• Genomics & Informatics
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• 제12권4호
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• pp.254-260
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• 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.

• Molecules and Cells
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• 제41권12호
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• pp.993-999
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• 2018

One of the most interesting findings from genome-wide expression analysis is that a considerable amount of noncoding RNA (ncRNA) is present in the cell. Recent studies have identified diverse biological functions of ncRNAs, which are expressed in a much wider array of forms than proteins. Certain ncRNAs associated with diseases, in particular, have attracted research attention as novel therapeutic targets and diagnostic markers. BC200 RNA, a 200-nucleotide ncRNA originally identified as a neuron-specific transcript, is abnormally over-expressed in several types of cancer tissue. A number of recent studies have suggested mechanisms by which abnormal expression of BC200 RNA contributes to the development of cancer. In this article, we first provide a brief review of a recent progress in identifying functions of BC200 RNA in cancer cells, and then offer examples of other ncRNAs as new therapeutic targets and diagnostic markers for human cancer. Finally, we discuss future directions of studies on BC200 RNA for new cancer treatments.

• 한국버섯학회지
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• 제19권4호
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• pp.336-340
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• 2021

본 연구에서는 국내에서 개발된 국내에서 개발된 10개의 양송이 품종을 CAPS 마커를 이용하여 구분하였다. An 등(2021)이 개발한 CAPS 마커 AB-gCAPs-017, AB-gCAPs-047, AB-gCAPs-055, AB-gCAPs-071을 이용하여 새아, 새도, 새한, 새연, 새정, 도담, 설강, 다향, 호감, 하담을 구분할 수 있었다. 본 연구의 결과는 국내 개발 양송이 품종에 대하여 품종간의 구별성과 유전적 다양성을 부여하여 품종보호에 대한 분자생물학적 근거를 마련하였다.

• 원예과학기술지
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• 제33권4호
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• pp.566-574
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• 2015

Yellow or transparent fruit peel color is caused by the accumulation or lack of naringenin chalcone (NG, C) in fruit peel and determines the red or pink appearance of tomato fruit, respectively. NGC biosynthesis is regulated by the SlMYB12 gene of the Y locus on chromosome 1, and DNA markers derived from SlMYB12 would be useful for marker-assisted selection (MAS) of tomato fruit color. To develop a gene-based marker, 4.9 kb of the SlMYB12 gene including a potential promoter region was sequenced from the red-fruited (YY) line 'FCR' and pink-fruited (yy) line 'FCP'. Sequence alignment of these SlMYB12 alleles revealed no sequence variations between 'FCR' and 'FCP'. To identify SlMYB12-linked single nucleotide polymorphisms (SNPs), 'FCR' and 'FCP' were genotyped using a SolCAP Tomato SNP array and CAPS markers (CAPS-456, 531, 13762, and 38123) were developed from the four SNPs (solcap_snp_sl_456, 531, 13762, and 38123) most closely flanking the SlMYB12. These CAPS markers were mapped using $F_2$ plants derived from 'FCR' ${\times}$ 'FCP'. The map positions of the fruit peel color locus (Y) were CAPS-13762 (0 cM) - 456 (11.09 cM) - Y (15.71 cM) - 38123 (17.82 cM) - 531 (30.86 cM), and the DNA sequence of SlMYB12 was physically anchored in the middle of CAPS-456 and CAPS-38123, indicating that fruit peel color in domesticated tomato is controlled by SlMYB12. A total of 64 SolCAP tomato germplasms were evaluated for their fruit peel color and SNPs located between solcap_snp_sl_456 and 38123. Seven SNPs that were detected in this interval were highly conserved for pink-fruited accessions and specific to transparent fruit peel traits, as depicted by a phenetic tree of 64 accessions based on the seven SNPs.

• 한국자원식물학회지
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• 제32권4호
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• pp.303-311
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• 2019

과피와 과육의 다양한 색은 복숭아 분류에 가장 널리 사용되는 상업적 기준 중 하나이다. 새로운 적색 과육 품종을 육성하기 위해서는 많은 교배 조합과 세대가 진전되어야 한다. 따라서 육종 효율을 높이기 위해서는 목적 형질을 가진 개체에 적용할 조기 선발 분자표지를 개발할 필요가 있다. 과육색이 다르게 발현되는 복숭아 품종의 유전자 발현을 비교하기 위해 2개의 cDNA library를 제작하였다. 적색 과육 품종인 '조생혈도'와 백색 과육 품종인 '미백도'의 유전자 발현 차이를 보기 위해 차세대 염기서열 분석(NGS) 기술을 사용하였고, 두 품종으로부터 얻은 EST의 염기서열을 결정하고 기존에 보고된 유전자와의 상동성을 분석하였다. '조생혈도'와 '미백도'의 EST database로부터 72쌍의 SNP 분자표지를 선발하였고, 적색 과육 품종 8개와 백색 과육 품종 24개를 구분할 수 있는 SNP 분자표지를 HRM 방법으로 분석하였다. 본 연구에서는 복숭아 EST database를 기반으로 HRM 분석 방법을 이용하여 복숭아 품종의 적육계와 백육계를 구분할 수 있는 효율적인 SNP 분자표지를 개발하였다. 이러한 SNP 분자표지는 복숭아 육종에 유용하게 사용할 수 있으며, 복숭아 품종의 다양한 색 변화에 관한 분자 기작 연구에 좋은 참고자료가 될 수 있을 것이다.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.391-403
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• 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.

• 한국수정란이식학회지
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• 제23권3호
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• pp.197-201
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• 2008

In order to provide information of genetic variants for Haptoglobin (Hp) gene, which may be related to weight traits in pig, a total of 235 animals from National Institute of Animal Science (NIAS) were screened with 3 primers. The primer sequences were selected using the porcine cDNA sequences based on NM_214000, and the exon boundaries were estimated. Genetic variants were observed using direct sequencing analysis, and there were 9 SNPs detected at nucleotide positions 503 (A/G), 509 (A/G), 709 (C/T), 734 (C/A), 742 (G/A), 769 (A/G), 840 (C/T), 876 (C/T) and 882 (C/A). All the SNPs were located in coding regions, and mutations caused amino acid changes at nucleotide positions 503, 509, 734, 742 and 769. Allele frequencies of SNPs were estimated for all segments. The SNPs at nucleotide position 509 (p<0.0001) and 734 (p<0.05) were significantly associated with average daily gain, but no significance was observed with other SNPs. From the results, the identified SNPs may be a useful candidate marker for the porcine weight gain traits.

• Asian-Australasian Journal of Animal Sciences
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• 제27권9호
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• pp.1244-1249
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• 2014

Goose fatty liver is one of the most delicious and popular foods in the world, but there is no reliable genetic marker for the early selection and breeding of geese with good liver-producing potential. In our study, one hundred and twenty-four 78-day-old Landes geese bred in Shunda Landes goose breeding farm, Jiutai, Jilin, China were selected randomly. The fatty livers were sampled each week after overfeeding during a three week period. Polymerase chain reaction-single strand conformation polymorphism and DNA sequencing were used to identify single nucleotide polymorphisms (SNPs) of fatty acid synthase (FAS), which is an important enzyme involved in the synthesis of fat under both physiological and pathological conditions. Least-squares correlation was established between these SNPs and fatty liver weight, abdominal fat weight, and intestinal fat weight of the overfed Landes geese, respectively. The results showed that fatty liver weight of geese with EF and FF genotypes (amplified by primer P1) was significantly higher than that of the EE genotype (p<0.05), and liver weight of CD and DD genotypes (amplified by primer P2) was significantly higher than that of the CC genotype (p<0.05). Different genotype combinations showed different liver weights, and from highest to lowest were ABDD, DDEF, DDFF, DDEE, ABEF, ABFF, AADD, and CDEF. Further analysis of DNA sequencing showed that there were two SNPs within the 5' promoter region the FAS gene. The geese of EF and FF genotypes carried a change of T to C, and the geese of CD and DD genotypes carried a change of A to G. The changes of the bases could potentially influence the binding of some transcription factors to this region as to regulate FAS gene. To our knowledge, this is the first report of SNPs found within the 5' promoter region of the Landes goose FAS gene, and our data will provide an insight for early selection of geese for liver production.

• Asian-Australasian Journal of Animal Sciences
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• 제29권11호
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• pp.1541-1546
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• 2016

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.

• Molecules and Cells
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• 제39권2호
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• pp.141-148
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• 2016

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.