Multi-INTACT: integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits by Jeffrey Okamoto, Xianyong Yin, Brady Ryan, Joshua Chiou, Francesca Luca, Roger Pique-Regi, Hae Kyung Im, Jean Morrison, Charles Burant, Eric B. Fauman, Markku Laakso, Michael Boehnke, Xiaoquan Wen

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A Two-Stage Method for Improving the Prediction Accuracy of Complex Traits by Incorporating Genotype by Environment Interactions in Brassica napus by Sican Xiong, Meng Wang, Jun Zou, Jinling Meng, Yanyan Liu

“…Improving the prediction accuracy of a complex trait of interest is key to performing genomic selection (GS) for crop breeding. …”
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The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study by Young-Sup Lee, Hyeon-Jeong Kim, Seoae Cho, Heebal Kim

“…Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. …”
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Network Graph Analysis of Gene-Gene Interactions in Genome-Wide Association Study Data by Sungyoung Lee, Min-Seok Kwon, Taesung Park

“…Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. …”
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Omics based technology application in poultry meat research by Huaijun Zhou, Austin Quach, Mahesh Nair, Behnam Abasht, Byungwhi Kong, Brian Bowker

“…The purpose of this symposium was not only to focus on how recent omics technologies can be used to gather, integrate, and interpret data produced by various methodologies in poultry research, but also to highlight how omics and bioinformatics have increased our understanding of poultry meat quality problems and other complex traits. This Poultry Science Association symposium paper includes 5 sections that cover: 1) functional annotation of cis-regulatory elements in the genome informs genetic control of complex traits in poultry, 2) mass spectrometry for proteomics, metabolomics, and lipidomics, 3) proteomic approaches to investigate meat quality, 4) spatial transcriptomics and metabolomics studies of wooden breast disease, and 5) multiomics analyses on chicken meat quality and spaghetti meat. …”
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Impact of rare non-coding variants on human diseases through alternative polyadenylation outliers by Xudong Zou, Zhaozhao Zhao, Yu Chen, Kewei Xiong, Zeyang Wang, Shuxin Chen, Hui Chen, Gong-Hong Wei, Shuhua Xu, Wei Li, Ting Ni, Lei Li

“…Abstract Although rare non-coding variants (RVs) play crucial roles in complex traits and diseases, understanding their mechanisms and identifying disease-associated RVs continue to be major challenges. …”
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MOLECULAR MARKERS IN GENETIC STUDIES AND BREEDING by E. K. Khlestkina

“…Back in the early decades in Genetics, it became clear that genetic markers may be useful in the analysis of complex traits. However, the low occurrence and a number of other shortcomings hampered wide application of classical genetic markers, and later then protein markers in the breeding. …”
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Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits. by Jingyi Zhang, Honglang Wang, Yuehua Cui

“…The genetic basis of complex traits involves the function of many genes with small effects as well as complex gene-gene and gene-environment interactions. …”
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metaGE: Investigating genotype x environment interactions through GWAS meta-analysis. by Annaïg De Walsche, Alexis Vergne, Renaud Rincent, Fabrice Roux, Stéphane Nicolas, Claude Welcker, Sofiane Mezmouk, Alain Charcosset, Tristan Mary-Huard

“…The procedure identified known and new QTLs, providing valuable insights into the genetic architecture of complex traits and QTL effects dependent on environmental stress conditions. …”
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Copy Number Variations in Short Tandem Repeats Modulate Growth Traits in Penaeid Shrimp Through Neighboring Gene Regulation by Hao Zhou, Guangfeng Qiang, Yan Xia, Jian Tan, Qiang Fu, Kun Luo, Xianhong Meng, Baolong Chen, Meijia Chen, Juan Sui, Ping Dai, Xupeng Li, Mianyu Liu, Qun Xing, Jie Kong, Sheng Luan

“…It offers a valuable framework for investigating complex traits and the biological functions of STRs in agricultural animals.…”
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Association mapping and candidate gene identification for yield traits in European hazelnut (Corylus avellana L.) by Asena Akköse Baytar, Ertuğrul Gazi Yanar, Anne Frary, Sami Doğanlar

“…This comprehensive study provides valuable insights for the development of breeding strategies and the improvement of hazelnut and enhances the understanding of the genetic architecture of complex traits by proposing candidate genes and potential functions.…”
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Genome-Wide Association Study for High Milk Yield in Saudi Arabian Dromedary using Whole Genome Sequencing by Faisal M. Alsubaie, Mohanad A. Ibrahim, Suheel Yousuf Wani, Ashraf Awad, Abdulwahed Fahad Alrefaei, Mikhlid H. Almutairi

“…Advances in molecular breeding have expanded our knowledge of the genetic architecture of complex traits through genome-wide association studies (GWAS). …”
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An Integrated Database for Exploring Alternative Promoters in Animals by Feiyang Xue, Yuqin Yan, Weiwei Jin, Haotian Zhu, Yanbo Yang, Zhanhui Yu, Xuewen Xu, Jing Gong, Xiaohui Niu

“…At present, hundreds of thousands of APs have been identified across human tissues, and a considerable number of APs have been demonstrated to be associated with complex traits and diseases. Recent researches have also proven important effects of APs on animals. …”
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GRAMMAR-Lambda Delivers Efficient Understanding of the Genetic Basis for Head Size in Catfish by Yunfeng Zhao, Jin Gao, Hong Feng, Li Jiang

“…These findings contribute to our understanding of the genetic architecture of head size and will support marker-assisted breeding in aquaculture, also reflecting the potential application of the GRAMMAR-Lambda method in genetic studies of complex traits.…”
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GPA-MDS: A Visualization Approach to Investigate Genetic Architecture among Phenotypes Using GWAS Results by Wei Wei, Paula S. Ramos, Kelly J. Hunt, Bethany J. Wolf, Gary Hardiman, Dongjun Chung

“…Recently, there has been accumulating evidence suggesting that different complex traits share a common risk basis, namely, pleiotropy. …”
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Assessment of Tools for Marker-Assisted Selection in a Marine Commercial Species: Significant Association between MSTN-1 Gene Polymorphism and Growth Traits by Irma Sánchez-Ramos, Ismael Cross, Jaroslav Mácha, Gonzalo Martínez-Rodríguez, Vladimir Krylov, Laureana Rebordinos

“…Molecular markers linked to quantitative trait loci (QTL) have been regarded as useful for marker-assisted selection in complex traits as growth. Polymorphisms have been studied in five candidate genes influencing growth in gilthead seabream (Sparus aurata): the growth hormone (GH), insulin-like growth factor-1 (IGF-1), myostatin (MSTN-1), prolactin (PRL), and somatolactin (SL) genes. …”
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Genetic control of N-glycosylation of human blood plasma proteins by S. Zh. Sharapov, A. N. Timoshchuk, Y. S. Aulchenko

“…Application of these methods has made it possible to find previously unknown regulators of N-glycosylation and expanded the understanding of the role of N-glycans in the control of multifactorial diseases and human complex traits. The present review considers the current knowledge of the genetic control of variability in the levels of N-glycosylation of plasma proteins in human populations. …”
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The Significant Effects of Threshold Selection for Advancing Nitrogen Use Efficiency in Whole Genome of Bread Wheat by Mohammad Bahman Sadeqi, Agim Ballvora, Said Dadshani, Md. Nurealam Siddiqui, Mohammad Kamruzzaman, Ahossi Patrice Koua, Jens Léon

“…ABSTRACT Currently in wheat breeding, genome wide association studies (GWAS) have successfully revealed the genetic basis of complex traits such as nitrogen use efficiency (NUE) and its biological processes. …”
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Genome-Wide Association Study of Metabolic Syndrome in Koreans by Seok Won Jeong, Myungguen Chung, Soo-Jung Park, Seong Beom Cho, Kyung-Won Hong

“…Conclusively, our approach using the conventional GWAS, reconsidering functional variants and pathway-based interpretation, suggests a useful method to understand the GWAS results of complex traits and can be expanded in other genomewide association studies.…”
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