Updating the Breeding Philosophy of Wheat to Fusarium Head Blight (FHB): Resistance Components, QTL Identification, and Phenotyping—A Review by Akos Mesterhazy

“…Type II QTL (quantitative trait locus) <i>Fhb1</i> on 3BS from Sumai 3 descendant CM82036 secures about the same resistance level as Type I QTL does on <i>5AS</i> and <i>5ASc</i> in terms of visual symptoms, FDK (Fusarium damaged kernel), and deoxynivalenol response. …”
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QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations by Jeekin Lau, Haramrit Gill, Cristiane H. Taniguti, Ellen L. Young, Patricia E. Klein, David H. Byrne, Oscar Riera-Lizarazu

“…With the use of newly developed software tools for autopolyploid genetics, two interconnected tetraploid garden rose F1 populations (phenotyped over the course of 3 years) were used for quantitative trait locus (QTL) analysis of black spot and cercospora leaf spot resistance as well as plant defoliation. …”
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A single nucleotide polymorphism of the porcine CXCL8 gene is associated with serum CXCL8 level by Shiwei Wang, Dongfeng Li, Mo Zhu, Rui Xie, Shuangli Duan, Zongjun Yin, Yang Liu

“…Previous studies have reported that the CXCL8 gene resides within the quantitative trait locus (QTL). In this report, the porcine CXCL8 gene was selected to investigate its effect on serum immune traits. …”
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DEPTOR Cell-Autonomously Promotes Adipogenesis, and Its Expression Is Associated with Obesity by Laplante, Mathieu, Horvat, Simon, Festuccia, William T., Birsoy, Kivanc, Prevorsek, Zala, Efeyan, Alejo, Sabatini, David M., Sabatini, David

“…Previous work indicates that Deptor is part of the Fob3a quantitative trait locus (QTL) linked to obesity/leanness in mice, with Deptor expression being elevated in white adipose tissue (WAT) of obese animals. …”
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Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells by Chen, L, Ge, B, Casale, FP, Vasquez, L, Kwan, T, Garrido-Martín, D, Watt, S, Yan, Y, Kundu, K, Ecker, S, Datta, A, Richardson, D, Burden, F, Mead, D, Mann, AL, Fernandez, JM, Rowlston, S, Wilder, SP, Farrow, S, Shao, X, Lambourne, JJ, Redensek, A, Albers, CA, Amstislavskiy, V, Ashford, S, Berentsen, K, Bomba, L, Bourque, G, Bujold, D, Busche, S, Caron, M, Chen, S-H, Cheung, W, Delaneau, O, Dermitzakis, ET, Elding, H, Colgiu, I, Bagger, FO, Flicek, P, Habibi, E, Iotchkova, V, Janssen-Megens, E, Kim, B, Lehrach, H, Lowy, E, Mandoli, A, Matarese, F, Maurano, MT, Morris, JA, Pancaldi, V, Pourfarzad, F, Rehnstrom, K, Rendon, A, Risch, T, Sharifi, N, Simon, M-M, Sultan, M, Valencia, A, Walter, K, Wang, S-Y, Frontini, M, Antonarakis, SE, Clarke, L, Yaspo, M-L, Beck, S, Guigo, R, Rico, D, Martens, JHA, Ouwehand, WH, Kuijpers, TW, Paul, DS, Stunnenberg, HG, Stegle, O, Downes, K, Pastinen, T, Soranzo, N

“…Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. …”

The impact of genetic variation on IFITM3 related influenza virus restriction by Laurenson-Schafer, H

“…We show that rs12252 is an expression Quantitative Trait Locus (eQTL) for IFITM3, and its activity is potentially tissue dependent. …”

High dimensional endophenotype ranking in the search for major depression risk genes by Glahn, D, Curran, J, Winkler, A, Carless, M, Kent, J, Charlesworth, J, Johnson, M, Göring, H, Cole, SA, Dyer, T, Moses, E, Olvera, R, Kochunov, P, Duggirala, R, Fox, P, Almasy, L, Blangero, J

“…A genome-wide significant quantitative trait locus was localized on chromsome 4p15 (logarithm of odds = 3.5) exhibiting pleiotropic effects on both the endophenotype (lymphocyte-derived expression levels of the <em>RNF123</em> gene) and disease risk.…”

Genome-Wide Association Study of Cryptosporidiosis in Infants Implicates PRKCA by Wojcik, GL, Korpe, P, Marie, C, Mentzer, AJ, Carstensen, T, Mychaleckyj, J, Kirkpatrick, BD, Rich, SS, Concannon, P, Faruque, ASG, Haque, R, Petri, WA, Duggal, P

“…The strongest meta-analytic association was with rs58296998 (P = 3.73 × 10−8), an intronic SNP and expression quantitative trait locus (eQTL) of protein kinase C alpha (PRKCA). …”

Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection by Durrant, C, Tayem, H, Yalcin, B, Cleak, J, Goodstadt, L, Pardo-Manuel De Villena, F, Mott, R, Iraqi, F

“…The survival time after infection varied significantly between CC lines. Quantitative trait locus (QTL) mapping identified genome-wide significant QTLs on chromosomes 2, 3, 8, 10 (two QTLs), 15, and 18. …”

Genetic and environmental risk factors for atherosclerosis regulate transcription of phosphatase and actin regulating gene PHACTR1. by Reschen, M, Lin, D, Chalisey, A, Soilleux, E, O'Callaghan, C

“…In primary human macrophages, we identified a novel expression quantitative trait locus (eQTL) specific for this short transcript, whereby the risk allele at CAD risk SNP rs9349379 is associated with reduced PHACTR1 expression, similar to the effect of an inflammatory stimulus.…”

Variation in the glucose transporter gene SLC2A2 is associated with glycaemic response to metformin by Kaixin, Z, Yee, S, Seiser, E, van Leeuwen, N, Tavendale, R, Bennett, A, Groves, C, Coleman, R, van der Heijden, A, Beulens, J, de Keyser, C, Zaharenko, L, Rotroff, D, Out, M, Jablonski, K, Chen, L, Javorský, M, Židzik, J, Levin, A, William, L, Dujic, T, Semiz, S, Kubo, M, Chien, H, Maeda, S, Witte, J, Wu, L, Tkáč, I, Kooy, A, van Schaik, R, Stehouwer, C, Logie, L, MetGen Investigators, DPP Investigators, ACCORD Investigators, Sutherland, C, Klovins, J, Pirags, V, Hofman, A, Stricker, B, Motsinger-Reif, A, Wagner, M, Innocenti, F, 't Hart, L, Holman, R, McCarthy, M, Hedderson, M, Palmer, C, Florez, J, Giacomini, K, Pearson, E

“…The C allele of rs8192675 in the intron of SLC2A2, which encodes the facilitated glucose transporter GLUT2, was associated with a 0.17% (P = 6.6 × 10−14) greater metformin-induced reduction in hemoglobin A1c (HbA1c) in 10,577 participants of European ancestry. rs8192675 was the top cis expression quantitative trait locus (cis-eQTL) for SLC2A2 in 1,226 human liver samples, suggesting a key role for hepatic GLUT2 in regulation of metformin action. …”

HLA-C level is regulated by a polymorphic Oct1 binding site in the HLA-C promoter region by Vince, N, Li, H, Ramsuran, V, Naranbhai, V, Duh, F, Fairfax, B, Saleh, B, Knight, J, Anderson, S, Carrington, M

“…This imputed expression quantitative trait locus, termed impeQTL, was also shown to associate with HLA-C expression in a genome-wide association study of 273 donors in which HLA-C mRNA expression levels were determined by quantitative PCR (qPCR) (p = 1.8 × 10(-20)) and in two cohorts where HLA-C cell surface levels were determined directly by flow cytometry (n = 369 combined, p &lt; 10(-15)). rs2395471 is located in an Oct1 transcription factor consensus binding site motif where the A allele is predicted to have higher affinity for Oct1 than the G allele. …”

Genetic and environmental risk factors for atherosclerosis regulate transcription of phosphatase and actin regulating gene PHACTR1 by Reschen, M, Lin, D, Chalisey, A, Soilleux, E, O'Callaghan, C

“…In primary human macrophages, we identified a novel expression quantitative trait locus (eQTL) specific for this short transcript, whereby the risk allele at CAD risk SNP rs9349379 is associated with reduced PHACTR1 expression, similar to the effect of an inflammatory stimulus. …”

The presence of methylation quantitative trait loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue by Drong, A, Nicholson, G, Hedman, A, Meduri, E, Grundberg, E, Small, K, Shin, S, Bell, J, Karpe, F, Soranzo, N, Spector, T, McCarthy, M, Deloukas, P, Rantalainen, M, Lindgren, C

“…We find that none of the 149 meQTL top SNPs is a significant expression quantitative trait locus in our expression data, but we observed association between expression levels of two mRNA transcripts and cis-methylation status. …”

Genetics and genomics of animal behaviour and welfare-Challenges and possibilities by Jensen, P, Buitenhuis, B, Kjaer, J, Zanella, A, Mormede, P, Pizzari, T

“…As a next step, it is necessary to map the loci involved in affecting these traits, and quantitative trait locus (QTL) analysis have been used for this. …”

Genome-wide and species-wide dissection of the genetics of arthritis severity in heterogeneous stock mice. by Johnsen, A, Valdar, W, Golden, L, Ortiz-Lopez, A, Hitzemann, R, Flint, J, Mathis, D, Benoist, C

“…In several instances, these regions proved to contain 2 quantitative trait loci: the region on chromosome 2 included the C5 fraction of complement known to be required for K/BxN serum-transfer arthritis but also contained a second adjacent quantitative trait locus, for which an intriguing candidate is Ptgs1 (Cox1). …”

Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice by Thomas A Sasani, Aaron R Quinlan, Kelley Harris

“…Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C&gt;A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). …”
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Transcriptome Analysis Reveals Inhibitory Effects of Lentogenic Newcastle Disease Virus on Cell Survival and Immune Function in Spleen of Commercial Layer Chicks by Jibin Zhang, Michael G. Kaiser, Rodrigo A. Gallardo, Terra R. Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont

“…Sprouty RTK signaling antagonist 1 (<i>SPRY1</i>), a DEG in the current study, is in a significant quantitative trait locus associated with virus load at 6 dpi in the same population. …”
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An Overview of the Bionomics, Host Plant Resistance and Molecular Perspectives of <i>Sesamia inferens</i> Walker in Cereals and Millets by Niranjanadevi Jeevanandham, Nalini Ramiah, Vanniarajan Chockalingam, Ramalingam Jegadeesan

“…Thus, molecular markers and Quantitative Trait Locus (QTL) mapping offer a more efficient approach to entomologists and plant breeders wherein they can work with traits like QTLs for stem borer resistance. …”
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Genetic basis of the early heading of high-latitude weedy rice by Zhuan Li, Rui Gui, Xiaoyu Yu, Chengwei Liang, Juan Cui, Xue Zhao, Xuemin Zhang, Pengcheng Yu, Wenfu Chen, Jian Sun

“…At the same time, we developed recombinant inbred lines (RILs) crossed by the early-heading weedy rice WR04-6 and its accompanied japonica cultivar ShenNong 265 (SN265) to carry out a QTL mapping analysis of the heading date and mapped four quantitative trait locus (QTLs) and three epistatic effect gene pairs. …”
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