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Plant phenotyping

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https://www.readbyqxmd.com/read/28550207/atx3-atx4-and-atx5-encode-putative-h3k4-methyltransferases-and-are-critical-for-plant-development
#1
Liqun Chen, Jinhong Luo, Zhenhai Cui, Ming Xue, Li Wang, Xiaoyu Zhang, Wojtek P Pawlowski, Yan He
Methylation of lysine residues in the tail of the H3 histone is a key regulator of chromatin state and gene expression, conferred by a large family of enzymes containing an evolutionarily-conserved SET domain. One of the main types of SET domain proteins are those controlling H3K4 di- and trimethylation. The genome of Arabidopsis encodes 12 such proteins, including five ARABIDOPSIS TRITHORAX (ATX) proteins and seven ATX-Related (ATXR) proteins. Here we examined three until-now-unexplored ATX proteins, ATX3, ATX4, and ATX5...
May 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28549454/genomic-adaptation-to-agricultural-environments-cabbage-white-butterflies-pieris-rapae-as-a-case-study
#2
Kristin L Sikkink, Megan E Kobiela, Emilie C Snell-Rood
BACKGROUND: Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades...
May 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28548604/quorum-sensing-systems-in-the-plant-growth-promoting-bacterium-paraburkholderia-phytofirmans-psjn-exhibit-cross-regulation-and-are-involved-in-biofilm-formation
#3
Ana Zúñiga, Raúl A Donoso, Daniela Ruiz, Gonzalo A Ruz, Bernardo González
Quorum-sensing systems play important roles in host colonization and host establishment of Burkholderiales species. Beneficial Paraburkholderia species share a conserved quorum-sensing (QS) system, designated BraI/R, that controls different phenotypes. In this context, the plant growth-promoting bacterium Paraburkholderia phytofirmans PsJN possesses two different homoserine lactone QS systems BpI.1/R.1 and BpI.2/R.2 (BraI/R-like QS system). The BpI.1/R.1 QS system was previously reported to be important to colonize and produce beneficial effects in Arabidopsis thaliana plants...
May 26, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28548242/enhanced-root-growth-in-phosphate-starved-arabidopsis-by-stimulating-de-novo-phospholipid-biosynthesis-through-the-overexpression-of-lysophosphatidic-acid-acyltransferase-2-lpat2
#4
Artik Elisa Angkawijaya, Van Cam Nguyen, Yuki Nakamura
Upon phosphate starvation, plants retard shoot growth but promote root development presumably to enhance phosphate assimilation from the ground. Membrane lipid remodeling is a metabolic adaptation that replaces membrane phospholipids by non-phosphorous galactolipids, thereby allowing plants to obtain scarce phosphate yet maintain the membrane structure. However, stoichiometry of this phospholipid-to-galactolipid conversion may not account for the massive demand of membrane lipids that enables active growth of roots under phosphate starvation, thereby suggesting the involvement of de novo phospholipid biosynthesis, which is not represented in the current model...
May 26, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28547891/large-scale-gene-expression-reveals-different-adaptations-of-hyalopterus-persikonus-to-winter-and-summer-host-plants
#5
Na Cui, Peng-Cheng Yang, Kun Guo, Le Kang, Feng Cui
Host alternation, an obligatory seasonal shifting between host plants of distant genetic relationship, has had significant consequences for the diversification and success of the superfamily of aphids. However, the underlying molecular mechanism remains unclear. In this study, the molecular mechanism of host alternation was explored through a large-scale gene expression analysis of the mealy aphid Hyalopterus persikonus on winter and summer host plants. More than four times as many unigenes of the mealy aphid were significantly upregulated on summer host Phragmites australis than on winter host Rosaceae plants...
June 2017: Insect Science
https://www.readbyqxmd.com/read/28547737/08sg2-osbak1-regulates-grain-size-and-number-and-functions-differently-in-indica-and-japonica-backgrounds-in-rice
#6
Hua Yuan, Shijun Fan, Juan Huang, Shijie Zhan, Shifu Wang, Peng Gao, Weilan Chen, Bin Tu, Bingtian Ma, Yuping Wang, Peng Qin, Shigui Li
BACKGROUND: Both grain size and grain number are significant for rice yield. In the past decade, a number of genes related to grain size and grain number have been documented, however, the regulatory mechanisms underlying them remains ambiguous. RESULTS: We identified a rice small grain (sg2) mutant in an EMS mutant library generated from an indica variety, Shuhui498. Using the MutMap gene mapping strategy, we identified two linkage regions on chromosome 7 and 8, respectively, consistent with the segregation ratios in the F2 population...
December 2017: Rice
https://www.readbyqxmd.com/read/28546830/antibiotic-resistance-serogroups-virulence-genes-and-phylogenetic-groups-of-escherichia-coli-isolated-from-yaks-with-diarrhea-in-qinghai-plateau-china
#7
Mujeeb Ur Rehman, Hui Zhang, Muhammad Kashif Iqbal, Khalid Mehmood, Shucheng Huang, Fazul Nabi, Houqiang Luo, Yanfang Lan, Jiakui Li
BACKGROUND: Ruminants serve as one of the most important reservoirs for pathogenic Escherichia coli. Infection with E. coli, a foodborne enteropathogen, can lead to asymptomatic infections that can cause life-threatening complications in humans. Therefore, from a clinical and human health perspective, it is important to know which virulence genes, phylogenetic groups, serogroups, and antibiotic resistance patterns are present in E. coli strains in yaks with diarrheic infections. METHODS: Two-hundred and ninety-two rectal swabs were collected from diarrheic yaks in Qinghai Plateau, China...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28546386/assessment-of-gene-flow-between-gossypium-hirsutum-and-gossypium-herbaceum-evidence-of-unreduced-gametes-in-the-diploid-progenitor
#8
E Montes, O Coriton, F Eber, V Huteau, J M Lacape, C Reinhardt, D Marais, J L Hofs, A M Chèvre, C Pannetier
In the framework of a gene flow assessment, we investigated the natural hybridization rate between Gossypium hirsutum (AADD genome) and G. herbaceum (AA genome). The latter species, a diploid progenitor of G. hirsutum, is spontaneously present in South Africa. Reciprocal crosses were performed without emasculation between G. herbaceum and G. hirsutum Neither examination of the morphological characteristics nor flow cytometry analysis of the 335 plants resulting from the G. hirsutum x G. herbaceum cross showed any hybrid features...
May 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28545405/genetic-complexity-of-miscanthus-cell-wall-composition-and-biomass-quality-for-biofuels
#9
Tim van der Weijde, Claire L Alvim Kamei, Edouard I Severing, Andres F Torres, Leonardo D Gomez, Oene Dolstra, Chris A Maliepaard, Simon J McQueen-Mason, Richard G F Visser, Luisa M Trindade
BACKGROUND: Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28545156/the-boron-transporter-bnac4-bor1-1c-is-critical-for-inflorescence-development-and-fertility-under-boron-limitation-in-brassica-napus
#10
Quan Zhang, Haifei Chen, Mingliang He, Zhuqing Zhao, Hongmei Cai, Guangda Ding, Lei Shi, Fangsen Xu
Boron (B) is an essential micronutrient for plants, but the molecular mechanisms underlying the uptake and distribution of B in allotetraploid rapeseed (Brassica napus) are unclear. Here, we identified a B transporter of rapeseed, BnaC4.BOR1;1c, which expressed in shoot nodes and involved in distributing B to the reproductive organs. Transgenic Arabidopsis plants containing a BnaC4.BOR1;1c promoter-driven GUS reporter gene showed strong GUS activity in roots, nodal regions of the shoots and immature floral buds...
May 25, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28545144/quantitative-descriptions-of-rice-plant-architecture-and-their-application
#11
Xumeng Li, Xiaohui Wang, Yulin Peng, Hailin Wei, Xinguang Zhu, Shuoqi Chang, Ming Li, Tao Li, Huang Huang
Plant architecture is an important agronomic trait, and improving plant architecture has attracted the attention of scientists for decades, particularly studies to create desirable plant architecture for high grain yields through breeding and culture practices. However, many important structural phenotypic traits still lack quantitative description and modeling on structural-functional relativity. This study defined new architecture indices (AIs) derived from the digitalized plant architecture using the virtual blade method...
2017: PloS One
https://www.readbyqxmd.com/read/28545065/influence-of-the-ferric-uptake-regulator-fur-protein-on-pathogenicity-in-pectobacterium-carotovorum-subsp-brasiliense
#12
Collins Kipngetich Tanui, Divine Yutefar Shyntum, Stefan Louis Priem, Jacques Theron, Lucy Novungayo Moleleki
Iron is an important nutrient for the survival and growth of many organisms. In order to survive, iron uptake from the environment must be strictly regulated and maintained to avoid iron toxicity. The ferric uptake regulator protein (Fur) regulates genes involved in iron homeostasis in many bacteria, including phytopathogens. However, to date, the role played by Fur in the biology of Pectobacterium carotovorum subsp. brasiliense (Pcb1692), an important pathogen of potatoes, has not yet been studied. To this end, we used the lambda recombineering method to generate a fur mutant strain of Pcb1692 and assessed the virulence and fitness of the mutant strain...
2017: PloS One
https://www.readbyqxmd.com/read/28542815/phenotypic-selection-varies-with-pollination-intensity-across-populations-of-sabatia-angularis
#13
Sarah L Emel, Steven J Franks, Rachel B Spigler
Pollinators are considered primary selective agents acting on plant traits, and thus variation in the strength of the plant-pollinator interaction might drive variation in the opportunity for selection and selection intensity across plant populations. Here, we examine whether these critical evolutionary parameters covary with pollination intensity across wild populations of the biennial Sabatia angularis. We quantified pollination intensity in each of nine S. angularis populations as mean stigmatic pollen load per population...
May 25, 2017: New Phytologist
https://www.readbyqxmd.com/read/28542571/quantitative-trait-loci-for-yield-and-grain-plumpness-relative-to-maturity-in-three-populations-of-barley-hordeum-vulgare-l-grown-in-a-low-rain-fall-environment
#14
Bulti Tesso Obsa, Jason Eglinton, Stewart Coventry, Timothy March, Maxime Guillaume, Thanh Phuoc Le, Matthew Hayden, Peter Langridge, Delphine Fleury
Identifying yield and grain plumpness QTL that are independent of developmental variation or phenology is of paramount importance for developing widely adapted and stable varieties through the application of marker assisted selection. The current study was designed to dissect the genetic basis of yield performance and grain plumpness in southern Australia using three doubled haploid (DH) populations developed from crosses between adapted parents that are similar in maturity and overall plant development. Three interconnected genetic populations, Commander x Fleet (CF), Commander x WI4304 (CW), and Fleet x WI4304 (FW) developed from crossing of Australian elite barley genotypes, were used to map QTL controlling yield and grain plumpness...
2017: PloS One
https://www.readbyqxmd.com/read/28541511/molecular-association-of-arabidopsis-rth-with-its-homolog-rte1-in-regulating-ethylene-signaling
#15
Fangfang Zheng, Xiankui Cui, Maximo Rivarola, Ting Gao, Caren Chang, Chun-Hai Dong
The plant hormone ethylene affects many biological processes during plant growth and development. Ethylene is perceived by ethylene receptors at the endoplasmic reticulum (ER) membrane. The ETR1 ethylene receptor is positively regulated by the transmembrane protein RTE1, which localizes to the ER and Golgi apparatus. The RTE1 gene family is conserved in animals, plants, and lower eukaryotes. In Arabidopsis, RTE1-HOMOLOG (RTH) is the only homolog of the Arabidopsis RTE1 gene family. The regulatory function of the Arabidopsis RTH in ethylene signaling and plant growth is largely unknown...
May 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28540573/optimization-of-multi-environment-trials-for-genomic-selection-based-on-crop-models
#16
R Rincent, E Kuhn, H Monod, F-X Oury, M Rousset, V Allard, J Le Gouis
We propose a statistical criterion to optimize multi-environment trials to predict genotype × environment interactions more efficiently, by combining crop growth models and genomic selection models. Genotype × environment interactions (GEI) are common in plant multi-environment trials (METs). In this context, models developed for genomic selection (GS) that refers to the use of genome-wide information for predicting breeding values of selection candidates need to be adapted. One promising way to increase prediction accuracy in various environments is to combine ecophysiological and genetic modelling thanks to crop growth models (CGM) incorporating genetic parameters...
May 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28540496/phenotyping-of-vigs-mediated-gene-silencing-in-rice-using-a-vector-derived-from-a-dna-virus
#17
Ravi Kant, Indranil Dasgupta
Target genes in rice can be optimally silenced if inserted in antisense or hairpin orientation in the RTBV-derived VIGS vector and plants grown at 28 °C and 80% humidity after inoculation. Virus induced gene silencing (VIGS) is a method used to transiently silence genes in dicot as well as monocot plants. For the important monocot species rice, the Rice tungro bacilliform virus (RTBV)-derived VIGS system (RTBV-VIGS), which uses agroinoculation to initiate silencing, has not been standardized for optimal use...
May 24, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28538736/leaf-bacterial-diversity-mediates-plant-diversity-and-ecosystem-function-relationships
#18
Isabelle Laforest-Lapointe, Alain Paquette, Christian Messier, Steven W Kembel
Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28537266/natural-allelic-variation-of-fro2-modulates-arabidopsis-root-growth-under-iron-deficiency
#19
Santosh B Satbhai, Claudia Setzer, Florentina Freynschlag, Radka Slovak, Envel Kerdaffrec, Wolfgang Busch
Low availability of Fe significantly limits crop yields in many parts of the world. However, it is largely unknown which genes and alleles adjust plant growth in Fe limited environments. Using natural variation of a geographically restricted panel of Arabidopsis thaliana accessions, we identify allelic variation at the FRO2 locus associated with root length under iron deficiency. We show that non-coding sequence variation at the FRO2 locus leads to variation of FRO2 transcript levels, as well as ferric chelate reductase activity, and is causal for a portion of the observed root length variation...
May 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28536596/sorghum-landrace-collections-from-cooler-regions-of-the-world-exhibit-magnificent-genetic-differentiation-and-early-season-cold-tolerance
#20
Frank Maulana, Dilooshi Weerasooriya, Tesfaye Tesso
Cold temperature is an important abiotic stress affecting sorghum production in temperate regions. It reduces seed germination, seedling emergence and seedling vigor thus limiting the production of the crop both temporally and spatially. The objectives of this study were (1) to assess early season cold temperature stress response of sorghum germplasm from cooler environments and identify sources of tolerance for use in breeding programs, (2) to determine population structure and marker-trait association among these germplasms for eventual development of marker tools for improving cold tolerance...
2017: Frontiers in Plant Science
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