This study has evaluated the genomic estimated breeding value (GEBV) of the commercial Hanwoo population using the genomic best linear unbiased prediction (GBLUP) method and genomic information. Furthermore, it analyzed the accuracy and realized accuracy of the GEBV. 1,740 heads of the Hanwoo population which were analyzed using a single nucleotide polymorphism (SNP) Chip has selected as the test population. For carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS), the mean GEBVs estimated using the GBLUP method were 3.819, 0.740, -0.248, and 0.041, respectively and the accuracy of each trait was 0.743, 0.728, 0.737, and 0.765, respectively. The accuracy of the breeding value was affected by heritability. The accuracy was estimated to be low in EMA with low heritability and high in MS with high heritability. Realized accuracy values of 0.522, 0.404, 0.444, and 0.539 for CWT, EMA, BFT, and MS, respectively, showing the same pattern as the accuracy value. The results of this study suggest that the breeding value of each individual can be estimated with higher accuracy by estimating the GEBV using the genomic information of 18,499 reference populations. If this method is used and applied to individual selection in a commercial Hanwoo population, more precise and economical individual selection is possible. In addition, continuous verification of the GBLUP model and establishment of a reference population suitable for commercial Hanwoo populations in Korea will enable a more accurate evaluation of individuals.

A previous studies depicting origin and sequence variability of the species using DNA barcoding region with the samples collected from Korea showed relatively low sequence variability. Thus, additional markers that reveal higher variability were necessitated to scrutinize population structure in connection with dispersal and invasive dynamics among international populations. Therefore, we sequenced two complete mitochondrial genomes (mitogenomes) of M. pruinosa from the two haplotypes occurring in Korea (H1 and H3). Comparison of the two mitogenomes each with 16,312 and 16,314 bp evidenced that one region located in the A+T-rich region to provide higher number of haplotypes (4 vs. 3), sequence divergence (1.636% vs. 0.636%), and variable sites (7 vs. 3) than those of DNA barcoding region from the screening test using 13 representative individuals. This variable region, in concatenation with the currently available DNA barcoding region might be useful for population genetic analysis of worldwide populations including those of Korea. †These authors contributed equally to this paper.

본 연구는 한우 보증씨수소 844두를 출생년도를 기준으로 8개 집단으로 분류하고, 각 개체들의 친자확인용 유전자 마커정보를 농협경제지주 한우개량사업소 홈페이지에서 제공 받아 유전적 다양성 및 구조 변화 분석에 활용하였다. 한우 보증씨수소 전체 집단의 대립유전자수(number of alleles)의 평균은 10.54개, 기대 및 관측 이형접합율(Hex, Hob)의 평균은 각각 0.764, 0.773, 다형성 정보량 지수(PIC)의 평균은 0.727 그리고 Fis의 평균은 –0.014로 확인되었다. 한우 보증씨수소 집단을 출생년도 별로 구분한 8개 집단의 유전적 다양성 및 구조 분석 결과, D집단(2005-2004년)의 기대이형접합율(0.777), 관측이형접합율(0.792) 그리고 다형성정보지수(0.740)가 가장 높은 것으로 확인되었다. C집단(2003-2004년)과 E집단(2007-2008년)에서는 기대이형접합율이 관측이형접합율 보다 큰 것으로 확인되었고, 나머지 그룹 모두에서는 관측이형접합율이 기대이형접합율 보다 큰 것으로 확인되었다. 대립유전자 출현빈도를 기반으로 유전적 조성과 구조를 추론하기 위해 STRUCTURE software를 이용하여 분석한 결과 세대가 지남에 따라 특정 유전적 성분의 변화 또는 비중의 증감을 확인 할 수 있었다. 이는 개량 목표를 설정하고 지속적으로 추진되고 있는 개량 사업이 한우 씨수소 집단의 유전적 구조 변화에 영향을 미치고 있음을 확인 할 수 있는 중요한 자료로, 한우 개량 사업의 효율적인 추진을 위해 유용하게 활용 될것으로 사료된다.

Bumblebee, Bombus ardens ardens (Apidae: Hymenopera), is an important resource for pollination that is most widely distributed in Korea. This study utilized microsatellite markers for investigation of genetic diversity and geographic relevance of the B. a. ardens populations in Korea. Through Next Generation Sequencing analysis, we identified 10 microsatellite markers and genotyped for 107 individuals of B. ardens collected from 10 populations. At each locus the number of alleles ranged from 10 to 23; the observed and expected heterozygosities ranged from 0.8909 to 1.0000 and 0.6641 to 0.8422, respectively; and inbreeding coefficient(FIS) ranged from –0.5053 to –0.0891. Significant deviation from the Hardy–Weinberg equilibrium was not observed at any locus. Population structure analysis indicated that there are three genetic groups in Korea with each Jeongseon and Ulleung-do composed of different gene pool from the remaining other populations. Similarly, Principal coordinates analysis also showed the same pattern. FST and RST analyses showed that each Jeongseon and Ulleung-do population had a significant genetic distance from other populations. Considering these results, genetic isolation of Ulleung-do may be explained by “Oceanic island” status and Jeongseon, which showed the positive FIS (0.069) and genetic isolation may be caused by its location on the east side of Baekdudaegan and by on-going inbreeding with a small population size.

The author undertook PCR-founded genetic platform to investigate the hierarchical dendrogram of Euclidean genetic distances of one razor clam population, particularly for Solen corneus, which was further associated with those of the other clam population, by engaging with the precisely designed oligonucleotide primer sets. Seven oligonucleotides primers were used producing a total of 639 counted bands in population A and 595 in population B, respectively, ranging in size of DNA fragments from larger than approximately 50 bp to less than 1,100 bp. Their primers generated 39 specific fragments (6.10%) in population A and 47 (7.90%) in population B, respectively Comparatively, individuals of one razor clam population were fairly related to that of the other clam population, as shown in the hierarchical dendrogram of Euclidean genetic distances. The analysis of genetic variation between razor clam populations could offer important statistics for fisheries and mariculture. Generally the results showed specific and/or conserved genetic loci between razor clam populations. Specific markers established by the author will be valuable for the genetic analysis, species protection and increase of razor clam individuals in coastal region of the Korean Peninsula.

Eleutherococcus senticosus (Siberian ginseng) is an important medicinal tree found in northeast Asia. In this study, we analyzed the genome-wide distribution of microsatellites in E. senticosus. By sequencing 711 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in E. senticosus accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 131 E. senticosus accessions in Korea and China. The number of alleles ranged from 2 to 11, with an average of 7.4 alleles. The mean values of observed heterozygosity (HO) and expected heterozygosity (HE) were 0.59 and 0.56, respectively. The average polymorphism information content (PIC) was 0.51 in all 131 E. senticosus accessions. E. senticosus accessions in Korea and China showed a close genetic similarity. Significantly low pairwise genetic divergence was observed between the two regions, suggesting a relatively narrow level of genetic basis among E. senticosus accessions. Our results not only provide molecular tools for genetic studies in E. senticosus but are also helpful for conservation and E. senticosus breeding programs.

We collected 32 maize inbred lines from eastern cereal and oilseed research center in Canada to develop new maize varieties. We also evaluated genetic diversity, genetic relationships, and population structure using 35 SSR markers. A total of 269 alleles were revealed in 35 loci with an average of 7.69 and a range between 3 and 15 alleles per locus. The genetic diversity values varied from 0.176 to 0.889 with an average of 0.691. The polymorphic information content varied from 0.171 to 0.879 with an average of 0.659. Population structure analysis indicated that 32 Canadian maize inbred lines comprised four major groups and one admixed group based on a membership probability threshold of 0.80. The four major groups contained 13, 2, 5 and 2 maize inbred lines, respectively. From genetic relationships analysis, the all inbred lines were divided into three main groups at 26% genetic similarity. Group I included 22 inbred lines, and Group II included 9 inbred lines. Group III consist of only one inbred line. The results in this study would be useful for the improvement and development of new cultivars, planning crosses for hybrids or development of inbred line in maize breeding program

We investigated the genetic diversity and structure of the 239 fixed lines with 47 simple sequence repeat (SSR) and 109 NGS-generated SNP markers evenly distributed in B. rapa genome. Phylogenetic analysis classified the vegetable fixed lines to four subgroups, with the three types forming a separate and relatively farther cluster. Population structure analysis identified four sub-populations corresponding to geographic origin and morphological traits, and revealed extensive admixture. The vegetable B. rapa fixed lines successfully developed in our study would be valuable materials for multinational B. rapa diversity resources establishment. Understanding the genetic diversity and population structure could be useful for utilization of the representing genetic variation and further genetic and genomic analysis.

Amaranth (Amaranthus sp. L.) is an important group of plants that includes grain, vegetable, and ornamental types. Centers of diversity for Amaranths are Central and South America, India, and South East Asia, with secondary centers of diversity in West and East Africa. The present study was performed to determine the genetic diversity and population structure of 75 amaranth accessions: 65 from South America and 10 from South Asia as controls using 14 SSR markers. Ninety-nine alleles were detected at an average of seven alleles per SSR locus. Model-based structure analysis revealed the presence of two subpopulations and 3 admixtures, which was consistent with clustering based on the genetic distance. The average major allele frequency and polymorphic information content (PIC) were 0.42 and 0.39, respectively. According to the model-based structure analysis based on genetic distance, 75 accessions (96%) were classified into two clusters, and only three accessions (4%) were admixtures. Cluster 1 had a higher allele number and PIC values than Cluster 2. Model-based structure analysis revealed the presence of two subpopulations and three admixtures in the 75 accessions. The results of this study provide effective information for future germplasm conservation and improvement programs in Amaranthus.

Amaranths (Amaranthus sp.) are cosmopolitan and include grain, vegetable, ornamental and weed types. Forteen simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 59 accessions of cultivated amaranth from Asian countries. A total of 63 alleles were detected with an average of 4.5 per locus. The averaged values of gene diversity and polymorphism information content (PIC) were 0.35 and 0.33, respectively. Alleles per locus in accessions from South Asia was 4.35, whereas 2.93 and 3.79 alleles per locus were found in Nepal and India, respectively. The mean gene diversity in Central Asia and East Asia was 0.36 and 0.28, respectively, whereas the mean PIC values were 0.27 and 0.22, respectively. The genetic diversity and PIC of the India amaranths were higher than that of other Asian countries. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 56.16% in contrast to 43.84% for the within-population component. The overall FST value was 0.56, reflecting genetic differentiation within Asian amaranths. These findings could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.

본 연구는 총 50개의 SSR primer를 이용하여 색소옥수수(색소종실 옥수수 12계통, 색소찰 옥수수 12계통) 및 비색소옥수수(종실옥수수 2계통, 찰옥수수 5계통) 계통들에 대하여 유전적 다양성, 계통유연관계 및 집단구조를 분석하였다.1. 그 결과 50 개의 SSR primer들은 색소 및 비색소옥수수 31계통들에서 총 282개의 대립단편을 증폭시켰으며, SSR primer들에서 증폭된 대립단편의 수는 최소 2개에서부터 최대 11개까지의 범위로 나타나 평균 5.64개가 증폭되었다. MAF(major allele frequency)는 0.23(bnlg279)에서 0.90(umc2338)의 범위로 나타나, SSR primer 당 평균 0.45개로 나타났고, 유전적 다양성(GD)값은 0.17(umc2338)에서 0.86(bnlg279)의 범위로 나타나, SSR primer 당 평균 0.67의 값을 나타내었다. 2. 31개의 색소 및 비색소옥수수 계통들의 집단구조를 분석한 결과, 이들 옥수수 계통들은 Groups I, II, III, IV, V, admixed로 구분되었다. Group I은 찰옥수수 1계통, 색소종실옥수수 1계통, 색소찰옥수수 5계통이 포함되었고, Group II는 찰옥수수 1계통, 색소찰옥수수 3계통이, Group III는 색소종실옥수수 3계통, Group IV는 색소종실옥수수 2계통이, Group V는 종실옥수수 2계통, 찰옥수수 2계통, 색소종실옥수수 5계통이 포함되어 있었다. 그리고 admixed group에는 찰옥수수 1계통, 색소종실옥수수 1계통, 색소찰옥수수 4계통 이 포함되어 있었다.3. UPGMA법에 의한 계통유연관계 분석 결과, 31개의 색소 및 비색소옥수수 계통들은 유전적 유사성 27.4%의 수준에서 크게 3개의 그룹으로 나누어졌다. Group I은 10개의 옥수수 계통(종실옥수수 2계통, 찰옥수수 2계통, 색소종실옥수수 6계통)을 포함하고 있었고, Group II는 20개의 옥수수 계통(찰옥수수 3계통, 색소종실옥수수 5계통, 색소찰옥수수 12계통)을, 그리고 Group III은 색소종실옥수수 1계통을 포함하고 있었다. 따라서 본 연구의 결과는 앞으로 강원도 농업기술원 옥수수시험장에서 색소옥수수 자식계통들에 대한 선발과 품종 육성 연구에 유용한 정보를 제공할 것으로 생각된다.

The genus Rubus belongs to the Rosaceae family and is comprised of 600-800 species distributed worldwide. Understanding the genetic relationships and genetic structure in Rubus species is important for enabling efficient management, conservation, characterization and utilization of the species. However, as a minor crop, genetic research foundation was limited to explore genetic diversity and relationships in Rubus species. The present study shows the results of application SSR markers that were developed from SSR-enriched libraries of the one Rubus species (Rubus coreanus Mique.) in our previous study. We used 34 polymorphic microsatellite markers to analysis of genetic diversity within the Rubus species, including redraspberry, blackraspberry, blackberry and mountainberry. All the 34 SSR primers pairs produced 483 polymorphic and reproducible amplification fragments. The largest number of alleles per primer pair was confirmed at GB-RC-167, GB-RC-100, GB-RC-076 and GB-RC-245, which contained 26, 25, 23 and 21, respectively. An average value of polymorphic information contents (PIC) were 0.74 with a range of 0.36 to 0.92. Population structure and phylogenetic analyses showed that all Rubus species formed three largely distinct clusters, which were confirmed by principal coordinate analysis (PCoA). We obtained the results that the developed SSR markers showed a substantial degree of genetic diversity in the various Rubus species distributed in Korea.