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Plant association mapping

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https://www.readbyqxmd.com/read/28214713/comparative-analysis-of-metagenomes-of-italian-top-soil-improvers
#1
Federica Gigliucci, Gianfranco Brambilla, Rosangela Tozzoli, Valeria Michelacci, Stefano Morabito
Biosolids originating from Municipal Waste Water Treatment Plants are proposed as top soil improvers (TSI) for their beneficial input of organic carbon on agriculture lands. Their use to amend soil is controversial, as it may lead to the presence of emerging hazards of anthropogenic or animal origin in the environment devoted to food production. In this study, we used a shotgun metagenomics sequencing as a tool to perform a characterization of the hazards related with the TSIs. The samples showed the presence of many virulence genes associated to different diarrheagenic E...
February 16, 2017: Environmental Research
https://www.readbyqxmd.com/read/28213475/wheat-landrace-genome-diversity
#2
Luzie U Wingen, Claire West, Michelle Leverington-Waite, Sarah Collier, Simon Orford, Richard Goram, Cai-Yun Yang, Julie King, Alexandra M Allen, Amanda Burridge, Keith J Edwards, Simon Griffiths
Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focussing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating bi-parental populations were developed mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity (WINGEN et al...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28211582/what-can-genome-wide-association-studies-tell-us-about-the-evolutionary-forces-maintaining-genetic-variation-for-quantitative-traits
#3
REVIEW
Emily B Josephs, John R Stinchcombe, Stephen I Wright
I. II. III. IV. V. References SUMMARY: Understanding the evolutionary forces that shape genetic variation within species has long been a goal of evolutionary biology. Integrating data for the genetic architecture of traits from genome-wide association mapping studies (GWAS) along with the development of new population genetic methods for identifying selection in sequence data may allow us to evaluate the roles of mutation-selection balance and balancing selection in shaping genetic variation at various scales...
February 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28209181/de-novo-sequencing-and-comparative-transcriptome-analysis-of-adventitious-root-development-induced-by-exogenous-indole-3-butyric-acid-in-cuttings-of-tetraploid-black-locust
#4
Jine Quan, Seng Meng, Erhui Guo, Sheng Zhang, Zhong Zhao, Xitian Yang
BACKGROUND: Indole-3-butyric acid (IBA) is applied to the cuttings of various plant species to induce formation of adventitious roots (ARs) in commercial settings. Tetraploid black locust is an attractive ornamental tree that is drought resistant, sand tolerant, can prevent sand erosion and has various commercial uses. To further elucidate the mechanisms of AR formation, we used Illumina sequencing to analyze transcriptome dynamics and differential gene expression at four developmental stages in control (CK) and IBA-treated groups...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28195333/arabidopsis-e3-ubiquitin-ligase-plant-u-box13-pub13-regulates-chitin-receptor-lysin-motif-receptor-kinase5-lyk5-protein-abundance
#5
Dehua Liao, Yangrong Cao, Xun Sun, Catherine Espinoza, Cuong T Nguyen, Yan Liang, Gary Stacey
Long-chain chitooligosaccharides are fungal microbe-associated molecular patterns (MAMPs) that are recognized by LYSIN MOTIF RECEPTOR KINASE5 (LYK5), inducing the formation of a complex with CHITIN ELICITOR RECEPTOR KINASE1 (CERK1). Formation of this complex leads to activation of the CERK1 intracellular kinase domain and induction of plant innate immunity in Arabidopsis. We found that addition of chitooctaose induced LYK5 protein accumulation as a result of de novo gene expression and the inhibition of LYK5 protein degradation...
February 14, 2017: New Phytologist
https://www.readbyqxmd.com/read/28187376/genome-wide-analysis-of-excretory-secretory-proteins-in-root-knot-nematode-meloidogyne-incognita-provides-potential-targets-for-parasite-control
#6
Shachi Gahoi, Budhayash Gautam
The root-knot nematode, Meloidogyne incognita causes significant damage to various economically important crops. Infection is associated with secretion of effector proteins into host cytoplasm and interference with host innate immunity. To combat this infection, the identification and functional annotations of Excretory/Secretory (ES) proteins serve as a key to produce durable control measures. The identification of ES proteins through experimental methods are expensive and time consuming while bioinformatics approaches are cost-effective by prioritizing the experimental analysis of potential drug targets for parasitic diseases...
February 1, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28174587/integrating-small-rna-sequencing-with-qtl-mapping-for-identification-of-mirnas-and-their-target-genes-associated-with-heat-tolerance-at-the-flowering-stage-in-rice
#7
Qing Liu, Tifeng Yang, Ting Yu, Shaohong Zhang, Xingxue Mao, Junliang Zhao, Xiaofei Wang, Jingfang Dong, Bin Liu
Although, microRNAs (miRNAs) have been reported to be associated with heat tolerance at the seedling stage in rice, their involvement in heat tolerance at the flowering stage is still unknown. In this study, small RNA profiling was conducted in a heat-tolerant variety Gan-Xiang-Nuo (GXN) and a heat-sensitive variety Hua-Jing-Xian-74 (HJX), respectively. Totally, 102 miRNAs were differentially expressed (DE) under heat stress. Compared to HJX, GXN had more DE miRNAs and its DE miRNAs changed earlier under heat stress...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28174273/h3k4me3-induces-allosteric-conformational-changes-in-the-dna-binding-and-catalytic-regions-of-the-v-d-j-recombinase
#8
John Bettridge, Chan Hyun Na, Akhilesh Pandey, Stephen Desiderio
V(D)J recombination is initiated by the recombination-activating gene (RAG) recombinase, consisting of RAG-1 and RAG-2 subunits. The susceptibility of gene segments to cleavage by RAG is associated with histone modifications characteristic of active chromatin, including trimethylation of histone H3 at lysine 4 (H3K4me3). Binding of H3K4me3 by a plant homeodomain (PHD) in RAG-2 stimulates substrate binding and catalysis, which are functions of RAG-1. This has suggested an allosteric mechanism in which information regarding occupancy of the RAG-2 PHD is transmitted to RAG-1...
February 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28173633/a-novel-functional-gene-associated-with-cold-tolerance-at-the-seedling-stage-in-rice
#9
Junliang Zhao, Shaohong Zhang, Jingfang Dong, Tifeng Yang, Xingxue Mao, Qing Liu, Xiaofei Wang, Bin Liu
Identification and cloning of cold-tolerant genes that can stably express under different cold environments are crucial for molecular rice breeding for cold tolerance. In the previous study, we identified a cold-tolerant QTL at the seedling stage, qCTS-9 which could be detected under different cold environments using a recombinant inbred line (RIL) population derived from a cold-tolerant variety Lijiangxintuanheigu (LTH) and a cold-sensitive variety Shanhuangzhan 2 (SHZ-2). In this study, eight candidate genes within the qCTS-9 interval were identified through integrated analysis of QTL mapping with genome-wide differential expression profiling of LTH...
February 7, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28167041/phenotypic-characterization-and-genetic-dissection-of-nine-agronomic-traits-in-tokachi-nagaha-and-its-derived-cultivars-in-soybean-glycine-max-l-merr
#10
Zhangxiong Liu, Huihui Li, Xuhong Fan, Wen Huang, Jiyu Yang, Zixiang Wen, Yinghui Li, Rongxia Guan, Yong Guo, Ruzhen Chang, Dechun Wang, Pengyin Chen, Shuming Wang, Li-Juan Qiu
By using the soybean founder parent Tokachi nagaha and its 137 derived cultivars as materials, a genome-wide association analysis was performed to identify the single nucleotide polymorphisms (SNPs) underlying soybean yield and quality related traits at two planting densities. Results of ANOVA showed that genotype, environment, and genotype by environment interaction effects were all significant for each trait. The Tokachi nagaha-derived soybean population could be divided into two subpopulations based on molecular data, and accessions in each subpopulation were almost all from the same Chinese province...
March 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28166212/a-study-of-allelic-diversity-underlying-flowering-time-adaptation-in-maize-landraces
#11
J Alberto Romero Navarro, Martha Wilcox, Juan Burgueño, Cinta Romay, Kelly Swarts, Samuel Trachsel, Ernesto Preciado, Arturo Terron, Humberto Vallejo Delgado, Victor Vidal, Alejandro Ortega, Armando Espinoza Banda, Noel Orlando Gómez Montiel, Ivan Ortiz-Monasterio, Félix San Vicente, Armando Guadarrama Espinoza, Gary Atlin, Peter Wenzl, Sarah Hearne, Edward S Buckler
Landraces (traditional varieties) of domesticated species preserve useful genetic variation, yet they remain untapped due to the genetic linkage between the few useful alleles and hundreds of undesirable alleles. We integrated two approaches to characterize the diversity of 4,471 maize landraces. First, we mapped genomic regions controlling latitudinal and altitudinal adaptation and identified 1,498 genes. Second, we used F-one association mapping (FOAM) to map the genes that control flowering time, across 22 environments, and identified 1,005 genes...
February 6, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28158253/qtls-associated-with-agronomic-traits-in-the-attila-%C3%A3-cdc-go-spring-wheat-population-evaluated-under-conventional-management
#12
Jun Zou, Kassa Semagn, Muhammad Iqbal, Hua Chen, Mohammad Asif, Amidou N'Diaye, Alireza Navabi, Enid Perez-Lara, Curtis Pozniak, Rong-Cai Yang, Harpinder Randhawa, Dean Spaner
Recently, we investigated the effect of the wheat 90K single nucleotide polymorphic (SNP) array and three gene-specific (Ppd-D1, Vrn-A1 and Rht-B1) markers on quantitative trait loci (QTL) detection in a recombinant inbred lines (RILs) population derived from a cross between two spring wheat (Triticum aestivum L.) cultivars, 'Attila' and 'CDC Go', and evaluated for eight agronomic traits at three environments under organic management. The objectives of the present study were to investigate the effect of conventional management on QTL detection in the same mapping population using the same set of markers as the organic management and compare the results with organic management...
2017: PloS One
https://www.readbyqxmd.com/read/28152092/a-genome-wide-association-study-for-agronomic-traits-in-soybean-using-snp-markers-and-snp-based-haplotype-analysis
#13
Rodrigo Iván Contreras-Soto, Freddy Mora, Marco Antônio Rott de Oliveira, Wilson Higashi, Carlos Alberto Scapim, Ivan Schuster
Mapping quantitative trait loci through the use of linkage disequilibrium (LD) in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max). The haplotype-based genome-wide association study (GWAS) has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW), plant height (PH) and seed yield (SY) in a soybean association mapping panel using single nucleotide polymorphism (SNP) markers and haplotype information...
2017: PloS One
https://www.readbyqxmd.com/read/28149680/increased-root-hair-density-by-loss-of-wrky6-in-arabidopsis-thaliana
#14
Markus G Stetter, Martin Benz, Uwe Ludewig
Root hairs are unicellular elongations of certain rhizodermal cells that improve the uptake of sparingly soluble and immobile soil nutrients. Among different Arabidopsis thaliana genotypes, root hair density, length and the local acclimation to low inorganic phosphate (Pi) differs considerably, when analyzed on split agar plates. Here, genome-wide association fine mapping identified significant single nucleotide polymorphisms associated with the increased root hair density in the absence of local phosphate on chromosome 1...
2017: PeerJ
https://www.readbyqxmd.com/read/28148242/exome-qtl-seq-maps-monogenic-locus-and-qtls-in-barley
#15
Hiroshi Hisano, Kazuki Sakamoto, Hiroki Takagi, Ryohei Terauchi, Kazuhiro Sato
BACKGROUND: QTL-seq, in combination with bulked segregant analysis and next-generation sequencing (NGS), is used to identify loci in small plant genomes, but is technically challenging to perform in species with large genomes, such as barley. A combination of exome sequencing and QTL-seq (exome QTL-seq) was used to map the mono-factorial Mendelian locus black lemma and pericarp (Blp) and QTLs for resistance to net blotch disease, a common disease of barley caused by the fungus Pyrenophora teres, which segregated in a population of 100 doubled haploid barley lines...
February 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28148225/novel-arabidopsis-microtubule-associated-proteins-track-growing-microtubule-plus-ends
#16
Jeh Haur Wong, Takashi Hashimoto
BACKGROUND: Microtubules (MTs) are polarized polymers with highly dynamic plus ends that stochastically switch between growth and shrinkage phases. In eukaryotic cells, a plethora of MT-associated proteins (MAPs) regulate the dynamics and higher-order organization of MTs to mediate distinct cellular functions. Plus-end tracking proteins (+TIPs) are a group of MAPs that specifically accumulate at the growing MT plus ends, where they modulate the behavior of the MT plus ends and mediate interactions with cellular targets...
February 2, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28145468/the-srnaome-mining-revealed-existence-of-unique-signature-small-rnas-derived-from-5-8srrna-from-piper-nigrum-and-other-plant-lineages
#17
Srinivasan Asha, E V Soniya
Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5' end of the putative long form of 5.8S rRNA (5.8SLrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5' consensus sequence of the 5...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28144698/fine-mapping-qfs07-1-controlling-fiber-strength-in-upland-cotton-gossypium-hirsutum-l
#18
Xiaomei Fang, Xueying Liu, Xiaoqin Wang, Wenwen Wang, Dexin Liu, Jian Zhang, Dajun Liu, Zhonghua Teng, Zhaoyun Tan, Fang Liu, Fengjiao Zhang, Maochao Jiang, Xiuling Jia, Jianwei Zhong, Jinghong Yang, Zhengsheng Zhang
KEY MESSAGE: qFS07.1 controlling fiber strength was fine-mapped to a 62.6-kb region containing four annotated genes. RT-qPCR and sequence of candidate genes identified an LRR RLK gene as the most likely candidate. Fiber strength is an important component of cotton fiber quality and is associated with other properties, such as fiber maturity, fineness, and length. Stable QTL qFS07.1, controlling fiber strength, had been identified on chromosome 7 in an upland cotton recombinant inbred line (RIL) population from a cross (CCRI35 × Yumian1) described in our previous studies...
January 31, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28143950/genomic-regions-associated-with-tolerance-to-freezing-stress-and-snow-mold-in-winter-wheat
#19
Erika B Kruse, Scott W Carle, Nuan Wen, Daniel Z Skinner, Timothy D Murray, Kimberly A Garland-Campbell, Arron H Carter
Plants grown through the winter are subject to selective pressures that vary with each year's unique conditions, necessitating tolerance of numerous abiotic and biotic stress factors. The objective of this study was to identify molecular markers in winter wheat (Triticum aestivum L.) associated with tolerance of two of these stresses, freezing temperatures and snow mold, a fungal disease complex active under snow cover. A population of 155 F2:5 recombinant inbred lines from a cross between soft white wheat cultivars 'Finch' and 'Eltan' were evaluated for snow mold tolerance in the field, and for freezing tolerance under controlled conditions...
January 30, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28143400/the-carotenoid-biosynthetic-and-catabolic-genes-in-wheat-and-their-association-with-yellow-pigments
#20
Pasqualina Colasuonno, Maria Luisa Lozito, Ilaria Marcotuli, Domenica Nigro, Angelica Giancaspro, Giacomo Mangini, Pasquale De Vita, Anna Maria Mastrangelo, Nicola Pecchioni, Kelly Houston, Rosanna Simeone, Agata Gadaleta, Antonio Blanco
BACKGROUND: In plants carotenoids play an important role in the photosynthetic process and photo-oxidative protection, and are the substrate for the synthesis of abscisic acid and strigolactones. In addition to their protective role as antioxidants and precursors of vitamin A, in wheat carotenoids are important as they influence the colour (whiteness vs. yellowness) of the grain. Understanding the genetic basis of grain yellow pigments, and identifying associated markers provide the basis for improving wheat quality by molecular breeding...
January 31, 2017: BMC Genomics
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