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Plant association mapping

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https://www.readbyqxmd.com/read/28525967/candidate-gene-based-association-mapping-in-fusarium-culmorum-for-field-quantitative-pathogenicity-and-mycotoxin-production-in-wheat
#1
Valheria Castiblanco, Jose J Marulanda, Tobias Würschum, Thomas Miedaner
BACKGROUND: Quantitative traits are common in nature, but quantitative pathogenicity has received only little attention in phytopathology. In this study, we used 100 Fusarium culmorum isolates collected from natural field environments to assess their variation for two quantitative traits, aggressiveness and deoxynivalenol (DON) production on wheat plants grown in four different field environments (location-year combinations). Seventeen Fusarium graminearum pathogenicity candidate genes were assessed for their effect on the aggressiveness and DON production of F...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28523639/association-mapping-of-yield-and-yield-related-traits-under-reproductive-stage-drought-stress-in-rice-oryza-sativa-l
#2
B P Mallikarjuna Swamy, Noraziyah Abd Aziz Shamsudin, Site Noorzuraini Abd Rahman, Ramil Mauleon, Wickneswari Ratnam, Ma Teressa Sta Cruz, Arvind Kumar
BACKGROUND: The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS: The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%...
December 2017: Rice
https://www.readbyqxmd.com/read/28520776/proteomic-analysis-of-tea-plants-camellia-sinensis-with-purple-young-shoots-during-leaf-development
#3
Qiongqiong Zhou, Zhidan Chen, Jinwook Lee, Xinghui Li, Weijiang Sun
Tea products made from purple leaves are highly preferred by consumers due to the health benefits. This study developed a proteome reference map related to color changes during leaf growth in tea (Camellia sinensis) plant with purple young shoots using two-dimensional electrophoresis (2-DE). Forty-six differentially expressed proteins were detected in the gel and successfully identified by using MALDI-TOF/TOF-MS. The pronounced changes in the proteomic profile between tender purple leaves (TPL) and mature green leaves (MGL) included: 1) the lower activity of proteins associated with CO2 assimilation, energy metabolism and photo flux efficiency and higher content of anthocyanins in TPL than those in MGL may protect tender leaves against photo-damage; 2) the higher abundance of chalcone synthase (CHS), chalcone isomerase (CHI) and flavonol synthase (FLS) likely contributes to the synthesis of anthocyanins, catechins and flavonols in TPL tissues; 3) higher abundance of stress response proteins, such as glutathione S-transferases (GST) and phospholipid hydroperoxide glutathione peroxidase (PHGPx), could enhance the tolerance of TPL tissues to adverse condition in; and 4) the increased abundance of proteins related to protein synthesis, nucleic acids and cell wall proteins should be beneficial for the proliferation and expansion of leaf cell in TPL tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28517039/genetics-of-mycorrhizal-symbiosis-in-winter-wheat-triticum-aestivum
#4
Heike Lehnert, Albrecht Serfling, Matthias Enders, Wolfgang Friedt, Frank Ordon
Bread wheat (Triticum aestivum) is a major staple food and therefore of prime importance for feeding the Earth's growing population. Mycorrhiza is known to improve plant growth, but although extensive knowledge concerning the interaction between mycorrhizal fungi and plants is available, genotypic differences concerning the ability of wheat to form mycorrhizal symbiosis and quantitative trait loci (QTLs) involved in mycorrhization are largely unknown. Therefore, a diverse set of 94 bread wheat genotypes was evaluated with regard to root colonization by arbuscular mycorrhizal fungi...
May 18, 2017: New Phytologist
https://www.readbyqxmd.com/read/28503182/genome-wide-snp-markers-based-on-slaf-seq-uncover-breeding-traces-in-rapeseed-brassica-napus-l
#5
Qinghong Zhou, Can Zhou, Wei Zheng, Annaliese S Mason, Shuying Fan, Caijun Wu, Donghui Fu, Yingjin Huang
Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28495892/lux-bacterial-biosensors-for-in-vivo-spatiotemporal-mapping-of-root-secretion
#6
Francesco Pini, Alison K East, Corinne Appia-Ayme, Jakub Tomek, Ramakrishnan Karunakaran, Marcela Mendoza-Suarez, Anne Edwards, Jason Terpolilli, Joshua Rowoth, J Allan Downie, Phil Poole
Plants engineer the rhizosphere to their advantage by secreting various nutrients and secondary metabolites. Coupling transcriptomic and metabolomic analysis of the Pisum sativum rhizosphere, a suite of bioreporters has been developed in Rhizobium leguminosarum bv. viciae 3841, and these detect metabolites secreted by roots in space and time. Fourteen bacterial lux-fusion bioreporters, specific for sugars, polyols, amino acids, organic acids or flavonoids, have been validated in vitro and in vivo. Using different bacterial mutants (nodC, nifH), the process of colonization and symbiosis has been analyzed, revealing compounds important in the different steps of the rhizobial-legume association...
May 11, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28493955/molecular-diversity-analysis-drought-related-marker-traits-association-mapping-and-discovery-of-excellent-alleles-for-100-day-old-plants-by-est-ssrs-in-cassava-germplasms-manihot-esculenta-cranz
#7
Bin Wang, Xin Guo, Pingjuan Zhao, Mengbin Ruan, Xiaoling Yu, Liangping Zou, Yiling Yang, Xiao Li, Deli Deng, Jixiang Xiao, Yiwei Xiao, Chunji Hu, Xue Wang, Xiaolin Wang, Wenquan Wang, Ming Peng
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2...
2017: PloS One
https://www.readbyqxmd.com/read/28493942/amplifying-recombination-genome-wide-and-reshaping-crossover-landscapes-in-brassicas
#8
Alexandre Pelé, Matthieu Falque, Gwenn Trotoux, Frédérique Eber, Sylvie Nègre, Marie Gilet, Virginie Huteau, Maryse Lodé, Thibaut Jousseaume, Sylvain Dechaumet, Jérôme Morice, Charles Poncet, Olivier Coriton, Olivier C Martin, Mathieu Rousseau-Gueutin, Anne-Marie Chèvre
Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male...
May 11, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28493303/comprehensive-profiling-of-rhizome-associated-alternative-splicing-and-alternative-polyadenylation-in-moso-bamboo-phyllostachys-edulis
#9
Taotao Wang, Huiyuan Wang, Dawei Cai, Yubang Gao, Hangxiao Zhang, Yongsheng Wang, Chentao Lin, Liuyin Ma, Lianfeng Gu
Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to their well-developed rhizomes system. However, the post-transcriptional mechanism has not been comprehensively studied for the development of rhizome system in bamboo. We therefore used a combination of single-molecule long-read sequencing technology and polyadenylation site sequencing (PAS-seq) to re-annotate the bamboo genome, and genome-wide identify alternative splicing (AS) and alternative polyadenylation (APA) in the rhizomes system...
May 10, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28491075/saturation-mapping-of-a-major-effect-qtl-for-stripe-rust-resistance-on-wheat-chromosome-2b-in-cultivar-napo-63-using-snp-genotyping-arrays
#10
Jianhui Wu, Qilin Wang, Shengjie Liu, Shuo Huang, Jingmei Mu, Qingdong Zeng, Lili Huang, Dejun Han, Zhensheng Kang
Stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum L.). Widespread deployment of resistant cultivars is the best means of achieving durable disease control. The red grain, spring wheat cultivar Napo 63 produced by CIMMYT in the 1960s shows a high level of adult-plant resistance to stripe rust in the field. To elucidate the genetic basis of resistance in this cultivar we evaluated 224 F2:3 lines and 175 F2:6 recombinant inbred lines (RILs) derived from a cross between Napo 63 and the Pst-susceptible line Avocet S...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28487704/a-combined-comparative-transcriptomic-metabolomic-and-anatomical-analyses-of-two-key-domestication-traits-pod-dehiscence-and-seed-dormancy-in-pea-pisum-sp
#11
Iveta Hradilová, Oldřich Trněný, Markéta Válková, Monika Cechová, Anna Janská, Lenka Prokešová, Khan Aamir, Nicolas Krezdorn, Björn Rotter, Peter Winter, Rajeev K Varshney, Aleš Soukup, Petr Bednář, Pavel Hanáček, Petr Smýkal
The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28483051/es7-encoding-a-ferredoxin-dependent-glutamate-synthase-functions-in-nitrogen-metabolism-and-impacts-leaf-senescence-in-rice
#12
Zhenzhen Bi, Yingxin Zhang, Weixun Wu, Xiaodeng Zhan, Ning Yu, Tingting Xu, Qunen Liu, Zhi Li, Xihong Shen, Daibo Chen, Shihua Cheng, Liyong Cao
Glutamate synthase (GOGAT) is a key enzyme for nitrogen metabolism and ammonium assimilation in plants. In this study, an early senescence 7 (es7) mutant was identified and characterized. The leaves of the es7 mutant begin to senesce at the tillering stage about 60day after sowing, and become increasingly senescent as the plants develop at the heading stage. When es7 plants are grown under photorespiration-suppressed conditions (high CO2), the senescence phenotype and chlorophyll content are rescued. qRT-PCR analysis showed that senescence- associated genes were up-regulated significantly in es7...
June 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28482802/high-density-genetic-map-construction-and-qtls-identification-for-plant-height-in-white-jute-corchorus-capsularis-l-using-specific-locus-amplified-fragment-slaf-sequencing
#13
Aifen Tao, Long Huang, Guifen Wu, Reza Keshavarz Afshar, Jianmin Qi, Jiantang Xu, Pingping Fang, Lihui Lin, Liwu Zhang, Peiqing Lin
BACKGROUND: Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping...
May 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28482306/mapping-allergenic-pollen-vegetation-in-uk-to-study-environmental-exposure-and-human-health
#14
Rachel N McInnes, Deborah Hemming, Peter Burgess, Donna Lyndsay, Nicholas J Osborne, Carsten Ambelas Skjøth, Sam Thomas, Sotiris Vardoulakis
Allergenic pollen is produced by the flowers of a number of trees, grasses and weeds found throughout the UK. Exposure to such pollen grains can exacerbate pollen-related asthma and allergenic conditions such as allergic rhinitis (hay fever). Maps showing the location of these allergenic taxa have many applications: they can be used to provide advice on risk assessments; combined with health data to inform research on health impacts such as respiratory hospital admissions; combined with weather data to improve pollen forecasting systems; or as inputs to pollen emission models...
May 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28468906/whole-genome-restriction-mapping-by-subhaploid-based-rad-sequencing-an-efficient-and-flexible-approach-for-physical-mapping-and-genome-scaffolding
#15
Jinzhuang Dou, Huaiqian Dou, Chuang Mu, Lingling Zhang, Yangping Li, Jia Wang, Tianqi Li, Yuli Li, Xiaoli Hu, Shi Wang, Zhenmin Bao
Assembly of complex genomes using short reads remains a major challenge, which usually yields highly fragmented assemblies. Generation of ultra-dense linkage maps is promising for anchoring such assemblies, but traditional linkage mapping methods are hindered by the infrequency and unevenness of meiotic recombination that limit attainable map resolution. Here we develop a sequencing-based "in vitro" linkage mapping approach (called RadMap), where chromosome breakage and segregation are realized by generating hundreds of "subhaploid" fosmid/BAC clone pools, and by restriction site-associated DNA (RAD) sequencing of these clone pools to produce an ultra-dense whole-genome restriction map to facilitate genome scaffolding...
May 3, 2017: Genetics
https://www.readbyqxmd.com/read/28460071/interactive-microbial-distribution-analysis-using-bioatlas
#16
Jesper Beltoft Lund, Markus List, Jan Baumbach
Massive amounts of 16S rRNA sequencing data have been stored in publicly accessible databases, such as GOLD, SILVA, GreenGenes (GG), and the Ribosomal Database Project (RDP). Many of these sequences are tagged with geo-locations. Nevertheless, researchers currently lack a user-friendly tool to analyze microbial distribution in a location-specific context. BioAtlas is an interactive web application that closes this gap between sequence databases, taxonomy profiling and geo/body-location information. It enables users to browse taxonomically annotated sequences across (i) the world map, (ii) human body maps and (iii) user-defined maps...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28458915/the-diversification-of-begomovirus-populations-is-predominantly-driven-by-mutational-dynamics
#17
Alison T M Lima, José C F Silva, Fábio N Silva, Gloria P Castillo-Urquiza, Fabyano F Silva, Yee M Seah, Eduardo S G Mizubuti, Siobain Duffy, F Murilo Zerbini
Begomoviruses (single-stranded DNA plant viruses) are responsible for serious agricultural threats. Begomovirus populations exhibit a high degree of within-host genetic variation and evolve as quickly as RNA viruses. Although the recombination-prone nature of begomoviruses has been extensively demonstrated, the relative contribution of recombination and mutation to the genetic variation of begomovirus populations has not been assessed. We estimated the genetic variability of begomovirus datasets from around the world...
January 2017: Virus Evolution
https://www.readbyqxmd.com/read/28455350/the-genomic-architecture-of-flowering-time-varies-across-space-and-time-in-mimulus-guttatus
#18
Patrick J Monnahan, John K Kelly
The degree to which genomic architecture varies across space and time is central to the evolution of genomes in response to natural selection. Bulked-segregant mapping combined with pooled sequencing provides an efficient means to estimate the effect of genetic variants on quantitative traits. We develop a novel likelihood framework to identify segregating variation within multiple populations and generations while accommodating estimation error on a sample-and SNP-specific basis. We use this method to map loci for flowering time within natural populations of Mimulus guttatus, collecting the early and late flowering plants from each of three neighboring populations and two consecutive generations...
April 28, 2017: Genetics
https://www.readbyqxmd.com/read/28452748/soleil-shining-on-the-solution-state-structure-of-biomacromolecules-by-synchrotron-x-ray-footprinting-at-the-metrology-beamline
#19
A Baud, L Aymé, F Gonnet, I Salard, Y Gohon, P Jolivet, K Brodolin, P Da Silva, A Giuliani, B Sclavi, T Chardot, P Mercère, P Roblin, R Daniel
Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France...
May 1, 2017: Journal of Synchrotron Radiation
https://www.readbyqxmd.com/read/28452349/wheat-ms2-encodes-for-an-orphan-protein-that-confers-male-sterility-in-grass-species
#20
Fei Ni, Juan Qi, Qunqun Hao, Bo Lyu, Ming-Cheng Luo, Yan Wang, Fengjuan Chen, Shuyun Wang, Chaozhong Zhang, Lynn Epstein, Xiangyu Zhao, Honggang Wang, Xiansheng Zhang, Cuixia Chen, Lanzhen Sun, Daolin Fu
Male sterility is a valuable trait for plant breeding and hybrid seed production. The dominant male-sterile gene Ms2 in common wheat has facilitated the release of hundreds of breeding lines and cultivars in China. Here, we describe the map-based cloning of the Ms2 gene and show that Ms2 confers male sterility in wheat, barley and Brachypodium. MS2 appears as an orphan gene within the Triticinae and expression of Ms2 in anthers is associated with insertion of a retroelement into the promoter. The cloning of Ms2 has substantial potential to assemble practical pipelines for recurrent selection and hybrid seed production in wheat...
April 28, 2017: Nature Communications
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