• Journal of the Korean Data and Information Science Society
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• v.25 no.4
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• pp.737-743
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• 2014

This experiment was conducted to compare heterogeneity for the variance in dairy cattle population and to induce homogeneity of variance using 502,228 performance test records of dairy cattle. The estimates of heritability for milk yields, fat yields and protein yields were 0.28, 0.26 and 0.24, respectively and the estimate of average breeding value by birth year was lower in HV (heterogenous variance) model than in animal model, collectively. The average breeding values of milk yields, fat yields and protein yields for 545 sire bulls applicable to the criteria of interbull MACE programme were 453.54kg, 10.75kg and 14.33kg, respectively and when the heterogeneity was adjusted they were 432.06kg, 10.15kg and 13.40kg, respectively, which were lower in all milk traits collectively. In animal model, coefficients of phenotypic correlation between dataset I and II were 0.839 in milk yields, 0.821 in fat yields, and 0.837 in protein yields, while in HV model, they were 0.841 in milk yields, 0.820 in fat yields, and 0.836 in protein yields, showing similar results in 2 models. When compared using animal model and HV model, the regression coefficient for ratio of number of daughters by calving year of milk yields increased from 15.157 to 16.105 and that of fat yields increased from =0.227 to =0.196, but that of protein yields decreased from 0.630 to 0.586.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.10
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• pp.1565-1574
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• 2018

Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits. Results: Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin 'eye' area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism. Conclusion: This study's results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.

• Korean Journal of Breeding Science
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• v.43 no.5
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• pp.464-469
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• 2011

Virus diseases often cause serious damage to rice production in Asia. The lack of information on virus resistance genes has been a major obstacle for the breeding of resistant varieties. In order to identify DNA marker associated with resistance against rice stripe virus (RSV), the quantitative trait locus (QTL) was carried out using advanced backcross population developed from a cross between RSV-resistant tongil type cultivar Shinkwang and susceptible japonica cultivar Ilpum. A RSV resistance QTL $qSTV11^{SG}$ explaining 44.2% of the phenotypic variation was identified on chromosome 11 of Tongil type rice cultivar 'Shingwang'. $qSTV11^{SG}$ was tightly linked to DNA marker RM6897. The RM6897 divided as resistance type allele and susceptible type alleles. Twenty seven resistant varieties showed the resistant-type allele and 23 susceptible varieties were susceptible-type allele to the marker of RM6897. This results and the molecular markers presented here may be useful in rice breeding for improving RSV resistance in japonica rice.

• Korean Journal of Breeding Science
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• v.43 no.1
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• pp.81-91
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• 2011

Rice wild relatives have been recognized as reservoirs of genetic reinforcements to improve cultivating rice against biotic and abiotic stresses. A wild relative, Oryza. minuta(BBCC; Acc. 101141), was hybridized with a Korean Japonica cultivar, 'Hwaseong'(AA), followed by ovule culture and several times of back crossings to overcome high level of sterility. During evaluation of the introgression lines, breeding line exhibited resistance to bacterial blight with reasonable agronomic performances, and nominated as an elite breeding line, the 'Suweon497'. A mapping population, to dissect genetic basis of the resistance, was constructed by using $F_2$ progenies of the 'Suweon497' ${\times}$ 'Milyang23'. Association analysis between SSR marker genotypes and pathogenisity levels of each $F_2$ progeny revealed the end terminal region of rice chromosome 11 as the nesting place for the wild rice derived bacterial blight resistance gene, where at least four other genes, Xa3, Xa4, Xa26 and Xa31, have been reported.

• Journal of Wetlands Research
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• v.20 no.3
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• pp.256-262
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• 2018

Multiple temporal scale can be a useful method to understand population dynamics in ecosystem. The multi-temporal scale approach for population dynamics has rarely been researched till lately. This study was carried out to identify the factors in affecting the population dynamics of herons, including Eastern Cattle Egret (Bubulcus coromadus), Grey Heron (Ardea cinerea), Great Egret (A. alba), Intermediate Egret (Egretta intermedia) and Little Egret (E. garzetta), at rice paddy fields of Seokmun-myeon in the city of Dangjin, South Chungcheong Province during the main breeding periods from 2014 to 2017. We identified the population dynamics of herons at different time interval (day and month) using the unmanned monitoring system. As a result, monthly population dynamics was mostly affected by time, mean temperature and mean precipitation, whereas daily population dynamics was affected by mean temperature and habitat types. The results suggest that there are differences in the factors affecting the population dynamics of herons according to the time scale.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.4
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• pp.441-451
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• 2009

In this study, 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity and population structure of 125 rice accessions from 40 different origins in Africa, Asia, Europe, South America, and Oceania. A total of 333 alleles were detected, with an average of 11.5 per locus. The mean values of major allele frequency, expected heterozygosity, and polymorphism information content (PIC) for each SSR locus were 0.39, 0.73, and 0.70, respectively. The highest mean PIC was 0.71 for Asia, followed by 0.66 for Africa, 0.59 for South America, 0.53 for Europe, and 0.47 for Oceania. Model-based structure analysis revealed the presence of five subpopulations, which was basically consistent with clustering based on genetic distance. Some accessions were clearly assigned to a single population in which >70% of their inferred ancestry was derived from one of the model-based populations. In addition, 12 accessions (9.6%) were categorized as having admixed ancestry. The results could be used to understanding the genetic structure of rice cultivars from these regions and to support effective breeding programs to broaden the genetic basis of rice varieties.

• Journal of Animal Science and Technology
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• v.56 no.8
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• pp.31.1-31.9
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• 2014

The objective of this study was to describe the population structure and inbreeding, and to quantify their effects on weights at different ages of Mehraban sheep in Iran. The analysis was based on the pedigree information of 26990 animals and 10278 body weight records from birth to yearling age. Data and pedigree information were collected during 1994 to 2011 by the breeding station of Mehraban sheep. The population structure was analyzed using the CFC program. Inbreeding of all animals was calculated by INBUPGF90 program. All animals were grouped into three classes according to their inbreeding coefficients: the first class included non-inbred animals (F=0); and the second and third classes included inbred animals (0$F{\geq}0.05$, respectively). The average inbreeding in Mehraban sheep was 1.69%. Founder equivalent ($f_e$) values were estimated to be 4244, 3116 and 2965 during 1994-1999, 2000-2005 and 2006-2011, respectively. The effective population sizes ($N_e$) were 363, 5080 and 5740 during 1994-1999, 2000-2005 and 2006-2011, respectively. Generation interval was 2.15 years for this breed of sheep. Regression coefficients of birth weight, 3-month weight, 6-month weight and yearling weight on lamb inbreeding were estimated to be -6.340.69, -14.685.33, 48.009.43 and 98.6515.65, respectively. Both positive and negative inbreeding effects were found in the current study. The utilization of a program for designed mating system, in the present flock, could be a suitable approach to keep the level of inbreeding under control.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.2
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• pp.176-183
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• 2016

A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.3
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• pp.316-323
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• 2014

We previously identified quantitative trait loci (QTL) for body weight and average daily gain in a common region between ADL0198 (chr 1: 171.7 Mb) and ABR0287 (chr 1: 173.4 Mb) on chicken chromosome 1 in an $F_2$ resource population produced by crossing low- and high-growth lines of the Hinai-dori breed. Motilin receptor (MLNR) is a candidate gene affecting growth traits in the region. In this study, we genotyped polymorphisms of the MLNR gene and investigated its association with growth traits in a Hinai-dori $F_2$ intercross population. All the exons of the MLNR gene in the parental population were subjected to PCR amplification, nucleotide sequenced and haplotypes identified. To distinguish resultant diplotype individuals in the $F_2$ population, a mismatch amplification mutation assay was performed. Three haplotypes (Haplotypes 1-3) were accordingly identified. Six genotypes produced by the combination of three haplotypes (Haplotype 1, 2, and 3) were examined in order to identify associations between MLNR haplotypes and growth traits. The data showed that Haplotype 1 was superior to Haplotype 2 and 3 in body weight at 10 and 14 weeks of age, average daily gain between 4 and 10 weeks, 10 and 14 weeks, and 0 and 14 weeks of age in female in $F_2$ females. It was concluded that MLNR is a useful marker of growth traits and could be used to develop strategies for improving growth traits in the Hinai-dori breed.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.53 no.4
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• pp.492-498
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• 2020

Despite its economic importance, olive flounder Paralichthys olivaceus aquaculture industry is facing a crisis with a continuous production decline. There have been many solutions to overcome the complicate predicament proposed. Increasing genetic diversity and discovering new commercial value through selective breeding are among them. The aims of the present study are to increase the selection power of the golden flounders. We examined the genetic diversity of the breeder population of golden flounders and developed selective markers for the golden flounder population. The 6 microsatellite (MS) markers were selected from melanogenesis-related genes, which are believed to be involved in the pigmentation of fish. All markers were polymorphic (except PO4) and 5 of them had PIC value of 0.6 or above. All makers had distinctive alleles indicating either normal or golden individuals. For examples, from PO4 marker, the frequency of an allele (316) in the golden population was 100% and in normal population was 0% (P<0.001). Although some more studies with more samples at the later generations should be performed to confirm this result, the 316 allele from PO4 marker could be a distinctive tool for decision of the colors in olive flounders at an early stage of the life cycle.