Review
Agronomy
Theo Meuwissen, Ben Hayes, Iona MacLeod, Michael Goddard
Summary: This review discusses the possibility of identifying causal variants for complex traits, stressing the importance of large and diverse samples, accurate genotypes, multiple phenotypes, annotation of genomic sites, and other types of evidence required for this task.
Article
Biotechnology & Applied Microbiology
Shaghayegh Soudi, Marc Crepeau, Travis C. Collier, Yoosook Lee, Anthony J. Cornel, Gregory C. Lanzaro
Summary: By integrating whole-genome sequencing data and topo-climate variables, this study identifies 112 genes associated with local environmental adaptation in Ae. aegypti populations in southern and central California. These findings provide insights into how environmental adaptation impacts the arboviral disease landscape and population control efforts.
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)
Review
Biochemistry & Molecular Biology
Michael Escamilla, Camille Merhi
Summary: Genetic studies of bipolar disorder have been conducted in Latin American populations, identifying significant loci and genes associated with the disorder. Studies have also found linkage loci for bipolar disorder endophenotypes in these populations. Candidate gene association analyses have confirmed the role of certain genes in conferring bipolar disorder risk in Latinos.
MOLECULAR PSYCHIATRY
(2023)
Article
Agriculture, Dairy & Animal Science
Abbas Hajihosseinlo, Ardeshir Nejati-Javaremi, Seyed Reza Miraei-Ashtiani
Summary: This research measured the extent of linkage disequilibrium, effective population size, haplotype block structure, and runs of homozygosity in several cattle populations using SNP genotypes. The results showed a decrease in genetic diversity with increasing distance between SNP pairs. The Iranian Holstein population had the lowest level of genomic inbreeding, while the French Holstein population had the highest. The number of runs of homozygosity decreased with increasing distance due to the increased recombination rate. This is concerning as it leads to a reduction in the effective population size.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Jose G. Cortes-Hernandez, Felipe J. Ruiz-Lopez, Carlos G. Vasquez-Pelaez, Adriana Garcia-Ruiz
Summary: This study aimed to investigate the runs of homozygosity (ROH) in the Mexican Holstein population and their associations with milk, fat and protein yields, and conformation final score. The results showed evidence of genomic regions preserved by genetic selection, which were associated with improved productivity and functionality of dairy cattle.
Article
Genetics & Heredity
Endashaw Terefe, Gurja Belay, Jianlin Han, Olivier Hanotte, Abdulfatai Tijjani
Summary: This study found genomic differences between cattle populations living in the Ethiopian mountains and lowlands, suggesting adaptations to high altitude. Some of the identified genes were also previously reported in human populations living in the Ethiopian highlands. The study also discovered new candidate genes associated with high-altitude adaptation in cattle.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Sungbong Jang, Roger Ros-Freixedes, John M. Hickey, Ching-Yi Chen, Justin Holl, William O. Herring, Ignacy Misztal, Daniela Lourenco
Summary: This study investigated the impact of using preselected variants from whole-genome sequence (WGS) data on single-step genomic predictions in maternal and terminal pig lines. The results showed that using preselected SNP sets improved prediction accuracy in maternal lines but resulted in a decrease in accuracy in terminal lines. Therefore, the benefit of using WGS data depends on the line and the method of preselecting variants.
GENETICS SELECTION EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Jose Marcelo Soriano Viana, Antonio Augusto Franco Garcia
Summary: Additive variance is generally the most important component of genotypic variance. LD and inbreeding have a significant effect on the magnitude of the genetic variances and covariances. In general, the additive x additive variance is the most important component of epistatic variance.
Article
Ecology
Soichiro Nishiyama, Mao Fujikawa, Hisayo Yamane, Kenta Shirasawa, Ebrahiem Babiker, Ryutaro Tao
Summary: Interspecific hybridization is a common breeding approach for introducing novel traits and genetic diversity. The study found that rabbiteye blueberry cultivars were genetically distinct from southern highbush blueberry and northern highbush blueberry cultivars, with the latter two being genetically indistinguishable. The allele selection strategies used by breeders may have influenced the genetic differentiation between the species.
Article
Multidisciplinary Sciences
Nandika Perera, Gayani Galhena, Gaya Ranawaka
Summary: A new 16 X-STR multiplex PCR system developed for Sri Lankans shows high forensic efficiency and subtle differences in allele frequency distribution among Indian Tamils, Sinhalese, and Moors, highlighting the need for separate databases. Sri Lankan ethnicities, except Indian Tamils, cluster closely with populations from Indian Bhil tribe, Bangladesh and Europe, indicating shared Indo-Aryan ancestry.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Tahere Akbarpour, Navid Ghavi Hossein-Zadeh, Abdol Ahad Shadparvar
Summary: This study investigated the impact of different rates of marker genotyping error on the accuracy of genomic prediction using stochastic simulation. The results showed that marker genotyping error can decrease the accuracy of genomic evaluations and result in biased estimates of genomic breeding values. It is recommended to minimize marker genotyping errors to zero in genomic evaluation programs in order to obtain accurate results.
MOLECULAR GENETICS AND GENOMICS
(2021)
Article
Ecology
Dengcheng Yang, Fan Li, Jing Wang, Ang Dong, Rongling Wu
Summary: LD in tetraploids is studied with a specific model for different loci disequilibrium, using EM algorithm for parameter estimation and experimental verification in populations. Analysis of switchgrass genomic data reveals the importance of LD in inferring evolutionary history.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Vivian Link, Yuomi Jhony A. Zavaleta, Rochelle-Jan Reyes, Linda Ding, Judy Wang, Rori V. Rohlfs, Michael D. Edge
Summary: The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are widely used in forensic genetics in the United States. Although CODIS loci were previously believed to contain limited information about ancestry or traits, recent research has shown that the regions surrounding CODIS loci are enriched with trait-related variants.
Article
Biochemistry & Molecular Biology
Jee Youn Hwang, Kesavan Markkandan, Kyudong Han, Mun Gyeong Kwon, Jung Soo Seo, Seung-il Yoo, Seong Don Hwang, Bo Young Ji, Maeng-Hyun Son, Jun-hyung Park
Article
Fisheries
Jee Youn Hwang, Kesavan Markkandan, Mun Gyeong Kwon, Jung Soo Seo, Seung-il Yoo, Seong Don Hwang, Maeng-Hyun Son, Junhyung Park
FISH & SHELLFISH IMMUNOLOGY
(2018)
Article
Environmental Sciences
Jae-Hyun Lim, Sang Heon Lee, Junhyung Park, Jiyoung Lee, Joo-Eun Yoon, Il-Nam Kim
JOURNAL OF COASTAL RESEARCH
(2018)
Article
Genetics & Heredity
Himansu Kumar, Woncheol Park, Krishnamoorthy Srikanth, Bong-Hwan Choi, Eun-Seok Cho, Kyung-Tai Lee, Jun-Mo Kim, Kwangmin Kim, Junhyung Park, Dajeong Lim, Jong-Eun Park
Article
Multidisciplinary Sciences
Jiyoung Lee, Sung-Ho Kang, Eun Jin Yang, Alison M. Macdonald, Hyoung Min Joo, Junhyung Park, Kwangmin Kim, Gi Seop Lee, Ju-Hyoung Kim, Joo-Eun Yoon, Seong-Su Kim, Jae-Hyun Lim, Il-Nam Kim
SCIENTIFIC REPORTS
(2019)
Article
Agriculture, Dairy & Animal Science
Himansu Kumar, Yu Na Jang, Kwangmin Kim, Junhyung Park, Min Woong Jung, Jong-Eun Park
Article
Entomology
Joon Ha Lee, Hoyong Chung, Yong Pyo Shin, In-Woo Kim, Sathishkumar Natarajan, Karpagam Veerappan, Minchul Seo, Junhyung Park, Jae Sam Hwang
Article
Entomology
Joon Ha Lee, Hoyong Chung, Yong Pyo Shin, In-Woo Kim, Sathishkumar Natarajan, Karpagam Veerappan, Minchul Seo, Junhyung Park, Jae Sam Hwang
Summary: The research analyzed antimicrobial peptides in locusts, predicted promising peptides with antimicrobial effects, and found that they were non-toxic, suggesting their potential as drug candidates.
JOURNAL OF ASIA-PACIFIC ENTOMOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Joon Ha Lee, Hoyong Chung, Yong Pyo Shin, Mi-Ae Kim, Sathishkumar Natarajan, Karpagam Veerappan, Seong Hyun Kim, Junhyung Park, Jae Sam Hwang
Summary: This study immunized the giant meal worm and predicted numerous novel antimicrobial peptides from the transcriptome data. Some of these peptides showed potential antimicrobial activity and could be candidates for the development of antimicrobial agents.
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS
(2021)
Article
Entomology
Kang-Woon Lee, Jae-Goo Kim, Karpagam Veerappan, Hoyong Chung, Sathishkumar Natarajan, Ki-Young Kim, Junhyung Park
Summary: Research extracted antimicrobial peptides from high-altitude red spotted apollo butterflies, identifying a promising candidate with antimicrobial activity against bacteria causing periodontitis.
Article
Biochemistry & Molecular Biology
Md Ataul Islam, V. P. Subramanyam Rallabandi, Sameer Mohammed, Sridhar Srinivasan, Sathishkumar Natarajan, Dawood Babu Dudekula, Junhyung Park
Summary: In this study, structure-based virtual screening and machine learning were used to identify potential drug compounds targeting key receptors involved in cardiovascular diseases. Four promising compounds for each beta 1- and beta 2-AR were identified, suggesting their potential importance for experimental validation in treating cardiovascular diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Kwangmin Kim, Karpagam Veerappan, Nahyun Woo, Bohyeon Park, Sathishkumar Natarajan, Hoyong Chung, Cheolmin Kim, Junhyung Park
Summary: The study investigated the impact of Ulmus macrocarpa Hance extract (UME) on human gut microbiota in healthy adults. The results showed that the microbial response to UME supplementation was personalized, with no significant differences in species richness and abundance. However, there was an increase in specific bacterial species and functional enrichment of bacterial genes related to bile acid biosynthesis in the UME group. This preliminary study suggests that UME supplementation may enhance host immunity by modulating gut microbiota, but further larger-scale clinical studies are needed for confirmation.
JOURNAL OF MICROBIOLOGY
(2021)
Review
Plant Sciences
Karpagam Veerappan, Sathishkumar Natarajan, Hoyong Chung, Junhyung Park
Summary: Fleshy fruits, particularly those from the genus Prunus, are highly demanded due to their diverse stone/drupe fruit varieties. Peach varieties have unique palatable qualities, but shorter post-harvest life due to excessive softening, which has led to studies focusing on the molecular mechanisms and genetic basis of the softening process.
Article
Entomology
Joon Ha Lee, Hoyong Chung, Yong Pyo Shin, Mi-Ae Kim, Sathishkumar Natarajan, Karpagam Veerappan, Seong Hyun Kim, Junhyung Park, Jae Sam Hwang
Article
Entomology
Rustem A. Ilyasov, Junhyung Park, Junichi Takahashi, Hyung Wook Kwon
JOURNAL OF APICULTURAL SCIENCE
(2018)