• Asian-Australasian Journal of Animal Sciences
• /
• 제20권4호
• /
• pp.466-470
• /
• 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.

• 농업과학연구
• /
• 제45권2호
• /
• pp.238-247
• /
• 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.

• 한국가금학회지
• /
• 제36권3호
• /
• pp.207-213
• /
• 2009

퓨린 합성의 반응을 촉진시키며 뇌기능장애, 성장장애 그리고 에너지대사에 핵심적인 역할을 하는 ADSL(Adenylosuccinate lyase)의 exon 영역을 중심으로 PCR을 수행하여 DNA 염기서열 분석을 통해 한국재래닭에서 단일염기다형성을 확인하였다. 염기분석 결과 총 11개(intron 5: T7724C, C7732T intron 8: G10108T intron 9: A10356T, G10375A, A10402 intron 10: A12716T, T12717A intron 12: C15491T exon 13: C15542T, C15550T)를 확인할 수 있었으며 특히 exon 13지역의 변이들은 각각 아미노산이 바뀌는 missense mutation 임이 확인되었다(Alanine$\rightarrow$Valine, Proline$\rightarrow$Serine). 또한 C15542T 변이는 NCBI의 SNP 데이터베이스에 등록된 것으로 확인되었고, C15550T는 SNP 데이터베이스에 등록되지 않은 신규 변이지역으로 확인되었다. 이는 단백질 발현이 향상되는 3'UTR 지역 근처인 exon 13 부위이며 추가적으로 ADSL 유전자의 아미노산 변이가 닭 집단의 성장 및 에너지 대사와의 연관성 검증을 통해 본 연구 결과는 중요하게 활용될 것으로 기대된다.

• 원예과학기술지
• /
• 제35권2호
• /
• pp.232-242
• /
• 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.

• 생명과학회지
• /
• 제19권1호
• /
• pp.152-155
• /
• 2009

old-gold-crimson ($og^c$) 과색 돌연변이는 라이코펜의 함량이 증가된 진붉은색 토마토 과실을 생산한다. 이러한 돌연변이는 토마토의 carotenoid 생합성경로에 관여하여 라이코펜을 ${\beta}$-carotene으로 전환시키는 라이코펜 ${\beta}$-cyclase (Crt-b) 유전자(B)에 point mutation을 일으켜 정상적인 효소생성을 저해한다. 높은 함량의 라이코펜을 생성시키는 토마토 품종개발은 유전자 연관 DNA 마커를 이용한 분자표지이용선발(MAS)을 통해 가속화 될 수 있다. $og^c$ 돌연변이는 라이코펜 ${\beta}$-cyclase(Crt-b) 유전자 내 poly-A 서열반복 지점에서 adenine (A) 단일 뉴클레오티드의 결손에 의한 frame-shift mutation에 의해 일어나며, 이러한 대립유전자의 운영과 검증을 위해 $og^c$ 대립유전자로부터 합성되는 PCR 산물에 Hin fI 제한효소 인식부위가 인위적으로 생성되도록 PCR 프라이머에 단일 뉴클레오티드 mismatch 부위를 만들어 dCAPS 마커를 개발하였다. 본 dCAPS 마커는 유전자 유래의 공우성 PCR 마커로서 고함량 라이코펜 토마토개발을 위한 육종 프로그램의 MAS에 효과적으로 사용될 수 있다.

• 원예과학기술지
• /
• 제34권6호
• /
• pp.912-923
• /
• 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.

• 원예과학기술지
• /
• 제33권5호
• /
• pp.722-729
• /
• 2015

딸기 흰가루병은 Podosphaera aphanis에 의해 발병되며 수확기에 가장 큰 피해를 주는 병으로 현재 유황, 농약으로 주로 방제 되고 있는 실정이다. 본 연구에서는 딸기 흰가루병 저항성 품종 육성을 위한 흰가루병 저항성 특이마커 개발로 내병성 육종효율을 높이고자 하였다. 흰가루병 저항성 계통 선발을 위한 분자마커를 개발하기 위해 아키히메${\times}$설향 집단을 대상으로 자가수분을 통해 후대 양성 후 병저항성을 검정하였다. 마커분석은 RAPD primer 200 세트 중 OPE10 331bp에서부터 흰가루병 저항성 특이 마커 선발하였다. 흰가루병 저항성 특이밴드만 선발하기 위하여 클로닝 후 유전자정보 분석하여 SP1F/R의 Primer를 제작하였다. 그러나 SP1F/R을 이용하여 PCR한 결과 저항성, 감수성간에 다형성이 확인되지 않아 염기서열을 정렬한 후 SNP, In/del의 다형성 유무를 확인한 결과 6개의 SNP를 확인하였다. 이들 PCR 산물을 해당 사이트와 연관된 제한효소로 절단한 결과 그 중 Eae I(Y/GGCCR)의 절단으로 231bp 위치에서 저항성과 감수성간의 다형성을 확인함으로써 흰가루병 저항성 계통선발을 위한 분자마커를 선발하였다. 이러한 과정을 통해 딸기 흰가루병 저항성 품종 육성을 위한 MAS(marker assisted selection) 체계 확립으로 내병성 육종효율 증진에 기여를 할 수 있을 것으로 기대된다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제24권11호
• /
• pp.1504-1513
• /
• 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
• /
• 제11권1호
• /
• pp.36-40
• /
• 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
• /
• 제5권4호
• /
• pp.193-195
• /
• 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.