• Animal Bioscience
• /
• v.37 no.5
• /
• pp.807-816
• /
• 2024

Objective: This study aims to identify the significant regions and candidate genes of growth-related traits (adjusted backfat thickness [ABF], average daily gain [ADG], and days to 90 kg [DAYS90]) in Korean commercial GGP pig (Duroc, Landrace, and Yorkshire) populations. Methods: A genome-wide association study (GWAS) was performed using single-nucleotide polymorphism (SNP) markers for imputation to Illumina PorcineSNP60. The BayesB method was applied to calculate thresholds for the significance of SNP markers. The identified windows were considered significant if they explained ≥1% genetic variance. Results: A total of 28 window regions were related to genetic growth effects. Bayesian GWAS revealed 28 significant genetic regions including 52 informative SNPs associated with growth traits (ABF, ADG, DAYS90) in Duroc, Landrace, and Yorkshire pigs, with genetic variance ranging from 1.00% to 5.46%. Additionally, 14 candidate genes with previous functional validation were identified for these traits. Conclusion: The identified SNPs within these regions hold potential value for future marker-assisted or genomic selection in pig breeding programs. Consequently, they contribute to an improved understanding of genetic architecture and our ability to genetically enhance pigs. SNPs within the identified regions could prove valuable for future marker-assisted or genomic selection in pig breeding programs.

• Journal of Animal Science and Technology
• /
• v.53 no.1
• /
• pp.1-6
• /
• 2011

This simulation study was performed to investigate the accuracy of the estimated breeding value by using genomic information (GEBV) by way of Bayesian framework. Genomic information by way of single nucleotide polymorphism (SNP) from a chromosome with length of 100cM were simulated with different marker distance (0.1cM, 0.5cM), heritabilities (0.1, 0.5) and half sibs families (20 heads, 4 heads). For generating the simulated population in which animals were inferred to genomic polymorphism, we assumed that the number of quantitative trait loci (QTL) were equal with the number of no effect markers. The positions of markers and QTLs were located with even and scatter distances, respectively. The accuracies of estimated breeding values by way of indicating correlations between true and estimated breeding values were compared on several cases of marker distances, heritabilities and family sizes. The accuracies of breeding values on animals only having genomic information were 0.87 and 0.81 in marker distances of 0.1cM and 0.5cM, respectively. These accuracies were shown to be influenced by heritabilities (0.87 at $h^2$ =0.10, 0.94 at $h^2$ =0.50). According to half sibs' family size, these accuracies were 0.87 and 0.84 in family size of 20 and 4, respectively. As half sibs family size is high, accuracy of breeding appeared high. Based on the results of this study it is concluded that the amount of marker information, heritability and family size would influence the accuracy of the estimated breeding values in genomic selection methodology for animal breeding.

• Horticultural Science & Technology
• /
• v.16 no.1
• /
• pp.18-20
• /
• 1998

The present research was conducted to study genetic relationship and cultivar identification in sweet potato (lpomoea batatas) using RAPD method. Thirteen cultivars of sweet potato in Korea were classified by UPGMA clustering method into three groups as follows; group I was corresponded to 'Choongsung100'; group II, 'Eunmi', 'Saengmi', 'Suwon147' and 'Yulmi'; group III, 'Hongmi', 'Jinmi', 'Kwandong95', 'Seonmi', 'Wonmi', 'Shinyulmi', 'Jeungmi', and 'Poongmi'. Identification using RAPD was generally consistent with breeding pedigree of those parents. However, inconsistent results may be caused by clonal variation. The results presented in this study suggest that RAPDs in sweetpotato are likely to be useful for cultivar identification and various procedures in breeding. The use of various DNA marker system assists selection programs for economically important trait, and may facilitate selection in earlier growing stage. This systems may enhance the prospects for improving sweet potato cultivar by accurate marking desirable traits at DNA level.

• Journal of Life Science
• /
• v.14 no.2
• /
• pp.339-344
• /
• 2004

Identification of individual quantitative trait loci (QTL) is a prerequisite to application of marker-assisted selection for stern length. Two simple sequence repeat (SSR)-based linkage maps were constructed from recombination inbred line populations between cross of Keunolkong and Shinpaldalkong. Two parents used differed greatly in stem length, which were 30.57 cm and 49.75 cm in Keunolkong and Shinpaldalkong, respectively. Using the constructed maps, regression analysis and interval mapping were performed to identify QTLs conferring stem length. Four QTLs for stem length on linkage groups (LG) F, J, N and O were identified in the Keunolkong ${\times}$ Shinpaldalkong population and they totally explained 37.83% of variation for stem length. In the population, two major QTLs on LG J and O conditioning 14.25% and 10.68% of the phenotypic variation in stem length were determined and two QTLs with minor effect were detected on LG F and N. Identification of QTLs for stem length and mapping individual locus should facilitate to describe genetic mechanisms for stem length in different population. SSR markers tightly linked to QTLs for stem length allow to accelerate the elimination of deleterious genes and selection for desirable recombinants at early stage in crop breeding programs.

• Journal of Ginseng Research
• /
• v.43 no.3
• /
• pp.482-487
• /
• 2019

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.

• Journal of applied mathematics & informatics
• /
• v.26 no.3_4
• /
• pp.493-500
• /
• 2008

In this paper, we first construct a mathematical model for tagSNP selection based on LD measure $r^2$, then aiming at this kind of model, we develop an efficient algorithm, which is called approximate greedy algorithm. This algorithm is able to make up the disadvantage of the greedy algorithm for tagSNP selection. The key improvement of our approximate algorithm over greedy algorithm lies in that it adds local replacement(or local search) into the greedy search, tagSNP is replaced with the other SNP having greater similarity degree with it, and the local replacement is performed several times for a tagSNP so that it can improve the tagSNP set of the local precinct, thereby improve tagSNP set of whole precinct. The computational results prove that our approximate greedy algorithm can always find more efficient solutions than greedy algorithm, and improve the tagSNP set of whole precinct indeed.

• Communications for Statistical Applications and Methods
• /
• v.26 no.2
• /
• pp.79-89
• /
• 2019

Classification models pertaining to receiver operating characteristic (ROC) curve analysis have been extended from univariate to multivariate setup by linearly combining available multiple markers. One such classification model is the multivariate ROC curve analysis. However, not all markers contribute in a real scenario and may mask the contribution of other markers in classifying the individuals/objects. This paper addresses this issue by developing an algorithm that helps in identifying the important markers that are significant and true contributors. The proposed variable selection framework is supported by real datasets and a simulation study, it is shown to provide insight about the individual marker's significance in providing a classifier rule/linear combination with good extent of classification.

• Journal of Life Science
• /
• v.21 no.12
• /
• pp.1659-1665
• /
• 2011

In Citrus, an $F_1$ segregation population of 150 plants was constructed from a cross between 'Kiyomi' (C. unshiu ${\times}$ C. sinensis) carrying the male sterility trait and 'Jinkyool' (C. sunki). Sequence-related amplification polymorphism (SRAP) combined with bulked segregant analysis was used to develop markers linked to male fertility. In the $F_1$ population, 66 out of 150 seedlings had aborted anthers and the ratio of male sterile plants to fertile plants in the progenies matched the expected Mendelian segregation ratio of 1:1 ($x^2$ =2.16 at p=0.05). From the profiling of the 197 SRAP primer sets, three SRAP primer sets (F4/R27, F39/R60, and F15/R37) that were closely linked to the target trait were identified and successfully converted into a sequence characterized amplified region (SCAR) marker for selection of male fertility in citrus. The SCAR marker, using the pMS 33U/pMS 1462L primer set specifically, produced a single 1.4-Kb fragment that was linked to male fertility. Our results suggested that this SCAR marker can be useful for marker-assisted selection of male sterile individuals in breeding $F_1$ progenies in Citrus.

• Journal of Crop Science and Biotechnology
• /
• v.11 no.2
• /
• pp.101-106
• /
• 2008

To identify inheritance of clubroot disease resistance genes in Chinese cabbage, seedling tests of $BC_1P_1,\;BC_1P_2$, and $F_2$ populations derived from $F_1$ hybrid(var. CR Saerona) using single spore isolate(race 4 identified with William's differential host) from Plasmodiophora brassciae were conducted. Resistance(R) and susceptible(S) plants segregated to 1:0 in backcross to the resistant parent. The $F_2$ population segregated in a 3(R):1(S) ratio. This result implied that the resistance of clubroot disease is controlled by a single dominant gene to the race 4 of P. brassicae in CR Saerona. To develop DNA markers linked to clubroot resistance genes, 185 plants of CR Saerona among $F_2$ populations were used. A total of 300 arbitrary decamer was applied to $F_2$ population using BSARAPD(Bulked segregant analysis-Randomly amplified polymorphic DNA). One RAPD marker linked to clubroot resistance gene in CR Saerona($OPJ_{1100}$) was identified. This marker was 3.1 cM in distance from resistance gene in $F_2$ population. This marker may be useful for a marker-assisted selection(MAS) and gene pyramiding of the clubroot disease resistant gene in Chinese cabbage breeding programs.

• The Korean Journal of Mycology
• /
• v.25 no.3 s.82
• /
• pp.191-201
• /
• 1997

A mutant (HSMl) of Cryphonectria parasitica created during transformation reproduced the hypovirulent symptoms in virus-free wild type. Its phenomena have been proved with morphological marker such as reduced sporulation, pigmentation, and laccase production. In addition to the changes in phenotypic characteristics, down-regulations of Lac1, Crp1, Vir1 and Vir2 were also observed. The integration of transforming vector was confirmed and located within genome by marker rescuing. Vector integration occurred between two genes, Cpg2 and Cpg3, which resulted in the disruption of neither Cpg2 nor Cpg3. Both Cpg2 and Cpg3 genes, sized at 1.8 kb and 1.9 kb respectively, were rarely transcribed genes in Cryphonectria parasitica. Cpg2 expression was significantly overexpressed from 4 to 5 day old culture of both UEP1 and HSM1 while no differences were observed in Cpg3 expression. It appears that an aberration from the normal expression of Cpg2, not Cpg3, results in the hypovirulent symptoms in virus-free wild type.