The Power of Single-Cell RNA Sequencing in eQTL Discovery by Maleeha Maria, Negar Pouyanfar, Tiit Örd, Minna U. Kaikkonen

“…During the last decade, functional genomics approaches combining genotype information with bulk RNA-sequencing data have identified genes regulated by GWAS loci through expression quantitative trait locus (eQTL) analysis. Single-cell RNA-Sequencing (scRNA-Seq) technologies have created new exciting opportunities for spatiotemporal assessment of changes in gene expression at the single-cell level in complex and inherited conditions. …”
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Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco by Guangdi Yuan, Kefan Sun, Wenlong Yu, Zipeng Jiang, Caihong Jiang, Dan Liu, Liuying Wen, Huan Si, Fengyan Wu, He Meng, Lirui Cheng, Aiguo Yang, Yuanying Wang

“…Multiparent Advanced Generation Inter-Cross (MAGIC) population is an ideal genetic and breeding material for quantitative trait locus (QTL) mapping and molecular breeding. …”
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Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease by Matteo D’Antonio, Jennifer P. Nguyen, Timothy D. Arthur, iPSCORE Consortium, Hiroko Matsui, Agnieszka D’Antonio-Chronowska, Kelly A. Frazer

“…Here, we leverage spatiotemporal information on 966 RNA-seq cardiac samples and perform an expression quantitative trait locus (eQTL) analysis detecting eQTLs considering both eGenes and eIsoforms. …”
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PRTN3 variant correlates with increased autoantigen levels and relapse risk in PR3-ANCA versus MPO-ANCA disease by Dhruti P. Chen, Claudia P. Aiello, DeMoris McCoy, Taylor Stamey, Jiajin Yang, Susan L. Hogan, Yichun Hu, Vimal K. Derebail, Eveline Y. Wu, J. Charles Jennette, Ronald J. Falk, Dominic J. Ciavatta

“…The variant (G allele) was shown to be an expression quantitative trait locus in healthy controls, but the clinical impact remains unknown. …”
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A Novel QTL and a Candidate Gene Are Associated with the Progressive Motility of Franches-Montagnes Stallion Spermatozoa after Thaw by Annik Imogen Gmel, Dominik Burger, Markus Neuditschko

“…We identified one significant (<i>p</i> < 1.69 × 10⁻⁷) quantitative trait locus (QTL) on ECA6 within the <i>SCN8A</i> gene for progressive motility after thaw, which was previously associated with progressive motility in boars. …”
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Genetic dissection of MHC-associated susceptibility to <it>Lepeophtheirus salmonis </it>in Atlantic salmon by MacDonald Elizabeth S, Stone Louise C, Glover Kevin A, Gharbi Karim, Matthews Louise, Grimholt Unni, Stear Michael J

“…In this study, we used quantitative trait locus (QTL) analysis to test the effect of genomic regions linked to MHC class I and II on linkage groups (LG) 15 and 6, respectively.…”
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Haplotype-based genome-wide association study identifies loci and candidate genes for milk yield in Holsteins. by Zhenliang Chen, Yunqiu Yao, Peipei Ma, Qishan Wang, Yuchun Pan

“…We further identified the nearest gene of each haplotype block and annotated the genes with milk-associated quantitative trait locus (QTL) intervals and ingenuity pathway analysis (IPA) networks. …”
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Accounting for isoform expression increases power to identify genetic regulation of gene expression. by Nathan LaPierre, Harold Pimentel

“…A core problem in genetics is molecular quantitative trait locus (QTL) mapping, in which genetic variants associated with changes in the molecular phenotypes are identified. …”
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Gene expression genetics of the striatum of Diversity Outbred mice by Vivek M. Philip, Hao He, Michael C. Saul, Price E. Dickson, Jason A. Bubier, Elissa J. Chesler

“…Abstract Brain transcriptional variation is a heritable trait that mediates complex behaviors, including addiction. Expression quantitative trait locus (eQTL) mapping reveals genomic regions harboring genetic variants that influence transcript abundance. …”
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The role of Sp140 revealed in IgE and mast cell responses in Collaborative Cross mice by Kazufumi Matsushita, Xin Li, Yuki Nakamura, Danyue Dong, Kaori Mukai, Mindy Tsai, Stephen B. Montgomery, Stephen J. Galli

“…Among strains tested, C57BL/6J and CC027 mice showed, respectively, moderate and uniquely potent MC activity. Quantitative trait locus analysis and RNA sequencing of BM-derived cultured MCs (BMCMCs) from CC027 mice suggested Sp140 as a candidate gene for MC activation. siRNA-mediated knock-down of Sp140 in BMCMCs decreased IgE-dependent histamine release and cytokine production. …”
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Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns. by Lukas Baumgarten, Bjorn Pieper, Baoxing Song, Sébastien Mane, Janne Lempe, Jonathan Lamb, Elizabeth L Cooke, Rachita Srivastava, Stefan Strütt, Danijela Žanko, Pedro Gp Casimiro, Asis Hallab, Maria Cartolano, Alexander D Tattersall, Bruno Huettel, Dmitry A Filatov, Pavlos Pavlidis, Barbara Neuffer, Christos Bazakos, Hanno Schaefer, Richard Mott, Xiangchao Gan, Carlos Alonso-Blanco, Stefan Laurent, Miltos Tsiantis

“…We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. …”
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Genetic variation on chromosome 6 influences F cell levels in healthy individuals of African descent and HbF levels in sickle cell patients. by Creary, L, Ulug, P, Menzel, S, McKenzie, C, Hanchard, N, Taylor, V, Farrall, M, Forrester, T, Thein, S

“…We investigated if a quantitative trait locus on chromosome 6q23 was significantly associated with HbF and F cell levels in individuals of African descent. …”

Susceptibility to klebsiella pneumonaie infection in collaborative cross mice is a complex trait controlled by at least three loci acting at different time points. by Vered, K, Durrant, C, Mott, R, Iraqi, F

“…We performed the first quantitative trait locus (QTL) mapping study of host susceptibility to Kp infection in immunocompetent Collaborative Cross mice (CC). …”

Colocalization analysis of polycystic ovary syndrome to identify potential disease-mediating genes and proteins by Censin, JC, Bovijn, J, Holmes, MV, Lindgren, CM

“…We evaluated the posterior probabilities of evidence consistent with shared causal variants between 14 PCOS genetic risk loci and intermediate cellular phenotypes in one protein (N = 3301) and two expression quantitative trait locus datasets (N = 31,684 and N = 80–491). …”

Inflammatory bowel disease: progress toward a gene. by van Heel, D, Satsangi, J, Carey, A, Jewell, D

“…Animal studies have provided insights from targeted mutations and quantitative trait locus analysis. The goals of continuing research include narrowing the regions of linkages and analysis of candidate genes, and possibly the application of newly developed methods using single nucleotide polymorphisms. …”

Measured haplotype analysis of the angiotensin-I converting enzyme gene. by Keavney, B, McKenzie, C, Connell, J, Julier, C, Ratcliffe, P, Sobel, E, Lathrop, M, Farrall, M

“…Linkage and segregation analysis have shown that circulating angiotensin-I converting enzyme (ACE) levels are influenced by a major quantitative trait locus that maps within or close to the ACE gene. …”

IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma by Taylor, CA, Watson, RA, Tong, O, Ye, W, Nassiri, I, Gilchrist, JJ, de Los Aires, AV, Sharma, PK, Koturan, S, Cooper, RA, Woodcock, VK, Jungkurth, E, Shine, B, Coupe, N, Payne, MJ, Church, DN, Naranbhai, V, Groha, S, Emery, P, Mankia, K, Freedman, ML, Choueiri, TK, Middleton, MR, Gusev, A, Fairfax, BP

“…We found that rs16906115 forms a B cell-specific expression quantitative trait locus (eQTL) to&nbsp;<em>IL7</em>&nbsp;in patients. …”

A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution by Warren, WC, Boggs, TE, Borowsky, R, Carlson, BM, Ferrufino, E, Gross, JB, Hillier, L, Hu, Z, Keene, AC, Kenzior, A, Kowalko, JE, Tomlinson, C, Kremitzki, M, Lemieux, ME, Graves-Lindsay, T, McGaugh, SE, Miller, JT, Mommersteeg, MTM, Moran, RL, Peuß, R, Rice, ES, Riddle, MR, Sifuentes-Romero, I, Stanhope, BA, Tabin, CJ, Thakur, S, Yamamoto, Y, Rohner, N

“…Using this resource, we performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss such as dusp26. …”

The presence of methylation quantitative trait loci indicate a direct genetic influence on the level of methylation in adipose tissue by Drong, A, Nicholson, G, Schuster, M, Karpe, F, McCarthy, M, Holmes, C, Rantalainen, M, Lindgren, C, Consortia, M

“…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. …”

Angiotensin-1-converting enzyme (ACE) plasma concentration is influenced by multiple ACE-linked quantitative trait nucleotides. by Cox, R, Bouzekri, N, Martin, S, Southam, L, Hugill, A, Golamaully, M, Cooper, R, Adeyemo, A, Soubrier, F, Ward, R, Lathrop, G, Matsuda, F, Farrall, M

“…The strong effect of the locus, and the interest in ACE as a candidate gene for cardiovascular disorders, has led to extensive investigation of its relationship to the ACE phenotype, providing one of the most complete examples of quantitative trait locus (QTL) analysis in humans. Resequencing of ACE followed by haplotype analysis in families of British and French origin has shown that the genetic variants that are primarily associated with the ACE trait map to an 18 kb interval flanked by two intragenic, ancestral recombination breakpoints. …”