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https://www.readbyqxmd.com/read/27912109/characterization-and-fine-mapping-of-a-novel-premature-leaf-senescence-mutant-yellow-leaf-and-dwarf-1-in-rice
#1
Luchang Deng, Peng Qin, Zhi Liu, Geling Wang, Weilan Chen, Jianhua Tong, Langtao Xiao, Bin Tu, Yuantao Sun, Wei Yan, Hang He, Jun Tan, Xuewei Chen, Yuping Wang, Shigui Li, Bingtian Ma
Leaves are the main organs in which photosynthates are produced. Leaf senescence facilitates the translocation of photosynthates and nutrients from source to sink, which is important for plant development and especially for crop yield. However, the molecular mechanism of leaf senescence is unknown. Here, we identified a mutant, yellow leaf and dwarf 1 (yld1), which exhibited decreased plant height and premature leaf senescence. Nitroblue tetrazolium and diamiobenzidine staining analyses revealed that the concentrations of reactive oxygen species were higher in yld1 leaves than in wild type leaves...
November 22, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27902795/genome-wide-association-study-identifies-candidate-loci-underlying-agronomic-traits-in-a-middle-american-diversity-panel-of-common-bean
#2
Samira Mafi Moghaddam, Sujan Mamidi, Juan M Osorno, Rian Lee, Mark Brick, James Kelly, Phillip Miklas, Carlos Urrea, Qijian Song, Perry Cregan, Jane Grimwood, Jeremy Schmutz, Phillip E McClean
Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27898815/germplasm-architecture-revealed-through-chromosomal-effects-for-quantitative-traits-in-maize
#3
Rex Bernardo, Addie M Thompson
Germplasm architecture refers to how favorable alleles for a given trait are distributed across the genome in a germplasm collection. Our objective was to assess germplasm architecture for quantitative traits among US maize ( L.) inbreds. A total of 271 inbreds were genotyped at 28,626 single nucleotide polymorphism (SNP) loci and phenotyped for anthesis date, plant height, starch and protein concentration, and resistance to northern corn leaf blight (NCLB, caused by ). Chromosomal effects were calculated as the sum of the trait effects of SNP alleles carried on a specific chromosome by an inbred...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898806/genome-wide-association-study-for-nine-plant-architecture-traits-in-sorghum
#4
Jing Zhao, Maria B Mantilla Perez, Jieyun Hu, Maria G Salas Fernandez
Sorghum [ (L) Moench], an important grain and forage crop, is receiving significant attention as a lignocellulosic feedstock because of its water-use efficiency and high biomass yield potential. Because of the advancement of genotyping and sequencing technologies, genome-wide association study (GWAS) has become a routinely used method to investigate the genetic mechanisms underlying natural phenotypic variation. In this study, we performed a GWAS for nine grain and biomass-related plant architecture traits to determine their overall genetic architecture and the specific association of allelic variants in gibberellin (GA) biosynthesis and signaling genes with these phenotypes...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898805/characterization-of-three-rice-multiparent-advanced-generation-intercross-magic-populations-for-quantitative-trait-loci-identification
#5
Lijun Meng, Longbiao Guo, Kimberly Ponce, Xiangqian Zhao, Guoyou Ye
Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker-trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27896743/analysis-of-quantitative-trait-loci
#6
David L Duffy
Although the term quantitative trait locus (QTL) strictly refers merely to a genetic variant that causes changes in a quantitative phenotype such as height, QTL analysis more usually describes techniques used to study oligogenic or polygenic traits where each identified locus contributes a relatively small amount to the genetic determination of the trait, which may be categorical in nature. Originally, too, it would be clear that it covered segregation and genetic linkage analysis, but now genetic association analysis in a genome-wide SNP or sequencing experiment would be the commonest application...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27872629/qtl-analysis-of-spike-morphological-traits-and-plant-height-in-winter-wheat-triticum-aestivum-l-using-a-high-density-snp-and-ssr-based-linkage-map
#7
Huijie Zhai, Zhiyu Feng, Jiang Li, Xinye Liu, Shihe Xiao, Zhongfu Ni, Qixin Sun
Wheat yield can be enhanced by modifying the spike morphology and the plant height. In this study, a population of 191 F9 recombinant inbred lines (RILs) was developed from a cross between two winter cultivars Yumai 8679 and Jing 411. A dense genetic linkage map with 10,816 markers was constructed by incorporating single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker information. Five spike morphological traits and plant height were evaluated under nine environments for the RILs and parental lines, and the number of detected environmentally stable QTLs were 18 and three, respectively...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27846199/height-height-related-snps-and-risk-of-non-melanoma-skin-cancer
#8
Xin Li, Liming Liang, Yen-Chen Anne Feng, Immaculata De Vivo, Edward Giovannucci, Jean Y Tang, Jiali Han
BACKGROUND: Adult height has been associated with risk of several site-specific cancers, including melanoma. However, less attention has been given to non-melanoma skin cancer (NMSC). METHODS: We prospectively examined the risk of squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) in relation to adult height in the Nurses' Health Study (NHS, n=117 863) and the Health Professionals Follow-up Study (HPFS, n=51 111). We also investigated the relationships between height-related genetic markers and risk of BCC and SCC in the genetic data sets of the NHS and HPFS (3898 BCC cases, and 8530 BCC controls; 527 SCC cases, and 8962 SCC controls)...
November 15, 2016: British Journal of Cancer
https://www.readbyqxmd.com/read/27829377/range-wide-phenotypic-and-genetic-differentiation-in-wild-sunflower
#9
Edward V McAssey, Jonathan Corbi, John M Burke
BACKGROUND: Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of growth, plant architecture, and seed traits, along with single-nucleotide polymorphism (SNP) genotyping to characterize range-wide patterns of diversity in 15 populations of wild sunflower (Helianthus annuus L.) sampled along a latitudinal gradient in central North America...
November 10, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27825992/prevalence-determinants-and-clinical-correlates-of-vitamin-d-deficiency-in-adults-with-inhaled-corticosteroid-treated-asthma-in-london-uk
#10
REVIEW
David A Jolliffe, Kate Kilpin, Beverley D MacLaughlin, Claire L Greiller, Richard L Hooper, Neil C Barnes, Peter M Timms, Raj K Rajakulasingam, Angshu Bhowmik, Aklak B Choudhury, David E Simcock, Elina Hyppönen, Christopher J Corrigan, Robert T Walton, Christopher J Griffiths, Adrian R Martineau
Vitamin D deficiency is common in children with asthma, and it associates with poor asthma control, reduced forced expiratory volume in one second (FEV1) and increased requirement for inhaled corticosteroids (ICS). Cross-sectional studies investigating the prevalence, determinants and clinical correlates of vitamin D deficiency in adults with asthma are lacking. We conducted a multi-centre cross-sectional study in 297 adults with a medical record diagnosis of ICS-treated asthma living in London, UK. Details of potential environmental determinants of vitamin D status, asthma control and medication use were collected by questionnaire; blood samples were taken for analysis of serum 25(OH)D concentration and DNA extraction, and participants underwent measurement of weight, height and fractional exhaled nitric oxide concentration (FeNO), spirometry and sputum induction for determination of lower airway eosinophil counts (n=35 sub-group)...
November 5, 2016: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27806077/linkage-and-association-mapping-for-two-major-traits-used-in-the-maritime-pine-breeding-program-height-growth-and-stem-straightness
#11
Jérôme Bartholomé, Marco Cam Bink, Joost van Heerwaarden, Emilie Chancerel, Christophe Boury, Isabelle Lesur, Fikret Isik, Laurent Bouffier, Christophe Plomion
BACKGROUND: Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches...
2016: PloS One
https://www.readbyqxmd.com/read/27782006/wrinkled-single-layer-graphenes-fabricated-by-silicon-nanopillar-arrays
#12
Zibo Li, Yutong Wu, Jingjie Nan, Xiaoduo Tang, Junhu Zhang, Bai Yang
The degree of crumpling affects the optoelectronic properties of graphene, which are very important for the performance of graphene-based devices and materials. In this article, we report an approach to tune the formation of wrinkles on single-layer graphene (SLG) by silicon nanopillar (SNP) arrays. By using gold nanoparticles as an etching mask, SNP arrays with different heights could be prepared by tuning the duration of etching. The formation of wrinkles on these SNP arrays was studied systematically. We found that thermal treatment could lead to a wrapping behavior of graphene around SNP arrays, which was accompanied by the emergence of many more wrinkles...
November 25, 2016: Nanotechnology
https://www.readbyqxmd.com/read/27755736/capturing-neutral-and-adaptive-genetic-diversity-for-conservation-in-a-highly-structured-tree-species
#13
Isabel Rodríguez-Quilón, Luis Santos-Del-Blanco, María Jesús Serra-Varela, Jarkko Koskela, Santiago C González-Martínez, Ricardo Alía
Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/27746787/mapping-qtls-for-fusarium-head-blight-resistance-in-an-interspecific-wheat-population
#14
Angelica Giancaspro, Stefania L Giove, Daniela Zito, A Blanco, Agata Gadaleta
Fusarium head blight (scab) is one of the most widespread and damaging diseases of wheat, causing grain yield and quality losses and production of harmful mycotoxins. Development of resistant varieties is hampered by lack of effective resistance sources in the tetraploid wheat primary gene pool. Here we dissected the genetic basis of resistance in a new durum wheat (Triticum turgidum ssp. durum) Recombinant inbred lines (RILs) population obtained by crossing an hexaploid resistant line and a durum susceptible cultivar...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27704615/role-of-runx2-polymorphisms-in-risk-and-prognosis-of-ossification-of-posterior-longitudinal-ligament
#15
Feng Chang, Lijun Li, Gang Gao, Shengqiang Ding, Jincai Yang, Ting Zhang, Genle Zuo
BACKGROUND: Our study was aimed at finding out if Runx2 SNPs (single-nucleotide polymorphisms) are related to susceptibility to and prognosis of ossification of posterior longitudinal ligament (OPLL). METHODS: We selected 80 OPLL patients and another 80 independent patients without OPLL from September 2013 to November 2014. Serum was collected to detect the genotypes of rs1321075, rs12333172, and rs1406846 on Runx2 with direct sequencing analysis. RESULTS: Differences in clinical characteristics, including age, weight, height, sex ratio, as well as smoking and drinking history, between OPLL and control groups appeared to be insignificant (all P-value >...
October 5, 2016: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/27703405/sequence-variants-of-biec2-808543-near-lcorl-are-associated-with-body-composition-in-thoroughbreds-under-training
#16
Teruaki Tozaki, Fumio Sato, Mutsuki Ishimaru, Mio Kikuchi, Hironaga Kakoi, Kei-Ichi Hirota, Shun-Ichi Nagata
Ligand-dependent nuclear receptor compressor-like (LCORL) encodes a transcription factor, and its polymorphisms are associated with measures of skeletal frame size and adult height in several species. Recently, the single nucleotide polymorphism (SNP) BIEC2-808543 located upstream of LCORL was identified as a genetic diagnostic marker associated with withers height in Thoroughbreds. In this study, 322 Thoroughbreds-in-training were genotyped for BIEC2-808543 to evaluate the association between genotype and body composition traits, including body weight, withers height, the ratio of body weight to withers height, chest circumference, and cannon circumference...
2016: Journal of Equine Science
https://www.readbyqxmd.com/read/27696287/molecular-dissection-of-seedling-salinity-tolerance-in-rice-oryza-sativa-l-using-a-high-density-gbs-based-snp-linkage-map
#17
Teresa B De Leon, Steven Linscombe, Prasanta K Subudhi
BACKGROUND: Salinity is one of the many abiotic stresses limiting rice production worldwide. Several studies were conducted to identify quantitative trait loci (QTLs) for traits associated to salinity tolerance. However, due to large confidence interval for the position of QTLs, utility of reported QTLs and the associated markers has been limited in rice breeding programs. The main objective of this study is to construct a high-density rice genetic map for identification QTLs and candidate genes for salinity tolerance at seedling stage...
December 2016: Rice
https://www.readbyqxmd.com/read/27684604/genetic-analysis-of-emerging-risk-factors-in-coronary-artery-disease
#18
Erik P A van Iperen, Suthesh Sivapalaratnam, Michael V Holmes, G Kees Hovingh, Aeilko H Zwinderman, Folkert W Asselbergs
BACKGROUND AND AIMS: Type 2 diabetes (T2D), low-density lipoprotein-cholesterol (LDL-c), body mass index (BMI), blood pressure and smoking are established risk factors that play a causal role in coronary artery disease (CAD). Numerous common genetic variants associating with these and other risk factors have been identified, but their association with CAD has not been comprehensively examined in a single study. Our goal was to comprehensively evaluate the associations of established and emerging risk factors with CAD using genetic variants identified from Genome-wide Association Studies (GWAS)...
September 13, 2016: Atherosclerosis
https://www.readbyqxmd.com/read/27625707/the-c1431t-polymorphism-of-peroxisome-proliferator-activated-receptor-%C3%AE-ppar%C3%AE-is-associated-with-low-risk-of-diabetes-in-a-pakistani-cohort
#19
Huma Butt, Shabana, Shahida Hasnain
BACKGROUND: Diabetes is a socioeconomic burden in Pakistan. International diabetes federation reported 6.9 million cases of diabetes and 87,548 deaths due to diabetes in Pakistan in 2014. Peroxisome proliferators-activated receptors are transcription factors, regulating several physiological processes. AIM: The aim of the current study was to determine the prevalence of silent variant C1431T in exon 6 of PPAR-y and analyze its effect on various anthropometric and biochemical parameters in a Pakistani cohort...
2016: Diabetology & Metabolic Syndrome
https://www.readbyqxmd.com/read/27616482/gwis-genome-wide-inferred-statistics-for-functions-of-multiple-phenotypes
#20
Harold A Nieuwboer, René Pool, Conor V Dolan, Dorret I Boomsma, Michel G Nivard
Here we present a method of genome-wide inferred study (GWIS) that provides an approximation of genome-wide association study (GWAS) summary statistics for a variable that is a function of phenotypes for which GWAS summary statistics, phenotypic means, and covariances are available. A GWIS can be performed regardless of sample overlap between the GWAS of the phenotypes on which the function depends. Because a GWIS provides association estimates and their standard errors for each SNP, a GWIS can form the basis for polygenic risk scoring, LD score regression, Mendelian randomization studies, biological annotation, and other analyses...
October 6, 2016: American Journal of Human Genetics
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