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Polymorphisms of the CAPN1, CAST and MSTN Genes,and Their Association with Histological and TexturalParameters of Beef from Polish Holstein-Friesian Cattle

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Journal of Agricultural Science and Technology(A) 2019年第6期9卷 364-370页

作者： Weglarz Andrzej Balakowska Anna Kulaj Dominika Department of Genetics Animal Breeding and EthologyUniversity of Agriculture in Krakowal.Mickiewicza 24/28Krakow 30-059Poland Technology Transfer Center University of Agriculture in Krakowal.Mickiewicza 21Krakow 31-120Poland Department of Animal Reproduction Anatomy and GenomicsUniversity of Agriculture in Krakowal.Mickiewicza 24/28Krakow 30-059Poland

The purpose of this study was to analyse polymorphisms of the CAPN1, CAST and MSTN genes and their association with the microstructure of the Musculus longissimus thoracis (MLT) and textural parameters in bulls of the Holstein-Friesian breeds, black-and-white variety. The polymorphisms at the three loci: in position 6536 of the 3’UTR region of the CAPN1 gene, in position 230 of intron 5 in CAST gene, and in position 371 of the promoter region of the MSTN gene were analysed. Given the inconsequential genetic diversity at the analysed CAPN1 and MSTN loci in the animal sample, it was considered unreasonable to perform further statistical analyses aimed at determining associations between polymorphisms in these positions and meat characteristics. Based on an analysis of the CAST gene polymorphism, a significant association with certain histological and textural parameters was identified.

关键词： Gene polymorphism beef histology texture calpain myostatin

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Integrative modeling of transmitted and de novo variants identifies novel risk genes for congenital heart disease

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Quantitative Biology 2021年第2期9卷 216-227页

作者： Mo Li Xue Zeng Chentian Jin Sheng Chih Jin Weilai Dong Martina Brueckner Richard Lifton Qiongshi Lu Hongyu Zhao Department of Biostatistics Yale School of Public HealthNew HavenCT 06510USA Department of Genetics Yale UniversityNew HavenCT 06510USA Department of Molecular Cellular&Developmental BiologyYale UniversityCT 06510USA Department of Genetics Washington University School of MedicineSt LouisMO 63110USA Department of Pediatrics Yale UniversityNew HavenCT 06510USA Laboratory of Human Genetics and genomics Rockefeller UniversityNew YorkNY 10065USA Department of Biostatistics and Medical Informatics University of Wisconsin-MadisonMadisonWl 53792USA Program of Computational Biology and Bioinformatics Yale UniversityNew HavenCT 06510USA

Background:Whole-exome sequencing(WES)studies have identified multiple genes enriched for de novo mutations(DNMs)in congenital heart disease(CHD)***,risk gene identification based on DNMs alone remains statistically challenging due to heterogenous etiology of CHD and low mutation rate in each ***:In this manuscript,we introduce a hierarchical Bayesian framework for gene-level association test which jointly analyzes de novo and rare transmitted *** integrative modeling of multiple types of genetic variants,gene-level annotations,and reference data from large population cohorts,our method accurately characterizes the expected frequencies of both de novo and transmitted variants and shows improved statistical power compared to analyses based on DNMs ***:Applied to WES data of 2,645 CHD proband-parent trios,our method identified 15 significant genes,half of which are novel,leading to new insights into the genetic bases of ***:These results showcase the power of integrative analysis of transmitted and de novo variants for disease gene discovery.

关键词： rare variants gene-level association test congenital heart disease de novo mutation

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Genomic regions underlying agronomic traits in linseed(Linum usitatissimum L.) as revealed by association mapping

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Journal of Integrative Plant Biology 2014年第1期56卷 75-87页

作者： Braulio J.Soto-Cerda Scott Duguid Helen Booker Gordon Rowland Axel Diederichsen Sylvie Cloutier Department of Plant Science University of Manitoba 66 Dafoe Road Cereal Research Center Agriculture and Agri-Food Canada 195 Dafoe Road Morden Research Station Agriculture and Agri-Food Canada 101 Route 100 Unit 100 Morden Department of Plant Sciences College of Agriculture and Bioresources University of Saskatchewan 51 Campus Drive Plant Gene Resources of Canada Agriculture and Agri-Food Canada 107 Science Place

The extreme climate of the Canadian Prairies poses a major chal enge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core col ection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bol s per area, 1,000 seed weight, seeds per bol , start of flowering, end of flowering, plant height, plant branching, and lodging col ected from up to eight environments was used for association mapping. Based on a mixed model （principal component analysis （PCA） t kinship matrix （K））, 12 significant marker-trait associations for six agronomic traits were identi-fied. Most of the associations were stable across environments as revealed by multivariate analyses. statistical simulation for five markers associated with 1000 seed weight indicated that the favorable al eles have additive effects. None of the modern cultivars carried the five favorable al eles and the maximum number of four observed in any accessions was mostly in＆amp;nbsp;breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while il ustrating the potential for improvement through marker-assisted selection.

关键词： Linum usitatissimum marker-assisted selection

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G-Quadruplex(G4) Motifs in the Maize(Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status,Hypoxia,Low Sugar,and Nutrient Deprivation

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Journal of Genetics and genomics 2014年第12期41卷 627-647页

作者： Carson M.Andorf Mykhailo Kopylov Drena Dobbs Karen E.Koch M.Elizabeth Stroupe Carolyn J.Lawrence Hank W.Bass USDA-ARS Corn Insects and Crop Genetics Research unit Iowa State University Department of Computer Science Iowa State University Institute of Molecular Biophysics Florida State University Department of Genetics Development and Cell BiologyIowa State University Plant Molecular and Cellular Biology Program Horticultural Sciences DepartmentGenetics InstituteUniversity of Florida Department of Biological Science Florida State University Department of Agronomy Iowa State University

The G-quadruplex （G4） elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This （34 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationaily identified 149,988 non-telomeric G4 motifs in maize （Zea mays L., B73 AGPv2）, 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5~ UTR and the other at the 5~ end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia （group VII ERFs）, oxidative stress （D J-1/GATasel）, and energy status （AMPK/ SnRK） pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel.

关键词： Maize G-quadruplex G4 Hypoxia Sucrose synthase

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Identification of telomere maintenance gene variations related to lung adenocarcinoma risk by genome-wide association and whole genome sequencing analyses

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Cancer Communications 2024年第2期44卷 287-293页

作者： Kouya Shiraishi Atsushi Takahashi Yukihide Momozawa Yataro Daigo Syuzo Kaneko Takahisa Kawaguchi Hideo Kunitoh Shingo Matsumoto Hidehito Horinouchi Akiteru Goto Takayuki Honda Kimihiro Shimizu Masahiro Torasawa Daisuke Takayanagi Motonobu Saito Akira Saito Yuichiro Ohe Shun-ichi Watanabe Koichi Goto Masahiro Tsuboi Katsuya Tsuchihara Sadaaki Takata Tomomi Aoi Atsushi Takano Masashi Kobayashi Yohei Miyagi Kazumi Tanaka Hiroyuki Suzuki Daichi Maeda Takumi Yamaura Maiko Matsuda Yoko Shimada Takaaki Mizuno Hiromi Sakamoto Teruhiko Yoshida Yasushi Goto Tatsuya Yoshida Taiki Yamaji Makoto Sonobe Shinichi Toyooka Kazue Yoneda Katsuhiro Masago Fumihiro Tanaka Megumi Hara Nobuo Fuse Satoshi S.Nishizuka Noriko Motoi Norie Sawada Yuichiro Nishida Kazuki Kumada Kenji Takeuchi Kozo Tanno Yasushi Yatabe Kuniko Sunami Tomoyuki Hishida Yasunari Miyazaki Hidemi Ito Mitsuhiro Amemiya Hirohiko Totsuka Haruhiko Nakayama Tomoyuki Yokose Kazuyoshi Ishigaki Toshiteru Nagashima Yoichi Ohtaki Kazuhiro Imai Ken Takasawa Yoshihiro Minamiya Kazuma Kobayashi Kenichi Okubo Kenji Wakai Atsushi Shimizu Masayuki Yamamoto Motoki Iwasaki Koichi Matsuda Johji Inazawa Yuichi Shiraishi Hiroyoshi Nishikawa Yoshinori Murakami Michiaki Kubo Fumihiko Matsuda Yoichiro Kamatani Ryuji Hamamoto Keitaro Matsuo Takashi Kohno Division of Genome Biology National Cancer Center Research InstituteTokyoJapan Department of Clinical genomics National Cancer Center Research InstituteTokyoJapan Laboratory for statistical Analysis Center for Integrative Medical SciencesRIKENYokohamaJapan Department of Genomic Medicine Research InstituteNational Cerebral and Cardiovascular CenterOsakaJapan Laboratory for Genotyping Development Center for Integrative Medical SciencesRIKENYokohamaJapan Center for Antibody and Vaccine Therapy Research HospitalInstitute of Medical ScienceThe University of TokyoTokyoJapan Department of Medical Oncology and Cancer Center and Center for Advanced Medicine against CancerShiga University of Medical ScienceOtsuJapan Division of Medical AI Research and Development National Cancer Center Research InstituteTokyoJapan Center for Genomic Medicine Graduate School of MedicineKyoto UniversityKyotoJapan Department of Medical Oncology Japanese Red Cross Medical CenterTokyoJapan Department of Thoracic Oncology National Cancer Center Hospital EastJapan Department of Thoracic Oncology National Cancer Center HospitalTokyoJapan Department of Cellular and Organ Pathology Graduate School of MedicineAkita UniversityAkitaJapan Department of Respiratory Medicine Tokyo Medical and Dental UniversityBunkyo-kuTokyoJapan Division of General Thoracic Surgery Department of SurgeryShinshu University School of MedicineMatsumotoNaganoJapan Department of General Surgical Science Division of General Thoracic SurgeryGunma University Graduate School of MedicineIntegrative Center of General SurgeryGunma University HospitalGunmaJapan Department of Gastrointestinal Tract Surgery Fukushima Medical University School of MedicineFukushimaJapan StaGen Co. LtdTokyoJapan Division of Thoracic Surgery National Cancer Center HospitalTokyoJapan Department of Thoracic Surgery National Cancer Center Hospital EastChibaJapan Division of Translational Informatics Exploratory Oncology Research and Clinical Trial Center(EPOC

Dear editor,Lung carcinoma is responsible for the highest fatal-ity rate among cancer-related deaths globally,with lung adenocarcinoma(LADC)emerging as the prevailing sub-type.

关键词： adenocarcinoma lung Lung

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