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Moysés Nascimento, Ana Carolina Campana Nascimento, Fabyano Fonseca E Silva, Leiri Daiane Barili, Naine Martins do Vale, José Eustáquio Carneiro, Cosme Damião Cruz, Pedro Crescêncio Souza Carneiro, Nick Vergara Lopes Serão
Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower-DFF; Days for flowering-DTF; Days to end of flowering-DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons...
2018: PloS One
Envel Kerdaffrec, Magnus Nordborg
Seed dormancy is a complex adaptive trait that controls the timing of seed germination, one of the major fitness components in many plant species. Despite being highly heritable, seed dormancy is extremely plastic and influenced by a wide range of environmental cues. Here, using a set of 92 Arabidopsis thaliana lines from Sweden, we investigate the effect of seed maturation temperature on dormancy variation at the population level. The response to temperature differs dramatically between lines, demonstrating that genotype and the maternal environment interact in controlling the trait...
2017: PloS One
Xiang Wang, Baohong Zou, Qiaolin Shao, Yongmei Cui, Shan Lu, Yan Zhang, Quansheng Huang, Ji Huang, Jian Hua
Low temperature affects seed germination in plants, and low-temperature germination (LTG) is an important agronomic trait. Natural variation of LTG has been reported in rice, but the molecular basis for this variation is largely unknown. Here we report the phenotypic analysis of LTG in 187 rice natural accessions and a genome-wide association study (GWAS) of LTG in this collection. A total of 53 quantitative trait loci (QTLs) were found to be associated with LTG, of which 20 were located in previously reported QTLs...
December 11, 2017: Journal of Experimental Botany
Xiao-Ming Zheng, Tingting Gong, Hong-Ling Ou, Dayuan Xue, Weihua Qiao, Junrui Wang, Sha Liu, Qingwen Yang, Kenneth M Olsen
Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (<i>Oryza sativa</i>) to perform a large scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1...
December 1, 2017: Genome Génome / Conseil National de Recherches Canada
Jens Keilwagen, Heike Lehnert, Thomas Berner, Holger Budahn, Thomas Nothnagel, Detlef Ulrich, Frank Dunemann
Terpenes are an important group of secondary metabolites in carrots influencing taste and flavor, and some of them might also play a role as bioactive substances with an impact on human physiology and health. Understanding the genetic and molecular basis of terpene synthases (TPS) involved in the biosynthesis of volatile terpenoids will provide insights for improving breeding strategies aimed at quality traits and for developing specific carrot chemotypes possibly useful for pharmaceutical applications. Hence, a combination of terpene metabolite profiling, genotyping-by-sequencing (GBS), and genome-wide association study (GWAS) was used in this work to get insights into the genetic control of terpene biosynthesis in carrots and to identify several TPS candidate genes that might be involved in the production of specific monoterpenes...
2017: Frontiers in Plant Science
Qian Gong, Zhaoen Yang, Eryong Chen, Gaofei Sun, Shoupu He, Hamama Islam Butt, Chaojun Zhang, Xueyan Zhang, Zuoren Yang, Xiongming Du, Fuguang Li
Verticillium wilt disease is one of the most destructive biotic stresses faced by cotton plants. Here, we performed a genome-wide association study (GWAS) in 215 Chinese Gossypium arboreum accessions inoculated as seedlings with Verticillium dahliae to identify candidate loci involved in wilt resistance. We identified 309 loci that had a significant association with Verticillium wilt resistance and Log (P) values greater than 5.0; the highest signal appeared on Ca3 in a 74 Kb haplotype block. Five genes were also located within this haplotype block...
November 20, 2017: Plant & Cell Physiology
Simerjeet Kaur, Xu Zhang, Amita Mohan, Haixiao Dong, Prashant Vikram, Sukhwinder Singh, Zhiwu Zhang, Kulvinder S Gill, Kanwarpal S Dhugga, Jaswinder Singh
Plant cell wall formation is a complex, coordinated and developmentally regulated process. Cellulose is the most dominant constituent of plant cell walls. Because of its paracrystalline structure, cellulose is the main determinant of mechanical strength of plant tissues. As the most abundant polysaccharide on earth, it is also the focus of cellulosic biofuel industry. To reduce culm lodging in wheat and for improved ethanol production, delineation of the variation for stem cellulose content could prove useful...
2017: Frontiers in Plant Science
Andrea Volante, Francesca Desiderio, Alessandro Tondelli, Rosaria Perrini, Gabriele Orasen, Chiara Biselli, Paolo Riccardi, Alessandra Vattari, Daniela Cavalluzzo, Simona Urso, Manel Ben Hassen, Agostino Fricano, Pietro Piffanelli, Paolo Cozzi, Filippo Biscarini, Gian Attilio Sacchi, Luigi Cattivelli, Giampiero Valè
A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for 26 traits related to phenology, plant and seed morphology, physiology and yield for 2 years in field conditions under permanent flooding (PF) and limited water (LW). A genome-wide analysis uncovered a total of 160 significant marker-trait associations (MTAs), of which 32 were LW-specific, 59 were PF-specific, and 69 were in common between the two water management systems. LW-specific associations were identified for several agronomic traits including days to maturation, days from flowering to maturation, leaf traits, plant height, panicle and seed traits, hundred grain weight, yield and tillering...
2017: Frontiers in Plant Science
Yajun He, Daoming Wu, Dayong Wei, Ying Fu, Yixin Cui, Hongli Dong, Chuandong Tan, Wei Qian
Branch number is an important trait in plant architecture that can influence crop yield and quality in Brassica napus. Here, we detected the QTLs responsible for branch number in a DH population and its reconstructed F2 population over two years. Further, a GWAS research on branch number was performed using a panel of 327 accessions with 33186 genomic SNPs from the 60 K Brassica Illumina® Infinium SNP array. Through combining linkage analysis and association mapping, a new QTL was fine mapped onto C03. Subsequently, we tested the correlations between the SNP polymorphisms and mRNA expression levels of genes in the target interval to identify potential loci or genes that control branch number through expression...
November 21, 2017: Scientific Reports
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
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
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
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
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
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
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
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
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
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
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
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