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https://www.readbyqxmd.com/read/29344848/current-status-and-future-possibilities-of-molecular-genetics-techniques-in-brassica-napus
#1
REVIEW
Muhammad Afzal, Salem Safer Alghamdi, Muhammad Habib Ur Rahman, Awais Ahmad, Tahir Farooq, Mukhtar Alam, Imtiaz Ali Khan, Hidayat Ullah, Wajid Nasim, Shah Fahad
As PCR methods have improved over the last 15 years, there has been an upsurge in the number of new DNA marker tools, which has allowed the generation of high-density molecular maps for all the key Brassica crop types. Biotechnology and molecular plant breeding have emerged as a significant tool for molecular understanding that led to a significant crop improvement in the Brassica napus species. Brassica napus possess a very complicated polyploidy-based genomics. The quantitative trait locus (QTL) is not sufficient to develop effective markers for trait introgression...
January 17, 2018: Biotechnology Letters
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
#2
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/29339742/slaf-based-high-density-genetic-map-construction-and-qtl-mapping-for-major-economic-traits-in-sea-urchin-strongylocentrotus-intermedius
#3
Yaqing Chang, Jun Ding, Yuhui Xu, Dan Li, Weijie Zhang, Lei Li, Jian Song
Sea urchin (Strongylocentrotus intermedius) has long been a model species for developmental and evolutionary research, but only a few studies have focused on gene mapping. Here, we reported a high-density genetic map containing 4,387 polymorphism specific-length amplified fragment (SLAF) markers spanning 21 linkage groups (LG) for sea urchin. Based on this genetic map and phenotyping data for eight economic traits, 33 potentially significant QTLs were detected on ten different LGs with explanations ranging from 9...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339072/deep-sequencing-of-a-qtl-rich-region-spanning-128-136mbp-of-pig-chromosome-15
#4
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/29331962/splicing-variant-of-wdfy4-augments-mda5-signalling-and-the-risk-of-clinically-amyopathic-dermatomyositis
#5
Yuta Kochi, Yoichiro Kamatani, Yuya Kondo, Akari Suzuki, Eiryo Kawakami, Ryosuke Hiwa, Yukihide Momozawa, Manabu Fujimoto, Masatoshi Jinnin, Yoshiya Tanaka, Takashi Kanda, Robert G Cooper, Hector Chinoy, Simon Rothwell, Janine A Lamb, Jiří Vencovský, Heřman Mann, Koichiro Ohmura, Keiko Myouzen, Kazuyoshi Ishigaki, Ran Nakashima, Yuji Hosono, Hiroto Tsuboi, Hidenaga Kawasumi, Yukiko Iwasaki, Hiroshi Kajiyama, Tetsuya Horita, Mariko Ogawa-Momohara, Akito Takamura, Shinichiro Tsunoda, Jun Shimizu, Keishi Fujio, Hirofumi Amano, Akio Mimori, Atsushi Kawakami, Hisanori Umehara, Tsutomu Takeuchi, Hajime Sano, Yoshinao Muro, Tatsuya Atsumi, Toshihide Mimura, Yasushi Kawaguchi, Tsuneyo Mimori, Atsushi Takahashi, Michiaki Kubo, Hitoshi Kohsaka, Takayuki Sumida, Kazuhiko Yamamoto
OBJECTIVES: Idiopathic inflammatory myopathies (IIMs) are a heterogeneous group of rare autoimmune diseases in which both genetic and environmental factors play important roles. To identify genetic factors of IIM including polymyositis, dermatomyositis (DM) and clinically amyopathic DM (CADM), we performed the first genome-wide association study for IIM in an Asian population. METHODS: We genotyped and tested 496 819 single nucleotide polymorphism for association using 576 patients with IIM and 6270 control subjects...
January 13, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29330432/developing-genome-wide-snps-and-constructing-an-ultrahigh-density-linkage-map-in-oil-palm
#6
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/29328911/western-diet-triggers-nlrp3-dependent-innate-immune-reprogramming
#7
Anette Christ, Patrick Günther, Mario A R Lauterbach, Peter Duewell, Debjani Biswas, Karin Pelka, Claus J Scholz, Marije Oosting, Kristian Haendler, Kevin Baßler, Kathrin Klee, Jonas Schulte-Schrepping, Thomas Ulas, Simone J C F M Moorlag, Vinod Kumar, Min Hi Park, Leo A B Joosten, Laszlo A Groh, Niels P Riksen, Terje Espevik, Andreas Schlitzer, Yang Li, Michael L Fitzgerald, Mihai G Netea, Joachim L Schultze, Eicke Latz
Long-term epigenetic reprogramming of innate immune cells in response to microbes, also termed "trained immunity," causes prolonged altered cellular functionality to protect from secondary infections. Here, we investigated whether sterile triggers of inflammation induce trained immunity and thereby influence innate immune responses. Western diet (WD) feeding of Ldlr-/- mice induced systemic inflammation, which was undetectable in serum soon after mice were shifted back to a chow diet (CD). In contrast, myeloid cell responses toward innate stimuli remained broadly augmented...
January 11, 2018: Cell
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
#8
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
#9
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/29322237/genome-wide-association-study-of-cold-tolerance-of-chinese-indica-rice-varieties-at-the-bud-burst-stage
#10
Mengchen Zhang, Jing Ye, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang, Xinghua Wei, Yaolong Yang
A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China...
January 10, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29321812/construction-of-an-ultrahigh-density-genetic-linkage-map-for-jatropha-curcas-l-and-identification-of-qtl-for-fruit-yield
#11
Zhiqiang Xia, Shengkui Zhang, Mingfu Wen, Cheng Lu, Yufang Sun, Meiling Zou, Wenquan Wang
Background: As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available. Results: An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29321599/splicing-qtl-of-human-adipose-related-traits
#12
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/29320498/molecular-mapping-of-qtl-alleles-of-brassica-oleracea-affecting-days-to-flowering-and-photosensitivity-in-spring-brassica-napus
#13
Habibur Rahman, Rick A Bennett, Berisso Kebede
Earliness of flowering and maturity are important traits in spring Brassica napus canola-whether grown under long- or short-day condition. By use of a spring B. napus mapping population carrying the genome content of B. oleracea and testing this population under 10 to 18 h photoperiod and 18 to 20 0C (day) temperature conditions, we identified a major QTL on the chromosome C1 affecting flowering time without being influenced by photoperiod and temperature, and a major QTL on C9 affecting flowering time under a short photoperiod (10 h); in both cases, the QTL alleles reducing the number of days to flowering in B...
2018: PloS One
https://www.readbyqxmd.com/read/29318417/identifying-a-major-qtl-associated-with-salinity-tolerance-in-nile-tilapia-using-qtl-seq
#14
Xiao Hui Gu, Dan Li Jiang, Yan Huang, Bi Jun Li, Chao Hao Chen, Hao Ran Lin, Jun Hong Xia
Selection of new lines with high salinity tolerance allows for economically feasible production of tilapias in brackish water areas. Mapping QTLs and identifying the markers linked to salinity-tolerant traits are the first steps in the improvement of the tolerance in tilapia through marker-assisted selection techniques. By using QTL-seq strategy and linkage-based analysis, two significant QTL intervals (chrLG4 and chrLG18) on salinity-tolerant traits were firstly identified in the Nile tilapia. Fine mapping with microsatellite and SNP markers suggested a major QTL region that located at 23...
January 9, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29315927/the-major-effect-qtl-csarn6-1-encodes-an-aaa-atpase-domain-containing-protein-that-is-associated-with-waterlogging-stress-tolerance-through-promoting-adventitious-root-formation
#15
Xuewen Xu, Jing Ji, Qiang Xu, Xiaohua Qi, Yiqun Weng, Xuehao Chen
In plants, the formation of hypocotyl-derived adventitious roots (AR) is an important morphological acclimation to waterlogging stress; however, its genetic basis remains fragmentary. Here, through combined use of bulked segregant analysis-based whole genome sequencing, SNP haplotyping and fine genetic mapping, we identified a candidate gene for a major-effect QTL ARN6.1 that was responsible for waterlogging tolerance due to increased AR formation in the cucumber line Zaoer-N. Through multiple lines of evidence, we show that the CsARN6...
January 8, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29315018/molecular-characterization-and-expression-of-pft-an-fhb-resistance-gene-at-the-fhb1-qtl-in-wheat
#16
Yi He, Xu Zhang, Yu Zhang, Dawood Ahmad, Lei Wu, Peng Jiang, Hongxiang Ma Ma
Fusarium head blight (FHB) is a destructive fungal disease in wheat worldwide. Efforts have been carried out to combat this disease, and the PFT (pore-forming toxin-like) gene at the quantitative trait locus (QTL) Fhb1 was isolated and found to confer resistance to FHB in Sumai 3. In this study, we characterized PFT in 348 wheat accessions. Four haplotypes of PFT were identified. The wild haplotype of PFT had higher resistance than other haplotypes and explained 13.8% of phenotypic variation in FHB resistance by association analysis...
January 9, 2018: Phytopathology
https://www.readbyqxmd.com/read/29314139/validating-genome-wide-associated-signals-for-clinical-mastitis-in-german-holstein-cattle
#17
H Abdel-Shafy, R H Bortfeldt, M Reissmann, G A Brockmann
A validation study for six genomic regions previously identified by a genome-wide association study for somatic cell score was conducted with data of clinical mastitis in German Holstein cattle. Out of 10 tested SNPs, five on chromosomes 6, 13 and 19 were significantly associated with clinical mastitis (P < 0.05). Three SNPs on chromosomes 6 and 19 had the same direction of effect as those previously reported in the initial genome-wide association study for somatic cell score. The other two SNPs on chromosome 13 had opposite effects...
January 4, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29313708/human-lung-dna-methylation-quantitative-trait-loci-colocalize-with-copd-genome-wide-association-loci
#18
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/29311653/meta-analysis-of-epigenome-wide-association-studies-of-cognitive-abilities
#19
Riccardo E Marioni, Allan F McRae, Jan Bressler, Elena Colicino, Eilis Hannon, Shuo Li, Diddier Prada, Jennifer A Smith, Letizia Trevisi, Pei-Chien Tsai, Dina Vojinovic, Jeannette Simino, Daniel Levy, Chunyu Liu, Michael Mendelson, Claudia L Satizabal, Qiong Yang, Min A Jhun, Sharon L R Kardia, Wei Zhao, Stefania Bandinelli, Luigi Ferrucci, Dena G Hernandez, Andrew B Singleton, Sarah E Harris, John M Starr, Douglas P Kiel, Robert R McLean, Allan C Just, Joel Schwartz, Avron Spiro, Pantel Vokonas, Najaf Amin, M Arfan Ikram, Andre G Uitterlinden, Joyce B J van Meurs, Tim D Spector, Claire Steves, Andrea A Baccarelli, Jordana T Bell, Cornelia M van Duijn, Myriam Fornage, Yi-Hsiang Hsu, Jonathan Mill, Thomas H Mosley, Sudha Seshadri, Ian J Deary
Cognitive functions are important correlates of health outcomes across the life-course. Individual differences in cognitive functions are partly heritable. Epigenetic modifications, such as DNA methylation, are susceptible to both genetic and environmental factors and may provide insights into individual differences in cognitive functions. Epigenome-wide meta-analyses for blood-based DNA methylation levels at ~420,000 CpG sites were performed for seven measures of cognitive functioning using data from 11 cohorts...
January 8, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29311651/identification-of-a-novel-gene-regulating-amygdala-mediated-fear-extinction
#20
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
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