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Plant association mapping

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https://www.readbyqxmd.com/read/28724060/genome-wide-association-mapping-of-crown-rust-resistance-in-oat-elite-germplasm
#1
Kathy Esvelt Klos, Belayneh A Yimer, Ebrahiem M Babiker, Aaron D Beattie, J Michael Bonman, Martin L Carson, James Chong, Stephen A Harrison, Amir M H Ibrahim, Frederic L Kolb, Curt A McCartney, Michael McMullen, Jennifer Mitchell Fetch, Mohsen Mohammadi, J Paul Murphy, Nicholas A Tinker
Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28716408/molecular-and-biochemical-characterization-of-a-vigna-mungo-map-kinase-associated-with-mungbean-yellow-mosaic-india-virus-infection-and-deciphering-its-role-in-restricting-the-virus-multiplication
#2
Anju Patel, Nrisingha Dey, Shubho Chaudhuri, Amita Pal
Yellow Mosaic Disease caused by the begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) severely affects many economically important legumes. Recent investigations in Vigna mungo - MYMIV incompatible interaction identified a MAPK homolog in the defense signaling pathway. An important branch of immunity involves phosphorylation by evolutionary conserved Mitogen-activated protein kinases (MAPK) that transduce signals of pathogen invasion to downstream molecules leading to diverse immune responses. However, most of the knowledge of MAPKs is derived from model crops, and functions of these versatile kinases are little explored in legumes...
September 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28715998/detection-of-active-transposable-elements-in-arabidopsis-thaliana-using-oxford-nanopore-sequencing-technology
#3
Emilie Debladis, Christel Llauro, Marie-Christine Carpentier, Marie Mirouze, Olivier Panaud
BACKGROUND: Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV)...
July 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28715485/characterization-of-the-maize-lipoxygenase-gene-family-in-relation-to-aflatoxin-accumulation-resistance
#4
Oluwaseun F Ogunola, Leigh K Hawkins, Erik Mylroie, Michael V Kolomiets, Eli Borrego, Juliet D Tang, W Paul Williams, Marilyn L Warburton
Maize (Zea mays L.) is a globally important staple food crop prone to contamination by aflatoxin, a carcinogenic secondary metabolite produced by the fungus Aspergillus flavus. An efficient approach to reduce accumulation of aflatoxin is the development of germplasm resistant to colonization and toxin production by A. flavus. Lipoxygenases (LOXs) are a group of non-heme iron containing dioxygenase enzymes that catalyze oxygenation of polyunsaturated fatty acids (PUFAs). LOX derived oxylipins play critical roles in plant defense against pathogens including A...
2017: PloS One
https://www.readbyqxmd.com/read/28702690/molecular-mapping-and-candidate-gene-analysis-of-a-new-epicuticular-wax-locus-in-sorghum-sorghum-bicolor-l-moench
#5
G Anurag Uttam, M Praveen, Y Venkateswara Rao, Vilas A Tonapi, R Madhusudhana
A new epicuticular wax (bloom) locus has been identified and fine mapped to the 207.89 kb genomic region on chromosome 1. A putative candidate gene, Sobic.001G269200, annotated as GDSL-like lipase/acylhydrolase, is proposed as the most probable candidate gene involved in bloom synthesis/deposition. Deposition of epicuticular wax on plant aerial surface is one strategy that plants adapt to reduce non-transpiration water loss. Epicuticular wax (bloom)-less mutants in sorghum with their glossy phenotypes exhibit changes in the accumulation of epicuticular wax on leaf and culm surfaces...
July 12, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28702072/development-of-a-phenotyping-platform-for-high-throughput-screening-of-nodal-root-angle-in-sorghum
#6
Dinesh C Joshi, Vijaya Singh, Colleen Hunt, Emma Mace, Erik van Oosterom, Richard Sulman, David Jordan, Graeme Hammer
BACKGROUND: In sorghum, the growth angle of nodal roots is a major component of root system architecture. It strongly influences the spatial distribution of roots of mature plants in the soil profile, which can impact drought adaptation. However, selection for nodal root angle in sorghum breeding programs has been restricted by the absence of a suitable high throughput phenotyping platform. The aim of this study was to develop a phenotyping platform for the rapid, non-destructive and digital measurement of nodal root angle of sorghum at the seedling stage...
2017: Plant Methods
https://www.readbyqxmd.com/read/28698237/maize-yabby-genes-drooping-leaf1-and-drooping-leaf2-regulate-plant-architecture
#7
Josh Strable, Jason G Wallace, Erica Unger-Wallace, Sarah Briggs, Peter Bradbury, Edward S Buckler, Erik Vollbrecht
Leaf architecture directly influences canopy structure, consequentially affecting yield. We discovered a maize (Zea mays) mutant with aberrant leaf architecture, which we named drooping leaf1 (drl1). Pleiotropic mutations in drl1 affect leaf length and width, leaf angle, and internode length and diameter. These phenotypes are enhanced by natural variation at the drl2 enhancer locus, including reduced expression of the drl2-Mo17 allele in the Mo17 inbred. A second drl2 allele, produced by transposon mutagenesis, interacted synergistically with drl1 mutants and reduced drl2 transcript levels...
July 11, 2017: Plant Cell
https://www.readbyqxmd.com/read/28690618/identification-of-major-effect-qtls-for-agronomic-traits-and-cssls-in-rice-from-swarna-oryza-nivara-derived-backcross-inbred-lines
#8
Malathi Surapaneni, Divya Balakrishnan, Sukumar Mesapogu, Krishnam Raju Addanki, Venkateswara Rao Yadavalli, V G N Tripura Venkata, Sarla Neelamraju
Backcross inbred lines (BILs) derived from elite x wild crosses are very useful for basic studies and breeding. The aim of this study was to map quantitative trait loci (QTLs) associated with yield and related traits and to identify chromosomal segment substitution lines (CSSLs) from unselected BC2F8 BILs of Swarna/Oryza nivara IRGC81848. In all, 94 BILs were field evaluated in 2 years (wet seasons, 2014 and 2015) for nine traits; days to 50% flowering, days to maturity (DM), plant height (PH), number of tillers, number of productive tillers, panicle weight, yield per plant, bulk yield, and biomass...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28688353/an-in-situ-method-for-the-high-resolution-mapping-of-137-cs-and-estimation-of-vertical-depth-penetration-in-a-highly-contaminated-environment
#9
Adam Varley, Andrew Tyler, Mark Dowdall, Yuri Bondar, Viachaslau Zabrotski
The Chernobyl nuclear power plant meltdown has to date been the single largest release of radioactivity into the environment. As a result, radioactive contamination that poses a significant threat to human health still persists across much of Europe with the highest concentrations associated with Belarus, Ukraine, and western Russia. Of the radionuclides still prevalent with these territories (137)Cs presents one of the most problematic remediation challenges. Principally, this is due to the localised spatial and vertical heterogeneity of contamination within the soil (~10's of meters), thus making it difficult to accurately characterise through conventional measurement techniques such as static in situ gamma-ray spectrometry or soil cores...
July 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28683804/mapk-triggered-chromatin-reprogramming-by-histone-deacetylase-in-plant-innate-immunity
#10
David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan Sebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptiste Genot, Ton Bisseling, Moussa Benhamed, Heribert Hirt
BACKGROUND: Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we determine whether microbial-associated molecular pattern-triggered gene expression involves modifications at the chromatin level. RESULTS: Histone acetylation and deacetylation are major regulators of microbial-associated molecular pattern-triggered gene expression and implicate the histone deacetylase HD2B in the reprogramming of defence gene expression and innate immunity...
July 6, 2017: Genome Biology
https://www.readbyqxmd.com/read/28674549/genome-wide-association-mapping-reveals-the-genetic-control-underlying-branch-angle-in-rapeseed-brassica-napus-l
#11
Hongge Li, Liping Zhang, Jihong Hu, Fugui Zhang, Biyun Chen, Kun Xu, Guizhen Gao, Hao Li, Tianyao Zhang, Zaiyun Li, Xiaoming Wu
Plant architecture is vital not only for crop yield, but also for field management, such as mechanical harvesting. The branch angle is one of the key factors determining plant architecture. With the aim of revealing the genetic control underlying branch angle in rapeseed (Brassica napus L.), the positional variation of branch angles on individual plants was evaluated, and the branch angle increased with the elevation of branch position. Furthermore, three middle branches of individual plants were selected to measure the branch angle because they exhibited the most representative phenotypic values...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28674545/identification-of-novel-associations-of-candidate-genes-with-resistance-to-late-blight-in-solanum-tuberosum-group-phureja
#12
María F Álvarez, Myrian Angarita, María C Delgado, Celsa García, José Jiménez-Gomez, Christiane Gebhardt, Teresa Mosquera
The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28674544/the-interactions-between-the-long-non-coding-rna-nerdl-and-its-target-gene-affect-wood-formation-in-populus-tomentosa
#13
Wan Shi, Mingyang Quan, Qingzhang Du, Deqiang Zhang
Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development, but little is known about the allelic interactions of lncRNAs with mRNA in perennial plants. Here, we analyzed the interaction of the NERD (Needed for RDR2-independent DNA methylation) Populus tomentosa gene PtoNERD with its putative regulator, the lncRNA NERDL (NERD-related lncRNA), which partially overlaps with the promoter region of this gene. Expression analysis in eight tissues showed a positive correlation between NERDL and PtoNERD (r = 0...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28671256/genome-wide-analysis-of-salinity-stress-induced-dna-methylation-alterations-in-cotton-gossypium-hirsutum-l-using-the-me-dip-sequencing-technology
#14
X K Lu, N Shu, J J Wang, X G Chen, D L Wang, S Wang, W L Fan, X N Guo, L X Guo, W W Ye
Cytosine DNA methylation is a significant form of DNA modification closely associated with gene expression in eukaryotes, fungi, animals, and plants. Although the reference genomes of cotton (Gossypium hirsutum L.) have been publically available, the salinity-stress-induced DNA methylome alterations in cotton are not well understood. Here, we constructed a map of genome-wide DNA methylation characteristics of cotton leaves under salt stress using the methylated DNA immunoprecipitation sequencing method. The results showed that the methylation reads on chromosome 9 were most comparable with those on the other chromosomes, but the greatest changes occurred on chromosome 8 under salt stress...
June 29, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28668354/the-use-of-metabolomic-quantitative-trait-locus-mapping-and-osmotic-adjustment-traits-for-the-improvement-of-crop-yields-under-environmental-stresses
#15
REVIEW
Mostafa Adbelrahman, David J Burritt, Lam-Son P Tran
The sustainable production of food to feed an increasing world population is a major challenge for plant scientists, especially due to the unpredictable and dynamic nature of global climatic conditions. Heat waves, drought, increased soil salinity, unseasonal cold and flooding are all becoming more common climate-related causes of stress for crop plants, and are already affecting yields and the geographical distributions of optimal growing regions for many crops. Therefore, the development and application of multi-faceted strategies, including sustainable agricultural practices and the development and cultivation of intraspecific hybrids containing genetic traits associated with abiotic stress tolerance from wild relatives, will either alone or together be essential to sustainably grow high-yielding crops under increasingly stressful environmental conditions...
June 28, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28667273/natural-and-induced-loss-of-function-mutations-in-slmbp21-mads-box-gene-led-to-jointless-2-phenotype-in-tomato
#16
Maria Victoria Gomez Roldan, Claire Périlleux, Halima Morin, Samuel Huerga-Fernandez, David Latrasse, Moussa Benhamed, Abdelhafid Bendahmane
Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, jointless (j) and jointless-2 (j-2), controlling pedicel abscission zone formation have been documented but only j-2 has been extensively used in breeding. J was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, Solyc12g038510, associated with j-2 phenotype...
June 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28664542/connecting-active-to-passive-fluorescence-with-photosynthesis-a-method-for-evaluating-remote-sensing-measurements-of-chl-fluorescence
#17
Troy S Magney, Christian Frankenberg, Joshua B Fisher, Ying Sun, Gretchen B North, Thomas S Davis, Ari Kornfeld, Katharina Siebke
Recent advances in the retrieval of Chl fluorescence from space using passive methods (solar-induced Chl fluorescence, SIF) promise improved mapping of plant photosynthesis globally. However, unresolved issues related to the spatial, spectral, and temporal dynamics of vegetation fluorescence complicate our ability to interpret SIF measurements. We developed an instrument to measure leaf-level gas exchange simultaneously with pulse-amplitude modulation (PAM) and spectrally resolved fluorescence over the same field of view - allowing us to investigate the relationships between active and passive fluorescence with photosynthesis...
June 30, 2017: New Phytologist
https://www.readbyqxmd.com/read/28659954/segregation-of-hydroxycinnamic-acid-esters-mediating-sweetpotato-weevil-resistance-in-storage-roots-of-sweetpotato
#18
Milton O Anyanga, Benard Yada, G C Yencho, Gorrettie N Ssemakula, Agnes Alajo, Dudley I Farman, Robert O M Mwanga, Philip C Stevenson
Resistance to sweetpotato weevils (Cylas spp.) has been identified in several sweetpotato (Ipomoea batatas) landraces from East Africa and shown to be conferred by hydroxycinnamic acids that occur on the surface of storage roots. The segregation of resistance in this crop is unknown and could be monitored using these chemical traits as markers for resistance in F1 offspring from breeding programs. For the first time in a segregating population, we quantified the plant chemicals that confer resistance and evaluated levels of insect colonization of the same progeny in field and laboratory studies...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28655869/analysis-of-the-grape-vitis-vinifera-l-thaumatin-like-protein-tlp-gene-family-and-demonstration-that-tlp29-contributes-to-disease-resistance
#19
Xiaoxiao Yan, Hengbo Qiao, Xiuming Zhang, Chunlei Guo, Mengnan Wang, Yuejin Wang, Xiping Wang
Thaumatin-like protein (TLP) is present as a large family in plants, and individual members play different roles in various responses to biotic and abiotic stresses. Here we studied the role of 33 putative grape (Vitis vinifera L.) TLP genes (VvTLP) in grape disease resistance. Heat maps analysis compared the expression profiles of 33 genes in disease resistant and susceptible grape species infected with anthracnose (Elsinoe ampelina), powdery mildew (Erysiphe necator) or Botrytis cinerea. Among these 33 genes, the expression level of TLP29 increased following the three pathogens inoculations, and its homolog from the disease resistant Chinese wild grape V...
June 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28653151/identification-of-quantitative-trait-loci-associated-with-resistance-to-net-form-net-blotch-in-a-collection-of-nordic-barley-germplasm
#20
Ronja Wonneberger, Andrea Ficke, Morten Lillemo
Association mapping of resistance to Pyrenophora teres f. teres in a collection of Nordic barley germplasm at different developmental stages revealed 13 quantitative loci with mostly small effects. Net blotch, caused by the necrotrophic fungus Pyrenophora teres, is one of the major diseases in barley in Norway causing quantitative and qualitative yield losses. Resistance in Norwegian cultivars and germplasm is generally insufficient and resistance sources have not been extensively explored yet. In this study, we mapped quantitative trait loci (QTL) associated with resistance to net blotch in Nordic germplasm...
June 26, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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