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Quantitative trait loci

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https://www.readbyqxmd.com/read/29352323/identification-of-a-molecular-marker-tightly-linked-to-bacterial-wilt-resistance-in-tomato-by-genome-wide-snp-analysis
#1
Boyoung Kim, In Sun Hwang, Hyung Jin Lee, Je Min Lee, Eunyoung Seo, Doil Choi, Chang-Sik Oh
Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29351903/integrative-genomic-analysis-predicts-causative-cis-regulatory-mechanisms-of-the-breast-cancer-associated-genetic-variant-rs4415084
#2
Yi Zhang, Mohith Manjunath, Shilu Zhang, Deborah Chasman, Sushmita Roy, Jun S Song
Previous genome-wide association studies (GWAS) have identified several common genetic variants that may significantly modulate cancer susceptibility. However, the precise molecular mechanisms behind these associations remain largely unknown; it is often not clear whether discovered variants are themselves functional or merely genetically linked to other functional variants. Here we provide an integrated method for identifying functional regulatory variants associated with cancer and their target genes by combining analyses of expression quantitative trait loci (eQTL), a modified version of allele-specific expression (ASE) that systematically utilizes haplotype information, transcription factor (TF) binding preference, and epigenetic information...
January 19, 2018: Cancer Research
https://www.readbyqxmd.com/read/29351588/sorghum-root-system-classification-in-contrasting-p-environments-reveals-three-main-rooting-types-and-root-architecture-related-marker-trait-associations
#3
Sebastian Parra-Londono, Mareike Kavka, Birgit Samans, Rod Snowdon, Silke Wieckhorst, Ralf Uptmoor
Background and Aims: Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions...
January 17, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29347909/identification-of-minor-effect-qtls-for-plant-architecture-related-traits-using-super-high-density-genotyping-and-large-recombinant-inbred-population-in-maize-zea-mays
#4
Baobao Wang, Han Liu, Zhipeng Liu, Xiaomei Dong, Jinjie Guo, Wei Li, Jing Chen, Chi Gao, Yanbin Zhu, Xinmei Zheng, Zongliang Chen, Jian Chen, Weibin Song, Andrew Hauck, Jinsheng Lai
BACKGROUND: Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. RESULTS: Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs)...
January 18, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29342893/qtl-mapping-for-fiber-quality-and-yield-traits-based-on-introgression-lines-derived-from-gossypium-hirsutum-%C3%A3-g-tomentosum
#5
Ayaz Ali Keerio, Chao Shen, Yichun Nie, Muhammad Mahmood Ahmed, Xianlong Zhang, Zhongxu Lin
The tetraploid species Gossypium hirsutum is cultivated widely throughout the world with high yield and moderate fiber quality, but its genetic basis is narrow. A set of 107 introgression lines (ILs) was developed with an interspecific cross using G. hirsutumacc. 4105 as the recurrent parent and G. tomentosum as the donor parent. A specific locus amplified fragment sequencing (SLAF-seq) strategy was used to obtain high-throughput single nucleotide polymorphism (SNP) markers. In total, 3157 high-quality SNP markers were obtained and further used for identification of quantitative trait loci (QTLs) for fiber quality and yield traits evaluated in multiple environments...
January 14, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29339072/deep-sequencing-of-a-qtl-rich-region-spanning-128-136mbp-of-pig-chromosome-15
#6
K Piórkowska, K Żukowski, K Ropka-Molik, M Tyra
The present study shows the characterization of the chromosome 15 (SSC15) region that is highly rich in quantitative traits loci (QTLs) associated with pork quality, growth performance, fat and meat carcass contents. The analytic method that was utilized included targeted enrichment DNA sequencing and RNA hybridisation probes. The research included two pig breeds (Puławska and Polish Landrace) that are significantly different in terms of carcass and meat quality features. Filtered sequences were aligned to the Sscrofa10...
January 12, 2018: Gene
https://www.readbyqxmd.com/read/29335020/ensemble-genomic-analysis-in-human-lung-tissue-identifies-novel-genes-for-chronic-obstructive-pulmonary-disease
#7
Jarrett D Morrow, Michael H Cho, John Platig, Xiaobo Zhou, Dawn L DeMeo, Weiliang Qiu, Bartholome Celli, Nathaniel Marchetti, Gerard J Criner, Raphael Bueno, George R Washko, Kimberly Glass, John Quackenbush, Edwin K Silverman, Craig P Hersh
BACKGROUND: Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context...
January 15, 2018: Human Genomics
https://www.readbyqxmd.com/read/29333270/lessons-from-ten-years-of-genome-wide-association-studies-of-asthma
#8
REVIEW
Cristina T Vicente, Joana A Revez, Manuel A R Ferreira
Twenty-five genome-wide association studies (GWAS) of asthma were published between 2007 and 2016, the largest with a sample size of 157242 individuals. Across these studies, 39 genetic variants in low linkage disequilibrium (LD) with each other were reported to associate with disease risk at a significance threshold of P<5 × 10-8, including 31 in populations of European ancestry. Results from analyses of the UK Biobank data (n=380 503) indicate that at least 28 of the 31 associations reported in Europeans represent true-positive findings, collectively explaining 2...
December 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/29330432/developing-genome-wide-snps-and-constructing-an-ultrahigh-density-linkage-map-in-oil-palm
#9
Bin Bai, Le Wang, Ying Jun Zhang, May Lee, Rahmadsyah Rahmadsyah, Yuzer Alfiko, Bao Qing Ye, Sigit Purwantomo, Antonius Suwanto, Nam-Hai Chua, Gen Hua Yue
Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29325965/genome-wide-association-mapping-for-seed-protein-and-oil-contents-using-a-large-panel-of-soybean-accessions
#10
Dongmei Li, Xue Zhao, Yingpeng Han, Wenbin Li, Futi Xie
Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0...
January 8, 2018: Genomics
https://www.readbyqxmd.com/read/29325110/impact-of-genetic-risk-loci-for-multiple-sclerosis-on-expression-of-proximal-genes-in-patients
#11
Tojo James, Magdalena Lindén, Hiromasa Morikawa, Sunjay Jude Fernandes, Sabrina Ruhrmann, Mikael Huss, Maya Brandi, Fredrik Piehl, Maja Jagodic, Jesper Tegnér, Mohsen Khademi, Tomas Olsson, David Gomez-Cabrero, Ingrid Kockum
Despite advancements in genetic studies, it is difficult to understand and characterize the functional relevance of disease-associated genetic variants, especially in the context of a complex multifactorial disease such as Multiple Sclerosis (MS). Since a large proportion of expression quantitative trait loci (eQTLs) are context-specific, we performed RNA-Seq in peripheral blood mononuclear cells (PBMCs) from MS patients (n = 145) to identify eQTLs in regions centered on 109 MS risk SNPs and seven associated HLA variants...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29324803/genetic-dissection-of-the-relationships-between-grain-yield-components-by-genome-wide-association-mapping-in-a-collection-of-tetraploid-wheats
#12
Giacomo Mangini, Agata Gadaleta, Pasqualina Colasuonno, Ilaria Marcotuli, Antonio M Signorile, Rosanna Simeone, Pasquale De Vita, Anna M Mastrangelo, Giovanni Laidò, Nicola Pecchioni, Antonio Blanco
Increasing grain yield potential in wheat has been a major target of most breeding programs. Genetic advance has been frequently hindered by negative correlations among yield components that have been often observed in segregant populations and germplasm collections. A tetraploid wheat collection was evaluated in seven environments and genotyped with a 90K SNP assay to identify major and stable quantitative trait loci (QTL) for grain yield per spike (GYS), kernel number per spike (KNS) and thousand-kernel weight (TKW), and to analyse the genetic relationships between the yield components at QTL level...
2018: PloS One
https://www.readbyqxmd.com/read/29322324/molecular-mapping-of-qbk1-wd-a-major-qtl-for-bakanae-disease-resistance-in-rice
#13
Sais-Beul Lee, Yeon-Jae Hur, Jun-Hyeon Cho, Jong-Hee Lee, Tae-Heon Kim, Soo-Min Cho, You-Chun Song, Young-Su Seo, Jungkwan Lee, Tae-Sung Kim, Yong-Jin Park, Myung-Kyu Oh, Dong-Soo Park
BACKGROUND: Bakanae or foot rot disease is a prominent disease of rice caused by Gibberella fujikuroi. This disease may infect rice plants from the pre-emergence stage to the mature stage. In recent years, raising rice seedlings in seed boxes for mechanical transplanting has increased the incidence of many seedling diseases; only a few rice varieties have been reported to exhibit resistance to bakanae disease. In this study, we attempted to identify quantitative trait loci (QTLs) conferring bakanae disease resistance from the highly resistant japonica variety Wonseadaesoo...
January 10, 2018: Rice
https://www.readbyqxmd.com/read/29321599/splicing-qtl-of-human-adipose-related-traits
#14
Liang Ma, Peilin Jia, Zhongming Zhao
Recently, genome-wide association studies (GWAS) have identified 11 loci associated with adipose-related traits across different populations. However, their functional roles still remain largely unknown. In this study, we aimed to explore the splicing regulation of these GWAS signals in a tissue-specific fashion. For adipose-related GWAS signals, we selected six adipose-related tissues (adipose subcutaneous, artery tibial, blood, heart left ventricle, muscle-skeletal, and thyroid) with the sample size greater than 80 for splicing quantitative trait loci (QTL) analysis using GTEx released datasets...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321353/identification-and-association-of-novel-lncrna-poumu1-gene-mutations-with-chicken-performance-traits
#15
Tuanhui Ren, Yanting Zhou, Yu Zhou, Weihua Tian, Zhenzhen Gu, Song Zhao, Yadi Chen, Ruili Han, Xiaojun Liu, Xiangtao Kang, Zhuanjian Li
The biological functions of long noncoding RNAs (lncRNAs), which play an important role in regulating development and gene expression, may be affected by variations in lncRNA gene loci or associated genomic sequences. However, the functions of many lncRNAs remain unknown. To analyse correlations between mutations in pouMU1 with chicken growth and carcass traits, 860 chickens from a Gushi×Anka F2 resource population and 96 Lushi, Xichuan, Changshun and recessive white chickens were used to evaluate the genetic effect of the pouMU1 gene...
December 2017: Journal of Genetics
https://www.readbyqxmd.com/read/29317604/beta-defensin-1-aryl-hydrocarbon-receptor-and-plasma-kynurenine-in-major-depressive-disorder-metabolomics-informed-genomics
#16
Duan Liu, Balmiki Ray, Drew R Neavin, Jiabin Zhang, Arjun P Athreya, Joanna M Biernacka, William V Bobo, Daniel K Hall-Flavin, Michelle K Skime, Hongjie Zhu, Gregory D Jenkins, Anthony Batzler, Krishna R Kalari, Felix Boakye-Agyeman, Wayne R Matson, Swati S Bhasin, Taisei Mushiroda, Yusuke Nakamura, Michiaki Kubo, Ravishankar K Iyer, Liewei Wang, Mark A Frye, Rima Kaddurah-Daouk, Richard M Weinshilboum
Major depressive disorder (MDD) is a heterogeneous disease. Efforts to identify biomarkers for sub-classifying MDD and antidepressant therapy by genome-wide association studies (GWAS) alone have generally yielded disappointing results. We applied a metabolomics-informed genomic research strategy to study the contribution of genetic variation to MDD pathophysiology by assaying 31 metabolites, including compounds from the tryptophan, tyrosine, and purine pathways, in plasma samples from 290 MDD patients. Associations of metabolite concentrations with depressive symptoms were determined, followed by GWAS for selected metabolites and functional validation studies of the genes identified...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29313708/human-lung-dna-methylation-quantitative-trait-loci-colocalize-with-copd-genome-wide-association-loci
#17
Jarrett D Morrow, Kimberly Glass, Michael H Cho, Craig P Hersh, Victor Pinto-Plata, Bartolome Celli, Nathaniel Marchetti, Gerard Criner, Raphael Bueno, George Washko, Augustine M K Choi, John Quackenbush, Edwin K Silverman, Dawn L DeMeo
RATIONALE: As the third leading cause of death in the United States, the impact of chronic obstructive pulmonary disease (COPD) makes identification of its molecular mechanisms of great importance. Genome-wide association studies have identified multiple genomic regions associated with COPD. However, genetic variation only explains a small fraction of the susceptibility to COPD and sub-genome-wide significant loci may play a role in pathogenesis. OBJECTIVES: Regulatory annotation with epigenetic evidence may give priority for further investigation, particularly for GWAS associations in non-coding regions...
January 9, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29311651/identification-of-a-novel-gene-regulating-amygdala-mediated-fear-extinction
#18
Ozge Gunduz-Cinar, Emma Brockway, Lauren Lederle, Troy Wilcox, Lindsay R Halladay, Ying Ding, Hyunjung Oh, Erica F Busch, Katie Kaugars, Shaun Flynn, Aaron Limoges, Olena Bukalo, Kathryn P MacPherson, Sophie Masneuf, Courtney Pinard, Etienne Sibille, Elissa J Chesler, Andrew Holmes
Recent years have seen advances in our understanding of the neural circuits associated with trauma-related disorders, and the development of relevant assays for these behaviors in rodents. Although inherited factors are known to influence individual differences in risk for these disorders, it has been difficult to identify specific genes that moderate circuit functions to affect trauma-related behaviors. Here, we exploited robust inbred mouse strain differences in Pavlovian fear extinction to uncover quantitative trait loci (QTL) associated with this trait...
January 8, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29307117/genetic-mapping-of-quantitative-trait-loci-for-tuber-cadmium-and-zinc-concentration-in-potato-reveals-associations-with-maturity-and-both-overlapping-and-independent-components-of-genetic-control
#19
Molla F Mengist, Sheila Alves, Denis Griffin, Joanne Creedon, Mike J McLaughlin, Peter W Jones, Dan Milbourne
Cd is a toxic metal, whilst Zn is an essential for plant and human health. Both can accumulate in potato tubers. We examine the genetic control of this process. The aim of this study was to map quantitative trait loci (QTLs) influencing tuber concentrations of cadmium (Cd) and zinc (Zn). We developed a segregating population comprising 188 F1 progeny derived from crossing two tetraploid cultivars exhibiting divergent tuber-Cd-accumulation phenotypes. These progeny were genotyped using the SolCap 8303 SNP array, and evaluated for Cd, Zn, and maturity-related traits...
January 6, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29305700/genetic-architecture-of-aerial-and-root-traits-in-field-grown-grafted-grapevines-is-largely-independent
#20
Jean-Pascal Tandonnet, Elisa Marguerit, Sarah J Cookson, Nathalie Ollat
QTLs were identified for traits assessed on field-grown grafted grapevines. Root number and section had the largest phenotypic variance explained. Genetic control of root and aerial traits was independent. Breeding new rootstocks for perennial crops remains challenging, mainly because of the number of desirable traits which have to be combined, these traits include good rooting ability and root development. Consequently, the present study analyzes the genetic architecture of root traits in grapevine. A segregating progeny of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera cv...
January 5, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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