• Asian-Australasian Journal of Animal Sciences
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• v.31 no.6
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• pp.791-797
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• 2018

Objective: Trimethylation of histone 3 (H3) at 4th lysine N-termini (H3K4me3) in gene promoter region was the universal marker of active genes specific to cell lineage. On the contrary, coexistence of trimethylation at 27th lysine (H3K27me3) in the same loci-the bivalent H3K4m3/H3K27me3 was known to suspend the gene transcription in germ cells, and could also be inherited to the developed stem cell. In galline species, throughout example of H3K4m3 and H3K27me3 ChIP-seq analysis was still not provided. We therefore designed and demonstrated such procedures using ChIP-seq and mRNA-seq data of chicken follicular mesenchymal cells and male germ cells. Methods: Analytical workflow was designed and provided in this study. ChIP-seq and RNA-seq datasets of follicular mesenchymal cells and male germ cells were acquired and properly preprocessed. Peak calling by Model-based analysis of ChIP-seq 2 was performed to identify H3K4m3 or H3K27me3 enriched regions ($Fold-change{\geq}2$, $FDR{\leq}0.01$) in gene promoter regions. Integrative genomics viewer was utilized for cellular retinoic acid binding protein 1 (CRABP1), growth differentiation factor 10 (GDF10), and gremlin 1 (GREM1) gene explorations. Results: The acquired results indicated that follicular mesenchymal cells and germ cells shared several unique gene promoter regions enriched with H3K4me3 (5,704 peaks) and also unique regions of bivalent H3K4m3/H3K27me3 shared between all cell types and germ cells (1,909 peaks). Subsequent observation of follicular mesenchyme-specific genes-CRABP1, GDF10, and GREM1 correctly revealed vigorous transcriptions of these genes in follicular mesenchymal cells. As expected, bivalent H3K4m3/H3K27me3 pattern was manifested in gene promoter regions of germ cells, and thus suspended their transcriptions. Conclusion: According the results, an example of chicken H3K4m3/H3K27me3 ChIP-seq data analysis was successfully demonstrated in this study. Hopefully, the provided methodology should hereby be useful for galline ChIP-seq data analysis in the future.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.10
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• pp.1394-1406
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• 2015

The AT motif-binding factor (ATBF1) not only interacts with protein inhibitor of activated signal transducer and activator of transcription 3 (STAT3) (PIAS3) to suppress STAT3 signaling regulating embryo early development and cell differentiation, but is required for early activation of the pituitary specific transcription factor 1 (Pit1) gene (also known as POU1F1) critically affecting mammalian growth and development. The goal of this study was to detect novel nucleotide variations and haplotypes structure of the ATBF1 gene, as well as to test their associations with growth-related traits in goats. Herein, a total of seven novel single nucleotide polymorphisms (SNPs) (SNP 1-7) within this gene were found in two well-known Chinese native goat breeds. Haplotypes structure analysis demonstrated that there were four haplotypes in Hainan black goat while seventeen haplotypes in Xinong Saanen dairy goat, and both breeds only shared one haplotype (hap1). Association testing revealed that the SNP2, SNP5, SNP6, and SNP7 loci were also found to significantly associate with growth-related traits in goats, respectively. Moreover, one diplotype in Xinong Saanen dairy goats significantly linked to growth related traits. These preliminary findings not only would extend the spectrum of genetic variations of the goat ATBF1 gene, but also would contribute to implementing marker-assisted selection in genetics and breeding in goats.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.5
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• pp.616-627
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• 2014

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index ($F_{ST}$) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values ($F_{IS}$) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity ($H_E$) or $F_{ST}$, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, $F_{ST}$ and D-scores were used. Only 6 to 8 markers ranking $H_E$, $F_{ST}$ or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, $F_{ST}$ and allelic number of close lineage populations.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.9
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• pp.1234-1238
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• 2017

Objective: The vertebral number is associated with body length and carcass traits, which represents an economically important trait in farm animals. The variation of vertebral number has been observed in a few mammalian species. However, the variation of vertebral number and quantitative trait loci in sheep breeds have not been well addressed. Methods: In our investigation, the information including gender, age, carcass weight, carcass length and the number of thoracic and lumbar vertebrae from 624 China Kazakh sheep was collected. The effect of vertebral number variation on carcass weight and carcass length was estimated by general linear model. Further, the polymorphic sites of Vertnin (VRTN) gene were identified by sequencing, and the association of the genotype and vertebral number variation was analyzed by the one-way analysis of variance model. Results: The variation of thoracolumbar vertebrae number in Kazakh sheep (18 to 20) was smaller than that in Texel sheep (17 to 21). The individuals with 19 thoracolumbar vertebrae (T13L6) were dominant in Kazakh sheep (79.2%). The association study showed that the numbers of thoracolumbar vertebrae were positively correlated with the carcass length and carcass weight, statistically significant with carcass length. To investigate the association of thoracolumbar vertebrae number with VRTN gene, we genotyped the VRTN gene. A total of 9 polymorphic sites were detected and only a single nucleotide polymorphism (SNP) (rs426367238) was suggested to associate with thoracic vertebral number statistically. Conclusion: The variation of thoracolumbar vertebrae number positively associated with the carcass length and carcass weight, especially with the carcass length. VRTN gene polymorphism of the SNP (rs426367238) with significant effect on thoracic vertebral number could be as a candidate marker to further evaluate its role in influence of thoracolumbar vertebral number.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.5
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• pp.704-711
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• 2020

Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc×Erhualian F₂ population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study. Methods: A whole-genome sequences association study was performed in the F₂ population. Genotyping was performed for 1,020 individuals (19 F₀, 68 F₁, and 933 F₂). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits. Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified. Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.

• Journal of Korean Society of Forest Science
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• v.102 no.4
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• pp.560-565
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• 2013

Population genetic structure and diversity of Ulmus davidiana var. japonica in South Korea were studied using ISSR markers. A total of 45 polymorphic ISSR amplicons were cropped from 7 ISSR primers and 171 individuals of 7 populations. The average of effective alleles and the proportion of polymorphic loci were 1.5 and 89% respectively. The Shannon's diversity index (I) was 0.435 and the expected heterozygosity from the frequentist's method ($H_e$) and the Bayesian inference (hs) were 0.289 and 0.323 respectively. From AMOVA, 4.2% of total genetic variation in the elm populations was explained with the difference among populations (${\Phi}_{ST}=0.042$) and the other 95.8% was distributed within populations. The ${\theta}^{II}$ value by Bayesian method which was comparable to the FST was 0.043. So the level of genetic diversity in the elm populations was similar to that in Genus Ulmus and the level of genetic differentiation was lower than that of others. No population showed a significant difference in the population-specific fixation indices (average of $PS-F_{IS}=0.822$) or the population-specific genetic differentiations (average of $PS-F_{ST}=0.101$). Seven populations were allocated into 3 groups in the UPGMA and the PCA, but the grouping patterns were different. Also, we could not confirm any geographic trend from Bayesian clustering.

• Reproductive and Developmental Biology
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• v.35 no.1
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• pp.77-83
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• 2011

One-step dilution and direct transfer would be a practical technique for the field application of frozen embryo. This study was to examine whether Jeju Black Cattle (JBC, Korean Cattle) can be successfully cloned from vitrified and one-tep diluted somatic cell nuclear transfer (SCNT) blastocyst after direct transfer. For vitrification, JBC-SCNT blastocysts were serially exposed in glycerol (G) and ethylene glycol (EG) mixtures [10%, (v/v) G for 5 min., 10% G plus 20% EG (v/v) for 5 min., and 25% G plus 25% EG (v/v) for 30 sec.] which is diluted in 10% FBS added D-PBS. And then SCNT blastocysts were loaded in 0.25 ml mini straw, placed in cold nitrogen vapor for 3 min. and then plunged into $LN_2$. One-step dilution in straw was done in $25^{\circ}C$ water for 1 min, by placing vertically in the state of plugged-end up and down for 0.5 min, respectively. When in vitro developmental capacity of vitrified SCNT blastocyst was examined at 48 h after one-step dilution, hatched rate (56.4%) was slightly lower than that of control group (62.5%). In field trial, when the vitrified-thawed SCNT blastocysts were transferred into uterus of synchronized 5 recipients, a cloned female JBC was delivered by natural birth on day 299 and healthy at present. In addition, when the short tandem repeat marker analysis of the cloned JBC was evaluated, microsatellite loci of 11 numbers was perfectly matched genotype with donor cell (BK94-14). This study suggested that our developed vitrification and one-step dilution technique can be applied effectively on field trial for cloned animal production, which is even no longer in existence.

• Journal of Korean Society of Forest Science
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• v.103 no.2
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• pp.182-188
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• 2014

Genetic diversity and genetic differentiation in six natural populations of Abies holophylla Max were investigated using ISSR marker system. From 6 ISSR primers, the average percentage of polymorphic loci was 85.6%, and the average expected heterozygosity ($H_e$) was 0.288. From the result of AMOVA, 94.4% of total genetic variation came from the differences among individuals within populations, and 5.6% was caused by those of among-populations. On the basis of Bayesian inference, genetic differentiation (${\theta}^{II}$ and $G_{ST}$) and inbreeding coefficient for all populations were 0.045, 0.038, and 0.509, respectively. The correlation between genetic distance and geographical distance was highly significant at the Mental's test (r = 0.74, P < 0.05). Six populations divided into two groups according to the results of UPGMA and PCA. One group included Namwon, Cheongdo and Mungyeong population. The other was Inje, Hongcheon and Pyeongchang population. Also, in Bayesian clustering analysis, 6 populations were divided into two clusters. But Cheongdo population was assigned into the other cluster unlike those of UPGMA or PCA. Taking the regions based on the results of the cluster analysis into consideration of AMOVA, 3.9% of genetic variation came from the regional difference. The dendrogram from UPGMA could provide the most genetically reasonable explanation for the distribution of Abies holophylla populations in South Korea.

• Korean Journal of Plant Taxonomy
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• v.42 no.4
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• pp.253-259
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• 2012

The genetic variation in populations of Eranthis byunsanensis, an endemic and rare species of Korea, was studied using starch gel electrophoresis. All five known populations were sampled for allozyme electrophoresis of nine enzymes coded by 10 loci. The overall genetic variation of E. byunsanensis population was shown to be considerably high within the populations (A = 2.4, P = 90.0, $H_E$ = 0.311). A positive $F_{IS}$ value of E. byunsanensis indicated an overall deficiency of heterozygotes, and a low $F_{ST}$ value (0.131) showed little differentiation among populations. The high genetic variation, less genetic differentiation among populations, and a significant amount of heterozygote deficiency propose the hypothesis that they have an experience of recent isolation and fragmentation of their habitat. Thus, the rate of gene flow has been drastically reduced, and the rate of inbreeding in E. byunsanensis populations has increased. Current habitats in Mai-san and Naro-do are vulnerable due to their small population size and the levels of anthropogenic activity in the region constantly threatening survival of this species. Because of the high genetic variation and low levels of differentiation among populations in E. byunsanensis, it is not issue which populations have a priority for protection, but we may concern the plan to maintain population continuously and diminish the rate of inbreeding.

• Journal of Life Science
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• v.14 no.5
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• pp.821-828
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• 2004

The increasing apparent photosynthetic rate per leaf area may improve seed yield in soybean. Leaf area, length and width are related to the photosynthetic capability of the plant. In this study, two populations derived from the cross of Keunolkong, Shinpaldalkong and Iksanl0 were evaluated with simple sequence repeat (SSR) markers to identify length, width and length/width ratio of leaf. Leaf length/width ratio were significantly negative correlation with leaf width in K/S and K/I populations. In the K/S population, two minor QTLs for leaf length (LL) were found on LG Dlb+W and 1. Two QTLs on LG J and L were related to LL in K/I population. Two and three minor QTLs were identified in leaf width with total phenotypic variation of 13% and 18.04 in K/S and K/I populations, respectively. The leaf length/width ratio, two QTLs on LG I and L, and three QTLs on LG Cl, E and L were related to K/S and K/I populations, respectively. Thus it is assumed that the leaf traits are very much dependent on the genotype used and different breeding approach should be considered for the selection of favorite leaf traits in soybean breeding programs.