• The Plant Pathology Journal
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• 제16권1호
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• pp.1-8
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• 2000

Worldwide, rice blast, caused by Magnaporthe grisea (Hebert) Barr. (anamorph, Pyricularia grisea Sacc.), is one of the most economically devastating crop diseases. Management of rice blast through the breeding of blast-resistant varieties has had only limited xuccess due to the frequent breakdown of resistance under field conditions (Bonman etal., 1992; Correa-Victoria and Zeigler, 1991; Kiyosawa, 1982). The frequent variation of race in pathogen populations has been proposed as the principal mechanism involved in the loss of resistance (Ou, 1980). Although it is generally accepted that race change in M. grisea occurs in nature, the degree of its variability has been a controversial subject. A number of studies have reported the appearance of new races at extremely high rates (Giatgong and Frederiksen, 1968; Ou and Ayad, 1968; Ou et al., 1970; Ou et al., 1971). Various potential mechanisms, including heterokaryosis (Suzuki, 1965), parasexual recombination (Genovesi and Magill, 1976), and aneuploidy (Kameswar Row et al., 1985; Ou, 1980), have been proposed to explain frequent race changes. In contrast, other studies have shown that although race change could occur, its frequency was much lower than that predicted by earlier studies (Bonman et al., 1987; Latterell and Rossi, 1986; Marchetti et al., 1976). Although questions about the frequency of race changes in M. grisea remain unanswered, the application of molecular genetic tools to study the fungus, ranging from its genes controlling host specificity to its population sturctures and dynamics, have begun to provide new insights into the potential mechanisms underlying race variation. In this review we aim to provide an overview on (a) the molecular basis of host specificity of M. grisea, (b) the population structure and dynamics of rice pathogens, and (c) the nature and mechanisms of genetic changes underpinning virulence variation in M. grisea.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.106-106
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• 2017

The soybean [Glycine max (L.) Merr.] is one of the most important crop resources worldwide as food and forage. It is also important and valuable that to hold crop resources to have high genetic diversities. Recently, a core collection has been constructed in many plants to preserve the genetic resources of various plants. A core collection is small population to represent the genetic diversity of the total collection, and is of strategic importance as they allow the use of a small part of a germplasm collection that is representative of the total collection. Here, we developed the core collection consisting of 816 accessions by using approximately 180,000 (180K) single nucleotide polymorphisms (SNPs) developed in previous study. In addition, we performed genetic diversity and population structure analysis to construct the core collection from entire 4,392 collections. there were excluded sample call rates less than 93% and duplicated samples more than 99.9% according to genotype analysis using 180K SNPs from entire collections. Furthermore, we were also excluded natural hybrid resources which Glycine max and Glycine soja are mixed in half through population structure analysis. As a result, we are constructed the core collection of genetic diversity that reflects 99% of the entire collections, including 430 cultivated soybeans (Glycine max) and 386 wild soybeans (Glycine soja). The core collection developed in this study should be to provide useful materials for both soybean breeding programs and genome-wide association studies.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.82-82
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• 2017

The production of spring wheat, the major crop in Mongolia, is accounting for 98% of the cultivated area. Collection, conservation and utilization of wheat germplasm resources play an important role in wheat breeding and production in Mongolia. Understanding genetic variability in the existing genebank accessions is important for collection and conservation of wheat germplasms. To determine the genetic diversity and population structure among a representative collection of Mongolian local wheat cultivars and lines, 200 wheat accessions were analyzed with 15 SSR markers distributed throughout the wheat genome. A total of 85 alleles were detected, with 3 to 5 alleles per locus and a mean genetic diversity value of 5.66. The average genetic diversity index was 0.68, with values ranging from 0.37 to 0.80. The 200 Mongolian wheat accessions were divided into two subgroups based on STRUCTURE, un-rooted NJ cluster and principal coordinate analyses. The results from this study will provide important information for future wheat germplasm conservation and improvement programs with Mongolian genebank.

• Asian-Australasian Journal of Animal Sciences
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• 제28권1호
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• pp.25-36
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• 2015

The complex analysis of the pedigree records of Czech Landrace (CLA), Czech Large White-dam line (CLWd), Czech Large White-sire line (CLWs), Duroc (DC), and Pietrain (PN) was performed to determine trends of genetic diversity (GD), and to find the main sources of the GD loss. The total size of the pedigree was 132,365, 391,151, 32,913, 13,299, and 7,160 animals in CLA, CLWd, CLWs, DC, and PN, respectively. Animals born in the years 2011 through 2013 were assumed as the reference population. The average pedigree completeness index for one generation back was 95.9%, 97.4%, 91.2%, 89.8%, and 94.2% for appropriate breeds. Number of ancestors explaining 100% of gene pool was 186, 373, 125, 157, and 37 in CLA, CLWd, CLWs, DC, and PN, respectively. The relative proportion of inbred animals (58%, 58%, 54%, 47%, and 25%), the average inbreeding (2.7%, 1.4%, 2.5%, 3.6%, and 1.3%) and the average co-ancestry (3.1%, 1.6%, 3.3%, 4.2%, and 3.3%) were found over the past decade in analysed breeds. The expected inbreeding under random mating increased during the last 10 years in CLWs and PN and varied from 1.27% to 3.2%. The effective population size computed on the basis of inbreeding was 76, 74, 50, 35, and 83 in 2012 in CLA, CLWd, CLWs, DC, and PN, respectively. The shortest generation interval (1.45) was observed for CLWd in sire to son selection pathway. The longest generation interval obtained PN (1.95) in sire to daughter pathway. The average relative GD loss within last generation interval was 7.05%, 4.70%, 9.81%, 7.47%, and 10.46%, respectively. The relative proportion of GD loss due to genetic drift on total GD loss was 85.04%, 84.51%, 89.46%, 86.19%, and 83.68% in CLA, CLWd, CLWs, DC, and PN, respectively. All breeds were characterized by a high proportion of inbred animals, but the average inbreeding was low. The most vulnerable breeds to loss of GD are DC and PN. Therefore, a breeding program should be more oriented to prevent the increase of GD loss in these breeds.

• Asian-Australasian Journal of Animal Sciences
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• 제33권12호
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• pp.1912-1921
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• 2020

Objective: This study assessed genomic prediction accuracies based on different selection methods, evaluation procedures, training population (TP) sizes, heritability (h²) levels, marker densities and pedigree error (PE) rates in a simulated Korean beef cattle population. Methods: A simulation was performed using two different selection methods, phenotypic and estimated breeding value (EBV), with an h² of 0.1, 0.3, or 0.5 and marker densities of 10, 50, or 777K. A total of 275 males and 2,475 females were randomly selected from the last generation to simulate ten recent generations. The simulation of the PE dataset was modified using only the EBV method of selection with a marker density of 50K and a heritability of 0.3. The proportions of errors substituted were 10%, 20%, 30%, and 40%, respectively. Genetic evaluations were performed using genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) with different weighted values. The accuracies of the predictions were determined. Results: Compared with phenotypic selection, the results revealed that the prediction accuracies obtained using GBLUP and ssGBLUP increased across heritability levels and TP sizes during EBV selection. However, an increase in the marker density did not yield higher accuracy in either method except when the h² was 0.3 under the EBV selection method. Based on EBV selection with a heritability of 0.1 and a marker density of 10K, GBLUP and ssGBLUP_0.95 prediction accuracy was higher than that obtained by phenotypic selection. The prediction accuracies from ssGBLUP_0.95 outperformed those from the GBLUP method across all scenarios. When errors were introduced into the pedigree dataset, the prediction accuracies were only minimally influenced across all scenarios. Conclusion: Our study suggests that the use of ssGBLUP_0.95, EBV selection, and low marker density could help improve genetic gains in beef cattle.

• Asian-Australasian Journal of Animal Sciences
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• 제21권11호
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• pp.1559-1571
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• 2008

A rule was developed to constrain the annual rate of inbreeding to a predefined value in a population with different lifetimes between sires and dams, and to maximize the selection response over generations. This rule considers that the animals in a population should be divided into sex-age classes based on the theory of gene flow, and restricts the increase of average inbreeding coefficient for new offspring by limiting the increase of the mean additive genetic relationship for parents selected. The optimization problem of this rule was formulated as a quadratic programming problem. Inputs for the rule were the BLUP estimated breeding values, the additive genetic relationship matrix of all animals, and the long-term contributions of sex-age classes. Outputs were optimal number and contributions of selected animals. In addition, this rule was combined with the optimization of emphasis given to QTL, and further increased the genetic gain over the planning horizon. Stochastic simulations of closed nucleus schemes for pigs were used to investigate the potential advantages obtained from this rule by combining the standard QTL selection, optimal QTL selection and conventional BLUP selection. Results showed that the predefined rates of inbreeding were actually achieved by this rule in three selection strategies. The rule obtained up to 9.23% extra genetic gain over truncation selection at the same rates of inbreeding. The combination of the extended rule and the optimization of emphasis given to QTL allowed substantial increases in selection response at a fixed annual rate of inbreeding, and solved substantially the conflict between short-term and long-term selection response in QTL-assisted selection schemes.

• The Plant Pathology Journal
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• 제31권1호
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• pp.33-40
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• 2015

Pigeonpea Sterility Mosaic Disease (PSMD) is an important foliar disease caused by Pigeonpea sterility mosaic virus (PPSMV) which is transmitted by eriophyid mites (Aceria cajani Channabasavanna). In present study, a F2 mapping population comprising 325 individuals was developed by crossing PSMD susceptible genotype (Gullyal white) and PSMD resistant genotype (BSMR 736). We identified a set of 32 out of 300 short decamer random DNA markers that showed polymorphism between Gullyal white and BSMR 736 parents. Among them, eleven DNA markers showed polymorphism including coupling and repulsion phase type of polymorphism across the parents. Bulked Segregant Analysis (BSA), revealed that the DNA marker, IABTPPN7, produced a single coupling phase marker (IABTPPN $7_{414}$) and a repulsion phase marker (IABTPPN $7_{983}$) co-segregating with PSMD reaction. Screening of 325 F2 population using IABTPPN7 revealed that the repulsion phase marker, IABTPPN $7_{983}$, was co-segregating with the PSMD responsive SV1 at a distance of 23.9 cM for Bidar PPSMV isolate. On the other hand, the coupling phase marker IABTPPN $7_{414}$ did not show any linkage with PSMD resistance. Additionally, single marker analysis both IABTPPN $7_{983}$ (P<0.0001) and IABTPPN $7_{414}$ (P<0.0001) recorded a significant association with the PSMD resistance and explained a phenotypic variance of 31 and 36% respectively in $F_2$ population. The repulsion phase marker, IABTPPN7983, could be of use in Marker-Assisted Selection (MAS) in the PPSMV resistance breeding programmes of pigeonpea.

• 생명과학회지
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• 제14권2호
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• pp.339-344
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• 2004

콩에서 경장과 연관된 DNA 표지인자를 개발하여 품종육성에 활용함으로서 육종효율 증진에 기여하고자 수행하였다. 본 시험은 육성된 큰올콩과 신팔달콩의 RIL 계통 및 SSR marker를 이용하여 유전자지도를 작성하고, 이를 바탕으로 경장과 관련된 양적형질 유전자좌(QTt)를 탐색하였다. 시험재료로 이용된 큰올콩과 신팔달콩은 경장이 각각 30.57 cm와 49.75 cm로 매우 큰 차이를 보였다. 경장과 연관된 QTL은 개별마커들과의 분산분석 결과, 연관군 F, J, N 및 O에서 전체변이의 37.83%를 설명할 수 있는 4개의 QTL을 탐색하였다. 특히, 연관군 J와 O에서 각각 14.25%와 10.68%를 설명할 수 있는 주요 QTL을 확인하였다. 따라서 경장 관련 QTL중 연관군 J와 O에서 확인된 주요 QTL은 품종 육성과정에서 경장 관련 선발 마커로서 활용가치가 높은 것으로 판단된다.

• 한국자원식물학회지
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• 제30권3호
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• pp.323-330
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• 2017

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 ($H_O$) and expected heterozygosity ($H_E$) 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.

• Asian-Australasian Journal of Animal Sciences
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• 제32권10호
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• pp.1491-1500
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• 2019

Objective: European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods: Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results: The results showed that Thai pig populations had a high genetic diversity with mean total and effective ($N_e$) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity ($H_e$) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher $H_e$ compared to observed heterozygosity ($H_o$) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei's genetic distance, mean $F_{ST}$ estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion: Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.