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Plant Genome

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July 2018: Plant Genome
Juan David Lobaton, Tamara Miller, Juanita Gil, Daniel Ariza, Juan Fernando de la Hoz, Alvaro Soler, Steve Beebe, Jorge Duitama, Paul Gepts, Bodo Raatz
Common bean ( L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to , (A...
July 2018: Plant Genome
Juan Manuel González-Camacho, Leonardo Ornella, Paulino Pérez-Rodríguez, Daniel Gianola, Susanne Dreisigacker, José Crossa
New methods and algorithms are being developed for predicting untested phenotypes in schemes commonly used in genomic selection (GS). The prediction of disease resistance in GS has its own peculiarities: a) there is consensus about the additive nature of quantitative adult plant resistance (APR) genes, although epistasis has been found in some populations; b) rust resistance requires effective combinations of major and minor genes; and c) disease resistance is commonly measured based on ordinal scales (e.g...
July 2018: Plant Genome
Arun Prabhu Dhanapal, Jeffery D Ray, James R Smith, Larry C Purcell, Felix B Fritschi
The mineral composition of crop shoot tissues is important for yield formation and nutrient remobilization to seeds. The natural diversity that exists within crop species can be used to investigate mechanisms that define plant mineral composition and to identify important genomic loci for these processes. The objective of this study was to determine shoot mineral nutrient concentrations in genetically diverse soybean [ (L.) Merr.] genotypes and to identify genomic regions associated with concentrations of different nutrients in shoot tissue...
July 2018: Plant Genome
Steven L Anderson, Adam L Mahan, Seth C Murray, Patricia E Klein
Multiparent advanced generation inter-cross (MAGIC) populations can provide improved genetic mapping resolution by increasing allelic diversity and effective recombination. The Four Parent Maize (FPM; L.) population implemented five different mating designs used in MAGIC and bi-parental populations to compare empirical effects on genetic resolution and power of quantitative trait locus (QTL) detection; the combined population here comprised of 1149 individuals with 118,509 genetic markers. Measurements were recorded for plant height (PH), ear height (EH), days to anthesis (DTA) and silking (DTS) in seven environments, spanning three years...
July 2018: Plant Genome
Hugo E Cuevas, Louis K Prom, Elizabeth A Cooper, Joseph E Knoll, Xinzhi Ni
The productivity and profitability of sorghum [ (L.) Moench] is reduced by susceptibility to fungal diseases, such as anthracnose ( P. Henn.). A limited number of resistant accessions are present in the temperate-adapted germplasm; other exotic sources of resistance are not currently available for breeding programs. Among 335 accessions available to breeders from a previously genotyped sorghum association panel (SAP), we found that 75 were resistant to anthracnose. A phylogenetic analysis of these accessions showed high genetic diversity and multiple resistance sources...
July 2018: Plant Genome
Mulusew Fikere, Denise M Barbulescu, Michelle M Malmberg, Fan Shi, Joshua C O Koh, Anthony T Slater, Iona M MacLeod, Phillip J Bowman, Phillip A Salisbury, German C Spangenberg, Noel O I Cogan, Hans D Daetwyler
Genomic prediction is becoming a popular plant breeding method to predict the genetic merit of lines. While some genomic prediction results have been reported in canola, none have been evaluated for blackleg disease. Here, we report genomic prediction for seedling emergence, survival rate, and internal infection), using 532 Spring and Winter canola lines. These lines were phenotyped in two replicated blackleg disease nurseries grown at Wickliffe and Green Lake, Victoria, Australia. A transcriptome genotyping-by-sequencing approach revealed 98,054 single nucleotide polymorphisms (SNPs) after quality control...
July 2018: Plant Genome
Carl-Erik Tornqvist, Megan Taylor, Yiwei Jiang, Joseph Evans, C Robin Buell, Shawn M Kaeppler, Michael D Casler
Flowering is an important developmental event in switchgrass (), as the time to complete the life cycle affects overall biomass accumulation. The objective of this study was to generate a linkage map using single nucleotide polymorphism (SNP) markers to identify quantitative trait loci (QTL) associated with flowering time. A pseudo-F population was created by crossing two siblings derived from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. Heading and anthesis dates were collected for 2 yr at two locations: DeKalb, IL and Lafayette, IN...
July 2018: Plant Genome
Yongfu Tao, Emma Mace, Barbara George-Jaeggli, Colleen Hunt, Alan Cruickshank, Robert Henzell, David Jordan
Grain weight has increased during domestication of cereals. Together with grain number it determines yield, but the two are often negatively correlated. Understanding the genetic architecture of grain weight and its relationship with grain number is critical to enhance crop yield. Sorghum is an important food, feed, and biofuel crop well-known for its adaptation to drought and heat. This study aimed to dissect the genetic basis of thousand grain weight (TGW) in a BCF population between a domesticated sorghum accession and its wild progenitor, subsp...
July 2018: Plant Genome
Adam Vanous, Candice Gardner, Michael Blanco, Adam Martin-Schwarze, Alexander E Lipka, Sherry Flint-Garcia, Martin Bohn, Jode Edwards, Thomas Lübberstedt
Flowering and height related traits are extensively studied in maize for three main reasons: 1) easily obtained phenotypic measurements, 2) highly heritable, and 3) importance of these traits to adaptation and grain yield. However, variation in flowering and height traits is extensive and findings from previous studies are genotype specific. Herein, a diverse panel of exotic derived doubled haploid lines, in conjunction with genome-wide association analysis, is used to further explore adaptation related trait variation of exotic germplasm for potential use in adapting exotic germplasm to the U...
July 2018: Plant Genome
Stella Salvo, Jason Cook, Alvar R Carlson, Candice N Hirsch, Shawn M Kaeppler, Heidi F Kaeppler
Embryogenic and regenerable tissue cultures are widely utilized in plant transformation, clonal propagation, and biological research applications. Germplasm utilized in those applications are limited, however, due to genotype-dependent culture response. The goal of this study was to identify genomic regions controlling embryogenic and regenerable tissue culture response in the globally important crop, maize ( L.), toward the long-term objective of developing approaches for genotype-independent plant genetic engineering and clonal propagation systems...
July 2018: Plant Genome
Cecile Richard, Jack Christopher, Karine Chenu, Andrew Borrell, Mandy Christopher, Lee Hickey
A current challenge for plant breeders is the limited ability to phenotype and select for root characteristics to enhance crop productivity. The development of a high-throughput phenotyping method has recently offered new opportunities for the selection of root characteristics in breeding programs. Here, we investigated prospects for phenotypic and molecular selection for seminal root angle (SRA), a key trait associated with mature root system architecture in wheat ( L.). We first investigated genetic diversity for this trait in a panel of 22 wheat lines adapted to Australian environments...
July 2018: Plant Genome
Maya Subedi, Kirstin E Bett, Hamid Khazaei, Albert Vandenberg
Milling qualities are key traits for the red lentil ( Medik.) industry as price is largely determined by recovery yield. milling involves removal of the seed coat and splitting of the cotyledon to produce either splits or footballs (cotyledons still attached). The objectives of the study were to determine the heritability of the milling traits dehulling efficiency (DE), milling recovery (MR), and football recovery (FR) and to identify the genomic regions controlling them. We used a lentil recombinant inbred population from the cross 'CDC Robin' × '946a-46', which have contrasting seed characteristics...
July 2018: Plant Genome
Moses Nyine, Brigitte Uwimana, Nicolas Blavet, Eva Hřibová, Helena Vanrespaille, Michael Batte, Violet Akech, Allan Brown, Jim Lorenzen, Rony Swennen, Jaroslav Doležel
Improving the efficiency of selection in conventional crossbreeding is a major priority in banana ( spp.) breeding. Routine application of classical marker assisted selection (MAS) is lagging in banana due to limitations in MAS tools. Genomic selection (GS) based on genomic prediction models can address some limitations of classical MAS, but the use of GS in banana has not been reported to date. The aim of this study was to evaluate the predictive ability of six genomic prediction models for 15 traits in a multi-ploidy training population...
July 2018: Plant Genome
Christian R Werner, Kai P Voss-Fels, Charlotte N Miller, Wei Qian, Wei Hua, Chun-Yun Guan, Rod J Snowdon, Lunwen Qian
Genomic selection (GS) has revolutionized breeding for quantitative traits in plants, offering potential to optimize resource allocation in breeding programs and increase genetic gain per unit of time. Modern high-density single nucleotide polymorphism (SNP) arrays comprising up to several hundred thousand markers provide a user-friendly technology to characterize the genetic constitution of whole populations and for implementing GS in breeding programs. However, GS does not build upon detailed genotype profiling facilitated by maximum marker density...
July 2018: Plant Genome
Sivakumar Sukumaran, Diego Jarquin, Jose Crossa, Matthew Reynolds
Genomic prediction studies incorporating genotype × environment (G×E) interaction effects are limited in durum wheat. We tested the genomic-enabled prediction accuracy (PA) of Genomic Best Linear Unbiased Predictor (GBLUP) models-six non-G × E and three G × E models-on three basic cross-validation (CV) schemes- in predicting incomplete field trials (CV2), new lines (CV1), and lines in untested environments (CV0)- in a durum wheat panel grown under yield potential, drought stress, and heat stress conditions...
July 2018: Plant Genome
Ben N Mansfeld, Rebecca Grumet
Next-Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G'. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G' values, and log (-values), enabling identification and plotting of QTL...
July 2018: Plant Genome
Rahul Chandnani, Changsoo Kim, Hui Guo, Tariq Shehzad, Jason G Wallace, Daohua He, Zhengsheng Zhang, Jinesh D Patel, Jeevan Adhikari, Sameer Khanal, Andrew H Paterson
In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. 'Acala Maxxa' (GH) and G. barbadense L. 'Pima S6' (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments...
March 2018: Plant Genome
Joseph Evans, Millicent D Sanciangco, Kin H Lau, Emily Crisovan, Kerrie Barry, Chris Daum, Hope Hundley, Jerry Jenkins, Megan Kennedy, Govindarajan Kunde-Ramamoorthy, Brieanne Vaillancourt, Ananta Acharya, Jeremy Schmutz, Malay Saha, Shawn M Kaeppler, E Charles Brummer, Michael D Casler, C Robin Buell
Switchgrass ( is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1...
March 2018: Plant Genome
Hamid Khazaei, Michael Fedoruk, Carolyn T Caron, Albert Vandenberg, Kirstin E Bett
The dimensions of lentil ( Medik.) seeds are important quality parameters that are major determinants of market preference, cooking time, and post-harvest milling quality. Knowledge of the genetic control of traits related to seed dimensions would be useful for crop improvement. The principal aim of this study was to identify single nucleotide polymorphism (SNP) markers linked to genes that control seed diameter, seed thickness, and seed plumpness. Association mapping analysis with SNP markers was used to study the seed dimensions of 138 diverse cultivated lentil accessions grown at two locations in Saskatchewan, Canada, in 2011 and 2012...
March 2018: Plant Genome
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