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Plant association mapping

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https://www.readbyqxmd.com/read/28431521/a-reference-floral-transcriptome-of-sexual-and-apomictic-paspalum-notatum
#1
Juan Pablo A Ortiz, Santiago Revale, Lorena A Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc, Silvina C Pessino
BACKGROUND: Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. RESULTS: We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28430019/characterization-of-rph24-a-gene-conferring-adult-plant-resistance-to-puccinia-hordei-in-barley
#2
Laura A Ziems, Lee T Hickey, Gregory J Platz, Jerome D Franckowiak, Peter M Dracatos, Davinder Singh, Robert F Park
We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers...
April 21, 2017: Phytopathology
https://www.readbyqxmd.com/read/28428796/expression-profiling-coupled-with-in-silico-mapping-identifies-candidate-genes-for-reducing-aflatoxin-accumulation-in-maize
#3
Ramesh Dhakal, Chenglin Chai, Ratna Karan, Gary L Windham, William P Williams, Prasanta K Subudhi
Aflatoxin, produced by Aspergillus flavus, is hazardous to health of humans and livestock. The lack of information about large effect QTL for resistance to aflatoxin accumulation is a major obstacle to employ marker-assisted selection for maize improvement. The understanding of resistance mechanisms of the host plant and the associated genes is necessary for improving resistance to A. flavus infection. A suppression subtraction hybridization (SSH) cDNA library was made using the developing kernels of Mp715 (resistant inbred) and B73 (susceptible inbred) and 480 randomly selected cDNA clones were sequenced to identify differentially expressed genes (DEGs) in response to A...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28418033/a-genome-wide-snp-based-genetic-map-and-qtl-mapping-for-agronomic-traits-in-chinese-cabbage
#4
Li Huang, Yafei Yang, Fang Zhang, Jiashu Cao
The aim of this work was to construct a high-resolution genetic map for the dissection of complex morphological and agronomic traits in Chinese cabbage (Brassica rapa L. syn. B. campestris). Chinese cabbage, an economically important vegetable, is a good model plant for studies on the evolution of morphologic variation. Herein, two high-generation inbred Chinese cabbage lines, 'Huangxiaoza' and 'Bqq094-11', were crossed. Then restriction-site-associated DNA sequencing (RAD-seq) was performed on the parents and 120 F2 individuals...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28405778/verification-and-fine-mapping-of-qgw1-05-a-major-qtl-for-grain-weight-in-maize-zea-mays-l
#5
Qiang Zhou, Yongbin Dong, Qingling Shi, Long Zhang, Huanqing Chen, Chunhui Hu, Yuling Li
Grain weight, one of the important factors to determine corn yield, is a typical quantitative inheritance trait. However, the molecular genetic basis of grain weight still remains limited. In our previous researches, a major QTL associated with grain weight, qGW1.05, has been identified between SSR markers umc1601 and umc1754 at bin locus 1.05-1.06 in maize. Here, its genetic and environmental stabiliteis were verified using a BC3F2 population to identify the effect of qGW1.05 on grain weight. Further, qGW1...
April 12, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28403820/characterization-of-genome-wide-segmental-duplications-reveals-a-common-genomic-feature-of-association-with-immunity-among-domestic-animals
#6
Xiaotian Feng, Jicai Jiang, Abinash Padhi, Chao Ning, Jinluan Fu, Aiguo Wang, Raphael Mrode, Jian-Feng Liu
BACKGROUND: Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species. RESULTS: Aiming at characterizing SDs across the genomes of diverse livestock species, we mapped genome-wide SDs of horse, rabbit, goat, sheep and chicken, and also enhanced the existing SD maps of cattle and pig genomes based on the most updated genome assemblies...
April 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28400567/genetic-dissection-of-yield-traits-in-super-hybrid-rice-xieyou9308-using-both-unconditional-and-conditional-genome-wide-association-mapping
#7
Yingxin Zhang, Liyuan Zhou, Xihong Shen, Daibo Chen, Weixun Wu, Xiaodeng Zhan, Qunen Liu, Aike Zhu, Xiangyang Lou, Haiming Xu, Shihua Cheng, Liyong Cao
With the development and application of super rice breeding, elite rice hybrids with super high-yielding potential have been widely developed in last decades in China. Xieyou9308 is one of the most famous super hybrid rice varieties. To uncover the genetic mechanism of Xieyou9308's high yield potential, a recombinant inbred line (RIL) population derived from cross of XieqingzaoB and Zhonghui9308 was re-sequenced and investigated on the grain yield (GYD) and its three component traits, number of panicles per plant (NP), number of filled grains per panicle (NFGP), and grain weight (GW)...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28400495/constitutively-active-arabidopsis-map-kinase-3-triggers-defense-responses-involving-salicylic-acid-and-summ2-resistance-protein
#8
Baptiste Genot, Julien Lang, Souha Berriri, Marie Garmier, Françoise Gilard, Stéphanie Pateyron, Katrien Haustraete, Dominique Van Der Straeten, Heribert Hirt, Jean Colcombet
Mitogen-activated protein kinases (MAPKs) are important regulators of plant immunity. Most of the knowledge about the function of these pathways is derived from loss-of-function approaches. Using a gain-of-function approach, we investigated the responses controlled by a constitutively active (CA) MPK3 in Arabidopsis thaliana. CA-MPK3 plants are dwarfed and display a massive de-repression of defense genes associated with spontaneous cell death as well as accumulation of reactive oxygen species (ROS), phytoalexins and the stress-related hormones ethylene and salicylic acid (SA)...
April 11, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28387006/novel-candidatus-liberibacter-species-identified-in-the-australian-eggplant-psyllid-acizzia-solanicola
#9
Jacqueline Morris, Jason Shiller, Rachel Mann, Grant Smith, Alan Yen, Brendan Rodoni
A novel candidate species of the liberibacter genus, 'Candidatus Liberibacter brunswickensis' (CLbr), was identified in the Australian eggplant psyllid, Acizzia solanicola. This is the first discovery of a species belonging to the liberibacter genus in Australia and the first report of a liberibacter species in the psyllid genus Acizzia. This new candidate liberibacter species has not been associated with plant disease, unlike other psyllid-vectored species in the genus including 'Candidatus Liberibacter asiaticus' (CLas), 'Candidatus Liberibacter africanus' (CLaf) and 'Ca...
April 7, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28385710/non-random-domain-organization-of-the-arabidopsis-genome-at-the-nuclear-periphery
#10
Xiuli Bi, Yingjuan Cheng, Bo Hu, Xiaoli Ma, Rui Wu, Jiawei Wang, Chang Liu
The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the non-random positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants...
April 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28384183/qtl-mapping-of-wheat-plant-architectural-characteristics-and-their-genetic-relationship-with-seven-qtls-conferring-resistance-to-sheath-blight
#11
Yan Guo, Ziyi Du, Jiang Chen, Zhongjun Zhang
Sheath blight is one of the most devastating wheat diseases worldwide. Breeding resistant cultivars is the most powerful strategy to defeat the disease. Plant resistance on "disease escape" works through modulation of morphological traits and shows sustainable resistance to disease. Plant architectural traits have been reported to play a significant role in disease response. Therefore, exploring the genetic relationship between plant architecture and disease resistance is of importance to the understanding of plant resistance via "disease escape"...
2017: PloS One
https://www.readbyqxmd.com/read/28383882/uptake-and-distribution-of-silver-in-the-aquatic-plant-landoltia-punctata-duckweed-exposed-to-silver-and-silver-sulfide-nanoparticles
#12
John P Stegemeier, Benjamin P Colman, Fabienne Schwab, Mark R Wiesner, Gregory V Lowry
Aquatic ecosystems are expected to receive Ag0 and Ag2S nanoparticles (NPs) through anthropogenic waste streams. The speciation of silver in Ag-NPs affects their fate in ecosystems, but its influence on interactions with aquatic plants is still unclear. Here, the Ag speciation and distribution was measured in an aquatic plant, duckweed (Landoltia punctata), exposed to Ag0 or Ag2S NPs, or to AgNO3. The silver distribution in duckweed roots was visualized using synchrotron-based micro X-ray fluorescence (XRF) mapping and Ag speciation was determined using extended X-ray absorption fine structure (EXAFS) spectroscopy...
April 6, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28370170/genome-wide-association-mapping-for-phenotypic-plasticity-in-rice
#13
Shinji Kikuchi, Raju Bheemanahalli, Krishna S V Jagadish, Etsushi Kumagai, Yusuke Masuya, Eiki Kuroda, Chitra Raghavan, Michael Dingkuhn, Akira Abe, Hiroyuki Shimono
Phenotypic plasticity of plants in response to environmental changes is important for adapting to changing climate. Less attention has been paid to exploring the advantages of phenotypic plasticity in resource-rich environments to enhance the productivity of agricultural crops. Here, we examined genetic variation in phenotypic plasticity in indica rice (Oryza sativa L.) across two diverse panels: (i) a Phenomics of Rice Adaptation and Yield (PRAY) population comprising 301 accessions and (ii) a Multi-parent-Advanced-Generation-Inter-Cross (MAGIC) indica population comprising 151 accessions...
March 31, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28369427/repeat-length-variation-in-a-wheat-cellulose-synthase-like-gene-is-associated-with-altered-tiller-number-and-stem-cell-wall-composition
#14
J Hyles, S Vautrin, F Pettolino, C MacMillan, Z Stachurski, J Breen, H Berges, T Wicker, W Spielmeyer
The tiller inhibition gene (tin) that reduces tillering in wheat (Triticum aestivum) is also associated with large spikes, increased grain weight, and thick leaves and stems. In this study, comparison of near-isogenic lines (NILs) revealed changes in stem morphology, cell wall composition, and stem strength. Microscopic analysis of stem cross-sections and chemical analysis of stem tissue indicated that cell walls in tin lines were thicker and more lignified than in free-tillering NILs. Increased lignification was associated with stronger stems in tin plants...
March 28, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28367154/genome-analysis-identified-novel-candidate-genes-for-ascochyta-blight-resistance-in-chickpea-using-whole-genome-re-sequencing-data
#15
Yongle Li, Pradeep Ruperao, Jacqueline Batley, David Edwards, Jenny Davidson, Kristy Hobson, Tim Sutton
Ascochyta blight (AB) is a fungal disease that can significantly reduce chickpea production in Australia and other regions of the world. In this study, 69 chickpea genotypes were sequenced using whole genome re-sequencing (WGRS) methods. They included 48 Australian varieties differing in their resistance ranking to AB, 16 advanced breeding lines from the Australian chickpea breeding program, four landraces, and one accession representing the wild chickpea species Cicer reticulatum. More than 800,000 single nucleotide polymorphisms (SNPs) were identified...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28363587/a-pp2c-1-allele-underlying-a-quantitative-trait-locus-enhances-soybean-100-seed-weight
#16
Xiang Lu, Qing Xiong, Tong Cheng, Qing-Tian Li, Xin-Lei Liu, Ying-Dong Bi, Wei Li, Wan-Ke Zhang, Biao Ma, Yong-Cai Lai, Wei-Guang Du, Wei-Qun Man, Shou-Yi Chen, Jin-Song Zhang
Cultivated soybeans may lose some useful genetic locus during domestication. Introgression of genes from wild soybeans may broaden the genetic background and improve soybean agronomic traits. Here, through whole-genome sequencing of an RIL population derived from a cross between a wild soybean ZYD7 and a cultivated soybean HN44, and mapping of QTLs for seed weight, we discover that a phosphatase 2C-1 (PP2C-1) allele from wild soybean ZYD7 contributes to the increase of seed weight/size in transgenic plants...
March 28, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28361363/fine-mapping-and-candidate-gene-analysis-of-qfl-chr1-a-fiber-length-qtl-in-cotton
#17
Peng Xu, Jin Gao, Zhibin Cao, Peng W Chee, Qi Guo, Zhenzhen Xu, Andrew H Paterson, Xianggui Zhang, Xinlian Shen
A fiber length QTL, qFL-chr1, was fine mapped to a 0.9 cM interval of cotton chromosome 1. Two positional candidate genes showed positive correlation between gene expression level and fiber length. Prior analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum L. and G. barbadense L. revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, a single NIIL, R01-40-08, was used to develop a large population segregating for the target region...
March 30, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28360923/adaptation-mechanisms-in-the-evolution-of-moss-defenses-to-microbes
#18
REVIEW
Inés Ponce de León, Marcos Montesano
Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28355304/isolation-and-characterization-of-the-tasnrk2-10-gene-and-its-association-with-agronomic-traits-in-wheat-triticum-aestivum-l
#19
Zhao-Gui Zhang, Guang-de Lv, Bing Li, Jia-Jia Wang, Yan Zhao, Fan-Mei Kong, Ying Guo, Si-Shen Li
Sucrose non-fermenting 1-related protein kinases (SnRKs) comprise a major family of signaling genes in plants and are associated with metabolic regulation, nutrient utilization and stress responses. This gene family has been proposed to be involved in sucrose signaling. In the present study, we cloned three copies of the TaSnRK2.10 gene from bread wheat on chromosomes 4A, 4B and 4D. The coding sequence (CDS) is 1086 bp in length and encodes a protein of 361 amino acids that exhibits functional domains shared with SnRK2s...
2017: PloS One
https://www.readbyqxmd.com/read/28349183/resveratrol-protects-the-loss-of-connexin-43-induced-by-ethanol-exposure-in-neonatal-mouse-cardiomyocytes
#20
Su Tu, Fu-Tao Cao, Xiao-Chun Fan, Cheng-Jian Yang
Excessive alcohol consumption provides risk to cardiomyopathy with unknown mechanisms. Resveratrol, a plant polyphenol, is widely reported for its cardiovascular benefits, while its effect on alcohol-induced impairments in cardiomyocytes largely remains unknown. Effects of resveratrol on the cardiomyocytes under ethanol insult were studied in vitro. Ethanol exposure in mouse neonatal cardiomyocytes increased cell death and induced a specific loss of tight junction protein, connexin 43. In spite of adverse effects at higher concentrations, resveratrol at 10 μM improved cell viability of cardiomyocytes in the presence of a deleterious dose of ethanol...
March 28, 2017: Naunyn-Schmiedeberg's Archives of Pharmacology
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