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Plant association mapping

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https://www.readbyqxmd.com/read/29150594/mating-design-and-genetic-structure-of-a-multi-parent-advanced-generation-inter-cross-magic-population-of-sorghum-sorghum-bicolor-l-moench
#1
Patrick O Ongom, Gebisa Ejeta
MAGIC populations are powerful next generation mapping resources. We describe here the mating design and structure of the first MAGIC population in sorghum and test its utility for mapping. The population was developed by intercrossing 19 diverse founder lines, through a series of paired crosses with a genetic male sterile source, followed by 10 generations of random mating. At the final stage of random mating, one thousand random fertile plants in the population were identified and subjected to six generations of selfing to produce 1000 immortal MAGIC inbred lines...
November 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29149280/whole-genome-re-sequencing-of-two-italian-tomato-landraces-reveals-sequence-variations-in-genes-associated-with-stress-tolerance-fruit-quality-and-long-shelf-life-traits
#2
Valentina Tranchida-Lombardo, Riccardo Aiese Cigliano, Irantzu Anzar, Simone Landi, Samuela Palombieri, Chiara Colantuono, Hamed Bostan, Pasquale Termolino, Riccardo Aversano, Giorgia Batelli, Maria Cammareri, Domenico Carputo, Maria Luisa Chiusano, Clara Conicella, Federica Consiglio, Nunzio D'Agostino, Monica De Palma, Antonio Di Matteo, Silvana Grandillo, Walter Sanseverino, Marina Tucci, Stefania Grillo
Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65...
November 14, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29147724/glabrous-cmgl-encodes-a-hd-zip-iv-transcription-factor-playing-roles-in-multicellular-trichome-initiation-in-melon
#3
Huayu Zhu, Xiaofen Sun, Qi Zhang, Pengyao Song, Qianmei Hu, Xiaojing Zhang, Xiang Li, Jianbin Hu, Junsong Pan, Shouru Sun, Yiqun Weng, Luming Yang
Map-based cloning identified CmGL that encodes a HD-ZIP type IV transcription factor that controls multicellular trichome initiation in melon. Trichomes are small hairs covering the aerial parts of plants that originate from the epidermal cells, which can protect plants against the damage by insects and pathogens. The regulatory pathway of unicellular trichomes has been well studied in the model plant Arabidopsis. Little is known about the genetic control and regulation of trichome development in melon (Cucumis melo L...
November 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29143603/evolution-of-vrn-1-homoeologous-loci-in-allopolyploids-of-triticum-and-their-diploid-precursors
#4
REVIEW
Andrey B Shcherban, Elena A Salina
BACKGROUND: The key gene in genetic system controlling the duration of the vegetative period in cereals is the VRN1 gene, whose product under the influence of low temperature (vernalization) promotes the transition of the apical meristem cells into a competent state for the development of generative tissues of spike. As early genetic studies shown, the dominant alleles of this gene underlie the spring forms of plants that do not require vernalization for this transition. In wheat allopolyploids various combinations of alleles of the VRN1 homoeologous loci (VRN1 homoeoalleles) provide diversity in such important traits as the time to heading, height of plants and yield...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143298/a-single-nucleotide-mutation-of-ispf-gene-involved-in-the-mep-pathway-for-isoprenoid-biosynthesis-causes-yellow-green-leaf-phenotype-in-rice
#5
Rui Huang, Yang Wang, Pingrong Wang, Chunmei Li, Fuliang Xiao, Nenggang Chen, Na Li, Caixia Li, Changhui Sun, Lihua Li, Rongjun Chen, Zhengjun Xu, Jianqing Zhu, Xiaojian Deng
We identified IspF gene through yellow-green leaf mutant 505ys in rice. OsIspF was expressed in all tissues detected, and its encoded protein was targeted to the chloroplast. On expression levels of genes in this mutant, OsIspF itself and the genes encoding other enzymes of the MEP pathway and chlorophyll synthase were all up-regulated, however, among eight genes associated with photosynthesis, only psaA, psaN and psbA genes for three reaction center subunits of photosystem obviously changed. Isoprenoids are the most abundant natural compounds in all organisms, which originate from the basic five-carbon units isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)...
November 15, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29140792/a-bayesian-hierarchical-model-for-identifying-significant-polygenic-effects-while-controlling-for-confounding-and-repeated-measures
#6
Christopher McMahan, James Baurley, William Bridges, Chase Joyner, Muhamad Fitra Kacamarga, Robert Lund, Carissa Pardamean, Bens Pardamean
Genomic studies of plants often seek to identify genetic factors associated with desirable traits. The process of evaluating genetic markers one by one (i.e. a marginal analysis) may not identify important polygenic and environmental effects. Further, confounding due to growing conditions/factors and genetic similarities among plant varieties may influence conclusions. When developing new plant varieties to optimize yield or thrive in future adverse conditions (e.g. flood, drought), scientists seek a complete understanding of how the factors influence desirable traits...
November 15, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29135338/convergent-and-divergent-signaling-in-pamp-triggered-immunity-and-effector-triggered-immunity
#7
Yujun Peng, Rowan van Wersch, Yuelin Zhang
Plants use diverse immune receptors to sense pathogen attacks. Recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors localized on the plasma membrane leads to PAMP-triggered immunity (PTI). Detection of pathogen effectors by intracellular or plasma membrane-localized immune receptors results in effector-triggered immunity (ETI). Despite the large variations in the magnitude and duration of immune responses triggered by different PAMPs or pathogen effectors during PTI and ETI, plasma membrane-localized immune receptors activate similar downstream molecular events such as MAP kinase activation, oxidative burst, ion influx and increased biosynthesis of plant defense hormones, indicating that defense signals initiated at the plasma membrane converge at later points...
November 14, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29132315/comprehensive-genomic-analysis-of-the-cngc-gene-family-in-brassica-oleracea-novel-insights-into-synteny-structures-and-transcript-profiles
#8
Kaleem U Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A Almoneafy, Raqeeb Ullah, Xue-Liang Ren, Qing-Yao Shu
BACKGROUND: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. RESULTS: In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29131848/high-throughput-m6a-seq-reveals-rna-m6a-methylation-patterns-in-the-chloroplast-and-mitochondria-transcriptomes-of-arabidopsis-thaliana
#9
Zegang Wang, Kai Tang, Dayong Zhang, Yizhen Wan, Yan Wen, Quanyou Lu, Lei Wang
This study is the first to comprehensively characterize m6A patterns in the Arabidopsis chloroplast and mitochondria transcriptomes based on our open accessible data deposited in NCBI's Gene Expression Omnibus with GEO Series accession number of GSE72706. Over 86% of the transcripts were methylated by m6A in the two organelles. Over 550 and 350 m6A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m6A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m6A methylation extent in the two organelles was greatly higher than that in the nucleus...
2017: PloS One
https://www.readbyqxmd.com/read/29123537/association-mapping-of-ferrous-zinc-and-aluminum-tolerance-at-the-seedling-stage-in-indica-rice-using-magic-populations
#10
Lijun Meng, Baoxiang Wang, Xiangqian Zhao, Kimberly Ponce, Qian Qian, Guoyou Ye
Excessive amounts of metal are toxic and severely affect plant growth and development. Understanding the genetic control of metal tolerance is crucial to improve rice resistance to Fe, Zn, and Al toxicity. The multi-parent advanced generation inter-cross (MAGIC) populations were genotyped using a 55 K rice SNP array and screened at the seedling stage for Fe, Zn, and Al toxicity using a hydroponics system. Association analysis was conducted by implementing a mixed linear model (MLM) for each of the five MAGIC populations double cross DC1 (founders were SAGC-08, HHZ5-SAL9-Y3-Y1, BP1976B-2-3-7-TB-1-1, PR33282-B-8-1-1-1-1-1), double cross DC2 (founders of double cross were FFZ1, CT 16658-5-2-2SR-2-3-6MP, IR 68, IR 02A127), eight parents population 8way (founders were SAGC-08, HHZ5-SAL9-Y3-Y1, BP1976B-2-3-7-TB-1-1, PR33282-B-8-1-1-1-1-1, FFZ1, CT 16658-5-2-2SR-2-3-6MP, IR 68, IR 02A127), DC12 (DC1+DC2) and rice multi-parent recombinant inbred line population RMPRIL (DC1+DC2+8way)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29118823/sequence-analysis-of-cultivated-strawberry-fragaria%C3%A2-%C3%A3-%C3%A2-ananassa-duch-using-microdissected-single-somatic-chromosomes
#11
Tomohiro Yanagi, Kenta Shirasawa, Mayuko Terachi, Sachiko Isobe
Background: Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA sequences, it is difficult to determine whether these sequences are derived from the same chromosome. To avoid the difficulties associated with homoeologous chromosomes and demonstrate the possibility of sequencing allopolyploids using single chromosomes, we conducted sequence analysis using microdissected single somatic chromosomes of cultivated strawberry...
2017: Plant Methods
https://www.readbyqxmd.com/read/29115920/genome-wide-association-mapping-of-resistance-to-a-brazilian-isolate-of-sclerotinia-sclerotiorum-in-soybean-genotypes-mostly-from-brazil
#12
Wei Wei, Ana Carolina Oliveira Mesquita, Adriana de A Figueiró, Xing Wu, Shilpa Manjunatha, Daniel P Wickland, Matthew E Hudson, Fernando C Juliatti, Steven J Clough
BACKGROUND: Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29081789/genetic-architecture-of-natural-variation-in-rice-nonphotochemical-quenching-capacity-revealed-by-genome-wide-association-study
#13
Quanxiu Wang, Hu Zhao, Junpeng Jiang, Jiuyue Xu, Weibo Xie, Xiangkui Fu, Chang Liu, Yuqing He, Gongwei Wang
The photoprotective processes conferred by nonphotochemical quenching (NPQ) serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice (Oryza sativa), and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS) for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29080185/genome-wide-association-mapping-analyses-applied-to-polyamines
#14
Luis Barboza-Barquero, Paul Esker, Rubén Alcázar
Genome Wide Association Studies (GWAS) allow the use of natural variation to understand the genetics controlling specific traits. Efficient methods to conduct GWAS in plants have been reported. This chapter provides the main steps to conduct and analyse GWAS in Arabidopsis thaliana using polyamine levels as trait. This approach is suitable for the discovery of genes that modulate the levels of polyamines, and can be used in combination with different types of stress.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29080179/generation-of-ems-mutagenized-populations-of-arabidopsis-thaliana-for-polyamine-genetics
#15
Kostadin E Atanasov, Changxin Liu, Antonio F Tiburcio, Rubén Alcázar
In the recent years, genetic engineering of polyamine biosynthetic genes has provided evidence for their involvement in plant stress responses and different aspects of plant development. Such approaches are being complemented with the use of reverse genetics, in which mutants affected on a particular trait, tightly associated with polyamines, are isolated and the causal genes mapped. Reverse genetics enables the identification of novel genes in the polyamine pathway, which may be involved in downstream signaling, transport, homeostasis, or perception...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29078746/qtl-mapping-and-candidate-gene-analysis-of-ferrous-iron-and-zinc-toxicity-tolerance-at-seedling-stage-in-rice-by-genome-wide-association-study
#16
Jian Zhang, Kai Chen, Yunlong Pang, Shahzad Amir Naveed, Xiuqin Zhao, Xiaoqian Wang, Yun Wang, Michael Dingkuhn, Julie Pasuquin, Zhikang Li, Jianlong Xu
BACKGROUND: Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity and greatly affect rice yield and quality. To improve rice production, understanding the genetic and molecular resistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is an effective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the genetic relationship between them in a genetically diverse population...
October 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29078140/ecosystem-services-urban-parks-under-a-magnifying-glass
#17
Teresa Mexia, Joana Vieira, Adriana Príncipe, Andreia Anjos, Patrícia Silva, Nuno Lopes, Catarina Freitas, Margarida Santos-Reis, Otília Correia, Cristina Branquinho, Pedro Pinho
Urban areas' population has grown during the last century and it is expected that over 60% of the world population will live in cities by 2050. Urban parks provide several ecosystem services that are valuable to the well-being of city-dwellers and they are also considered a nature-based solution to tackle multiple environmental problems in cities. However, the type and amount of ecosystem services provided will vary with each park vegetation type, even within same the park. Our main goal was to quantify the trade-offs in ecosystem services associated to different vegetation types, using a spatially detailed approach...
October 24, 2017: Environmental Research
https://www.readbyqxmd.com/read/29077764/detection-of-quantitative-trait-loci-controlling-grain-zinc-concentration-using-australian-wild-rice-oryza-meridionalis-a-potential-genetic-resource-for-biofortification-of-rice
#18
Ryo Ishikawa, Masahide Iwata, Kenta Taniko, Gotaro Monden, Naoya Miyazaki, Chhourn Orn, Yuki Tsujimura, Shusaku Yoshida, Jian Feng Ma, Takashige Ishii
Zinc (Zn) is one of the essential mineral elements for both plants and humans. Zn deficiency in human is one of the major causes of hidden hunger, a serious health problem observed in many developing countries. Therefore, increasing Zn concentration in edible part is an important issue for improving human Zn nutrition. Here, we found that an Australian wild rice O. meridionalis showed higher grain Zn concentrations compared with cultivated and other wild rice species. The quantitative trait loci (QTL) analysis was then performed to identify the genomic regions controlling grain Zn levels using backcross recombinant inbred lines derived from O...
2017: PloS One
https://www.readbyqxmd.com/read/29076604/mass-spectrometry-characterization-of-endophytic-bacterium-curtobacterium-sp-strain-er1-6-isolated-from-citrus-sinensis
#19
Francisca Diana da Silva Araújo, Daiene Souza Santos, Carolina Clepf Pagotto, Welington Luiz de Araújo, Marcos Nogueira Eberlin
The bacteria of the genus Curtobacterium are usually seen as plant pathogen, but some species have been identified as endophytes of different crops, and could as such present a potential for disease control and plant growth promotion. We have therefore applied the desorption electrospray ionization mass spectrometry imaging (DESI-MSI) in the direct analysis of living Curtobacterium sp. strain ER1/6 colonies to map the surface metabolites, and electrospray ionization tandem mass spectrometry (ESI-MS/MS) for characterization of these compounds...
October 27, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/29075283/molecular-basis-of-resistance-to-fusarium-ear-rot-in-maize
#20
REVIEW
Alessandra Lanubile, Valentina Maschietto, Virginia M Borrelli, Lorenzo Stagnati, Antonio F Logrieco, Adriano Marocco
The impact of climate change has been identified as an emerging issue for food security and safety, and the increased incidence of mycotoxin contamination in maize over the last two decades is considered a potential emerging hazard. Disease control by chemical and agronomic approaches is often ineffective and increases the cost of production; for this reason the exploitation of genetic resistance is the most sustainable method for reducing contamination. The review focuses on the significant advances that have been made in the development of transcriptomic, genetic and genomic information for maize, Fusarium verticillioides molds, and their interactions, over recent years...
2017: Frontiers in Plant Science
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