Genetic polymorphisms within immunity-related candidate genes in pigs have been identified to control variations in immune functions and/or disease resistance. It has become necessary to evaluate the effects of other genetic markers of economically important traits prior to introducing them into marker-assisted selection programs. In this study, polymorphisms of porcine genes coding Interferon-induced Gunylate binding protein 1 (GBP1), GBP2, CD163, and CD169 were investigated for their association with growth and meat quality traits in a Korean native pig breed -Yorkshire inter-crossed F2 pig population (KY-F2). KY-F2 animals (n=346) have been successfully used for linkage mapping to identify quantitative loci that control meat quality, growth, and immunity traits. In our results, polymorphisms in genes GBP1 and GBP2 showed association with pig growth rate as well as meat quality traits such as crude fat, drip loss, and meat color (yellowness) in the KY-F2 population. The polymorphism in gene CD163 only showed association with crude fat, as a meat quality trait. CD169 gene was associated with pork tenderness. In conclusion, four immune-related genetic markers were validated for their association with growth and meat quality traits to gauge their potential use in a swine selection program. The results warrant further studies in other commercial pig populations.

국내에서 재배하여 생산되고 있는 상황버섯의 일종인 PMO-P4균주에 대한 ITS 영역의 염기서열 분석을 실시하였으며 목질 진흙버섯으로 잘 알려져 있는 P. linteus와 함께 RFLP분석을 통하여 상호 비교한 결과 PMO-P4균주는 P. baumii로 판명되었다. 이 결과를 토대로 이미 보고 되어 있는 Phellinus속 균주들과의 종간 ITS 영역의 상동성을 비교한 결과 48.6%-72.2%였으며 본 연구에서 비교한 종들 가운데서는 P. linteus와 상동성이 가장 높았으며 P. gilvus와 상동성이 가장 낮았다.

Six field bean (GI-vcine soza S and Z ) plants were examined for their genetic polymorphisms and intraspecific variations using randomly amplified polymorphic DNA(RAPD) markers. In RAPD analysis of 5 random primers (Rp-1, Rp2, Rp-3, Rp-4, Rp-5), 30 of tot

Eleven Italian ryegrass cultivars were examined for their genetic polymorphisms and phylogenetic relationships using randomly amplified polymorphic DNA (RAPD) markers. In RAPD analysis of 34 random primers, 96 of total 162 bands obtained from 16 primers w

복숭아혹진딧물(Myzus persicae Sulzer)은 두가지 서로 다른 기주선호성을 가지는데 이 기주선호성과 형태적 특징에 기초하여 담배진닷물(Myzus nicotinae Blackman)과 담배 이외의 다른 채소류에 서식하는 복숭아 혹진딧물(M. persicae)로 분류하였지만(Blachmean, 1987) 이 분류 방법에 동의하지 않는 학자들도 많다. 이런 이유로 RAPD-PCR 기법을 이용하여 한국에 서식하는 복숭아혹진딧물에 대하여 그들의 2차 숙주선호성에 따른 DNA의 변이 정도를 살펴보았다. 실험곤충으로는 담배와 배추에서 채집하여 사육한 진딧물 각 4 clones 씩을 사용하였다. 각 clone은 한 개체를 사육하여 얻은 자손들과 그들의 후손으로 이루어졌으며, 사육한 진딧물에서 핵 DNA를 추출하고, 10개 nucleotide 길이의 random primer 100가지를 사용하여 PCR한 후 1 % agarose gel 전기영동법으로 분석하였다. 사용한 100종류의 random primer 중 83가지에서 DNA 단편이 합성되었다. 증폭된 1개의 primer당 단편의 수는 1개에서 22개였고 평균 단편 수는 약 13개였으며, 각 각 단편의 길이는 500에서 20,000 base pair사이에 분포하였다. 82가지 primer의 경우에 일부 단편의 짙기에는 차이가 있었으나 단편종류의 분포는 동일하게 나타났다. 한가지 primer경우에만 담배섭식형 1개 c clone에서 다른 7가지 clones에 없는 band가 1개 나타났다. 이때 나머지 7 clones의 단편 분포 형태는 모두 동일하였다. 따라서 이 band는 숙주 선호성과는 무관한 것으로 보인다. 결국 이 실험에 사용한 100종류의 primer에 기초하여 RAPD-PCR기법으로 DNA를 증폭한 결과 복숭아혹진딧물의 숙주선호성이 개체군간의 유전적인 차이점에 기인한다는 가설을 뒷받침할 만한 증거를 찾지 못하였다.

This study analyzed the mitochondrial DNA (mtDNA) sequences of the Red-spotted grouper, Epinephelus akaara (Perciformes, Serranidae), and used for construction of molecular phylogeny and for association between maternal haplotypes and phenotypic differences of F1 progeny. This study revealed phylogenetic position of the endangered red-spotted grouper, Epinephelus akaara (Perciformes, Serranidae) based on the nucleotide sequences of complete mt genome. Complete nucleotide sequences were determined from the mt genomes of two individuals of the red-spotted grouper caught in South Korea. The mitochondrial genome had 16,795 base pairs (bp) and 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region. The two mt genomes were highly homologous (99.71% similarity). The two mt genomes of E. akaara determined in this study were found in Clade I in the phylogenetic tree with those of E. awoara, E. fasciatomaculosus, E. sexfasciatus, E. diacanthus, E. sticus, and E. morio, suggesting that this may be helpful to understand phylogenetic position of Epinephelus species including red-spotted grouper. The genetic structure and phylogenetic relationship were investigated in the red-spotted grouper populations using the sequence polymorphisms of the cytochrome c oxidase subunit I(COI) gene and variable number of tandem repeats (VNTRs) of the control region (CR). A total of forty-one COIhaplotypes were found from 174 COIsequences from East Asia. The Jeju Island population (n=5) had four haplotypes, and the South Sea population (n=105) had twenty-five haplotypes. The Hong Kong population had nineteen haplotypes from fifty-nine COIsequences determined in this study. Among the COIhaplotypes, EAC_03 is commonly found in all populations (Jeju Island and South Sea of Korea, China, Hong Kong and Taiwan). In addition, there were four haplotypes (EAC_12, EAC_14, EAC_28 and EAC_35) also common among the populations tested in this study and collected from NCBI database. However, twenty haplotypes were specific in the Korean populations, and fifteen haplotypes were specific in the China and Hong Kong populations. The neighbor-joining (NJ) trees constructed from the phylogenetic analyses based on the polymorphisms of the COIhaplotypes showed the monophyletic branching pattern within the genus Epinephelus, indicating that the red spotted grouper populations had evolved from common maternal ancestors. Consequently, East Asian red-spotted grouper populations are maternally related at least in part, as well as sharing the same evolutionary history, and still affected by the East Asian ocean current (Kuroshio). From the haplotype analysis for mtDNA CR, we obtained VNTR polymor-phisms in all populations tested. We found five haplotypes for the CR VNTR patterns. The 133-bp repeat units were counted two to five. Using CR VNTR haplotypes, the statistical association was examined between mtDNA haplotypes and growth traits of aquafarming young fishes of the red-spotted grouper. A total of 386 F1 progeny, which were randomly selected from a progeny population produced by artificial insemination in the farm, were genotyped and statistically compared their body length (BL), body weights (BW) and length-weight indexes (LWI) at 11-months after hatching. There haplotypes H03, H04 and H05 were detected for CR in the parents and progeny populations. The significant difference was found in the BL values among three haplotypes (p<0.05). The F1 animals with haplotype H03 had freater level of BL (19.22±2.000 cm) than those of H04 (18.64±1.964 cm) and H05 (18.86±1.512 cm). There were no significant differences in BW and LWI among haplotypes (p<0.05). These results concluded that the maternal lineages affected the growth rates during early developmental stage in the red-spotted grouper. These findings suggested that the mitochondrial background of the fertilized eggs may play an important role in the early development, and the markerassisted selection system for broodstork animals may be helpful in improving performance traits for aquaculture industry as well as for conservation biology of the endangered red-spotted grouper. However, the results from the association analysis between haplotypes and phenotypes of F1 progeny (n=1,093) at 60-days after hatching showed that there were no significant difference (p>0.05). Consequently, the results of this study may be useful information for understanding the evolutionary relation with other species and may be good genetic markers for breeding management in the red-spotted grouper aquaculture system.

Cultivated tomato (Solanum lycopersicum L.) is an economically important vegetable and has a narrow genetic base due to intensive human selection through domestication and breeding. The low level of genetic variation between cultivated tomatoes has made it difficult to develop molecular markers for elite breeding lines. Recently, genome-wide 145,695 InDels were identified from in silico analysis of two tomato genome sequences, Heinz 1706 (S. lycoperiscum) and LA1589 (S. pimpnellifolium). Of these, 2,272 InDels were validated and 717 InDels showed polymorphism in cultivated tomatoes. In the present study, we selected 48 out of 717 InDels based on PIC value (> 0.3) and size (> 10 bp) to develop a DNA database for commercial tomato cultivars. We also used an additional set of 28 InDels that have been previously reported. These markers were distributed across 11 chromosomes with an average of 6.6 markers. A total of 48 F1 hybrid cultivars were collected from 20 seed companies and a subset of eight cultivars were used to test polymorphism of the InDel markers. The 37 InDel markers were polymorphic in these cultivars and were used to genotype additional 40 cultivars. Genetic distances and relationships between cultivars were assessed using the InDel genotypes of 48 cultivars. This analysis revealed that the InDel markers detected genetic variations to identify 46 cultivars. Our results demonstrate that the InDel markers will be a useful resource to construct a DNA database for tomato cultivars and to protect tomato breeder’s rights via variety identification.

With the rapid development of sequencing technologies, next-generation sequencing is widely utilized for molecular breeding in several crops including rice. We performed whole genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. In total, 2,448 million raw reads were generated with over 58x coverage of Nipponbare genome. We mapped the reads from each of the ten accessions onto genomic sequence of japonica rice cultivar, Nipponbare. We detected 3,144,016 SNPs, which estimated to be one per 2.2kb on average. We found SNPs in genes that have been reported to be involved in rice flowering time regulation and bacterial blight resistance among ten rice accessions. Unmapped region against Nipponbare genome occupied about 1 ~ 2% in each accession. Over 50% of the unmapped region were found in the repeat region. The minimum length of gap in all accessions were 1bp and the maximum length of gap was 45,967bp in Ilpum. We also identified 3,497 possible gene loss events within these unmapped regions. The frequency of gene loss in each chromosome ranged from 33 on chromosome 5 to 913 on chromosome 11. The genetic variations we detected among ten rice accessions will provide invaluable resources for identification of genes associated with diverse traits of agronomical importance for molecular breeding.

Progress in next-generation sequencing technologies have enabled discovery of massive amount of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs) and insertion-deletion (InDels), which are an invaluable resource to analyze genetic diversity in a population. We performed whole-genome resequencing of ten Korean rice accessions including six cultivars and four mutant lines. A total of 2,448 million raw reads was generated with 58-fold coverage and uniquely mapped to 87.5% of the Nipponbare as a reference genome. We identified 3,240,025 DNA polymorphisms including 2,867,878 SNPs, 151,845 insertions and 220,302 deletions between the Korean rice accessions and Nipponbare. We observed that in ten Korean rice accessions, the frequency of potential SNPs was estimated to be one per 2.1kb on Nipponbare (382Mb). According to annotation of DNA polymorphisms, 634,617 SNPs were found in gene region, and only 169,738 SNPs were occurred in coding region. Altogether, 86,251 non-synonymous SNPs were located on 76,891 genes. We also examined the cultivar-specific SNPs to select candidate SNPs which would have possibility of being associated with unique phenotype or agronomical trait of each cultivar. It was estimated that the portion of cultivar specific SNPs is 1~12% of the total SNPs. These DNA polymorphisms obtained from our result will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.

Genetic background and phylogenetic relationships among 20 Korean wheat cultivars were assessed using microsatellites after amplifying with 13 SSR primer pairs. Average allele number per primer pair was 3.36. Genetic similarities for every pair of cultivars ranged from 0.42 to 0.97, with 0.69 of overall average. Korean cultivars were divided into two major groups based on microsatellite DNA polymorphisms. Group I consisted of relatively old cultivars developed until 1970s, and group II contained the recent cultivars developed during 1980s and 1990s. Amongst old elite cultivars/lines, ‘Yukseung 3’, ‘Norin 12’ and ‘Norin 72’ contributed most to the genetic background of cultivars belonging to group I, and ‘Norin 4’, ‘Norin 12’, ‘Norin 43’ and ‘Norin 72’ to group II, respectively. The phylogenetic relationship of Korean wheat cultivars was in accordance with the genealogical data of each cultivar. The genetic background of each cultivar was assessed from the point of breeding and germplasm management such as variety identification and duplicated accessions for assisting in developing a system for the registration of new variety based on the molecular characterization in future.