• Korean Journal of Fisheries and Aquatic Sciences
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• v.56 no.4
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• pp.411-418
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• 2023

Genome wide association studies (GWAS) identify genetic loci associated with quantitative traits in genomic selection. Although several studies have compared performance of various algorithms, no study compares them in olive flounder Paralichthys olivaceus. This study compared the GWAS results of four mixed linear model (MLM) algorithms and one Fixed and random model Circulating Probability Unification (FarmCPU) algorithm in olive flounder. Considering gender and genetic association matrices as fixed and random effects, the MLM had stable performance without inflation for λ_GC (genomic inflation factor) of -log₁₀P. The FarmCPU algorithm had some appropriate λ_GC of -log₁₀P, and an upward tail was identified in quantile-quantile plots. Therefore, the models were suitable for detecting genetic variants associated with olive flounder growth traits. Moreover, significant genotypes appeared several times at chromosome 22, around which quantitative trait loci are expected to exist. Finally, in both models, some of the most genetic variants were found in genes related to growth traits, confirming their reliability. These results will be helpful when applied to the genomic selection of olive flounder growth traits in the future.

• Journal of Aquaculture
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• v.21 no.4
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• pp.317-324
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• 2008

This study estimated the genetic parameters and breeding values for the growth-related traits of the 1st generation produced in 2005. The heritability of body weight, total length, body height, body shape and condition factor of 180 days old olive flounders Paralichthys olivaceus, the 1st generation of selection, was estimated as 0.564, 0.590, 0.588, 0.306 and 0.332, respectively. And reproductivity of genetic evaluation for crossing superior flounders and inferior ones was tested using the subsequent generation produced in 2006 based on the breeding values of 1st generation. In the least-squares means of body weight and total length for each group of crossing, the values of crossing group between superior flounders ($S{\times}S$) showed $145.6{\pm}1.8\;g$ and $22.4{\pm}0.1\;cm$, respectively. The values of crossing group between superior and inferior flounders ($S{\times}I$) showed $133.2{\pm}2.5\;g$ and $22.1{\pm}0.1\;cm$, respectively. The values of crossing group between inferior flounders ($I{\times}I$) showed $114.0{\pm}2.1\;g$ and $21.08{\pm}0.12\;cm$, respectively. In the results, flounders are determined as appropriate selective breeding fish with the high heritability of flounders in early ages at 180 days old, and the reproductivity of genetic evaluation was also high.

• Korean Journal of Ichthyology
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• v.32 no.4
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• pp.210-221
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• 2020

Since the introduction of Israeli carp into Korea for farming in 1973, there are no breeding studies on developing Korea Israeli carp (domestic) so far. This study performed gene-based cross-breeding studies to restore genetic diversity of lowered Israeli carp through continuous inbreeding, and for rapid growth and better scales. This study produced four cross-breeding groups (F1) using Koean Israeli carp and Chinese Songpu mirror carp for the improvement of growth and scale of Israeli carp in Korea. And mating scheme for breeding groups was set in consideration of the morphological analysis and genetic distance of broodstock. In addition, this study used microsatellite markers and genotype data to analyze genetic diversity and parentage analysis. As a result, the average N_A and H_E values of Korean select broodstock are 8.3 and 0.743, and F1 is 13.0 and 0.764. This study shows that the genetic diversity of F1 has been recovered over Korean Israeli carp through breeding between Korean Israeli carp and Chinese Songpu mirror carp. Common Israeli carp in Korea reached 1.7 kg in 17 months, and improved Israeli carp reached to 2.2 kg. The KC (Korea×China, KC) group was 2.52 and broodstock group was 3.15. F1 showed lower scale score (0.63) than broodstock. The improved carp (F1; CK, KC) had 20% better scales than the parent group (F0), which improved 27% in weight and 25% in scales compared to common Israeli carp. The Israeli carp developed by the genetics-based breeding grew quicker and had improved genetic diversity and fewer scales, which will be of great value for Korean Israeli aquaculture industry due to good marketability.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.87-99
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• 2010

Genetic diversity and relationships within and among Korean, Japanese and Chinese Jilin provincial wild soybeans based on SSR markers were evaluated to enlarge genetic variation in soybean breeding in the future. A total of 184 wild soybeans including 67 Korean, 71 Japanese and 46 Chinese Jilin provincial wild soybeans were analyzed to evaluate genetic diversity and relationships based on 23 SSR markers. Korean and Japanese wild soybeans were obtained from National Agrobiodiversity Center, Korea, and Biological Resource Center in Lotus and Glycine, Frontier Science Research Center, University of Miyazaki, Japan, respectively. Chinese wild soybeans were collected from Jilin province, China. Twenty three SSR markers generated a total of 964 alleles with an average of 41.9 alleles per marker. Number of alleles ranged from 23 (Satt635) to 56 (Satt157). Genetic diversity (PIC value) of 184 wild soybeans ranged from 0.880 to 0.968 with an average of 0.945. Number of alleles for Korean, Japanese and Chinese Jilin provincial wild soybeans was 513 with an average of 22.3, 511 with an average of 22.2, and 312 with an average of 13.6 per marker, respectively. PIC value for Korean, Japanese and Chinese Jilin provincial wild soybeans was similar with an average of 0.905, 0.897, and 0.850, respectively. Cluster analysis based on genetic distances estimated by SSR markers classified wild soybeans into 3 clusters. Cluster I included only Chinese Jilin provincial wild soybeans. Cluster II included most of Japanese wild soybeans including 5 Korean wild soybeans. Cluster III included most of Korean wild soybeans including 6 Japanese and 1 Chinese Jilin provincial wild soybeans. Cluster I was not subclassified, but cluster II and III were subclassified into various groups. Genetic distance evaluated by SSR markers between Korean and Japanese wild soybeans was closer than that of between Korean and Chinese Jilin provincial, and between Japanese and Chinese Jilin provincial wild soybeans.

• Journal of Korean Society of Forest Science
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• v.112 no.1
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• pp.40-56
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• 2023

Tree species within the Populus genus grow rapidly and have an excellent capacity to absorb carbon, conferring substantial ability to effective purify the environment. Poplar breeding can be achieved rapidly and efficiently if a genetic linkage map is constructed and quantitative trait loci (QTLs) are identified. Here, a high-density genetic linkage map was constructed for the control pollinated progeny using the genotyping-by-sequencing (GBS) technique, which is a next-generation sequencing method. A search was also performed for the genes associated with quantitative traits located in the genetic linkage map by examining the variables of height and diameter at root collar, and resilience to insect damage. The height and diameter at root collar were measured directly, while the ability to recover from insect damage was scored in a 4-year-old breeding population of aspen hybrids (Odae19 × Bonghyeon4 F1) established in the research forest of Seoul National University. After DNA extraction, paternity was confirmed using five microsatellite markers, and only the individuals for which paternity was confirmed were used for the analysis. The DNA was cut using restriction enzymes and the obtained DNA fragments were prepared using a GBS library and sequenced. The analyzed results were sorted using Populus trichocarpa as a reference genome. Overall, 58,040 aligned single-nucleotide polymorphism (SNP) markers were identified, 17,755 of which were used for mapping genetic linkages. The genetic linkage map was divided into 19 linkage groups, with a total length of 2,129.54 cM. The analysis failed to identify any growth-related QTLs, but a gene assumed to be related to recovery from insect damage was identified on linkage group (chromosome) 4 through genome-wide association study.

• Horticultural Science & Technology
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• v.32 no.1
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• pp.77-83
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• 2014

To improve the breeding efficiency of oriental pear, the inheritance of major fruit traits were analyzed using 4,035 seedlings of 15 cross combinations combined with 13 cultivars. Yearly variation of parental cultivars, broad-sense heritability of the traits, and frequency of seedlings with commercially acceptable characteristics by the mid-parent values were studied. Despite the heritabilities of traits related with pear the fruit texture were different depending on cross combination, the average narrow-sense heritability ($h^2$) for firmness, flesh hardness, flesh density and grit were over 0.6, a relatively high value. However fruit firmness showed different heritability among the cross combination and its value of cross combination between 'Niitaka' and 'Choju' was very low as 0.11. Positive correlation was not observed on fresh hardness, fresh density and grit but observed on firmness between mid-parent value and average value of offspring. Regression of offspring on firmness, fresh hardness, fresh density and grit between mid-parent value and average value of offspring were 0.778, 0.343, -0.273, 0.313, respectively. Frequency distributions of fruit texture in 15 cross combinations of pear seedling was influenced by parental characteristics. When fruit firmness was estimated as low, low ${\times}$ high and high ${\times}$ high values in parental fruits, firmness in their offspring exhibited low, medium and high, respectively. In addition, when parental grit by sensory evaluation were light ${\times}$ light and light-medium ${\times}$ medium-heavy, most of offsprings showed light and medium grit, respectively.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.342-349
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• 2015

Kiwifruit is a new fruit crop that was commercialized in the late 1970s. Recently, its cultivation and consumption have increased rapidly worldwide. Kiwifruit is a dioecious, deciduous, and climbing plant having fruit with hairs and various flesh colors and a variation in ploidy level; however, the industry consists of very simple cultivars or genotypes. The need for efficient cultivar improvement together with the evolutional and biological perspectives based on unique plant characteristics, have recently encouraged genome analysis and bioinformatics application. The draft genome sequence and chloroplast genome sequence of kiwifruit were released in 2013 and 2015, respectively; and gene annotation has been in progress. Recently, transcriptome analysis has shifted from previous ESTs analysis to the RNA-seq platform for intensive exploration of controlled genetic expression and gene discovery involved in fruit ascorbic acid biosynthesis, flesh coloration, maturation, and vine bacterial canker tolerance. For improving conventional breeding efficiency, molecular marker development and genetic linkage map construction have advanced from basic approaches using RFLP, RAPD, and AFLP to the development of NGS-based SSR and SNP markers linked to agronomically important traits and the construction of highly saturated linkage maps. However, genome and transcriptome studies have been limited in Korea. In the near future, kiwifruit genome and transcriptome studies are expected to translate to the practical application of molecular breeding.

• The Korean Journal of Food And Nutrition
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• v.23 no.4
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• pp.582-587
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• 2010

본 연구에서는 녹두 유전자원의 지방산 함량을 신속 대량 검정하는 기술을 개발하여 유전자원 활용 및 육종 촉진에 기여하고자 하였다. 유전자원 평가에 적합한 신속하고 비파괴적인 지방산 함량 평가기술을 개발하기 위해 공시자원 1,125점의 녹두 종자를 종실상태와 분쇄한 분말상태로 근적외선분광분석기(NIR)를 이용하여 1,104~2,494 nm에서의 스펙트럼을 얻고 이들 중 스펙트럼이 중복되지 않는 원산지가 다양한 대표자원 106점을 선발하여 일반적인 방법으로 지방산 함량을 분석하고, 이 값과 NIR 스펙트럼 흡광도값 간의 상관분석을 위한 calibration set로 활용하였다. 그 결과 palmitic acid, stearic acid, oleic acid, linoleic acid, linolenic acid 및 total fatty acid에 대한 NIR 흡광도와의 상관계수 $R^2$이 각각 0.74, 0.18, 0.12, 0.72, 0.48 및 0.78로 나타났고, 이들 중 $R^2$가 높은 검량식을 미지의 시료 10점으로 검증한 결과, palmitic, linoleic 및 total fatty acid에 대한 검증 상관계수 $R^2$이 0.96, 0.74, 0.81로 나타나, 다양한 녹두 유전자원의 지방산함량 신속 대량 예측에 유효하게 활용될 수 있는 것으로 나타났다. 한편, 공시된 녹두 유전자원 115점 중에서 자원번호 IT208075 자원은 저 지방산 자원($14.24\;mg\;g^{-1}$)으로 선발되었고, IT163279 자원은 고 지방산 자원($18.43\;mg\;g^{-1}$)으로 선발되어 향후 녹두작물의 성분육종에 유용할 것으로 생각된다.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.29 no.1
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• pp.55-61
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• 1984

A Korean local maize line, MET, which has multi-ears and tillers has been proved as a potential source for silage production. However, no fundamental genetic nature for the line has been investigated. Therefore, this study was done to find genetic information on the multi-earing and -tillering habits of MET line. MET line and a hybrid. (Mo 17 ${\times}$ B68), with monoculm and single ear per plant were used for production of F$_1$(F$\_$1-12/ and F$\_$1-21/), F$\_$2-12/, F$\_$2-21/, BC$\_$1-12/ and BC$\_$1-21/ generations. From the comparison of reciprocal crosses, it was found that the tillering and earing habits of the MET line are controlled by cytoplasmic factors. The tiller and ear numbers, and barren ears were all characters associated with the MET cytoplasm. The cytoplasmic effect of MET on tiller and ear numb en was not evident in F$_1$ generation, probably because of suppressing effect of heterosis on appearance of tillers or ears. Genetic parameters for the gene action for both tiller and ear number also indicated a lack of mono- or digenic-chromosomal gene effects. The heritability (broad) was very low for both characters. Therefore, it is strongly concluded that the tillering and earing characters of MET line are due to cytoplasmic reasons.

• Korean Journal of Breeding Science
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• v.43 no.5
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• pp.405-412
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• 2011

Knowledge of genetic diversity and genetic relationships among inbred lines gives a significant impact on the selection of parental lines for hybrid maize varieties. Genetic diversity and genetic relationships among 86 popcorn inbred lines were analyzed using 50 SSR markers distributed over the whole genome. A total of 256 alleles were identified at all the SSR loci with an average of 5.1 and a range between two and sixteen per locus. The gene diversity values varied from 0.21 to 0.831 with an average of 0.579. The cluster tree generated using the described SSR markers recognized three major groups at 35.8% genetic similarity. Groups I, II, III respectively included 40, 39 and 7 inbred lines. The present study indicates that the SSR markers chosen for this analysis are effective for the assessment of genetic diversity and genetic relationships among 86 popcorn inbred lines in Korea.