• Asian-Australasian Journal of Animal Sciences
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• v.32 no.4
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• pp.494-500
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• 2019

Objective: Feed consumption contributes a large percentage for total production costs in the poultry industry. Detecting genes associated with feeding traits will be of benefit to improve our understanding of the molecular determinants for feed efficiency. The objective of this study was to identify candidate genes associated with feed conversion ratio (FCR) via genomewide association study (GWAS) using sequence data imputed from single nucleotide polymorphism (SNP) panel in a Chinese indigenous chicken population. Methods: A total of 435 Chinese indigenous chickens were phenotyped for FCR and were genotyped using a 600K SNP genotyping array. Twenty-four birds were selected for sequencing, and the 600K SNP panel data were imputed to whole sequence data with the 24 birds as the reference. The GWAS were performed with GEMMA software. Results: After quality control, 8,626,020 SNPs were used for sequence based GWAS, in which ten significant genomic regions were detected to be associated with FCR. Ten candidate genes, ubiquitin specific peptidase 44, leukotriene A4 hydrolase, ETS transcription factor, R-spondin 2, inhibitor of apoptosis protein 3, sosondowah ankyrin repeat domain family member D, calmodulin regulated spectrin associated protein family member 2, zinc finger and BTB domain containing 41, potassium sodium-activated channel subfamily T member 2, and member of RAS oncogene family were annotated. Several of them were within or near the reported FCR quantitative trait loci, and others were newly reported. Conclusion: Results from this study provide valuable prior information on chicken genomic breeding programs, and potentially improve our understanding of the molecular mechanism for feeding traits.

• Journal of Korean Medicine for Obesity Research
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• v.20 no.2
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• pp.138-148
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• 2020

Objectives: The aim of this study is to evaluate the effects of Bangpungtongseong-san (Fangfengtongsheng-san, BTS) and Daesiho-tang (Dachaihu-tang, DST) on weight loss and improvement in lipid metabolism and glucose metabolism. Furthermore, we intend to develop a prediction model for drug effects through the analysis of the single nucleotide polymorphism (SNP), gut-microbiota, and the expression of immune-related biomarkers. Methods: This study is a single-center, randomized, double-blind, parallel-design clinical trial. One hundred twenty-eight participants will be assigned to the BTS group (n=64) and DST group (n=64). Both groups will be administered 4 g medication three times a day for up to 2 weeks. The primary outcomes is weight loss. The secondary outcomes include bioelectrical impedance analysis, waist circumstance, body mass index, total cholesterol, high-density lipoprotein, triglyceride, insulin resistance. The exploratory outcomes include 3-day dietary recall, food frequency questionnaire, quality of life questionnaire, gut microbiota analysis, immune biomarkers analysis, and SNP analysis. Assessment will be made at baseline and at week 4, 8, and 12. Conclusions: This protocol will be implemented by approval of the Institutional Review Board of Dongguk University. The results of this trial will provide a systematic evidence for the treatment of obesity and enable more precise herbal medicine prescriptions.

• Animal Bioscience
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• v.35 no.10
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• pp.1512-1523
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• 2022

Objective: The growth of pigs involves multiple regulatory mechanisms, and modern molecular breeding techniques can be used to understand the skeletal muscle growth and development to promote the selection process of pigs. This study aims to explore candidate lncRNAs and mRNAs related to skeletal muscle growth and development among Duroc pigs with different average daily gain (ADG). Methods: A total of 8 pigs were selected and divided into two groups: H group (high-ADG) and L group (low-ADG). And followed by whole transcriptome sequencing to identify differentially expressed (DE) lncRNAs and mRNAs. Results: In RNA-seq, 703 DE mRNAs (263 up-regulated and 440 down-regulated) and 74 DE lncRNAs (45 up-regulated and 29 down-regulated) were identified. In addition, 1,418 Transcription factors (TFs) were found. Compared with mRNAs, lncRNAs had fewer exons, shorter transcript length and open reading frame length. DE mRNAs and DE lncRNAs can form 417 lncRNA-mRNA pairs (antisense, cis and trans). DE mRNAs and target genes of lncRNAs were enriched in cellular processes, biological regulation, and regulation of biological processes. In addition, quantitative trait locus (QTL) analysis was used to detect the functions of DE mRNAs and lncRNAs, the most of DE mRNAs and target genes of lncRNAs were enriched in QTLs related to growth traits and skeletal muscle development. In single-nucleotide polymorphism/insertion-deletion (SNP/INDEL) analysis, 1,081,182 SNP and 131,721 INDEL were found, and transition was more than transversion. Over 60% of percentage were skipped exon events among alternative splicing events. Conclusion: The results showed that different ADG among Duroc pigs with the same diet maybe due to the DE mRNAs and DE lncRNAs related to skeletal muscle growth and development.

• Journal of Animal Science and Technology
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• v.65 no.4
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• pp.735-747
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• 2023

The composition of fatty acids determines the flavor and quality of meat. Flavor compounds are generated during the cooking process by the decomposition of volatile fatty acids via lipid oxidation. A number of research on candidate genes related to fatty acid content in livestock species have been published. The majority of these studies focused on pigs and cattle; the association between fatty acid composition and meat quality in chickens has rarely been reported. Therefore, this study investigated candidate genes associated with fatty acid composition in chickens. A genome-wide association study (GWAS) was performed on 767 individuals from an F2 crossbred population of Yeonsan Ogye and White Leghorn chickens. The Illumina chicken 60K significant single-nucleotide polymorphism (SNP) genotype data and 30 fatty acids (%) in the breast meat of animals slaughtered at 10 weeks of age were analyzed. SNPs were shown to be significant in 15 traits: C10:0, C14:0, C18:0, C18:1n-7, C18:1n-9, C18:2n-6, C20:0, C20:2, C20:3n-6, C20:4n-6, C20:5n-3, C24:0, C24:1n-9, monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA). These SNPs were mostly located on chromosome 10 and around the following genes: ACSS3, BTG1, MCEE, PPARGC1A, ACSL4, ELOVL4, CYB5R4, ME1, and TRPM1. Both oleic acid and arachidonic acid contained the candidate genes: MCEE and TRPM1. These two fatty acids are antagonistic to each other and have been identified as traits that contribute to the production of volatile fatty acids. The results of this study improve our understanding of the genetic mechanisms through which fatty acids in chicken affect the meat flavor.

• Animal Bioscience
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• v.37 no.7
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• pp.1168-1176
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• 2024

Objective: As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future. Methods: Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations. Results: Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations. Conclusion: The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.

• Journal of Animal Science and Technology
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• v.66 no.4
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• pp.682-701
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• 2024

This study estimated the heritabilities (h²) and genetic and phenotypic correlations between reproductive traits, including calving interval (CI), age at first calving (AFC), gestation length (GL), number of artificial inseminations per conception (NAIPC), and carcass traits, including carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) in Korean Hanwoo cows. In addition, the accuracy of genomic predictions of breeding values was evaluated by applying the genomic best linear unbiased prediction (GBLUP) and the weighted GBLUP (WGBLUP) method. The phenotypic data for reproductive and carcass traits were collected from 1,544 Hanwoo cows, and all animals were genotyped using Illumina Bovine 50K single nucleotide polymorphism (SNP) chip. The genetic parameters were estimated using a multi-trait animal model using the MTG2 program. The estimated h² for CI, AFC, GL, NAIPC, CWT, EMA, BF, and MS were 0.10, 0.13, 0.17, 0.11, 0.37, 0.35, 0.27, and 0.45, respectively, according to the GBLUP model. The GBLUP accuracy estimates ranged from 0.51 to 0.74, while the WGBLUP accuracy estimates for the traits under study ranged from 0.51 to 0.79. Strong and favorable genetic correlations were observed between GL and NAIPC (0.61), CWT and EMA (0.60), NAIPC and CWT (0.49), AFC and CWT (0.48), CI and GL (0.36), BF and MS (0.35), NAIPC and EMA (0.35), CI and BF (0.30), EMA and MS (0.28), CI and AFC (0.26), AFC and EMA (0.24), and AFC and BF (0.21). The present study identified low to moderate positive genetic correlations between reproductive and CWT traits, suggesting that a heavier body weight may lead to a longer CI, AFC, GL, and NAIPC. The moderately positive genetic correlation between CWT and AFC, and NAIPC, with a phenotypic correlation of nearly zero, suggesting that the genotype-environment interactions are more likely to be responsible for the phenotypic manifestation of these traits. As a result, the inclusion of these traits by breeders as selection criteria may present a good opportunity for developing a selection index to increase the response to the selection and identification of candidate animals, which can result in significantly increased profitability of production systems.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.69 no.2
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• pp.111-122
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• 2024

This study was conducted to evaluate agronomic traits and classify phylogenetic characteristics of Korean wheat landraces (KWLs) collected in Gyeongnam province. We used the squash method for chromosome observation, image analysis to examine seed characteristics, and genotyping using commercial single-nucleotide polymorphism chips to construct a phylogenetic tree. All KWLs contained 42 chromosomes and two pairs of microsatellites as observed in Keumgang, a Korean wheat cultivar. All KWLs showed smaller seed traits compared with those of Keumgang, although KWL-3 had a larger embryo length than that of Keumgang. Among agronomic traits compared with those of Keumgang, all KWLs had a late heading date and ripening period except for KWL-3, which showed the smallest culm and spike length. KWL-1 had the lowest tiller, highest floret, and grain number. All KWLs showed a lower thousand grain weight than that of Keumgang because of their smaller seeds. In the variation of variety and area, the heading date, ripening period, tiller number, and floret number were affected by the cultivation area, whereas the culm length, spike length, and 1000 grain weight were affected by the variety. Correlation distribution analysis showed differences in agronomic traits according to the cultivation area, and the heading date was positively correlated with the culm length and floret number in three cultivation areas. Principal component analysis explained that the heading date had a positive relationship with the ripening period and floret number and a negative relationship with the tiller number. Principal component analysis also revealed that all KWLs had a lower thousand grain weight than that of Keumgang. Phylogenetic tree showed that KWL-1 was near KWL-3, while KWL-2 was near KWL-4. All KWLs were genetically near the Korean wheat cultivars milsung and saeol, whereas they were genetically far from the Korean wheat cultivars goso and olgrue.

• The Plant Pathology Journal
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• v.40 no.5
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• pp.451-462
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• 2024

Xanthomonas oryzae pv. oryzae (Xoo) is a pathogenic bacterium responsible for bacterial blight (BB) disease in rice, primarily mediated by the interaction between the plant and pathogen. The virulence mechanism involves the activation of the Sugars Will Eventually be Exported Transporter (SWEET) gene family in rice by transcription activator-like effectors derived from Xoo. The BB resistance gene xa5 has been identified as one of the most effective genes against Thai Xoo isolates, but xa5-mediated resistance-breaking Xoo strains have emerged. This study aimed to develop a single nucleotide polymorphism (SNP) marker for precise identification of xa5-mediated resistance-breaking Xoo. Comparative genomics of Thai Xoo isolates Xoo16PK001 and Xoo16PK002, which were incompatible and compatible with rice variety IRBB5 carrying xa5, respectively, identified eight SNP positions for the development of an SNP marker. The SNP marker XooE6 yields a specific 1,143 bp PCR product unique to Xoo16PK002. Screening 61 Thai isolates using XooE6 identified two positives: Xoo20PL010 and Xoo20UT002. Inoculation tests on rice varieties IRBB5 and IRBB13 demonstrated compatibility with IRBB5 and incompatibility with IRBB13, which bears Xa5 and xa13. Xoo16PK001 (XooE6-negative) showed different virulence. Inoculation on IRBB21 harboring Xa5, Xa13, and Xa21 resulted in partial resistance to both XooE6-positive and -negative strains. XooE6-positive strains up-regulated SWEET11 and suppressed SWEET14 in IRBB5, while Xoo16PK001 slightly induced SWEET11 but activated SWEET14 in IRBB13. This highlights the potential of XooE6 to identify xa5-mediated resistance-breaking Xoo strains and elucidate their pathogenic mechanisms through the upregulation of SWEET11.

• Journal of Animal Science and Technology
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• v.44 no.2
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• pp.181-190
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• 2002

This study was performed to determine sequences of the mt DNA D-loop region, including $tRNA^{Pro}$ and $tRNA^{Pre}$ and to analysis sequence variation polymorphism in Korean cattle. The resulting sequencies were compared with previously published sequences for other cattle breeds(GenBank J01394). The PCR was used to amplify an 1142bp between nucleotides 15061 and 404 within the D-loop region of mt DNA using specific primers. Korean cattle showed 24 polymorphic sites by nucleotide substitutions and insertions of single base pairs. About 50% of polymorphic sites were found in positions 16042 to 16122 with the most variable region. Among these polymorphic sites, variations at 16055, 16230 and 16260 bp were detected as new sequence variants in Korean cattle. These specific polymorphic sites have not been reported in the Japanese black cattle and European cattle. Therefore, mt DNA variants in the D-loop region may be used as genetic markers for specifying Korean cattle. The frequencies of positions 169, 16302, 16093, 16042, 16119 with a high level of sequence polymorphism were 0.81, 0.56, 0.56, 0.50 and 0.43, respectively. In comparison of genetic distances, Korean cattle showed the more closely to European cattle as Bos taurus than Bos indicus such as African and India breeds. In conclusion, these mt DNA sequence polymorphisms in the D-loop region for Korean cattle may be useful for the analysis of cytoplasmic genetic variation and associations with economic important traits and genetic analysis of maternal lineage.

• Korean Journal of Poultry Science
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• v.40 no.2
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• pp.139-145
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• 2013

There are several loci controlling the feather color of birds, of which one of the most studied is Extended black (E) encoding the melanocortin 1-receptor (MC1R). Mutations in this gene affect the relative distribution of eumelanin, phaeomelanin. The association of feather color and sequence polymorphism in the melanocortin 1-receptor (MC1R) gene was investigated using Korean native chicken H breed (H_PL) and 'Woorimatdag' commercial chickens (Woorimatdag_CC). In order to correlate gene mutation to Korean native chicken feather color, single nucleotide polymorphism (SNP) from MC1R gene sequence were investigated. A total of 307 birds from H_PL and Woorimatdag_CC were used. H_PL have black, black-brown feather color and Woorimatdag_CC have black with brown spots or brown with black spots. There are 6 SNPs in MC1R gene, locus T69C, C212T, A274G, G376A, G636A, T637C. 3 SNPs are nonsynonymous that change amino acid. But it is difficult to find correlation of feather color and polymorphisms. It will be needed to increase the population of Korean native chicken H breed and correlation analysis of genetic variation with feather colors.