Article
Agriculture, Dairy & Animal Science
Haoqiang Ye, Zhenqiang Xu, Semiu Folaniyi Bello, Qianghui Zhu, Shaofen Kong, Ming Zheng, Xiang Fang, Xinzheng Jia, Haiping Xu, Xiquan Zhang, Qinghua Nie
Summary: In this study, the performance of haplotype models for genomic prediction in a Chinese yellow-feathered chicken population was comprehensively evaluated. It was found that haplotype methods were beneficial for genomic prediction, and the accuracy could be further increased by incorporating genomic annotation information. Moreover, using LD information would potentially improve the performance of genomic prediction.
Article
Genetics & Heredity
Haoqiang Ye, Zipeng Zhang, Duanyang Ren, Xiaodian Cai, Qianghui Zhu, Xiangdong Ding, Hao Zhang, Zhe Zhang, Jiaqi Li
Summary: The size of reference population is important for genomic prediction. This study used WGS data to construct LD-based haplotypes and explored the impact of different SNP densities, variant representation, and reference population size on prediction accuracy. The results showed that GBLUP using WGS data improved prediction accuracy in multi-population and haplotype method had better performance in multi-population genomic evaluation.
FRONTIERS IN GENETICS
(2022)
Article
Evolutionary Biology
Hongwei Li, Zezhao Wang, Lei Xu, Qian Li, Han Gao, Haoran Ma, Wentao Cai, Yan Chen, Xue Gao, Lupei Zhang, Huijiang Gao, Bo Zhu, Lingyang Xu, Junya Li
Summary: In this study, haplotype blocks were constructed using LD-based and fixed-SNP methods in beef cattle. The predictive performance of different haplotype block partitioning methods was evaluated, and it was found that LD-based and fixed-SNP haplotype Bayesian methods outperform the Bayesian models. Filtering minor haplotype allele frequency can also improve the performance of genomic prediction.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Agronomy
Sang He, Shanshan Liang, Lijun Meng, Liyong Cao, Guoyou Ye
Summary: Multi-environment genomic selection is important in rice breeding for selecting resilient varieties. To achieve this, a robust training set with multi-environment phenotypic data is necessary. Optimizing genomic prediction methods and considering haplotype-based models can improve the accuracy of selection.
Article
Genetics & Heredity
Masoumeh Naserkheil, Hossein Mehrban, Deukmin Lee, Mi Na Park
Summary: This study compared the prediction accuracy of conventional pedigree-based BLUP and single-step genomic BLUP methods for 10 primal cut traits in Hanwoo cattle, with ssGBLUP showing better performance overall. The ssGBLUP method demonstrated more accurate and less biased predictions across the studied traits, making it more suitable for improving accuracy in predicting primal cut yields.
Article
Agriculture, Dairy & Animal Science
Rostam Abdollahi-Arpanahi, Daniela Lourenco, Ignacy Misztal
Summary: Genomic selection has been widely adopted in various livestock and plant species nationally and internationally. The start date of genomic selection for economically important traits in pigs, cattle, and broiler chickens can be determined by analyzing the differences between genetic and Realized Mendelian sampling (RMS) trends obtained using BLUP and single-step genomic BLUP (ssGBLUP). The results showed that the effective onset of genomic selection varied across species, with notable divergences in trends between BLUP and ssGBLUP for certain traits.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Reza Seyed Sharifi, Fatemeh Ala Noshahr, Jamal Seifdavati, Nemat Hedayat Evrigh, Moises Cipriano-Salazar, Maria A. Mariezcurrena-Berasain
Summary: The study found that when the length of haploblocks is properly characterized, covariates suitable for haplotype alleles instead of SNPs will improve the accuracy of the genome. Longer haploblocks are more negatively affected by increasing the frequency threshold, leading to a greater impact on accuracy and bias.
SMALL RUMINANT RESEARCH
(2021)
Article
Biochemical Research Methods
Shan-Shan Dong, Wei-Ming He, Jing-Jing Ji, Chi Zhang, Yan Guo, Tie-Lin Yang
Summary: LDBlockShow is an open source software that visualizes LD and haplotype blocks, providing faster speed and lower memory consumption compared to other tools.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Chen Cao, Jingni He, Lauren Mak, Deshan Perera, Devin Kwok, Jia Wang, Minghao Li, Tobias Mourier, Stefan Gavriliuc, Matthew Greenberg, A. Sorana Morrissy, Laura K. Sycuro, Guang Yang, Daniel C. Jeffares, Quan Long
Summary: DNA sequencing technologies offer unprecedented opportunities to study within-host evolution of microorganism populations, but current instruments struggle to directly distinguish long haplotypes. PoolHapX is a computational approach that integrates information from genetic sharing and genomic sequencing, outperforming other tools and capable of inferring whole-chromosome-scale haplotypes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Anna R. Rogers, Yang Bian, Matthew Krakowsky, David Peters, Clint Turnbull, Paul Nelson, James B. Holland
Summary: The Germplasm Enhancement of Maize (GEM) project is a collaborative effort between public and private maize breeders to enhance the genetic diversity of the U.S. maize crop. Through hybridization and genetic selection, the project has developed hundreds of useful breeding lines. Evaluation of the prediction ability of genomic selection (GS) models showed that the predicted genetic gain is higher than that of phenotypic selection.
Article
Genetics & Heredity
Andre C. Araujo, Paulo L. S. Carneiro, Hinayah R. Oliveira, Flavio S. Schenkel, Renata Veroneze, Daniela A. L. Lourenco, Luiz F. Brito
Summary: Haplotype-based models did not improve the performance of genomic predictions in genetically diverse populations.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Jie Zheng, Yuan-yuan Wu, Wen-liang Fang, Xin-ying Cai, Zeng-yun-ou Zhang, Chong-xian Yu, Xiao-dong Zheng, Feng-li Xiao
Summary: This study confirmed the association between the TMEM232 gene and AD through haplotype analysis and targeted capture sequencing. The most strongly associated haplotype with AD was H15.
SCIENTIFIC REPORTS
(2021)
Article
Mathematics
Armalia Desiyanti, Irlandia Ginanjar, Toni Toharudin
Summary: Data at a smaller regional level is necessary for local governments. The current average data on household expenditure does not include subdistrict-level statistics. Small area estimation is one method to address this issue.
Article
Plant Sciences
Leandro Tonello Zuffo, Rodrigo Oliveira DeLima, Thomas Lubberstedt
Summary: Combining maize association panels with different genetic backgrounds can improve the efficiency of identifying candidate genes associated with root traits. In this study, the combined panel successfully identified SNPs associated with root traits and showed higher prediction accuracy compared to using individual panels.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Agriculture, Dairy & Animal Science
Artem Kabanov, Ekaterina Melnikova, Sergey Nikitin, Maria Somova, Oleg Fomenko, Valeria Volkova, Olga Kostyunina, Tatiana Karpushkina, Elena Martynova, Elena Trebunskikh
Summary: This study compared three methods for assessing the breeding value of pigs and evaluated the changes in accuracy of genomic estimates using different reference groups. The results showed that the wssGBLUP method has higher reliability compared to ssGBLUP, and a reference group size of more than 1000 individuals leads to more stable results.
Article
Genetics & Heredity
Bryan Irvine M. Lopez, Narae An, Krishnamoorthy Srikanth, Seunghwan Lee, Jae-Don Oh, Dong-Hyun Shin, Woncheoul Park, Han-Ha Chai, Jong-Eun Park, Dajeong Lim
Summary: This study aimed to improve the predictive performance of a customized 50k SNP panel for four carcass traits in commercial Hanwoo cattle by adding highly predictive variants from sequence data. Results showed that adding 3000 pre-selected variants from each trait significantly improved prediction accuracy, with gains of up to 9.9% for backfat thickness, 9.2% for carcass weight, 6.4% for longissimus muscle area, and 4.7% for marbling score. The strategy used to select variants based on functional annotation did not show a clear advantage compared to using whole-genome data, indicating that using WGS data remained more accurate.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Han-Ha Chai, Tae-Hun Kim, Young Ran Kim, Dajeong Lim
Summary: The study predicted the structure of the pig TAP transporter and its inhibition complex by the herpes simplex virus-encoded ICP47 inhibitor, revealing the specificity determinants and functional effects of the ICP47 inhibitor on TAP. The research also demonstrated the specialized structure-function relationship of the pig TAP exporter and its implications for antiviral resistance and disease susceptibility.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Bo-Hye Nam, Hyaekang Kim, Donghyeok Seol, Heebal Kim, Eun Soo Noh, Eun Mi Kim, Jae Koo Noh, Young-Ok Kim, Jung Youn Park, Woori Kwak
Summary: Continuous monitoring of genetic status is crucial for preserving the genetic resource of wild populations. This study used GBS to sequence Pacific abalone samples from around the Korean peninsula, revealing genetic diversity and population structure differences, as well as population-specific SNVs potentially associated with phenotype differences in Korean abalone populations.
Article
Multidisciplinary Sciences
Devender Arora, Krishnamoorthy Srikanth, Jongin Lee, Daehwan Lee, Nayoung Park, Suyeon Wy, Hyeonji Kim, Jong-Eun Park, Han-Ha Chai, Dajeong Lim, In-Cheol Cho, Jaebum Kim, Woncheoul Park
Summary: This study comprehensively investigated the genomic selection and functional characteristics of candidate genes in Nanchukmacdon pig breed, revealing selective sweep and differential expression in muscle-related pathways. The results demonstrate low genetic diversity and the critical role of DNA methylation pattern in enhancing meat variety in Nanchukmacdon.
SCIENTIFIC REPORTS
(2021)
Correction
Genetics & Heredity
Sohyoung Won, Jong-Eun Park, Ju-Hwan Son, Seung-Hwan Lee, Byeong Ho Park, Mina Park, Won-Chul Park, Han-Ha Chai, Heebal Kim, Jungjae Lee, Dajeong Lim
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Clementine Charton, Dong-Jae Youm, Byung June Ko, Donghyeok Seol, Bongsang Kim, Han-Ha Chai, Dajeong Lim, Heebal Kim
Summary: This study investigated the transcriptomic effects of molt in Korean long-tailed chickens, revealing tissue-specific impacts on gene expression, especially in the nervous system. Blood was the most affected tissue by molt, with gender differences in gene expression. miRNA was found to play potential roles in molt, and reliable candidate biomarkers related to molt were identified, providing new insights for future transcriptome analyses in chickens.
Article
Genetics & Heredity
Jihye Cha, Hyojun Choo, Krishnamoorthy Srikanth, Seung-Hwan Lee, Ju-Whan Son, Mi-Rim Park, Nayeon Kim, Gul Won Jang, Jong-Eun Park
Summary: A study identified 12 SNPs associated with body weight in Korean native chickens and these SNPs were located near or within 11 candidate genes. Gene set enrichment analysis revealed that genes related to body weight were significantly enriched in pathways involving transcription regulation, motor activity, mitogen-activated protein kinase signaling, and tight junction. These findings suggest the potential use of identified SNPs as biomarkers in Korean native chicken breeding.
Article
Agriculture, Dairy & Animal Science
Hana Kim, Hyeran Kim, Pilnam Seong, Devender Arora, Donghyun Shin, Woncheoul Park, Jong-Eun Park
Summary: This study investigated the heat stress response in chickens through transcriptome analysis, identifying DEGs involved in various biological processes and revealing gene regulation and metabolic changes under heat stress environment. These findings provide a comprehensive understanding of the heat stress response in poultry.
Article
Agriculture, Dairy & Animal Science
Swati Srivastava, Bryan Irvine Lopez, Himansu Kumar, Myoungjin Jang, Han-Ha Chai, Woncheoul Park, Jong-Eun Park, Dajeong Lim
Summary: This study evaluated the predictive performance of three machine learning methods in predicting carcass traits of Hanwoo cattle. The results showed that XGB and GBLUP had the best predictive correlations for different traits, suggesting that GBLUP is still recommended for predicting genomic breeding values in Hanwoo cattle.
Article
Agriculture, Dairy & Animal Science
Kyu-Sang Lim, Hyung-Chul Kim, Bong-Hwan Choi, Ju-Whan Son, Kyung-Tai Lee, Tae-Jeong Choi, Yong-Min Cho, Han-Ha Chai, Jong-Eun Park, Woncheoul Park, Chiwoong Lim, Jun-Mo Kim, Dajeong Lim
Summary: In this study, genes with monoallelic expression were identified in Korean cattle (Hanwoo) using genome-wide and transcriptome-wide screening. Tissue-specific expression patterns were observed, and these genes were associated with breeding values for economically important traits in Hanwoo. This study provides potential selective targets for genetic improvement in Hanwoo.
Article
Multidisciplinary Sciences
Devender Arora, Jong-Eun Park, Dajeong Lim, In-Cheol Cho, Kyung Soo Kang, Tae-Hun Kim, Woncheoul Park
Summary: The size distribution of the Korean minipig is an important feature that makes it an ideal model for biomedical research. However, the large minipig breed has a comparatively frail and vulnerable immune response, requiring additional care. In this study, we identified genes under selection in the large breed that could contribute to the development of a better variety of the extremely tiny minipig breed.
Article
Agriculture, Dairy & Animal Science
Do-Young Kim, Byeonghwi Lim, Dajeong Lim, Woncheol Park, Kyung-Tai Lee, Eun-Seok Cho, Kyu-Sang Lim, Si Nae Cheon, Bong-Hwan Choi, Jong-Eun Park, Jun-Mo Kim
Summary: Fat is involved in the synthesis of fatty acids, circulation of fatty acids, and lipid metabolism. This study aimed to investigate the epigenetic differences in abdominal fat during the growth of pigs. The results showed changes in DNA methylation and gene expression with growth. Genes that were differentially methylated or expressed were found to be involved in immune response and lipid metabolism. The effects of DNA methylation on gene expression were analyzed through cis-regulation and trans-regulation analysis. This research provides insights into the underlying mechanisms of epigenetic regulation in porcine abdominal fat during aging.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Food Science & Technology
Do Manh Cuong, Dae Kyeong Kim, Meran Keshawa Ediriweera, Jong-Eun Park, Jeong Yong Moon, Somi Kim Cho
Summary: This study explores the extraction and drying techniques of Melosira nummuloides and finds that freeze-drying method and chloroform:methanol extraction solvent are effective in extracting products with antioxidant and anti-inflammatory activity.
APPLIED BIOLOGICAL CHEMISTRY
(2023)