smyda-dajmund, paulina szajko, katarzyna sołtys-kalina, dorota marczewski, waldemar śliwka, jadwiga
The production of chips is an increasing part of the potato market. While the potato tubers are stored at low temperatures to minimize storage problems, they tend to accumulate reducing sugars, which negatively impact the quality and color of fried products. The goal of this study was to analyze the impact of cytoplasm type on chip color after harv...
Przytycki, Pawel Pollard, Katherine
While context-type-specific regulation of genes is largely determined by cis-regulatory regions, attempts to identify cell type-specific eQTLs are complicated by the nested nature of cell types. We present hierarchical eQTL (H-eQTL), a network-based model for hierarchical annotation of bulk-derived eQTLs to levels of a cell type tree using single-c...
Guo, Weier Bastiaanse, Héloïse Maloof, Julin Comai, Luca Henry, Isabelle
The genetic control of many plant traits can be highly complex. Both allelic variation (sequence change) and dosage variation (copy number change) contribute to a plants phenotype. While numerous studies have investigated the effect of allelic or dosage variation, very few have documented both within the same system, leaving their relative contribu...
Zhang, Yuanyuan Yang, Zhiquan He, Yizhou Liu, Dongxu Liu, Yueying Liang, Congyuan Xie, Meili Jia, Yupeng Ke, Qinglin Zhou, Yongming
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Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions...
Fu, Boyang Anand, Prateek Anand, Aakarsh Mefford, Joel Sankararaman, Sriram
Our knowledge of the contribution of genetic interactions (epistasis) to variation in human complex traits remains limited, partly due to the lack of efficient, powerful, and interpretable algorithms to detect interactions. Recently proposed approaches for set-based association tests show promise in improving the power to detect epistasis by examin...
Xu, Shizhong Osorio Y Fortéa, José
BACKGROUND: Traditional recombinant inbred lines (RILs) are generated from repeated self-fertilization or brother-sister mating from the F1 hybrid of two inbred parents. Compared with the F2 population, RILs cumulate more crossovers between loci and thus increase the number of recombinants, resulting in an increased resolution of genetic mapping. S...
Lara, Montana Kay Chitre, Apurva S Chen, Denghui Johnson, Benjamin B Nguyen, Khai‐Minh Cohen, Katarina A Muckadam, Sakina A Lin, Bonnie Ziegler, Shae Beeson, Angela
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Delay discounting refers to the behavioral tendency to devalue rewards as a function of their delay in receipt. Heightened delay discounting has been associated with substance use disorders and multiple co-occurring psychopathologies. Human and animal genetic studies have established that delay discounting is heritable, but only a few associated ge...
Lee, Seung Hyuk Garske, Kristina Arasu, Uma Kar, Asha Miao, Zong Alvarez, Marcus Koka, Amogha Darci-Maher, Nicholas Benhammou, Jihane Pan, David
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BACKGROUND: Abdominal obesity increases the risk for non-alcoholic fatty liver disease (NAFLD), now known as metabolic dysfunction-associated steatotic liver disease (MASLD). METHODS: To elucidate the directional cell-type level biological mechanisms underlying the association between abdominal obesity and MASLD, we integrated adipose and liver sin...
Akdeniz, Bayram Frei, Oleksandr Shadrin, Alexey Vetrov, Dmitry Kropotov, Dmitry Hovig, Eivind Andreassen, Ole Dale, Anders
Genome-wide association studies (GWAS) implicate broad genomic loci containing clusters of highly correlated genetic variants. Finemapping techniques can select and prioritize variants within each GWAS locus which are more likely to have a functional influence on the trait. Here, we present a novel method, Finemap-MiXeR, for finemapping causal vari...
Verma, Anurag Huffman, Jennifer E Rodriguez, Alex Conery, Mitchell Liu, Molei Ho, Yuk-Lam Kim, Youngdae Heise, David A Guare, Lindsay Panickan, Vidul Ayakulangara
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One of the justifiable criticisms of human genetic studies is the underrepresentation of participants from diverse populations. Lack of inclusion must be addressed at-scale to identify causal disease factors and understand the genetic causes of health disparities. We present genome-wide associations for 2068 traits from 635,969 participants in the ...
