Mapping rheumatoid arthritis susceptibility through integrative bioinformatics and genomics by Nining Medi Sushanti, Wirawan Adikusuma, Arief Rahman Afief, Anita Silas La’ah, Firdayani, Rockie Chong, Zainul Amiruddin Zakaria, Barkah Djaka Purwanto, Rahmat Dani Satria, Riat El Khair, Abdi Wira Septama, Lalu Muhammad Irham

“…These functional annotations include missense/nonsense mutations, cis-expression quantitative trait locus (cis-eQTL), overlap knockout mouse phenotype (KMP), protein-protein interaction (PPI), molecular pathway analysis (MPA), and primary immunodeficiency (PID). 119 genetic variants mapped had a potential high risk for RA based on functional scoring. …”
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Genetically Modified Rice Is Associated with Hunger, Health, and Climate Resilience by Kaori Kobayashi, Xiaohui Wang, Weiqun Wang

“…Specifically, a quantitative trait locus called grain weight on chromosome 6 has been identified, which was amplified by the Kasa allele, resulting in a substantial increase in grain weight and brown grain. …”
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Using social interaction models for genetic analysis of skin damage in gilts by Natália Galoro Leite, Egbert Knol, Shogo Tsuruta, Stefanie Nuphaus, Roos Vogelzang, Daniela Lourenco

“…The results of the genome-wide association study indicate that CSD has a polygenic architecture and no major quantitative trait locus was detected.…”
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Transcriptome profiling reveals the expression and regulation of genes associated with Fusarium wilt resistance in chickpea (Cicer arietinum L.) by Vanika Garg, Annapurna Chitikineni, Mamta Sharma, Raju Ghosh, Srinivasan Samineni, Rajeev K. Varshney, Himabindu Kudapa

“…Further, a considerable number of the identified DEGs (287) co‐localized with previously reported quantitative trait locus for FW resistance. Several resistance/susceptibility‐related genes, such as SERINE/THREONINE PROTEIN KINASE, DIRIGENT, and MLO exhibiting contrasting expression patterns in resistant and susceptible genotypes upon Foc inoculation, were identified. …”
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QTL mapping for seed density per silique in Brassica napus by Jifeng Zhu, Lei Lei, Weirong Wang, Jianxia Jiang, Xirong Zhou

“…In this study, a quantitative trait locus (QTL) for SDPS was detected on chromosome A09 using the QTL-seq approach and confirmed via linkage analysis in the mapping population obtained from 4263 × 3001 cross. …”
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Integration of genomic variants and bioinformatic-based approach to drive drug repurposing for multiple sclerosis by Arief Rahman Afief, Lalu Muhammad Irham, Wirawan Adikusuma, Dyah Aryani Perwitasari, Ageng Brahmadhi, Rocky Cheung

“…The prioritization was performed based on six defined categories of functional annotations, namely missense mutation, cis-expression quantitative trait locus (cis-eQTL), molecular pathway analysis, protein-protein interaction (PPI), genes overlap with knockout mouse phenotype, and primary immunodeficiency (PID). …”
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Natural sequence variants of yeast environmental sensors confer cell‐to‐cell expression variability by Steffen Fehrmann, Hélène Bottin‐Duplus, Andri Leonidou, Esther Mollereau, Audrey Barthelaix, Wu Wei, Lars M Steinmetz, Gaël Yvert

“…These results demonstrate that an expression quantitative trait locus (eQTL) can simultaneously have a deterministic effect in cis and a probabilistic effect in trans. …”
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A Quantitative Proteomics View on the Function of Qfhb1, a Major QTL for Fusarium Head Blight Resistance in Wheat by Moustafa Eldakak, Aayudh Das, Yongbin Zhuang, Jai S. Rohila, Karl Glover, Yang Yen

“…Fusarium head blight (FHB) is a highly detrimental disease of wheat. A quantitative trait locus for FHB resistance, Qfhb1, is the most utilized source of resistance in wheat-breeding programs, but very little is known about its resistance mechanism. …”
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A major QTL identification and candidate gene analysis of watermelon fruit cracking using QTL-seq and RNA-seq by Yuanfeng Zhan, Yuanfeng Zhan, Wei Hu, Huang He, Xuanmin Dang, Songbi Chen, Zhilong Bie

“…The cracking tolerance capacity (CTC), depth of fruit cracking (DFC), rind thickness (RT), and rind hardness (RH) were measured for quantitative trait locus (QTL) analysis. Of the four traits analyzed, one major QTL with high phenotypic variation (41.04%–61.37%) was detected at 76.613–76.919 cM on chromosome 2, which contained 104 annotated genes. …”
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Development of a SNP resource and a genetic linkage map for Atlantic cod (<it>Gadus morhua</it>) by Higgins Brent, Hubert Sophie, Borza Tudor, Bowman Sharen

“…They have been used to build a genetic linkage map that can be applied to quantitative trait locus (QTL) discovery. Since these SNPs were generated from ESTs, they are linked to specific genes. …”
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meQTL mapping in the GENOA study reveals genetic determinants of DNA methylation in African Americans by Lulu Shang, Wei Zhao, Yi Zhe Wang, Zheng Li, Jerome J. Choi, Minjung Kho, Thomas H. Mosley, Sharon L. R. Kardia, Jennifer A. Smith, Xiang Zhou

“…Abstract Identifying genetic variants that are associated with variation in DNA methylation, an analysis commonly referred to as methylation quantitative trait locus (meQTL) mapping, is an important first step towards understanding the genetic architecture underlying epigenetic variation. …”
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Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration by Nelson Rex T, Avraham Shulamit, Shoemaker Randy C, May Gregory D, Ware Doreen, Gessler Damian DG

“…</p> <p>Methods</p> <p>We selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. …”
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Gene expression changes in sickle cell reticulocytes and their clinical associations by Xu Zhang, Jihyun Song, Binal N. Shah, Jin Han, Taif Hassan, Galina Miasniakova, Adelina Sergueeva, Sergei Nekhai, Roberto F. Machado, Mark T. Gladwin, Santosh L. Saraf, Josef T. Prchal, Victor R. Gordeuk

“…An erythroid expression quantitative trait locus of one of these genes, LNX2 encoding an E3 ubiquitin ligase, associated with severe pain episodes in 774 SCA patients (OR = 1.7, P = 3.9 × 10–5). …”
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Domestication and improvement genes reveal the differences of seed size- and oil-related traits in soybean domestication and improvement by Jian-Fang Zuo, Muhammad Ikram, Jin-Yang Liu, Chun-Yu Han, Yuan Niu, Jim M. Dunwell, Yuan-Ming Zhang

“…To address domestication and improvement studies of soybean seed size- and oil-related traits, a series of domesticated and improved regions, loci, and candidate genes were identified in 286 soybean accessions using domestication and improvement analyses, genome-wide association studies, quantitative trait locus (QTL) mapping and bulked segregant analyses in this study. …”
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A systems genetics approach identifies CXCL14, ITGAX, and LPCAT2 as novel aggressive prostate cancer susceptibility genes. by Kendra A Williams, Minnkyong Lee, Ying Hu, Jonathan Andreas, Shashank J Patel, Suiyuan Zhang, Peter Chines, Abdel Elkahloun, Settara Chandrasekharappa, J Silvio Gutkind, Alfredo A Molinolo, Nigel P S Crawford

“…The goal of this work is to identify susceptibility genes using the C57BL/6-Tg(TRAMP)8247Ng/J (TRAMP) mouse model of neuroendocrine prostate cancer. Quantitative trait locus (QTL) mapping was performed in transgene-positive (TRAMPxNOD/ShiLtJ) F2 intercross males (n = 228), which facilitated identification of 11 loci associated with aggressive disease development. …”
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An animal model of differential genetic risk for methamphetamine intake by Tamara ePhillips, Tamara ePhillips, Shkelzen eShabani

“…Using selective breeding, we created lines of mice that differ in genetic risk for voluntary MA intake and identified the chromosomal addresses of contributory genes. A quantitative trait locus was identified on chromosome 10 that accounts for more than 50% of the genetic variance in MA intake in the selected mouse lines. …”
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GAHP: An integrated software package on genetic analysis with bi-parental immortalized heterozygous populations by Luyan Zhang, Xinhui Wang, Kaiyi Wang, Jiankang Wang, Jiankang Wang

“…Four functionalities have been implemented in the current version of GAHP, i.e., 1) MHP: visualization of genetic linkage maps; 2) VHP: analysis of variance (ANOVA) and estimation of heritability on phenotypic data; 3) QHP: quantitative trait locus (QTL) mapping on both genotypic and phenotypic data; 4) SHP: simulation of bi-parental immortalized heterozygous and pure-line populations, and power analysis of QTL mapping. …”
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Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (<it>HMGA2</it>) as a positional candidate gene by Li Pinghua, Xiao Shijun, Wei Na, Zhang Zhiyan, Huang Ruihua, Gu Yueqing, Guo Yuanmei, Ren Jun, Huang Lusheng, Chen Congying

“…Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian F₂resource population. …”
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Genetic analysis of a phenotypic loss in the mechanosensory entrainment of a circalunar clock by Dušica Briševac, Celine Prakash, Tobias S. Kaiser

“…By combining quantitative trait locus mapping and genome-wide screens, we explored the genetics of this phenotypic loss. …”
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Integrated analysis of genome-wide association studies and 3D epigenomic characteristics reveal the BMP2 gene regulating loin muscle depth in Yorkshire pigs. by Yuanxin Miao, Yunxia Zhao, Siqi Wan, Quanshun Mei, Heng Wang, Chuanke Fu, Xinyun Li, Shuhong Zhao, Xuewen Xu, Tao Xiang

“…<h4>Results</h4>Five single nucleotide polymorphisms (SNPs) located on porcine chromosome 17 were significantly associated with LMD in Yorkshire pigs. A 10 kb quantitative trait locus (QTL) was identified as a candidate functional genomic region through the integration of linkage disequilibrium and linkage analysis (LDLA) and high-throughput chromosome conformation capture (Hi-C) analysis. …”
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