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https://www.readbyqxmd.com/read/29150594/mating-design-and-genetic-structure-of-a-multi-parent-advanced-generation-inter-cross-magic-population-of-sorghum-sorghum-bicolor-l-moench
#1
Patrick O Ongom, Gebisa Ejeta
MAGIC populations are powerful next generation mapping resources. We describe here the mating design and structure of the first MAGIC population in sorghum and test its utility for mapping. The population was developed by intercrossing 19 diverse founder lines, through a series of paired crosses with a genetic male sterile source, followed by 10 generations of random mating. At the final stage of random mating, one thousand random fertile plants in the population were identified and subjected to six generations of selfing to produce 1000 immortal MAGIC inbred lines...
November 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29143671/gwas-of-agronomic-traits-in-soybean-collection-included-in-breeding-pool-in-kazakhstan
#2
Alibek Zatybekov, Saule Abugalieva, Svetlana Didorenko, Yelena Gerasimova, Ivan Sidorik, Shynar Anuarbek, Yerlan Turuspekov
BACKGROUND: In recent years soybean is becoming one of the most important oilseed crops in Kazakhstan. Only within the last ten years (2006-2016), the area under soybean is expanded from 45 thousand hectares (ha) in 2006 to 120 thousand ha in 2016. The general trend of soybean expansion is from south-eastern to eastern and northern regions of the country, where average temperatures are lower and growing seasons are shorter. These new soybean growing territories were poorly examined in terms of general effects on productivity level among the diverse sample of soybean accessions...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143598/gwas-for-plant-growth-stages-and-yield-components-in-spring-wheat-triticum-aestivum-l-harvested-in-three-regions-of-kazakhstan
#3
Yerlan Turuspekov, Aida Baibulatova, Kanat Yermekbayev, Laura Tokhetova, Vladimir Chudinov, Grigoriy Sereda, Martin Ganal, Simon Griffiths, Saule Abugalieva
BACKGROUND: Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29115920/genome-wide-association-mapping-of-resistance-to-a-brazilian-isolate-of-sclerotinia-sclerotiorum-in-soybean-genotypes-mostly-from-brazil
#4
Wei Wei, Ana Carolina Oliveira Mesquita, Adriana de A Figueiró, Xing Wu, Shilpa Manjunatha, Daniel P Wickland, Matthew E Hudson, Fernando C Juliatti, Steven J Clough
BACKGROUND: Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29114015/genetic-components-of-root-architecture-remodeling-in-response-to-salt-stress
#5
Magdalena Julkowska, Iko Tamar Koevoets, Selena Mol, Huub Cj Hoefsloot, Richard Feron, Mark Tester, Joost J B Keurentjes, Arthur Korte, Michel A Haring, Gert-Jan de Boer, Christa Testerink
Salinity of the soil is highly detrimental to plant growth. Plants respond by a redistribution of root mass between main and lateral roots, yet the genetic machinery underlying this process is still largely unknown. Here, we describe the natural variation among 347 Arabidopsis thaliana accessions in root system architecture (RSA) and identify the traits with highest natural variation in their response to salt. Salt-induced changes in RSA were associated with 100 genetic loci using genome-wide association studies (GWAS)...
November 7, 2017: Plant Cell
https://www.readbyqxmd.com/read/29081789/genetic-architecture-of-natural-variation-in-rice-nonphotochemical-quenching-capacity-revealed-by-genome-wide-association-study
#6
Quanxiu Wang, Hu Zhao, Junpeng Jiang, Jiuyue Xu, Weibo Xie, Xiangkui Fu, Chang Liu, Yuqing He, Gongwei Wang
The photoprotective processes conferred by nonphotochemical quenching (NPQ) serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice (Oryza sativa), and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS) for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29080185/genome-wide-association-mapping-analyses-applied-to-polyamines
#7
Luis Barboza-Barquero, Paul Esker, Rubén Alcázar
Genome Wide Association Studies (GWAS) allow the use of natural variation to understand the genetics controlling specific traits. Efficient methods to conduct GWAS in plants have been reported. This chapter provides the main steps to conduct and analyse GWAS in Arabidopsis thaliana using polyamine levels as trait. This approach is suitable for the discovery of genes that modulate the levels of polyamines, and can be used in combination with different types of stress.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29078746/qtl-mapping-and-candidate-gene-analysis-of-ferrous-iron-and-zinc-toxicity-tolerance-at-seedling-stage-in-rice-by-genome-wide-association-study
#8
Jian Zhang, Kai Chen, Yunlong Pang, Shahzad Amir Naveed, Xiuqin Zhao, Xiaoqian Wang, Yun Wang, Michael Dingkuhn, Julie Pasuquin, Zhikang Li, Jianlong Xu
BACKGROUND: Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity and greatly affect rice yield and quality. To improve rice production, understanding the genetic and molecular resistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is an effective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the genetic relationship between them in a genetically diverse population...
October 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29044609/phenomics-allows-identification-of-genomic-regions-affecting-maize-stomatal-conductance-with-conditional-effects-of-water-deficit-and-evaporative-demand
#9
Santiago Alvarez Prado, Llorenç Cabrera-Bosquet, Antonin Grau, Aude Coupel-Ledru, Emilie J Millet, Claude Welcker, François Tardieu
Stomatal conductance is central for the trades-off between hydraulics and photosynthesis. We aimed at deciphering its genetic control and that of its responses to evaporative demand and water deficit, a nearly impossible task with gas exchanges measurements. Whole-plant stomatal conductance was estimated via inversion of the Penman Monteith equation from data of transpiration and plant architecture collected in a phenotyping platform. We have analyzed jointly four experiments with contrasting environmental conditions imposed to a panel of 254 maize hybrids...
October 17, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28983305/genetic-architecture-of-charcoal-rot-macrophomina-phaseolina-resistance-in-soybean-revealed-using-a-diverse-panel
#10
Sara M Coser, R V Chowda Reddy, Jiaoping Zhang, Daren S Mueller, Alemu Mengistu, Kiersten A Wise, Tom W Allen, Arti Singh, Asheesh K Singh
Charcoal rot (CR) disease caused by Macrophomina phaseolina is responsible for significant yield losses in soybean production. Among the methods available for controlling this disease, breeding for resistance is the most promising. Progress in breeding efforts has been slow due to the insufficient information available on the genetic mechanisms related to resistance. Genome-wide association studies (GWAS) enable unraveling the genetic architecture of resistance and identification of causal genes. The aims of this study were to identify new sources of resistance to CR in a collection of 459 diverse plant introductions from the USDA Soybean Germplasm Core Collection using field and greenhouse screenings, and to conduct GWAS to identify candidate genes and associated molecular markers...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28981780/genetic-architecture-of-photosynthesis-in-sorghum-bicolor-under-non-stress-and-cold-stress-conditions
#11
Diego Ortiz, Jieyun Hu, Maria G Salas Fernandez, Tracy Lawson
Sorghum (Sorghum bicolor L. Moench) is a C4 species sensitive to the cold spring conditions that occur at northern latitudes, especially when coupled with excessive light, and that greatly affect the photosynthetic rate. The objective of this study was to discover genes/genomic regions that control the capacity to cope with excessive energy under low temperature conditions during the vegetative growth period. A genome-wide association study (GWAS) was conducted for seven photosynthetic gas exchange and chlorophyll fluorescence traits under three consecutive temperature treatments: control (28 °C/24 °C), cold (15 °C/15 °C), and recovery (28 °C/24 °C)...
July 20, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28980023/unlocking-new-alleles-for-leaf-rust-resistance-in-the-vavilov-wheat-collection
#12
Adnan Riaz, Naveenkumar Athiyannan, Sambasivam K Periyannan, Olga Afanasenko, Olga P Mitrofanova, Gregory J Platz, Elizabeth A B Aitken, Rod J Snowdon, Evans S Lagudah, Lee T Hickey, Kai P Voss-Fels
Thirteen potentially new leaf rust resistance loci were identified in a Vavilov wheat diversity panel. We demonstrated the potential of allele stacking to strengthen resistance against this important pathogen. Leaf rust (LR) caused by Puccinia triticina is an important disease of wheat (Triticum aestivum L.), and the deployment of genetically resistant cultivars is the most viable strategy to minimise yield losses. In this study, we evaluated a diversity panel of 295 bread wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources (St Petersburg, Russia) for LR resistance and performed genome-wide association studies (GWAS) using 10,748 polymorphic DArT-seq markers...
October 4, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28961930/a-highly-specific-genome-wide-association-study-integrated-with-transcriptome-data-reveals-the-contribution-of-copy-number-variations-to-specialized-metabolites-in-arabidopsis-thaliana-accessions
#13
Kazumasa Shirai, Fumio Matsuda, Ryo Nakabayashi, Masanori Okamoto, Maho Tanaka, Akihiro Fujimoto, Minami Shimizu, Kazuo Shinozaki, Motoaki Seki, Kazuki Saito, Kousuke Hanada
Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication events contribute to the diversity of specialized metabolites within species. We identified metabolome quantitative trait genes (mQTGs) associated with quantitative metabolite variations and examined the relationship between mQTGs and CNVs...
September 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28922760/the-roles-of-pleiotropy-and-close-linkage-as-revealed-by-association-mapping-of-yield-and-correlated-traits-of-wheat-triticum-aestivum-l
#14
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
https://www.readbyqxmd.com/read/28835210/high-density-80%C3%A2-k-snp-array-is-a-powerful-tool-for-genotyping-g-hirsutum-accessions-and-genome-analysis
#15
Caiping Cai, Guozhong Zhu, Tianzhen Zhang, Wangzhen Guo
BACKGROUND: High-throughput genotyping platforms play important roles in plant genomic studies. Cotton (Gossypium spp.) is the world's important natural textile fiber and oil crop. Upland cotton accounts for more than 90% of the world's cotton production, however, modern upland cotton cultivars have narrow genetic diversity. The amounts of genomic sequencing and re-sequencing data released make it possible to develop a high-quality single nucleotide polymorphism (SNP) array for intraspecific genotyping detection in cotton...
August 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28828506/an-innovative-procedure-of-genome-wide-association-analysis-fits-studies-on-germplasm-population-and-plant-breeding
#16
Jianbo He, Shan Meng, Tuanjie Zhao, Guangnan Xing, Shouping Yang, Yan Li, Rongzhan Guan, Jiangjie Lu, Yufeng Wang, Qiuju Xia, Bing Yang, Junyi Gai
The innovative RTM-GWAS procedure provides a relatively thorough detection of QTL and their multiple alleles for germplasm population characterization, gene network identification, and genomic selection strategy innovation in plant breeding. The previous genome-wide association studies (GWAS) have been concentrated on finding a handful of major quantitative trait loci (QTL), but plant breeders are interested in revealing the whole-genome QTL-allele constitution in breeding materials/germplasm (in which tremendous historical allelic variation has been accumulated) for genome-wide improvement...
November 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28797221/use-of-genotyping-by-sequencing-to-determine-the-genetic-structure-in-the-medicinal-plant-chamomile-and-to-identify-flowering-time-and-alpha-bisabolol-associated-snp-loci-by-genome-wide-association-mapping
#17
Lars-Gernot Otto, Prodyut Mondal, Jonathan Brassac, Susanne Preiss, Jörg Degenhardt, Sang He, Jochen Christoph Reif, Timothy Francis Sharbel
BACKGROUND: Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active. In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28770301/genome-wide-association-mapping-reveals-a-rich-genetic-architecture-of-stripe-rust-resistance-loci-in-emmer-wheat-triticum-turgidum-ssp-dicoccum
#18
Weizhen Liu, Marco Maccaferri, Xianming Chen, Gaetano Laghetti, Domenico Pignone, Michael Pumphrey, Roberto Tuberosa
SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated...
November 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28769955/genome-wide-association-study-reveals-candidate-genes-for-control-of-plant-height-branch-initiation-height-and-branch-number-in-rapeseed-brassica-napus-l
#19
Ming Zheng, Cheng Peng, Hongfang Liu, Min Tang, Hongli Yang, Xiaokang Li, Jinglin Liu, Xingchao Sun, Xinfa Wang, Junfeng Xu, Wei Hua, Hanzhong Wang
Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number (BN) and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH, and BN) in a panel of 333 rapeseed accessions across 4 years. A genome-wide association study (GWAS) was performed via Q + K model and the panel was genotyped using the 60 k Brassica Infinium SNP array. We identified seven loci for PH, four for BIH, and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15, and 17 candidate genes for these traits, respectively...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747922/identification-of-major-quantitative-trait-loci-for-seed-oil-content-in-soybeans-by-combining-linkage-and-genome-wide-association-mapping
#20
Yongce Cao, Shuguang Li, Zili Wang, Fangguo Chang, Jiejie Kong, Junyi Gai, Tuanjie Zhao
Soybean oil is the most widely produced vegetable oil in the world and its content in soybean seed is an important quality trait in breeding programs. More than 100 quantitative trait loci (QTLs) for soybean oil content have been identified. However, most of them are genotype specific and/or environment sensitive. Here, we used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley...
2017: Frontiers in Plant Science
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