence alignment performed for searching polymorphisms and six single nucleotide polymorphism (SNP) were found in amplified regions. To develop polymorphic marker for distinguishing between resistant and susceptible, RAPD was converted to cleaved amplified polymorphic sequence (CAPS) marker. Among restriction enzymes associated with six SNPs, Eae I (Y/GGCCR) was successfully digested to 231bp in susceptible. The results suggest that the selected CAPS marker could be used for increasing efficiency of selecting powdery mildew resistant strawberry in breeding system.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.11
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• pp.1504-1513
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• 2011

It is important to identify genetic interactions related to human diseases or animal traits. Many linear statistical models have been reported but they did not consider genetic interactions. Genotype matrix mapping (GMM) has been developed to identify genetic interactions. This study uses the GMM method to detect superior SNP combinations of the CCDC158 gene that influences average daily gain, marbling score, cold carcass weight and longissimus muscle dorsi area traits in Hanwoo. We evaluated the statistical significance of the major SNP combinations selected by implementing the permutation test of the F-measure. The effect of g.34425+102 A>T (AA), g.8778G>A (GG) and g.4102+36T>G (GT) SNP combinations produced higher performance of average daily gain, marbling score, cold carcass weight and the longissimus muscle dorsi area traits than the effect of a single SNP. GMM is a fast and reliable method for multiple SNP analysis with potential application in marker-assisted selection. GMM may prospectively be used for genetic assessment of quantitative traits after further development.

• Fisheries and Aquatic Sciences
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• v.11 no.1
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• pp.36-40
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• 2008

We analyzed the nucleotide sequences of about 500 bp of the mitochondrial NADH dehydrogenase subunit 3 (ND3) gene to estimate the genetic variation of Korean masu salmon (Oncorhynchus masou) populations. DNA samples were collected from 104 river-only specimens and 52 anadromous specimens from three hatcheries and one river. There are no records of artificial release into the river. We amplified the ND3 gene by polymerase chain reaction, targeting areas that included parts of the cytochrome oxidase III gene and the NADH dehydrogenase subunit 4L gene, and defined 14 haplotypes based on 12 variable nucleotide sites in the examined region. Among the haplotypes, ten were specific to river-only specimens within hatchery populations. Haplotype diversity of river-only populations in hatcheries was higher than that of anadromous and wild populations. Pairwise population $F_{ST}$ estimates and neighbor-joining tree analyses inferred that anadromous and river-only populations were distinct. These results suggest that sequence polymorphism in the ND3 region may be a useful marker for analyzing the genetic variation and population structure of masu salmon.

• Journal of Plant Biotechnology
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• v.5 no.4
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• pp.193-195
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• 2003

A major goal of agricultural biotechnology is the discovery of genes or genetic loci which are associated with characteristics beneficial to crop production. This knowledge of genetic loci may then be applied to improve crop breeding. Agriculturally important genes may also benefit crop production through transgenic technologies. Recent years have seen an application of high throughput technologies to agricultural biotechnology leading to the production of large amounts of genomic data. The challenge today is the effective structuring of this data to permit researchers to search, filter and importantly, make robust associations within a wide variety of datasets. At the Plant Biotechnology Centre, Primary Industries Research Victoria in Melbourne, Australia, we have developed a series of tools and computational pipelines to assist in the processing and structuring of genomic data to aid its application to agricultural biotechnology resear-ch. These tools include a sequence database, ASTRA, for the processing and annotation of expressed sequence tag data. Tools have also been developed for the discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular markers from large sequence datasets. Application of these tools to Brassica research has assisted in the production of genetic and comparative physical maps as well as candidate gene discovery for a range of agronomically important traits.