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Plant association mapping

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https://www.readbyqxmd.com/read/28820491/mapping-of-qtls-for-seed-phorbol-esters-a-toxic-chemical-in-jatropha-curcas-l
#1
Kitiya Amkul, Kularb Laosatit, Prakit Somta, Sangrea Shim, Suk-Ha Lee, Patcharin Tanya, Peerasak Srinives
Jatropha (Jatropha curcas L.) is an oil-bearing plant that has potential to be cultivated as a biodiesel crop. The seed cake after oil extraction has 40-50% protein that can be used in animal feeds. A major limitation in utilizing the cake is the presence of phorbol esters (PE), a heat-tolerant toxic chemical. To identify the quantitative trait loci (QTLs) for PE, we constructed a genetic linkage map from an F₂ population of 95 individuals from a cross "Chai Nat" × "M10" using 143 simple sequence repeat (SSR) markers...
August 18, 2017: Genes
https://www.readbyqxmd.com/read/28819820/genome-wide-characterization-of-the-wrky-gene-family-in-radish-raphanus-sativus-l-reveals-its-critical-functions-under-different-abiotic-stresses
#2
Bernard Kinuthia Karanja, Lianxue Fan, Liang Xu, Yan Wang, Xianwen Zhu, Mingjia Tang, Ronghua Wang, Fei Zhang, Everlyne M'mbone Muleke, Liwang Liu
The radish WRKY gene family was genome-widely identified and played critical roles in response to multiple abiotic stresses. The WRKY is among the largest transcription factors (TFs) associated with multiple biological activities for plant survival, including control response mechanisms against abiotic stresses such as heat, salinity, and heavy metals. Radish is an important root vegetable crop and therefore characterization and expression pattern investigation of WRKY transcription factors in radish is imperative...
August 17, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28817232/crystal-structure-of-the-melampsora-lini-effector-avrp-reveals-insights-into-a-possible-nuclear-function-and-recognition-by-the-flax-disease-resistance-protein-p
#3
Xiaoxiao Zhang, Nadya Farah, Laura Rolston, Daniel J Ericsson, Ann-Maree Catanzariti, Maud Bernoux, Thomas Ve, Katerina Bendak, Chunhong Chen, Joel P Mackay, Gregory J Lawrence, Adrienne Hardham, Jeffrey G Ellis, Simon J Williams, Peter N Dodds, David A Jones, Bostjan Kobe
The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in loss of P-mediated recognition...
August 17, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28814642/an-indel-in-the-promoter-of-al-activated-malate-transporter-9-selected-during-tomato-domestication-determines-fruit-malate-contents-and-aluminum-tolerance
#4
Jie Ye, Xin Wang, Ti Xu Hu, Feng Xia Zhang, Bing Wang, Chang Xin Li, Tian Xia Yang, Han Xia Li, Yong En Lu, James J Giovannoni, Yuyang Zhang, Zhibiao Ye
Deciphering the mechanism of malate accumulation in plants would contribute to a greater understanding of plant chemistry, which has implications for improving flavor quality in crop species and enhancing human health benefits. However, the regulation of malate metabolism is poorly understood in crops such as tomato (Solanum lycopersicum). Here, we integrated a metabolite-based genome-wide association study (mGWAS) with linkage mapping and gene functional studies to characterize the genetics of malate accumulation in a global collection of tomato accessions with broad genetic diversity...
August 16, 2017: Plant Cell
https://www.readbyqxmd.com/read/28810059/targeted-genome-editing-in-caenorhabditis-elegans-using-crispr-cas9
#5
REVIEW
Behnom Farboud
Utilization of programmable nucleases to generate DNA lesions at precise endogenous sequences has transformed the ability to edit genomes from microbes to plants and animals. This is especially true in organisms that previously lacked the means to engineer precise genomic changes, like Caenorhabditis elegans. C. elegans is a 1 mm long free-living, nonparasitic, nematode worm, which is easily cultivated in a laboratory. Its detailed genetic map and relatively compact genome (~100 megabases) helped make it the first metazoan to have its entire genome sequenced...
August 15, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28806927/mapping-of-a-major-qtl-for-salt-tolerance-of-mature-field-grown-maize-plants-based-on-snp-markers
#6
Meijie Luo, Yanxin Zhao, Ruyang Zhang, Jinfeng Xing, Minxiao Duan, Jingna Li, Naishun Wang, Wenguang Wang, Shasha Zhang, Zhihui Chen, Huasheng Zhang, Zi Shi, Wei Song, Jiuran Zhao
BACKGROUND: Salt stress significantly restricts plant growth and production. Maize is an important food and economic crop but is also a salt sensitive crop. Identification of the genetic architecture controlling salt tolerance facilitates breeders to select salt tolerant lines. However, the critical quantitative trait loci (QTLs) responsible for the salt tolerance of field-grown maize plants are still unknown. RESULTS: To map the main genetic factors contributing to salt tolerance in mature maize, a double haploid population (240 individuals) and 1317 single nucleotide polymorphism (SNP) markers were employed to produce a genetic linkage map covering 1462...
August 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28806731/climatic-niche-of-selinum-alatum-apiaceae-selineae-a-new-invasive-plant-species-in-central-europe-and-its-alterations-according-to-the-climate-change-scenarios-are-the-european-mountains-threatened-by-invasion
#7
Kamil Konowalik, Małgorzata Proćków, Jarosław Proćków
In recent years, a few established populations of Selinum alatum have been found in the Eastern Carpathians outside its native range that is the Caucasus and the Armenian Highlands. The species is spreading predominantly in Poland where it can outcompete native plants in certain cases. This study addresses a potential climatic niche of the plant with the special aims to illuminate future spreading and indicate areas suitable for invasion. Our results show that the extent of the favourable habitat of the species is broader than currently known...
2017: PloS One
https://www.readbyqxmd.com/read/28806681/human-biomonitoring-of-polycyclic-aromatic-hydrocarbonsand-metals-in-the-general-population-residing-near-the-municipal-solid-waste-incinerator-of-modena-italy
#8
Maria Giulia Gatti, Petra Bechtold, Laura Campo, Giovanna Barbieri, Giulia Quattrini, Andrea Ranzi, Sabrina Sucato, Luca Olgiati, Elisa Polledri, Michael Romolo, Laura Iacuzio, Giuliano Carrozzi, Paolo Lauriola, Carlo A Goldoni, Silvia Fustinoni
BACKGROUND AND OBJECTIVES: A cross-sectional biomonitoring study was carried out to investigate exposure to incinerator emission in relation to the body burden of selected biomarkers in the population living around the plant. METHODS: Approximately 500 people, aged 18-69 yrs, living within 4 km from the incinerator were randomly selected form the population register. Exposure was measured through fall-out maps of particulate matter (PM), used as tracer for incinerator emissions...
August 5, 2017: Chemosphere
https://www.readbyqxmd.com/read/28805500/chitin-receptor-mediated-activation-of-map-kinases-and-ros-production-in-rice-and-arabidopsis
#9
Tsutomu Kawasaki, Kenta Yamada, Satomi Yoshimura, Koji Yamaguchi
Rapid induction of plant immune responses is essential to inhibit colonization and invasion by pathogens. Plants can recognize pathogen-associated molecular patterns (PAMPs) including fungal chitin and bacterial flagellin using pattern-recognition receptors (PRRs), which trigger the intracellular activation of mitogen-activated protein kinase (MAPK) cascades and the production of reactive oxygen species (ROS). MAPK activation and ROS production play pivotal roles in the induction of robust immune responses...
August 14, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28798752/qtl-analysis-and-nested-association-mapping-for-adult-plant-resistance-to-powdery-mildew-in-two-bread-wheat-populations
#10
Yan Ren, Weixiu Hou, Caixia Lan, Bhoja R Basnet, Ravi P Singh, Wei Zhu, Xiyong Cheng, Dangqun Cui, Feng Chen
CIMMYT wheat (Triticum aestivum L.) lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR) to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL) populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014-2015 and 2015-2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers) and DArT (diversity arrays technology) markers...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28797656/plant-associated-odor-perception-and-processing-in-two-parasitoid-species-with-different-degrees-of-host-specificity-implications-for-host-location-strategies
#11
Prithwiraj Das, Tolulope Morawo, Henry Fadamiro
Microplitis croceipes and Cotesia marginiventris (Hymenoptera: Braconidae) are parasitoids of lepidopteran larvae with different degrees of host specificity. Both parasitoid species rely on host-related plant volatiles as odor cues to locate their herbivore hosts. To better understand mechanisms of odor processing in parasitoids, we tested responses of olfactory sensory neurons (OSNs) in the antennal sensilla placodea of female parasitoids to select plant volatiles and mixtures. The compounds tested include two green leaf volatiles (i...
August 8, 2017: Journal of Insect Physiology
https://www.readbyqxmd.com/read/28797221/use-of-genotyping-by-sequencing-to-determine-the-genetic-structure-in-the-medicinal-plant-chamomile-and-to-identify-flowering-time-and-alpha-bisabolol-associated-snp-loci-by-genome-wide-association-mapping
#12
Lars-Gernot Otto, Prodyut Mondal, Jonathan Brassac, Susanne Preiss, Jörg Degenhardt, Sang He, Jochen Christoph Reif, Timothy Francis Sharbel
BACKGROUND: Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active. In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28796917/single-base-methylome-analysis-reveals-dynamic-epigenomic-differences-associated-with-water-deficit-in-apple
#13
Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan
Cytosine methylation is an essential feature of epigenetic regulation and is involved in various biological processes. Although cytosine methylation has been analyzed at the genomic scale for several plant species, there is a general lack of understanding of the dynamics of global and genic DNA methylation in plants growing in environments challenged with biotic and abiotic stresses. In this study, we mapped cytosine methylation at single-base resolution in the genome of commercial apple (Malus x domestica), and analyzed changes in methylation patterns associated with water deficit in representative drought-sensitive and drought-tolerant cultivars...
August 10, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28795235/impact-of-seed-protein-alleles-from-three-soybean-sources-on-seed-composition-and-agronomic-traits
#14
Lillian F Brzostowski, Timothy I Pruski, James E Specht, Brian W Diers
Evaluation of seed protein alleles in soybean populations showed that an increase in protein concentration is generally associated with a decrease in oil concentration and yield. Soybean [Glycine max (L.) Merrill] meal is one of the most important plant-based protein sources in the world. Developing cultivars high in seed protein concentration and seed yield is a difficult task because the traits have an inverse relationship. Over two decades ago, a protein quantitative trait loci (QTL) was mapped on chromosome (chr) 20, and this QTL has been mapped to the same position in several studies and given the confirmed QTL designation cqSeed protein-003...
August 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28795202/predicting-genomic-selection-efficiency-to-optimize-calibration-set-and-to-assess-prediction-accuracy-in-highly-structured-populations
#15
R Rincent, A Charcosset, L Moreau
We propose a criterion to predict genomic selection efficiency for structured populations. This criterion is useful to define optimal calibration set and to estimate prediction reliability for multiparental populations. Genomic selection refers to the use of genotypic information for predicting the performance of selection candidates. It has been shown that prediction accuracy depends on various parameters including the composition of the calibration set (CS). Assessing the level of accuracy of a given prediction scenario is of highest importance because it can be used to optimize CS sampling before collecting phenotypes, and once the breeding values are predicted it informs the breeders about the reliability of these predictions...
August 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28780664/unique-sequence-organization-and-small-rna-expression-of-a-selfish-b-chromosome
#16
Yue Li, Xueyuan A Jing, John C Aldrich, C Clifford, Jian Chen, Omar S Akbari, Patrick M Ferree
B chromosomes are found in numerous plants and animals. These nonessential, supernumerary chromosomes are often composed primarily of noncoding DNA repeats similar to those found within transcriptionally "silenced" heterochromatin. In order to persist within their resident genomes, many B chromosomes exhibit exceptional cellular behaviors, including asymmetric segregation into gametes and induction of genome elimination during early development. An important goal in understanding these behaviors is to identify unique B chromosome sequences and characterize their transcriptional contributions...
August 5, 2017: Chromosoma
https://www.readbyqxmd.com/read/28770301/genome-wide-association-mapping-reveals-a-rich-genetic-architecture-of-stripe-rust-resistance-loci-in-emmer-wheat-triticum-turgidum-ssp-dicoccum
#17
Weizhen Liu, Marco Maccaferri, Xianming Chen, Gaetano Laghetti, Domenico Pignone, Michael Pumphrey, Roberto Tuberosa
SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated...
August 2, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28769936/genetic-mapping-of-quantitative-trait-loci-for-yield-affecting-traits-in-a-barley-doubled-haploid-population-derived-from-clipper-%C3%A3-sahara-3771
#18
Fatemeh Vafadar Shamasbi, Seyed Hossein Jamali, Behzad Sadeghzadeh, Babak Abdollahi Mandoulakani
Many traits play essential roles in determining crop yield. Wide variation for morphological traits exists in Hordeum vulgare L., but the genetic basis of this morphological variation is largely unknown. To understand genetic basis controlling morphological traits affecting yield, a barley doubled haploid population (146 individuals) derived from Clipper × Sahara 3771 was used to map chromosome regions underlying days to awn appearance, plant height, fertile spike number, flag leaf length, spike length, harvest index, seed number per plant, thousands kernel weight, and grain yield...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28764648/association-mapping-of-starch-chain-length-distribution-and-amylose-content-in-pea-pisum-sativum-l-using-carbohydrate-metabolism-candidate-genes
#19
Margaret A Carpenter, Martin Shaw, Rebecca D Cooper, Tonya J Frew, Ruth C Butler, Sarah R Murray, Leire Moya, Clarice J Coyne, Gail M Timmerman-Vaughan
BACKGROUND: Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea...
August 1, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28760746/insights-into-the-evolution-and-function-of-auxin-signaling-f-box-proteins-in-arabidopsis-thaliana-through-synthetic-analysis-of-natural-variants
#20
R Clay Wright, Mollye L Zahler, Stacey R Gerben, Jennifer L Nemhauser
The evolution of complex body plans in land plants has been paralleled by gene duplication and divergence within nuclear auxin-signaling networks. A deep mechanistic understanding of auxin signaling proteins therefore may allow rational engineering of novel plant architectures. Towards that end, we analyzed natural variation in the auxin receptor F-box family of wild accessions of the reference plant Arabidopsis thaliana and used this information to populate a structure/function map. We employed a synthetic assay to identify natural hypermorphic F-box variants, and then assayed auxin-associated phenotypes in accessions expressing these variants...
July 31, 2017: Genetics
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