• Asian-Australasian Journal of Animal Sciences
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• v.24 no.2
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• pp.162-172
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• 2011

In this paper, simulation was used to determine accuracies of genomic breeding values for polygenic traits associated with many thousands of markers obtained from high density genome scans. The statistical approach was based upon stochastically simulating a pedigree with a specified base population and a specified set of population parameters including the effective and noneffective marker distances and generation time. For this population, marker and quantitative trait locus (QTL) genotypes were generated using either a single linkage group or multiple linkage group model. Single nucleotide polymorphism (SNP) was simulated for an entire bovine genome (except for the sex chromosome, n = 29) including linkage and recombination. Individuals drawn from the simulated population with specified marker and QTL genotypes were randomly mated to establish appropriate levels of linkage disequilibrium for ten generations. Phenotype and genomic SNP data sets were obtained from individuals starting after two generations. Genetic prediction was accomplished by statistically modeling the genomic relationship matrix and standard BLUP methods. The effect of the number of linkage groups was also investigated to determine its influence on the accuracy of breeding values for genomic selection. When using high density scan data (0.08 cM marker distance), accuracies of breeding values on juveniles were obtained of 0.60 and 0.82, for a low heritable trait (0.10) and high heritable trait (0.50), respectively, in the single linkage group model. Estimates of 0.38 and 0.60 were obtained for the same cases in the multiple linkage group models. Unexpectedly, use of BLUP regression methods across many chromosomes was found to give rise to reduced accuracy in breeding value determination. The reasons for this remain a target for further research, but the role of Mendelian sampling may play a fundamental role in producing this effect.

• Journal of Ecology and Environment
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• v.30 no.2
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• pp.121-126
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• 2007

We monitored gold-spotted pond frog (Rana chosenica) populations near the Korea National University of Education in Chungbuk, Korea, from 19 May to 8 August, 2006 to examine the spatial distribution of populations in local areas and to investigate patterns of migration of adult gold-spotted pond frogs from terrestrial hibernation sites to breeding sites, We captured individuals from the largest population using a drift fence with 22 pitfall traps surrounding the breeding site. A total of 22 individuals (19 males and 3 females) were captured between 23 May and 15 June. No peak in breeding migration was detected, but the onset of the breeding migration may correspond with increased humidity. Male body weights were negatively correlated with sampling dates. Seven of 22 individuals were captured at the 4th pitfall trap, which was placed between two culverts. The capture rate per pitfall trap was higher in traps close to the rice field banks (1.44, traps $1{\sim}9$) than in traps facing hilly land (0.33, traps $13{\sim}18$). Comparative data from the Korean frog (Rana coreana), a sympatric species in the study area, were also collected and compared with those of the gold-spotted pond frog.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.53 no.4
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• pp.421-426
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• 2008

Freshly harvested seed of Chinese milk vetch (Astragalus sinicus L.; CMV) was strongly dormant because of hardseedness. Seeds of freshly harvested germinated only 8% while clipping the seed coat completely overcome the innate dormancy, which indicates inhibition of germination of the seed is mainly due to seed coat (87%). The dormant (intact) hard seeds did not imbibe water whereas the non-dormant (clipped) seeds took up rapidly. In natural environment condition, the hard seed coat dormancy was broken only after 5 months after seed harvest. To break such a strong seed coat dormancy, the chemical and heat treatments were effective. Concentrated sulfuric acid was more effective than dry heat and hot water treatments. Hot water treatment improved germination but the germination percentage was less than 41%. Treatments increased germination due to its effect on the seed coat integrity. A scanning electron microscope reveled that disruption of seed coat layers and subsequent development of numerous crack in the hilum region of the seed and on the seed coat surface of concentrated sulfuric acid treatment and formation of cracks in the dry heat treatments, respectively, were observed in the seed coat surface, which served as water entry points.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.1
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• pp.1-6
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• 2010

The objectives of this study were to i) investigate genetic performance for linear type traits of individual Holstein dairy cows, especially focusing on comparative traits, and to estimate genetic variances for these traits using actual data, and ii) compare genetic performance and improvement of progeny by birth country of the cows. Linear type traits defined with five comparative traits on this study were general stature composite (GSC), dairy capacity composite (DCC), body size composite (BSC), foot and leg composite (FLC), and udder composite (UDC). These traits were scored from 1 to 6 with 1 = poor, 2 = fair, 3 = good, 4 = good plus, 5 = very good and 6 = excellent. Final scores (FS) were also included in this study. Data used was collected from the years 2000 to 2004 by the Korea Animal Improvement Association (KAIA). Only data of more than five tested cows by herd appraisal date and by sires having more than ten daughters were included to increase the reliability of the data analyses. A total of 30,204 records of the selected traits, which was collected from 26,701 individuals having pedigree information were used. Herd appraisal date, year of age, lactation stage (grouped by month), and time lagged for milking (in hours) were assumed as fixed effects on the model. Animal additive genetic effects considering pedigree relationship and residual errors were assumed with random effects. Year of age at appraisal date was classified from one to nine years of age, assigning the value of nine years of age for animals that were greater than or equal to nine years of age. From our results, the estimate for heritability was 0.463, 0.346, 0.473, 0.290, and 0.430 on GSC, DCC, BSC, FLC and UDC, respectively. The estimate for FS heritability was 0.539. The greatest breeding values for GSC were estimated for Canada, with the breeding values for American lines increasing for 10 years starting in 1989 but tending to decrease after that until 2004. For DCC, the breeding values for American and Canadian lines showed similar patterns until 1999, after which the breeding values for the American lines declined sharply. For BSC, data from Korea, Canada and the USA followed similar trends overall except when the breeding values of the American lines decreased starting in 1999. Overall, the methods used to evaluate genetic performance in this study were acceptable and allowed for the discovery of differences by country of genetic origin, likely due in part to the American use of selection indexes based primarily on milk yield traits until methods for evaluating other traits began to emerge.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.4
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• pp.467-475
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• 2015

Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.

• Korean Journal of Breeding Science
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• v.40 no.1
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• pp.1-7
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• 2008

An attempt was made to link rice embryo proteins to DNA sequences and to understand their functions. One hundred of the 700 spots detected on the embryo 2-DE gels were microsequenced. Of these, 28% of the embryo proteins were matched to DNA sequences with known functions, but 72% of the proteins were unknown in functions as previously reported (Woo et al. 2002). In addition, twenty-four protein spots with 100% of homology and nine with over 80% were matched to ESTs (expressed sequence tags) after expanding the amino acid sequences of the protein spots by Database searches using the available rice EST databases at the NCBI (http://www/ncbi.nlm.nih.gov/) and DDBJ (http://www.ddbj.nig.ac.jp/). The chromosomal location of some proteins were also obtained from the rice genetic map provided by Japanese Rice Genome Research Program (http://rgp.dna.affrc.go.jp). The DNA sequence databases including EST have been reported for rice (Oryza sativa L.) now provides whole or partial gene sequence, and recent advances in protein characterization allow the linking proteins to DNA sequences in the functional analysis. This work shows that proteome analysis could be a useful tool strategy to link sequence information and to functional genomics.

• Korean Journal of Environment and Ecology
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• v.26 no.2
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• pp.186-191
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• 2012

The Chinese Sparrowhawk($Accipiter$ $soloensis$) is the most common breeding raptor in Korea, but its spatial use in the breeding season has been poorly documented. Therefore, to estimate the territory and home range sizes of breeding sparrowhawks, six territorial males(four in 2005 and two in 2006) were observed from June to July in Gyeonggi Province, the Republic of Korea. Main perches, which were used repeatedly(more than three times) or where apparent territorial behaviors were observed, were identified and the locations were analyzed by GIS software. According to the 100% Minimum Convex Polygons which were identified from $25.2{\pm}5.3$ perches, Chinese Sparrowhawks occupied $4.62{\pm}0.90$ ha for breeding territories and used $22.57{\pm}5.12$ ha for their home ranges. These estimates showed larger spatially occupied areas than those in one previous report, but this study suggests that Chinese Sparrowhawks intensively use small areas throughout the breeding season. This result also implies that the sparrowhawks have the potential to be significantly affected by any habitat changes and resource exploitation in the small areas(particularly in small rice paddies of 0.6-2.0 ha) which they largely rely on for food. Although this study was based on observations solely for territory size estimations, this study may be worthwhile as preliminary pilot research for Chinese Sparrowhawk conservation, management, and further studies.

• Korean Journal of Environment and Ecology
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• v.29 no.4
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• pp.508-515
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• 2015

Post-fire restoration can affect breeding bird communities and species compositions over a long-term period by determining pot-fire succession, and a long-term monitoring is therefore required to understand its impacts on forest birds. This study aimed to document the effects of post-fire restoration methods on breeding bird communities in three areas: unburned and two burned (nonintervention and intervention with clear-cut logging and planting) stands 13 years after the stand-replacing Samcheok forest fire at Mt. Geombong in Samcheok, South Korea. According to 108 point counts during the breeding season from April to June 2013, we found that the number of individuals, observed bird species, and species diversity index in intervention stands with clear-cut logging and planting were lower than that in nonintervention and unburned control stands. Foraging and nesting guild analysis also showed a lower abundance of foliage searchers, timber drillers, primary cavity nesters and secondary cavity nesters in intervention stands than in the other stands, while no significant difference was detected between the nonintervention and unburned stands. These results imply that an interventional restoration method may deter the recovery of avian breeding communities after forest fires, and also suggest that non-interventional restoration methods may be an effective way to benefit the species diversity and density of breeding bird communities.

• Korean Journal of Environment and Ecology
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• v.32 no.1
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• pp.39-46
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• 2018

Breeding bird surveys provide the reference information for understanding bird community structure and function in the ecosystem and conserving biodiversity. Recent rapid change of biodiversity due to climate change and other factors has made it necessary to utilize acoustic sensors for accuracy and spatial expansion of forest bird survey data and for time-series monitoring of forest birds. The objective of this study is to investigate the possibility of using acoustic recording sensor to evaluate the diversity of forest birds at breeding season by comparing and analyzing the recorded data of bird songs and field bird survey data. We conducted the site survey and recording in 186 points in 48 areas of 4 regions of Gombaeryeong and Jochimryeong around Jeombongsan Mountain and Jugryeong and Gochiryeong around Sobaeksan Mountain from May 2nd to 16th in 2013. The analysis of the correlation between the recording result and Bird Community Index based on the field survey showed that the number of bird species, population, and the number of bird songs by recording was significantly correlated to the number of species and population by field survey. Moreover, the number of bird species and the number of bird songs by recording showed a significant correlation to species diversity and species richness but no or low significant correlation to species evenness by the field study (observation and listing in parallel). As a result, it was possible to check species composition and species diversity of bird communities by analyzing acoustic recording data on the field. The acoustic recordings of bird songs in the breeding period were more reliable than the non-breeding period in the correlation of recording result and species diversity and for utilization.

• Korean Journal of Environment and Ecology
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• v.32 no.1
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• pp.47-54
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• 2018

This study examined the behavior of red fox (Vulpes vulpes) during the estrus period, breeding period, and mating including the estrus period along as well as the effect of environmental factors in an outdoor breeding facility. The average mating duration was 19.95 min (n = 13, range = 1.17-35.25 min). The breeding season was mainly early February (56.6%) for foxes aged more than one year and mid-March (60.0%) for foxes aged less than one year. The mating duration was longest when both male and female were more than one year old ($24.4{\pm}11.08min$), although copulation took place regardless of partner's age. Females that mated twice within two days after estrus started or with two males had 100% pregnancy rate. In addition, the pregnancy rate was highest (87%) when both mating partners were more than one year old. Foxes preferred daytime to nighttime for mating, and thus mating usually took place on sunny days or between 10:00 and 12:00 on partly cloudy days. A male mated with different females for a maximum of five times, and the higher the mating frequency of a male, the longer the mating duration. Interest in mating decreased after three copulations in the case of males and after two copulations in the case of females. Males required at least 4 hours and 46 minutes between the first and second copulation. For this study, we collected reference data that might be applied to breeding programs for the red fox to secure the restoration of individuals of this important species.