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https://www.readbyqxmd.com/read/27902791/genome-wide-association-mapping-of-leaf-rust-response-in-a-durum-wheat-worldwide-germplasm-collection
#1
Meriem Aoun, Matthew Breiland, M Kathryn Turner, Alexander Loladze, Shiaoman Chao, Steven S Xu, Karim Ammar, James A Anderson, James A Kolmer, Maricelis Acevedo
Leaf rust (caused by Erikss. []) is increasingly impacting durum wheat ( L. var. ) production with the recent appearance of races with virulence to widely grown cultivars in many durum producing areas worldwide. A highly virulent race on durum wheat was recently detected in Kansas. This race may spread to the northern Great Plains, where most of the US durum wheat is produced. The objective of this study was to identify sources of resistance to several races from the United States and Mexico at seedling stage in the greenhouse and at adult stage in field experiments...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27898806/genome-wide-association-study-for-nine-plant-architecture-traits-in-sorghum
#2
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/27896995/muse-a-multi-locus-sampling-based-epistasis-algorithm-for-quantitative-genetic-trait-prediction
#3
Dan He, Laxmi Parida
Quantitative genetic trait prediction based on high-density genotyping arrays plays an important role for plant and animal breeding, as well as genetic epidemiology such as complex diseases. The prediction can be very helpful to develop breeding strategies and is crucial to translate the findings in genetics to precision medicine. Epistasis, the phenomena where the SNPs interact with each other, has been studied extensively in Genome Wide Association Studies (GWAS) but received relatively less attention for quantitative genetic trait prediction...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27872244/network-guided-gwas-improves-identification-of-genes-affecting-free-amino-acids
#4
Ruthie Angelovici, Albert Batushansky, Nicholas Deason, Sabrina Gonzalez-Jorge, Michael A Gore, Aaron Fait, Dean DellaPenna
Amino acids (AA) are essential for proper growth and development in plants. AAs serve as building blocks for proteins but also are important for responses to stresses and the biosynthesis of numerous essential compounds. In seed, the pool of free amino acids (FAA) also contributes to alternative energy, desiccation, and seed vigor; thus, manipulating FAA levels can significantly impact a seed's nutritional qualities. While genome-wide association studies (GWAS) on branched chain amino acids have identified some regulatory genes controlling seed FAAs, the genetic regulation of FAA levels, composition, and homeostasis in seeds remains mostly unresolved...
November 21, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27859799/multilocus-resistance-evolution-to-azole-fungicides-in-fungal-plant-pathogen-populations
#5
Norfarhan Mohd-Assaad, Bruce A McDonald, Daniel Croll
Evolution of fungicide resistance is a major threat to food production in agricultural ecosystems. Fungal pathogens rapidly evolved resistance to all classes of fungicides applied to the field. Resistance to the commonly used azole fungicides is thought to be driven mainly by mutations in a gene (CYP51) encoding a protein of the ergosterol biosynthesis pathway. However, some fungi gained azole resistance independently of CYP51 mutations and the mechanisms leading to CYP51-independent resistance are poorly understood...
November 14, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27822217/genome-wide-association-study-identifies-new-loci-for-resistance-to-leptosphaeria-maculans-in-canola
#6
Harsh Raman, Rosy Raman, Neil Coombes, Jie Song, Simon Diffey, Andrzej Kilian, Kurt Lindbeck, Denise M Barbulescu, Jacqueline Batley, David Edwards, Phil A Salisbury, Steve Marcroft
Key message "We identified both quantitative and quantitative resistance loci to Leptosphaeria maculans, a fungal pathogen, causing blackleg disease in canola. Several genome-wide significant associations were detected at known and new loci for blackleg resistance. We further validated statistically significant associations in four genetic mapping populations, demonstrating that GWAS marker loci are indeed associated with resistance to L. maculans. One of the novel loci identified for the first time, Rlm12, conveys adult plant resistance in canola...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27814357/a-novel-tiller-angle-gene-tac3-together-with-tac1-and-d2-largely-determine-the-natural-variation-of-tiller-angle-in-rice-cultivars
#7
Haijiao Dong, Hu Zhao, Weibo Xie, Zhongmin Han, Guangwei Li, Wen Yao, Xufeng Bai, Yong Hu, Zilong Guo, Kai Lu, Lin Yang, Yongzhong Xing
Tiller angle is one of the most important components of the ideal plant architecture that can greatly enhance rice grain yield. Understanding the genetic basis of tiller angle and mining favorable alleles will be helpful for breeding new plant-type varieties. Here, we performed genome-wide association studies (GWAS) to identify genes controlling tiller angle using 529 diverse accessions of Oryza sativa including 295 indica and 156 japonica accessions in two environments. We identified 7 common quantitative trait loci (QTLs), including the previously reported major gene Tiller Angle Control 1 (TAC1), in the two environments, 10 and 13 unique QTLs in Hainan and Wuhan, respectively...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27802269/genome-wide-association-of-stem-water-soluble-carbohydrates-in-bread-wheat
#8
Yan Dong, Jindong Liu, Yan Zhang, Hongwei Geng, Awais Rasheed, Yonggui Xiao, Shuanghe Cao, Luping Fu, Jun Yan, Weie Wen, Yong Zhang, Ruilian Jing, Xianchun Xia, Zhonghu He
Water soluble carbohydrates (WSC) in stems play an important role in buffering grain yield in wheat against biotic and abiotic stresses; however, knowledge of genes controlling WSC is very limited. We conducted a genome-wide association study (GWAS) using a high-density 90K SNP array to better understand the genetic basis underlying WSC, and to explore marker-based breeding approaches. WSC was evaluated in an association panel comprising 166 Chinese bread wheat cultivars planted in four environments. Fifty two marker-trait associations (MTAs) distributed across 23 loci were identified for phenotypic best linear unbiased estimates (BLUEs), and 11 MTAs were identified in two or more environments...
2016: PloS One
https://www.readbyqxmd.com/read/27799070/capture-hi-c-identifies-a-novel-causal-gene-il20ra-in-the-pan-autoimmune-genetic-susceptibility-region-6q23
#9
Amanda McGovern, Stefan Schoenfelder, Paul Martin, Jonathan Massey, Kate Duffus, Darren Plant, Annie Yarwood, Arthur G Pratt, Amy E Anderson, John D Isaacs, Julie Diboll, Nishanthi Thalayasingam, Caroline Ospelt, Anne Barton, Jane Worthington, Peter Fraser, Stephen Eyre, Gisela Orozco
BACKGROUND: The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific assays in T and B cell lines, we provide compelling evidence that redefines causal genes at the 6q23 locus, one of the most important loci that confers autoimmunity risk...
November 1, 2016: Genome Biology
https://www.readbyqxmd.com/read/27769176/genome-wide-association-analysis-of-forage-quality-in-maize-mature-stalk
#10
Hongwu Wang, Kun Li, Xiaojiao Hu, Zhifang Liu, Yujin Wu, Changling Huang
BACKGROUND: Plant digestibility of silage maize (Zea mays L.) has a large influence on nutrition intake for animal feeding. Improving forage quality will enhance the utilization efficiency and feeding value of forage maize. Dissecting the genetic basis of forage quality will improve our understanding of the complex nature of cell wall biosynthesis and degradation, which is also helpful for breeding good quality silage maize. RESULTS: Acid detergent fiber (ADF), neutral detergent fiber (NDF) and in vitro dry matter digestibility (IVDMD) of stalk were evaluated in a diverse maize population, which is comprised of 368 inbred lines and planted across seven environments...
October 21, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27760136/combined-use-of-genome-wide-association-data-and-correlation-networks-unravels-key-regulators-of-primary-metabolism-in-arabidopsis-thaliana
#11
Si Wu, Saleh Alseekh, Álvaro Cuadros-Inostroza, Corina M Fusari, Marek Mutwil, Rik Kooke, Joost B Keurentjes, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman
Plant primary metabolism is a highly coordinated, central, and complex network of biochemical processes regulated at both the genetic and post-translational levels. The genetic basis of this network can be explored by analyzing the metabolic composition of genetically diverse genotypes in a given plant species. Here, we report an integrative strategy combining quantitative genetic mapping and metabolite‒transcript correlation networks to identify functional associations between genes and primary metabolites in Arabidopsis thaliana...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27742723/genome-wide-association-study-and-qtl-mapping-reveal-genomic-loci-associated-with-fusarium-ear-rot-resistance-in-tropical-maize-germplasm
#12
Jiafa Chen, Rosemary Shrestha, Junqiang Ding, Hongjian Zheng, Chunhua Mu, Jianyu Wu, George Mahuku
Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance...
October 14, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27730302/systems-biology-and-genome-wide-approaches-to-unveil-the-molecular-players-involved-in-the-pre-germinative-metabolism-implications-on-seed-technology-traits
#13
Anca Macovei, Andrea Pagano, Paola Leonetti, Daniela Carbonera, Alma Balestrazzi, Susana S Araújo
The pre-germinative metabolism is among the most fascinating aspects of seed biology. The early seed germination phase, or pre-germination, is characterized by rapid water uptake (imbibition), which directs a series of dynamic biochemical events. Among those are enzyme activation, DNA damage and repair, and use of reserve storage compounds, such as lipids, carbohydrates and proteins. Industrial seedling production and intensive agricultural production systems require seed stocks with high rate of synchronized germination and low dormancy...
October 11, 2016: Plant Cell Reports
https://www.readbyqxmd.com/read/27729396/leaf-growth-response-to-mild-drought-natural-variation-in-arabidopsis-sheds-light-on-trait-architecture
#14
Pieter Clauw, Frederik Coppens, Arthur Korte, Dorota Herman, Bram Slabbinck, Stijn Dhondt, Twiggy Van Daele, Liesbeth De Milde, Mattias Vermeersch, Katrien Maleux, Steven Maere, Nathalie Gonzalez, Dirk Inzé
Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under nonlethal drought conditions is lacking. Recent advances in genomics, phenomics, and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves...
October 2016: Plant Cell
https://www.readbyqxmd.com/read/27698483/comparative-and-parallel-genome-wide-association-studies-for-metabolic-and-agronomic-traits-in-cereals
#15
Wei Chen, Wensheng Wang, Meng Peng, Liang Gong, Yanqiang Gao, Jian Wan, Shouchuang Wang, Lei Shi, Bin Zhou, Zongmei Li, Xiaoxi Peng, Chenkun Yang, Lianghuan Qu, Xianqing Liu, Jie Luo
The plant metabolome is characterized by extensive diversity and is often regarded as a bridge between genome and phenome. Here we report metabolic and phenotypic genome-wide studies (mGWAS and pGWAS) in rice grain that, in addition to previous metabolic GWAS in rice leaf and maize kernel, show both distinct and overlapping aspects of genetic control of metabolism within and between species. We identify new candidate genes potentially influencing important metabolic and/or morphological traits. We show that the differential genetic architecture of rice metabolism between different tissues is in part determined by tissue specific expression...
October 4, 2016: Nature Communications
https://www.readbyqxmd.com/read/27696619/genotyping-by-sequencing-approaches-to-characterise-crop-genomes-choosing-the-right-tool-for-the-right-application
#16
Armin Scheben, Jacqueline Batley, David Edwards
In the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practise. New methods allowing rapid, high-throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping by sequencing (GBS) methods include over a dozen reduced representation sequencing (RRS) approaches and at least four whole genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best-suited method seem a daunting task...
October 3, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27695390/using-phenomic-analysis-of-photosynthetic-function-for-abiotic-stress-response-gene-discovery
#17
Tepsuda Rungrat, Mariam Awlia, Tim Brown, Riyan Cheng, Xavier Sirault, Jiri Fajkus, Martin Trtilek, Bob Furbank, Murray Badger, Mark Tester, Barry J Pogson, Justin O Borevitz, Pip Wilson
Monitoring the photosynthetic performance of plants is a major key to understanding how plants adapt to their growth conditions. Stress tolerance traits have a high genetic complexity as plants are constantly, and unavoidably, exposed to numerous stress factors, which limits their growth rates in the natural environment. Arabidopsis thaliana, with its broad genetic diversity and wide climatic range, has been shown to successfully adapt to stressful conditions to ensure the completion of its life cycle. As a result, A...
2016: Arabidopsis Book
https://www.readbyqxmd.com/read/27662898/characterization-of-biosynthetic-pathways-for-the-production-of-the-volatile-homoterpenes-dmnt-and-tmtt-in-zea-mays
#18
Annett Richter, Claudia Schaff, Zhiwu Zhang, Alexander E Lipka, Feng Tian, Tobias G Köllner, Christiane Schnee, Susanne Preiss, Sandra Irmisch, Georg Jander, Wilhelm Boland, Jonathan Gershenzon, Edward S Buckler, Jorg Degenhardt
Plant volatiles not only have multiple defense functions against herbivores, fungi, and bacteria, but also have been implicated in signaling within the plant and towards other organisms. Elucidating the function of individual plant volatiles will require more knowledge of their biosynthesis and regulation in response to external stimuli. By exploiting the variation of herbivore-induced volatiles among 26 maize (Zea mays) inbred lines, we conducted a nested association mapping (NAM) and genome-wide association study (GWAS) to identify a set of quantitative trait loci (QTLs) for investigating the pathways of volatile terpene production...
September 23, 2016: Plant Cell
https://www.readbyqxmd.com/read/27596807/genome-wide-association-study-reveals-putative-regulators-of-bioenergy-traits-in-populus-deltoides
#19
Annette M Fahrenkrog, Leandro G Neves, Márcio F R Resende, Ana I Vazquez, Gustavo de Los Campos, Christopher Dervinis, Robert Sykes, Mark Davis, Ruth Davenport, William B Barbazuk, Matias Kirst
Genome-wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides, a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low-frequency single-nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals...
September 6, 2016: New Phytologist
https://www.readbyqxmd.com/read/27554097/advantages-of-continuous-genotype-values-over-genotype-classes-for-gwas-in-higher-polyploids-a-comparative-study-in-hexaploid-chrysanthemum
#20
Fabian Grandke, Priyanka Singh, Henri C M Heuven, Jorn R de Haan, Dirk Metzler
BACKGROUND: Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing technologies. While genotype classification is an established noise reduction step in diploids, it gains complexity with increasing ploidy levels. Eventually, the errors produced by misclassifications exceed the benefits of genotype classes...
2016: BMC Genomics
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