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Plant association mapping

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https://www.readbyqxmd.com/read/28081268/the-rice-dynamin-related-protein-osdrp1e-negatively-regulates-programmed-cell-death-by-controlling-the-release-of-cytochrome-c-from-mitochondria
#1
Zhiqiang Li, Bo Ding, Xueping Zhou, Guo-Liang Wang
Programmed cell death (PCD) mediated by mitochondrial processes has emerged as an important mechanism for plant development and responses to abiotic and biotic stress. However, the role of translocation of cytochrome c from the mitochondria to the cytosol during PCD remains unclear. Here, we demonstrate that the rice dynamin-related protein 1E (OsDRP1E) negatively regulates PCD by controlling mitochondrial structure and cytochrome c release. We used a map-based cloning strategy to isolate OsDRP1E from the lesion mimic mutant dj-lm and confirmed that the E409V mutation in OsDRP1E causes spontaneous cell death in rice...
January 12, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28078746/a-gly65val-substitution-in-an-actin-ghact_li1-disrupts-cell-polarity-and-f-actin-organization-resulting-in-dwarf-lintless-cotton-plants
#2
Gregory N Thyssen, David D Fang, Rickie B Turley, Christopher B Florane, Ping Li, Christopher P Mattison, Marina Naoumkina
Actin polymerizes to form part of the cytoskeleton and organize polar growth in all eukaryotic cells. Species with numerous actin genes are especially useful for the dissection of actin molecular function due to redundancy and neofunctionalization. Here, we investigated the role of a cotton (Gossypium hirsutum) actin gene in the organization of actin filaments in lobed cotyledon pavement cells and the highly-elongated single-celled trichomes that comprise cotton lint fibers. Using mapping-by-sequencing, virus-induced gene silencing, and molecular modeling, we identified the causative mutation of the dominant dwarf Ligon-lintless Li1 short fiber mutant as a single Gly65Val amino acid substitution in a polymerization domain of an actin gene, GhACT_LI1 (Gh_D04G0865)...
January 12, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28077090/gbs-based-single-dosage-markers-for-linkage-and-qtl-mapping-allow-gene-mining-for-yield-related-traits-in-sugarcane
#3
Thiago Willian Almeida Balsalobre, Guilherme da Silva Pereira, Gabriel Rodrigues Alves Margarido, Rodrigo Gazaffi, Fernanda Zatti Barreto, Carina Oliveira Anoni, Cláudio Benício Cardoso-Silva, Estela Araújo Costa, Melina Cristina Mancini, Hermann Paulo Hoffmann, Anete Pereira de Souza, Antonio Augusto Franco Garcia, Monalisa Sampaio Carneiro
BACKGROUND: Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068350/genome-wide-association-mapping-and-genomic-selection-for-alfalfa-medicago-sativa-forage-quality-traits
#4
Elisa Biazzi, Nelson Nazzicari, Luciano Pecetti, E Charles Brummer, Alberto Palmonari, Aldo Tava, Paolo Annicchiarico
Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest)...
2017: PloS One
https://www.readbyqxmd.com/read/28049428/pergola-fast-and-deterministic-linkage-mapping-of-polyploids
#5
Fabian Grandke, Soumya Ranganathan, Nikkie van Bers, Jorn R de Haan, Dirk Metzler
BACKGROUND: A large share of agriculturally and horticulturally important plant species are polyploid. Linkage maps are used to locate associations between genes and traits by breeders and geneticists. Linkage map creation for polyploid species is not supported by standard tools. We want to overcome this limitation and validate our results with simulation studies. RESULTS: We developed PERGOLA, a deterministic and heuristic method that addresses this problem. We show that it creates correct linkage groups, marker orders and distances for simulated and real datasets...
January 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28041874/economic-and-social-activities-on-ancient-cypriot-terraced-landscapes
#6
Elizabeth Ridder, Christopher S Galletti, Patricia L Fall, Steven E Falconer
We investigate ancient agricultural terraces and their associated social and economic activities across the site complex consisting of the village at Politiko-Troullia and its more extensive associated taskscape. Surface artifact distributions mapped over 12 ha are integrated with evidence excavated from this Bronze Age settlement in central Cyprus. Contrary to expectations, artifact densities do not diminish with distance from the village architecture. In particular, concentrations of Prehistoric Bronze Age ceramics and ground stone artifacts are most pronounced on nearby terraced hillsides...
December 29, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/28039516/defeating-the-warrior-genetic-architecture-of-triticale-resistance-against-a-novel-aggressive-yellow-rust-race
#7
Dominik Losert, Hans Peter Maurer, Willmar L Leiser, Tobias Würschum
Genome-wide association mapping of resistance against the novel, aggressive 'Warrior' race of yellow rust in triticale revealed a genetic architecture with some medium-effect QTL and a quantitative component, which in combination confer high levels of resistance on both leaves and ears. Yellow rust is an important destructive fungal disease in small grain cereals and the exotic 'Warrior' race has recently conquered Europe. The aim of this study was to investigate the genetic architecture of yellow rust resistance in hexaploid winter triticale as the basis for a successful resistance breeding...
December 30, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28039515/genome-wide-association-mapping-for-seedling-and-field-resistance-to-puccinia-striiformis-f-sp-tritici-in-elite-durum-wheat
#8
Weizhen Liu, Marco Maccaferri, Peter Bulli, Sheri Rynearson, Roberto Tuberosa, Xianming Chen, Michael Pumphrey
Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide. Improving resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major objective for wheat breeding. To identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using 232 elite durum wheat (Triticum turgidum ssp. durum) lines from worldwide breeding programs...
December 30, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28028612/qtls-for-cell-wall-bound-phenolics-in-relation-to-the-photosynthetic-apparatus-activity-and-leaf-water-status-under-drought-stress-at-different-growth-stages-of-triticale
#9
Tomasz Hura, Mirosław Tyrka, Katarzyna Hura, Agnieszka Ostrowska, Kinga Dziurka
The present study aimed at identifying the regions of triticale genome responsible for cell wall saturation with phenolic compounds under drought stress during vegetative and generative growth. Moreover, the loci determining the activity of the photosynthetic apparatus, leaf water content (LWC) and osmotic potential (Ψ o) were identified, as leaf hydration and functioning of the photosynthetic apparatus under drought are associated with the content of cell wall-bound phenolics (CWPh). Compared with LWC and Ψ o, CWPh fluctuations were more strongly associated with changes in chlorophyll fluorescence...
December 27, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28028582/genetic-dissection-of-sorghum-grain-quality-traits-using-diverse-and-segregating-populations
#10
Richard E Boyles, Brian K Pfeiffer, Elizabeth A Cooper, Bradley L Rauh, Kelsey J Zielinski, Matthew T Myers, Zachary Brenton, William L Rooney, Stephen Kresovich
Coordinated association and linkage mapping identified 25 grain quality QTLs in multiple environments, and fine mapping of the Wx locus supports the use of high-density genetic markers in linkage mapping. There is a wide range of end-use products made from cereal grains, and these products often demand different grain characteristics. Fortunately, cereal crop species including sorghum [Sorghum bicolor (L.) Moench] contain high phenotypic variation for traits influencing grain quality. Identifying genetic variants underlying this phenotypic variation allows plant breeders to develop genotypes with grain attributes optimized for their intended usage...
December 27, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28018403/comparative-analysis-of-phenolic-compound-characterization-and-their-biosynthesis-genes-between-two-diverse-bread-wheat-triticum-aestivum-varieties-differing-for-chapatti-unleavened-flat-bread-quality
#11
Monica Sharma, Rajat Sandhir, Anuradha Singh, Pankaj Kumar, Ankita Mishra, Sanjay Jachak, Sukhvinder P Singh, Jagdeep Singh, Joy Roy
Phenolic compounds (PCs) affect the bread quality and can also affect the other types of end-use food products such as chapatti (unleavened flat bread), now globally recognized wheat-based food product. The detailed analysis of PCs and their biosynthesis genes in diverse bread wheat (Triticum aestivum) varieties differing for chapatti quality have not been studied. In this study, the identification and quantification of PCs using UPLC-QTOF-MS and/or MS/MS and functional genomics techniques such as microarrays and qRT-PCR of their biosynthesis genes have been studied in a good chapatti variety, "C 306" and a poor chapatti variety, "Sonalika...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28012227/widespread-selective-sweeps-throughout-the-genome-of-model-plant-pathogenic-fungi-and-identification-of-effector-candidates
#12
H Badouin, P Gladieux, J Gouzy, S Siguenza, G Aguileta, A Snirc, S Le Prieur, C Jeziorski, A Branca, T Giraud
Identifying the genes underlying adaptation, their distribution in genomes, and the evolutionary forces shaping genomic diversity, are key challenges in evolutionary biology. Very few studies have investigated the abundance and distribution of selective sweeps in species with high-quality reference genomes, outside of a handful of model species. Pathogenic fungi are tractable eukaryote models for investigating the genomics of adaptation. By sequencing 53 genomes of two species of anther-smut fungi and mapping them against a high-quality reference genome, we showed that selective sweeps were abundant and scattered throughout the genome in one species, affecting near 17% of the genome, but much less numerous and in different genomic regions in its sister species, where they left footprints in only 1% of the genome...
December 24, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28011790/high-throughput-interpretation-of-gene-structure-changes-in-human-and-nonhuman-resequencing-data-using-ace
#13
William H Majoros, Michael S Campbell, Carson Holt, Erin DeNardo, Doreen Ware, Andrew S Allen, Mark Yandell, Timothy E Reddy
MOTIVATION: The accurate interpretation of genetic variants is critical for characterizing genotype-phenotype associations. Because the effects of genetic variants can depend strongly on their local genomic context, accurate genome annotations are essential. Furthermore, as some variants have the potential to disrupt or alter gene structure, variant interpretation efforts stand to gain from the use of individualized annotations that account for differences in gene structure between individuals or strains...
December 23, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28008334/transcriptome-analysis-highlights-defense-and-signaling-pathways-mediated-by-rice-pi21-gene-with-partial-resistance-to-magnaporthe-oryzae
#14
Yu Zhang, Jianhua Zhao, Yali Li, Zhengjie Yuan, Haiyan He, Haihe Yang, Haiyan Qu, Chenyan Ma, Shaohong Qu
Rice blast disease is one of the most destructive rice diseases worldwide. The pi21 gene confers partial and durable resistance to Magnaporthe oryzae. However, little is known regarding the molecular mechanisms of resistance mediated by the loss-of-function of Pi21. In this study, comparative transcriptome profiling of the Pi21-RNAi transgenic rice line and Nipponbare with M. oryzae infection at different time points (0, 12, 24, 48, and 72 hpi) were investigated using RNA sequencing. The results generated 43,222 unique genes mapped to the rice genome...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27999231/adverse-reproductive-outcomes-associated-with-exposure-to-a-municipal-solid-waste-incinerator
#15
Michele Santoro, Fabrizio Minichilli, Nunzia Linzalone, Alessio Coi, Maria Teresa Maurello, Domenico Sallese, Fabrizio Bianchi
INTRODUCTION: The association between reproductive health outcomes and exposure to municipal solid waste incinerators (MSWIs) is inconclusive. This study investigates the association between exposure to a MSWI and various reproductive outcomes (preterm birth, low birth weight, small for gestational age, and sex ratio), taking into account other sources of pollution (industrial plants, highway, major roads with high traffic flows) and maternal factors, including the socioeconomic status...
October 2016: Annali Dell'Istituto Superiore di Sanità
https://www.readbyqxmd.com/read/27998268/mapping-the-membrane-proteome-of-anaerobic-gut-fungi-identifies-a-wealth-of-carbohydrate-binding-proteins-and-transporters
#16
Susanna Seppälä, Kevin V Solomon, Sean P Gilmore, John K Henske, Michelle A O'Malley
BACKGROUND: Engineered cell factories that convert biomass into value-added compounds are emerging as a timely alternative to petroleum-based industries. Although often overlooked, integral membrane proteins such as solute transporters are pivotal for engineering efficient microbial chassis. Anaerobic gut fungi, adapted to degrade raw plant biomass in the intestines of herbivores, are a potential source of valuable transporters for biotechnology, yet very little is known about the membrane constituents of these non-conventional organisms...
December 20, 2016: Microbial Cell Factories
https://www.readbyqxmd.com/read/27997751/identifying-the-plant-associated-microbiome-across-aquatic-and-terrestrial-environments-the-effects-of-amplification-method-on-taxa-discovery
#17
Sara L Jackrel, Sarah M Owens, Jack A Gilbert, Catherine A Pfister
Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater, and marine environments...
December 20, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27996306/mapping-qtls-associated-with-agronomic-and-physiological-traits-under-terminal-drought-and-heat-stress-conditions-in-wheat-triticum-aestivum-l
#18
Sirous Tahmasebi, Bahram Heidari, Hassan Pakniyat, C Lynne McIntyre
Wheat crops frequently experience a combination of abiotic stresses in the field, but most quantitative trait loci (QTL) studies have focused on the identification of QTLs for traits under single stress field conditions. A recombinant inbred line (RIL) population derived from SeriM82 × Babax was used to map QTLs under well-irrigated, heat, drought, and a combination of heat and drought stress conditions in two years. A total of 477 DNA markers were used to construct linkage groups that covered 1619.6 cM of the genome, with an average distance of 3...
January 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27994192/mapping-of-stripe-rust-resistance-gene-in-an-aegilops-caudate-introgression-line-in-wheat-and-its-genetic-association-with-leaf-rust-resistance
#19
Puneet Inder Toor, Satinder Kaur, Mitaly Bansal, Bharat Yadav, Parveen Chhuneja
A pair of stripe rust and leaf rust resistance genes was introgressed from Aegilops caudata, a nonprogenitor diploid species with the CC genome, to cultivated wheat. Inheritance and genetic mapping of stripe rust resistance gene in backcrossrecombinant inbred line (BC-RIL) population derived from the cross of a wheat-Ae. caudata introgression line (IL) T291- 2(pau16060) with wheat cv. PBW343 is reported here. Segregation of BC-RILs for stripe rust resistance depicted a single major gene conditioning adult plant resistance (APR) with stripe rust reaction varying from TR-20MS in resistant RILs signifying the presence of some minor genes as well...
December 2016: Journal of Genetics
https://www.readbyqxmd.com/read/27994177/cytological-behaviour-of-floral-organs-and-in-silico-characterization-of-differentially-expressed-transcript-derived-fragments-associated-with-floral-bud-distortion-in-soybean
#20
Prashant B Kale, Pravin V Jadhav, Rachana S Wakekar, M P Moharil, A G Deshmukh, M S Dudhare, R S Nandanwar, S S Mane, J G Manjaya, R G Dani
An attempt was made to understand the 'floral bud distortion' (FBD), an unexplored disorder prevailing in soybean. Cytological behaviour of floral reproductive organs and in silico characterization of differentially expressed transcript-derived fragments (TDFs) in symptomatic and asymptomatic soybean plants were carried out. Pollens in asymptomatic plants do not have defects in number, size, shape and function. However, in symptomatic plant, pollens were found nonviable, abnormal in shape and with reduced germination ability...
December 2016: Journal of Genetics
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