A scalable Bayesian functional GWAS method accounting for multivariate quantitative functional annotations with applications for studying Alzheimer disease by Junyu Chen, Lei Wang, Philip L. De Jager, David A. Bennett, Aron S. Buchman, Jingjing Yang

“…Applying BFGWAS_QUANT to study five Alzheimer disease (AD)-related phenotypes using individual-level GWAS data (n = ∼1,000), we found that histone modification annotations have higher enrichment than expression quantitative trait locus (eQTL) annotations for all considered phenotypes, with the highest enrichment in H3K27me3 (polycomb regression). …”
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Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping by Matuszkiewicz Mateusz, Grądzielewska Agnieszka, Święcicka Magdalena, Ozturk Alperen, Mokrzycka Monika, Igbari Aramide Dolapo, Song Jie, Kilian Andrzej, Rakoczy-Trojanowska Monika

“…Despite intensive research using various analytical and methodological approaches, such as quantitative trait locus (QTL) mapping, candidate gene expression analysis, and transcriptome sequencing, the genetic basis of the rye immune response to LR remains unclear. …”
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Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Capsicum annuum L.) by Hector Lopez-Moreno, Ana Celia Basurto-Garduño, Maria Alejandra Torres-Meraz, Eric Diaz-Valenzuela, Sergio Arellano-Arciniega, Juan Zalapa, Juan Zalapa, Ruairidh J. H. Sawers, Angelica Cibrián-Jaramillo, Luis Diaz-Garcia

“…A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. …”
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Dissection of the multigenic wheat stem rust resistance present in the Montenegrin spring wheat accession PI 362698 by Jason D. Zurn, Matthew N. Rouse, Shiaoman Chao, Meriem Aoun, Godwin Macharia, Colin W. Hiebert, Zacharias A. Pretorius, J. Michael Bonman, Maricelis Acevedo

“…A genetic map was constructed using the Illumina iSelect 90 K wheat assay and the markers csLv34, NB-LRR3, and wMAS000003 and quantitative trait locus (QTL) analysis was performed. Results QTL analysis identified five significant QTLs (α = 0.05) on chromosomes 2B, 3B, 6A, 6D, and 7A associated with wheat stem rust resistance. …”
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Analysis of Genetic Diversity in Adzuki Beans (<i>Vigna angularis</i>): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement by Xiaohan Wang, Yu-Mi Choi, Young-ah Jeon, JungYoon Yi, Myoung-Jae Shin, Kebede Taye Desta, Hyemyeong Yoon

“…A large number of genes related to biotic/abiotic stress resistance and defense were found in most quantitative trait locus (QTL) for yield-related traits using genome-wide association studies (GWAS). …”
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Transcriptional mechanisms influencing glycaemic traits and risk of type 2 diabetes by Payne, A

“…</p> <p>Using these models along with expression quantitative trait locus models, I identified 33 candidate expression mediators of genetic associations with T2D and glycaemic traits. …”

Evidence that the 5p12 variant rs10941679 confers susceptibility to estrogen receptor-positive breast cancer through FGF10 and MRPS30 regulation. by Ghoussaini, M, French, J, Michailidou, K, Nord, S, Beesley, J, Canisus, S, Hillman, K, Kaufmann, S, Sivakumaran, H, Moradi Marjaneh, M, Lee, J, Dennis, J, Bolla, M, Wang, Q, Dicks, E, Milne, R, Hopper, J, Southey, M, Schmidt, M, Broeks, A, Muir, K, Lophatananon, A, Fasching, P, Beckmann, M, Fletcher, O, Johnson, N, Sawyer, E, Tomlinson, I, Burwinkel, B, Marme, F, Guénel, P, Truong, T, Bojesen, S, Flyger, H, Benitez, J, González-Neira, A, Alonso, M, Pita, G, Neuhausen, S, Anton-Culver, H, Brenner, H, Arndt, V, Meindl, A, Schmutzler, R, Brauch, H, Hamann, U, Tessier, D, Vincent, D, Nevanlinna, H, Khan, S, Matsuo, K, Ito, H, Dörk, T, Bogdanova, N, Lindblom, A, Margolin, S, Mannermaa, A, Kosma, V, Wu, A, Van Den Berg, D, Lambrechts, D, Floris, G, Chang-Claude, J, Rudolph, A, Radice, P, Barile, M, Couch, F, Hallberg, E, Giles, G, Haiman, C, Le Marchand, L, Goldberg, M, Teo, S, Yip, C, Borresen-Dale, A, Zheng, W, Cai, Q, Winqvist, R, Pylkäs, K, Andrulis, I, Devilee, P, Tollenaar, R, García-Closas, M, Figueroa, J, Hall, P, Czene, K, Brand, J, Darabi, H, Eriksson, M, Hooning, M, Koppert, L, Li, J, Shu, X, Zheng, Y, Cox, A, Cross, S, Shah, M, Rhenius, V, Choi, J, Kang, D, Hartman, M, Chia, K, Kabisch, M, Torres, D, Luccarini, C, Conroy, D, Jakubowska, A, Lubinski, J, Sangrajrang, S, Brennan, P, Olswold, C, Slager, S, Shen, C, Hou, M, Swerdlow, A, Schoemaker, M, Simard, J, Pharoah, P, Kristensen, V, Chenevix-Trench, G, Easton, D, Dunning, A, Edwards, S

“…After adjustment for rs10941679, we detected signal 2, consisting of 38 SNPs more strongly associated with ER-negative (ER−) breast cancer (lead SNP rs6864776: per-a allele OR ER− = 1.10; 95% CI 1.05–1.14; p conditional = 1.44 × 10−12), and a single signal 3 SNP (rs200229088: per-t allele OR ER+ = 1.12; 95% CI 1.09–1.15; p conditional = 1.12 × 10−05). Expression quantitative trait locus analysis in normal breast tissues and breast tumors showed that the g (risk) allele of rs10941679 was associated with increased expression of FGF10 and MRPS30. …”

A Genome-Wide Association Study of Genetic Variants of Apolipoprotein A1 Levels and Their Association with Vitamin D in Korean Cohorts by Young Lee, Ji Won Yoon, Ye An Kim, Hyuk Jin Choi, Byung Woo Yoon, Je Hyun Seo

“…Additionally, an expression quantitative trait locus (eQTL) and differentially expressed genes (DEGs) analysis were performed. …”
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Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild by Sonia Pascoal, Judith E. Risse, Xiao Zhang, Mark Blaxter, Timothee Cezard, Richard J. Challis, Karim Gharbi, John Hunt, Sujai Kumar, Emma Langan, Xuan Liu, Jack G. Rayner, Michael G. Ritchie, Basten L. Snoek, Urmi Trivedi, Nathan W. Bailey

“…We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a flatwing quantitative trait locus covering a large region of the X chromosome. …”
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Identification of novel candidate loci and genes for seed vigor-related traits in upland cotton (Gossypium hirsutum L.) via GWAS by Libei Li, Yu Hu, Yongbo Wang, Shuqi Zhao, Yijin You, Ruijie Liu, Jiayi Wang, Mengyuan Yan, Fengli Zhao, Juan Huang, Shuxun Yu, Zhen Feng

“…A total of 26 significant SNPs were detected and divided into six quantitative trait locus regions, including 121 predicted candidate genes. …”
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QTL Detection for Rice Grain Length and Fine Mapping of a Novel Locus qGL6.1 by Mingzhu Zhao, Yuanzheng Wang, Na He, Xiu Pang, Lili Wang, Zuobin Ma, Zhiqiang Tang, Hong Gao, Liying Zhang, Liang Fu, Changhua Wang, Jingang Liu, Wenjing Zheng

“…Although abundant quantitative trait locus (QTL) associated with GL have been identified, it was still relatively weak to identify QTL for GL from japonica genetic background, as the shortage of japonica germplasms with long grains. …”
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Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS by Fuchen Zhou, Jianping Quan, Donglin Ruan, Yibin Qiu, Rongrong Ding, Cineng Xu, Yong Ye, Gengyuan Cai, Langqing Liu, Zebin Zhang, Jie Yang, Zhenfang Wu, Enqin Zheng

“…Through haplotype block analysis, we discovered a novel quantitative trait locus (QTL) associated with TLNW, spanning a 5 kb region on SSC12, and a novel RIBW-associated QTL spanning 1.42 Mb on SSC13. …”
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QTL Mapping for Cucumber Fruit Size and Shape with Populations from Long and Round Fruited Inbred Lines by Zhihui Gao, Haiyang Zhang, Chenxing Cao, Jing Han, Hao Li, Zhonghai Ren

“…ABSTRACT: To gain insight into the molecular and genetic basis of fruit size and shape in cucumber, we conducted Quantitative Trait Locus (QTL) mapping with F2 and BC1F1 populations derived from a cross between the Northern-China type inbred line CNS21 and the Southern-China type inbred line RNS7. …”
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Mutations in the <i>FOXO3</i> Gene and Their Effects on Meat Traits in Gannan Yaks by Youpeng Qi, Xiangyan Wang, Chune Zhu, Baohong Mi, Changze Cui, Shaopeng Chen, Zhidong Zhao, Fangfang Zhao, Xiu Liu, Jiqing Wang, Bingang Shi, Jiang Hu

“…The <i>FOXO3</i> gene, a prominent member of the FOXO family, has been identified as a potential quantitative trait locus for muscle atrophy and lipid metabolism in livestock. …”
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Effect of a QTL on wheat chromosome 5B associated with enhanced root dry mass on transpiration and nitrogen uptake under contrasting drought scenarios in wheat by Stjepan Vukasovic, Andreas H. Eckert, Anna L. Moritz, Christian Borsch, Silvia Rudloff, Rod J. Snowdon, Andreas Stahl

“…It included the Chinese variety Ning0604, carrying a quantitative trait locus (QTL) on chromosome 5B associated with a higher root dry biomass, and three elite German varieties, Elixer, Genius, and Leandrus. …”
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Genetic and molecular analysis of stem rot (Sclerotinia sclerotiorum) resistance in Brassica napus (canola type) by Muhammad Azam Khan, Wallace A. Cowling, Surinder Singh Banga, Martin J. Barbetti, Aldrin Y. Cantila, Junrey C. Amas, William J.W. Thomas, Ming Pei You, Vikrant Tyagi, Baudh Bharti, David Edwards, Jacqueline Batley

“…In a genome wide association study (GWAS), a significant quantitative trait locus (QTL) was identified for SLL. Several putative candidate marker trait associations (MTA) were located within this QTL region. …”
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A Nuclear Factor Y-B Transcription Factor, <i>GmNFYB17</i>, Regulates Resistance to Drought Stress in Soybean by Maolin Sun, Yue Li, Jiqiang Zheng, Depeng Wu, Chunxia Li, Zeyang Li, Ziwei Zang, Yanzheng Zhang, Qingwei Fang, Wenbin Li, Yingpeng Han, Xue Zhao, Yongguang Li

“…Via a genome-wide association study (GWAS) combined with linkage analysis, we identified 11 single-nucleotide polymorphisms (SNPs) and 22 quantitative trait locus (QTLs) that are significantly associated with soybean drought tolerance. …”
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Ultra-low-coverage genome-wide association study—insights into gestational age using 17,844 embryo samples with preimplantation genetic testing by Shumin Li, Bin Yan, Thomas K. T. Li, Jianliang Lu, Yifan Gu, Yueqiu Tan, Fei Gong, Tak-Wah Lam, Pingyuan Xie, Yuexuan Wang, Ge Lin, Ruibang Luo

“…From 1744 born embryos, we identified 11 genomic risk loci associated with gestational ages and 166 genes mapped to these loci according to positional, expression quantitative trait locus, and chromatin interaction strategies. …”
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Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome r... by Xin Zhang, Xin Zhang, Xiaoji Zhang, Luhuan Wang, Qimei Liu, Yuying Liang, Jiayu Zhang, Yunyun Xue, Yuexia Tian, Huiqi Zhang, Na Li, Cong Sheng, Pingping Nie, Suping Feng, Boshou Liao, Dongmei Bai

“…Then, we constructed a high density SNP-based genetic linkage map through whole genome re-sequencing (WGRS) technique and identified a major quantitative trait locus (QTL), qRGRB09, on chromosome B09. …”
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Mitochondrial Inner Membrane ABC Transporter Bcmdl1 Is Involved in Conidial Germination, Virulence, and Resistance to Anilinopyrimidine Fungicides in Botrytis cinerea by Fei Fan, Yong-Xu Zhu, Min-Yi Wu, Wei-Xiao Yin, Guo-Qing Li, Matthias Hahn, Mohamed S. Hamada, Chao-Xi Luo

“…In this study, we identified several AP resistance-related mutations by quantitative trait locus sequencing (QTL-seq) and confirmed that mutation E407K in Bcmdl1 conferred AP resistance. …”
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