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Genetic Mapping of Quantitative Trait Loci Underlying Flowering Time in Chrysanthemum (Chrysanthemum morifolium)

Genetic Mapping of Quantitative Trait Loci Underlying Flowering Time in Chrysanthemum (Chrysanthemum morifolium) | Plant Breeding and Genomics News | Scoop.it

 

Flowering time is an important trait in chrysanthemum, but its genetic basis remains poorly understood. An intraspecific mapping population bred from the cross between the autumn-flowering cultivar 'Yuhualuoying’ and the summer-flowering ‘Aoyunhanxiao’ was used to determine the number and relative effect of QTL segregating for five

measures of flowering time.

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Tomato Yield Heterosis Is Triggered by a Dosage Sensitivity of the Florigen Pathway That Fine-Tunes Shoot Architecture

Tomato Yield Heterosis Is Triggered by a Dosage Sensitivity of the Florigen Pathway That Fine-Tunes Shoot Architecture | Plant Breeding and Genomics News | Scoop.it

The superiority of hybrids has long been exploited in agriculture, and although many models explaining “heterosis” have been put forth, direct empirical support is limited. Particularly elusive have been cases of heterozygosity for single gene mutations causing heterosis under a genetic model known as overdominance. In tomato (Solanum lycopersicum), plants carrying mutations in SINGLE FLOWER TRUSS (SFT) encoding the flowering hormone florigen are severely delayed in flowering, become extremely large, and produce few flowers and fruits, but when heterozygous, yields are dramatically increased. . . .

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Probability genotype imputation method and integrated weighted lasso for QTL identification

Many QTL studies have two common features: (1) often there is missing marker information, (2) among many markers involved in the biological process only a few are causal.
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MAPfastR: Quantitative Trait Loci Mapping in Outbred Line Crosses

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Abstract:  MAPfastR is a software package developed to analyze quantitative trait loci data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate quantitative trait loci analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7

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2013 Plant Breeding and Genetics Symposium "Genetics of Seed Quality, Germination and Evolution" at Michigan State University on Friday, Dec 13th

2013 Plant Breeding and Genetics Symposium "Genetics of Seed Quality, Germination and Evolution" at Michigan State University on Friday, Dec 13th | Plant Breeding and Genomics News | Scoop.it

Join the symposium live from Michigan State University by registering at the link below.  . 

 

Title: Genetics of Seed Quality, Germination and Evolution

Date: Friday, December 13, 2013

Time: 9:00 am - 4:00 pm Eastern Time

Register: https://www1.gotomeeting.com/register/919017808

 

9:10 - 10:00  Dr. Hiro Nonogaki, Oregon State University

“Transcriptional and Post-transcriptional Regulation of Gene Expression Associated with Hormone Signaling in Seeds.”

 

10:40 - 11:30  Dr. Kristin Mercer, Ohio State University

“Evolutionary Ecology Of Seeds In Crop-Wild Hybrid Zones.”


1:35 - 2:25 pm Dr. Chris Richards, US National Center for Genetic Preservation

"Genetic Dynamics in Conservation Collections"


3:05 - 3:55 pm Dr. Oswald Crasta, Leader, Genomics Assisted Breeding, Dow AgroSciences

"Next-generation breeding"

 

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PLOS ONE: Impacts of Population Structure and Analytical Models in Genome-Wide Association Studies of Complex Traits in Forest Trees: A Case Study in Eucalyptus globulus

PLOS ONE: Impacts of Population Structure and Analytical Models in Genome-Wide Association Studies of Complex Traits in Forest Trees: A Case Study in Eucalyptus globulus | Plant Breeding and Genomics News | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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BMC Genomics | Full text | A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton

The study of quantitative trait loci (QTL) in cotton (Gossypium spp.) is focused on traits of agricultural significance.
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Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus

“ Single nucleotide polymorphisms (SNPs), the most abundant variations in a genome, have been widely used in various studies.”
Via Biswapriya Biswavas Misra
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Traditional and Modern Plant Breeding Methods with Examples in Rice (Oryza sativa L.)

Traditional and Modern Plant Breeding Methods with Examples in Rice (Oryza sativa L.) | Plant Breeding and Genomics News | Scoop.it
Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.
Via Jean-Pierre Zryd
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Science advances providing a boost for plant breeding | Features | Farmers Guardian

Science advances providing a boost for plant breeding | Features | Farmers Guardian | Plant Breeding and Genomics News | Scoop.it
RAPID developments in new areas of science such as genomics and bioinformatics are helping to deliver advances in plant breeding that will benefit farmers across the globe.
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Fighting poverty, hunger and malnutrition with neglected and underutilized species (NUS): needs, challenges and the way forward

Fighting poverty, hunger and malnutrition with neglected and underutilized species (NUS): needs, challenges and the way forward | Plant Breeding and Genomics News | Scoop.it

Neglected and underutilized species (NUS) are those to which little attention is paid or which are entirely ignored by agricultural researchers, plant breeders and policymakers1. Typically, NUS are not traded as commodities. They are wild or semi-domesticated varieties and non-timber forest species adapted to particular, often quite local, environments. Many of these varieties and species, along with a wealth of traditional knowledge about their cultivation and use, are being lost at an alarming rate. Yet NUS present tremendous opportunities for fighting poverty, hunger and malnutrition. And they can help make agricultural production systems more resilient to climate change. Not least, acknowledgment of the value of NUS in traditional foods and cultures can empower indigenous communities (women in particular) and reaffirm their identity. The time for action on NUS is now. There is a growing realization that agriculture must diversify. NUS have an important role to play in advancing agricultural development beyond the Green Revolution model of improving and raising the yields of staple crops.

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Free PDF it the book is available.

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Genome-Wide Survey on Genomic Variation, Expression Divergence, and Evolution in Two Contrasting Rice Genotypes under High Salinity Stress

Expression profiling is one of the most important tools for dissecting biological functions of genes and the upregulation or downregulation of gene expression is sufficient for recreating phenotypic differences. Expression divergence of genes significantly contributes to phenotypic variations. However, little is known on the molecular basis of expression divergence and evolution among rice genotypes with contrasting phenotypes. In this study, we have implemented an integrative approach using bioinformatics and experimental analyses to provide insights into genomic variation, expression divergence, and evolution between salinity-sensitive rice variety Nipponbare and tolerant rice line Pokkali under normal and high salinity stress conditions. We have detected thousands of differentially expressed genes between these two genotypes and thousands of up- or downregulated genes under high salinity stress. Many genes were first detected with expression evidence using custom microarray analysis. Some gene families were preferentially regulated by high salinity stress and might play key roles in stress-responsive biological processes. Genomic variations in promoter regions resulted from single nucleotide polymorphisms, indels (1–10 bp of insertion/deletion), and structural variations significantly contributed to the expression divergence and regulation. Our data also showed that tandem and segmental duplication, CACTA and hATelements played roles in the evolution of gene expression divergence and regulation between these two contrasting genotypes under normal or high salinity stress conditions.

  
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PLOS ONE: Enhanced Methanol Production in Plants Provides Broad Spectrum Insect Resistance

PLOS ONE: Enhanced Methanol Production in Plants Provides Broad Spectrum Insect Resistance | Plant Breeding and Genomics News | Scoop.it

Plants naturally emit methanol as volatile organic compound. Methanol is toxic to insect pests; but the quantity produced by most of the plants is not enough to protect them against invading insect pests. In the present study, we demonstrated that the over-expression of pectin methylesterase, derived fromArabidopsis thaliana and Aspergillus niger, in transgenic tobacco plants enhances methanol production and resistance to polyphagous insect pests. Methanol content in the leaves of transgenic plants was measured using proton nuclear spectroscopy (1H NMR) and spectra showed up to 16 fold higher methanol as compared to control wild type (WT) plants. A maximum of 100 and 85% mortality in chewing insectsHelicoverpa armigera and Spodoptera litura larvae was observed, respectively when fed on transgenic plants leaves. The surviving larvae showed less feeding, severe growth retardation and could not develop into pupae. In-planta bioassay on transgenic lines showed up to 99 and 75% reduction in the population multiplication of plant sap sucking pests Myzus persicae (aphid) and Bemisia tabaci (whitefly), respectively. Most of the phenotypic characters of transgenic plants were similar to WT plants. Confocal microscopy showed no deformities in cellular integrity, structure and density of stomata and trichomes of transgenic plants compared to WT. Pollen germination and tube formation was also not affected in transgenic plants. Cell wall enzyme transcript levels were comparable with WT. This study demonstrated for the first time that methanol emission can be utilized for imparting broad range insect resistance in plants.

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BMC Plant Biology | Full text | New stable QTLs for berry weight do not colocalize with QTLs for seed traits in cultivated grapevine (Vitis vinifera L.)

BMC Plant Biology | Full text | New stable QTLs for berry weight do not colocalize with QTLs for seed traits in cultivated grapevine (Vitis vinifera L.) | Plant Breeding and Genomics News | Scoop.it
In grapevine, as in other fruit crops, fruit size and seed content are key components of yield and quality; however, very few Quantitative Trait Loci (QTLs) for berry weight and seed content (number, weight, and dry matter percentage) have been...
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A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East.
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Genetic mapping and marker development for resistance of wheat against the root lesion nematode Pratylenchus neglectus

The Rlnn1 locus, which resides on chromosome 7A of bread wheat (Triticum aestivum L.) confers moderate resistance against the root lesion nematode Pratylenchus neglectus.
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Increased Genomic Prediction Accuracy in Wheat Breeding Through Spatial Adjustment of Field Trial Data

In crop breeding, the interest of predicting the performance of candidate cultivars in the field has increased due to recent advances in molecular breeding technologies. However, the complexity of the wheat genome presents some challenges for applying new technologies in molecular marker identification with next-generation sequencing. We applied genotyping-by-sequencing, a recently developed method to identify single-nucleotide polymorphisms, in the genomes of 384 wheat (Triticum aestivum) genotypes that were field tested under three different water regimes in Mediterranean climatic conditions: rain-fed only, mild water stress, and fully irrigated. We identified 102,324 single-nucleotide polymorphisms in these genotypes, and the phenotypic data were used to train and test genomic selection models intended to predict yield, thousand-kernel weight, number of kernels per spike, and heading date. Phenotypic data showed marked spatial variation. Therefore, different models were tested to correct the trends observed in the field. A mixed-model using moving-means as a covariate was found to best fit the data. When we applied the genomic selection models, the accuracy of predicted traits increased with spatial adjustment. Multiple genomic selection models were tested, and a Gaussian kernel model was determined to give the highest accuracy. The best predictions between environments were obtained when data from different years were used to train the model. Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models.

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Recorded Webinar Available: Use of GAPIT in Genome-Wide Association Studies - eXtension

Recorded Webinar Available:  Use of GAPIT in Genome-Wide Association Studies - eXtension | Plant Breeding and Genomics News | Scoop.it
This tutorial demonstrates the use of the R package, GAPIT, in a barley genome-wide association study. The video was recorded live October...
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BMC Genomics | Abstract | Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits.
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PLOS ONE: Genomics Assisted Ancestry Deconvolution in Grape

PLOS ONE: Genomics Assisted Ancestry Deconvolution in Grape | Plant Breeding and Genomics News | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Summer undergraduate internships for US citizens or permanent residents at Boyce Thompson Institute

Summer undergraduate internships for US citizens or permanent residents at Boyce Thompson Institute | Plant Breeding and Genomics News | Scoop.it

Via Mary Williams
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How might open data in agriculture help achieve food security?

How might open data in agriculture help achieve food security? | Plant Breeding and Genomics News | Scoop.it
The policy support for improving the ability to store and share data on agriculture is growing. But how do you ensure farmers in developing countries benefit and will it achieve food security?
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Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Most methods for next-generation sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy–Weinberg equilibrium (HWE) as a prior. However, many organisms including those that are domesticated, partially selfing, or with asexual life cycles show strong deviations from HWE. For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual before calling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. We assess the impact of taking inbreeding into account when calling genotypes or estimating the site frequency spectrum (SFS), and demonstrate a marked increase in accuracy on low-coverage highly inbred samples. We demonstrate the applicability and efficacy of these methods in both simulated and real data sets.
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Where Catastrophic Droughts and Floods Are Bound to Happen in the U.S.

Where Catastrophic Droughts and Floods Are Bound to Happen in the U.S. | Plant Breeding and Genomics News | Scoop.it
A new NASA map shows what parts of the country will likely soon suffer from extreme floods, major droughts, and other water-related calamities.
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Civilizations rise and fall on the quality of their soil

Civilizations rise and fall on the quality of their soil | Plant Breeding and Genomics News | Scoop.it
Great civilizations have fallen because they failed to prevent the degradation of the soils on which they were founded. The modern world could suffer the same fate.
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