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Plant association mapping

Albert W Schulthess, Jochen C Reif, Jie Ling, Jörg Plieske, Sonja Kollers, Erhard Ebmeyer, Viktor Korzun, Odile Argillier, Gunther Stiewe, Martin W Ganal, Marion S Röder, Yong Jiang
Grain yield (GY) of bread wheat (Triticum aestivum L.) is quantitatively inherited. Correlated GY-syndrome traits such as plant height (PH), heading date (HD), thousand grain weight (TGW), test weight (TW), grains per ear (GPE), and ear weight (EW) influence GY. Most quantitative genetics studies assessed the multiple-trait (MT) complex of GY-syndrome using single-trait approaches, and little is known about its underlying pleiotropic architecture. We investigated the pleiotropic architecture of wheat GY-syndrome through MT association mapping (MT-GWAS) using 372 varieties phenotyped in up to eight environments and genotyped with 18 832 single nucleotide polymorphisms plus 24 polymorphic functional markers...
July 10, 2017: Journal of Experimental Botany
Pascale Jolivet, Laure Aymé, Alexandre Giuliani, Frank Wien, Thierry Chardot, Yann Gohon
Lipid droplets are the major stock of lipids in oleaginous plant seeds. Despite their economic importance for oil production and biotechnological issues (biofuels, lubricants and plasticizers), numerous questions about their formation, structure and regulation are still unresolved. To determine water accessible domains of protein coating at lipid droplets surface, a structural proteomic approach has been performed. This technique relies on the millisecond timescale production of hydroxyl radicals by the radiolysis of water using Synchrotron X-ray white beam...
September 14, 2017: Journal of Proteomics
Neha Samir Roy, Kyong-Cheul Park, Sung-Il Lee, Min-Ji Im, Rahul Vasudeo Ramekar, Nam-Soo Kim
Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population...
September 15, 2017: Genetica
Daniel Antony Pass, Emily Sornay, Angela Marchbank, Margaret R Crawford, Konrad Paszkiewicz, Nicholas A Kent, James A H Murray
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes...
September 2017: PLoS Genetics
Stephen A Smith, Joseph W Brown, Ya Yang, Riva Bruenn, Chloe P Drummond, Samuel F Brockington, Joseph F Walker, Noah Last, Norman A Douglas, Michael J Moore
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species...
September 11, 2017: New Phytologist
Jyoti Bhadouria, Ajit Pal Singh, Poonam Mehra, Lokesh Verma, Rishi Srivastawa, Swarup K Parida, Jitender Giri
Purple acid phosphatases (PAPs) play important roles in phosphate (Pi) acquisition and utilization. These PAPs hydrolyze organic Phosphorus (P) containing compounds in rhizosphere as well as inside the plant cell. However, roles of PAPs in one of the most widely cultivated legumes, chickpea (Cicer arietnum L.), have not been unraveled so far. In the present study, we identified 25 putative PAPs in chickpea (CaPAPs) which possess functional PAP motifs and domains. Differential regulation of CaPAPs under different nutrient deficiencies revealed their roles under multiple nutrient stresses including Pi deficiency...
September 8, 2017: Scientific Reports
Erik S J Gontijo, Cláudia H Watanabe, Adnívia S C Monteiro, Gilmare A da Silva, Hubert M P Roeser, Andre H Rosa, Kurt Friese
Humic substances (HS) are ubiquitous organic compounds able to affect mobility and availability of arsenic (As) in aquatic systems. Although it is known that associations between HS and As occur mainly via iron (Fe)-cationic bridges, the behaviour and distribution of this metalloid in HS- and Fe-rich environments is still not fully understood. In this paper, the quality of HS from different rivers in Brazil and Germany and its influence on the behaviour of As(V) under different Fe(III) concentrations were investigated...
August 29, 2017: Chemosphere
Xingtan Zhang, Xuequn Chen, Pingping Liang, Haibao Tang
Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with phenotypic variations. Building on the next generation sequencing (NGS) technologies, research on plant structural variations are gaining momentum and have revolutionized our view on the functional impact of the 'hidden' diversity that were largely understudied before. Herein, we first describe the current state of plant genomic SV research based on NGS and in particular focus on the biological insights gained from the large-scale identification of various types of plant SVs...
September 8, 2017: Current Issues in Molecular Biology
Mengzhou Liu, Zhengwen Wang, Shanshan Li, Xiaotao Lü, Xiaobo Wang, Xingguo Han
Specific leaf area (SLA) is a key trait with great ecological importance as it correlates with whole plant growth. We aimed to investigate how SLA varies with environmental factors at a geographical scale in temperate grasslands. We measured SLA and mass-based leaf nitrogen content (N mass) of four dominant plant genera along a 2500 km climatic gradient in northern China grassland, and correlated SLA with mean annual precipitation (MAP), mean annual temperature (MAT), soil nitrogen concentration (soil N), soil C:N and N mass...
September 7, 2017: Scientific Reports
Nathalie Aoun, Laetitia Tauleigne, Fabien Lonjon, Laurent Deslandes, Fabienne Vailleau, Fabrice Roux, Richard Berthomé
In the context of climate warming, plants will be facing an increased risk of epidemics as well as the emergence of new highly aggressive pathogen species. Although a permanent increase of temperature strongly affects plant immunity, the underlying molecular mechanisms involved are still poorly characterized. In this study, we aimed to uncover the genetic bases of resistance mechanisms that are efficient at elevated temperature to the Ralstonia solanacearum species complex (RSSC), one of the most harmful phytobacteria causing bacterial wilt...
2017: Frontiers in Plant Science
Aladje Baldé, Dina Neves, Francisco J García-Breijo, Maria Salomé Pais, Alfredo Cravador
BACKGROUND: Phlomis plants are a source of biological active substances with potential applications in the control of phytopathogens. Phlomis purpurea (Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to Phytophthora cinnamomi. Phlomis purpurea has revealed antagonistic effect in the rhizosphere of Quercus suber and Q. ilex against P. cinnamomi. Phlomis purpurea roots produce bioactive compounds exhibiting antitumor and anti-Phytophthora activities with potential to protect susceptible plants...
September 6, 2017: BMC Genomics
Changbin Yin, Huihui Li, Zhigang Zhao, Zhiquan Wang, Shijia Liu, Liangming Chen, Xi Liu, Yunlu Tian, Juan Ma, Lidong Xu, Dashuang Zhang, Susong Zhu, Danting Li, Jianmin Wan, Jiankang Wang
The size of the top three leaves of rice plants is strongly associated with yield; thus, it is important to consider quantitative traits representing leaf size (e.g., length and width) when breeding novel rice varieties. It is challenging to measure such traits on a large scale in the field, and little is known about the genetic factors that determine the size of the top three leaves. In this study, a population of recombinant inbred lines (RILs) and reciprocal single chromosomal segment substitution lines (SSSLs) derived from the progeny of a japonica Asominori × indica IR24 cross were grown under four diverse environmental conditions...
September 6, 2017: Journal of Integrative Plant Biology
Ana Giner, Laura Pascual, Michael Bourgeois, Gabor Gyetvai, Pablo Rios, Belén Picó, Christelle Troadec, Abdel Bendahmane, Jordi Garcia-Mas, Ana Montserrat Martín-Hernández
In the melon exotic accession PI 161375, the gene cmv1, confers recessive resistance to Cucumber mosaic virus (CMV) strains of subgroup II. cmv1 prevents the systemic infection by restricting the virus to the bundle sheath cells and impeding viral loading to the phloem. Here we report the fine mapping and cloning of cmv1. Screening of an F2 population reduced the cmv1 region to a 132 Kb interval that includes a Vacuolar Protein Sorting 41 gene. CmVPS41 is conserved among plants, animals and yeast and is required for post-Golgi vesicle trafficking towards the vacuole...
September 5, 2017: Scientific Reports
Reetika Mahajan, Sajad Majeed Zargar, R K Salgotra, Ravinder Singh, Aijaz Ahmad Wani, Muslima Nazir, Parvaze A Sofi
Micronutrient deficiencies are of major concern in human health and plant metabolism. Iron (Fe), zinc (Zn), iodine (I), selenium (Se) are regarded as micronutrients having major impact on human health. More than 50% of populations mainly from developing countries are suffering from one or the other micronutrient malnutrition. Ensuring adequate supply of these micronutrients through diet consisting of staple foods, such as common bean (Phaseolus vulgaris L.) is must. Here, we evaluated common bean genotypes that were collected from various regions of Jammu and Kashmir, India for Fe, Zn and protein contents and used SSRs to identify the markers associated with these traits...
October 2017: 3 Biotech
Min Cui, Bo Jia, Huanhuan Liu, Xin Kan, Yu Zhang, Ronghua Zhou, Zhipeng Li, Liang Yang, Dexiang Deng, Zhitong Yin
The leaf number above the primary ear (LA) is a major contributing factor to plant architecture in maize. The yield of leafy maize, which has extra LA compared to normal maize, is higher than normal maize in some regions. One major concern is that increasing LA may be accompanied by increased plant height and/or flowering time. Using an F2:3 population comprising 192 families derived from a leafy maize line and a normal maize line, an association population comprising 437 inbred maize lines, and a pair of near-isogenic maize lines, we mapped the quantitative trait loci (QTL) associated with LA and assessed its genetic relationship with flowering time and plant height...
2017: Frontiers in Plant Science
Qiaojun Jia, Junmei Wang, Jinghuan Zhu, Wei Hua, Yi Shang, Jianming Yang, Zongsuo Liang
Black barley is caused by phytomelanin synthesized in lemma and/or pericarp and the trait is controlled by one dominant gene Blp1. The gene is mapped on chromosome 1H by molecular markers, but it is yet to be isolated. Specific-locus amplified fragment sequencing (SLAF-seq) is an effective method for large-scale de novo single nucleotide polymorphism (SNP) discovery and genotyping. In the present study, SLAF-seq with bulked segregant analysis (BSA) was employed to obtain sufficient markers to fine mapping Blp1 gene in an F2 population derived from Hatiexi No...
2017: Frontiers in Plant Science
Amit Gur, Galil Tzuri, Ayala Meir, Uzi Sa'ar, Vitaly Portnoy, Nurit Katzir, Arthur A Schaffer, Li Li, Joseph Burger, Yaakov Tadmor
Cucumis melo is highly diverse for fruit traits providing wide breeding and genetic research opportunities, including genome-wide association (GWA) analysis. We used a collection of 177 accessions representing the two C. melo subspecies and 11 horticultural groups for detailed characterization of fruit traits variation and evaluation of the potential of GWA for trait mapping in melon. Through genotyping-by-sequencing, 23,931 informative SNPs were selected for genome-wide analyses. We found that linkage-disequilibrium decays at ~100 Kb in this collection and that population structure effect on association results varies between traits...
August 29, 2017: Scientific Reports
Jean-Félix Dallery, Nicolas Lapalu, Antonios Zampounis, Sandrine Pigné, Isabelle Luyten, Joëlle Amselem, Alexander H J Wittenberg, Shiguo Zhou, Marisa V de Queiroz, Guillaume P Robin, Annie Auger, Matthieu Hainaut, Bernard Henrissat, Ki-Tae Kim, Yong-Hwan Lee, Olivier Lespinet, David C Schwartz, Michael R Thon, Richard J O'Connell
BACKGROUND: The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. RESULTS: Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7...
August 29, 2017: BMC Genomics
Mercedes García-Sánchez, Zdeněk Košnář, Filip Mercl, Elisabet Aranda, Pavel Tlustoš
Biological treatments are considered an environmentally option to clean-up polluted soil with polycyclic aromatic hydrocarbons (PAHs). A pot experiment was conducted to comparatively evaluate four different strategies, including natural attenuation (NA), mycoaugmentation (M) by using Crucibulum leave, phytoremediation (P) using maize plants, and microbial-assisted phytoremediation (MAP) for the bioremediation of an aged PAH-polluted soil at 180 days. The P treatment had higher affinity degrading 2-3 and 4 ring compounds than NA and M treatments, respectively...
August 23, 2017: Ecotoxicology and Environmental Safety
Yunlei Zhao, Hongmei Wang, Wei Chen, Pei Zhao, Haiyan Gong, Xiaohui Sang, Yanli Cui
BACKGROUND: Verticillium wilt is one of the most destructive diseases affecting global cotton production. The most effective way to control wilt disease has been the development of new cotton varieties that are resistant to VW. VW-resistant Upland cotton cultivars have been created in both the USA and China by Gossypium barbadense introgression. More than 100 VW resistance quantitative trait loci have been detected. RESULTS: Three clustered VW resistance-related QTL were detected in a 120-line association population and assigned to a genome region of 14,653,469-55,190,112 bp in Dt_chr9...
August 25, 2017: BMC Genomics
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