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Prevalence of gene expression additivity in genetically stable wheat allohexaploids - Chelaifa - 2012 - New Phytologist - Wiley Online Library

Prevalence of gene expression additivity in genetically stable wheat allohexaploids - Chelaifa - 2012 - New Phytologist - Wiley Online Library | Plant Breeding and Genomics News | Scoop.it
The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents.In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the AB genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome-wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted.Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34 820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near-complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploidTriticum turgidum as the AB genome progenitor.Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids.
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Construction of a SSR-Based Genetic Map and Identification of QTLs for Catechins Content in Tea Plant (Camellia sinensis)

Construction of a SSR-Based Genetic Map and Identification of QTLs for Catechins Content in Tea Plant (Camellia sinensis) | 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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nosehound's comment, April 6, 10:25 PM
Thats helpful
nosehound's comment, April 6, 10:25 PM
Its superb
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Borlaug's Contributions Remembered On Ag Day - Farm Futures

Borlaug's Contributions Remembered On Ag Day - Farm Futures | Plant Breeding and Genomics News | Scoop.it
Farm Futures
Borlaug's Contributions Remembered On Ag Day
Farm Futures
A new statue in the U.S. Capitol building's statuary hall to recognize the contributions of Dr.
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University of Minnesota honors 100-year legacy of graduate Norman Borlaug ... - Minneapolis Star Tribune

University of Minnesota honors 100-year legacy of graduate Norman Borlaug ... - Minneapolis Star Tribune | Plant Breeding and Genomics News | Scoop.it
AgWeb
University of Minnesota honors 100-year legacy of graduate Norman Borlaug ...
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Paleo-evolutionary plasticity of plant disease resistance genes

The recent access to a large set of genome sequences, combined with a robust evolutionary scenario of modern monocot (i.e. grasses) and eudicot (i.e. rosids) species from their founder ancestors, offered the opportunity to gain insights into disease resistance genes (R-genes) evolutionary plasticity.

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, March 17, 1:24 PM
Abstract (provisional)Background

The recent access to a large set of genome sequences, combined with a robust evolutionary scenario of modern monocot (i.e. grasses) and eudicot (i.e. rosids) species from their founder ancestors, offered the opportunity to gain insights into disease resistance genes (R-genes) evolutionary plasticity.

Results

We unravel in the current article (i) a R-genes repertoire consisting in 7883 for monocots and 15758 for eudicots, (ii) a contrasted R-genes conservation with 23.8% for monocots and 6.6% for dicots, (iii) a minimal ancestral founder pool of 384 R-genes for the monocots and 150 R-genes for the eudicots, (iv) a general pattern of organization in clusters accounting for more than 60% of mapped R-genes, (v) a biased deletion of ancestral duplicated R-genes between paralogous blocks possibly compensated by clusterization, (vi) a bias in R-gene clusterization where Leucine-Rich Repeats acts as a 'glue' for domain association, (vii) a R-genes/miRNAs interome enriched toward duplicated R-genes..

Conclusions

Together, our data may suggest that R-genes family plasticity operated during plant evolution (i) at the structural level through massive duplicates loss counterbalanced by massive clusterization following polyploidization; as well as at (ii) the regulation level through microRNA/R-gene interactions acting as a possible source of functional diploidization of structurally retained R-genes duplicates. Such evolutionary shuffling events leaded to CNVs (i.e. Copy Number Variation) and PAVs (i.e. Presence Absence Variation) between related species operating in the decay of R-genes colinearity between plant species.

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Natural Variations and Genome-Wide Association Studies in Crop Plants - Annual Review of Plant Biology, 65(1):

Natural Variations and Genome-Wide Association Studies in Crop Plants - Annual Review of Plant Biology, 65(1): | Plant Breeding and Genomics News | Scoop.it

Natural variants of crops are generated from wild progenitor plants under both natural and human selection. Diverse crops that are able to adapt to various environmental conditions are valuable resources for crop improvements to meet the food demands of the increasing human population. With the completion of reference genome sequences, the advent of high-throughput sequencing technology now enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops. Comprehensive maps of genome variations facilitate genome-wide association studies of complex traits and functional investigations of evolutionary changes in crops. These advances will greatly accelerate studies on crop designs via genomics-assisted breeding. Here, we first discuss crop genome studies and describe the development of sequencingbased genotyping and genome-wide association studies in crops. We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs.


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Play it Hard - Norman Borlaug 100 Year Tribute - YouTube

The International Center for Maize and Wheat Improvement (CIMMYT) and Biology Fortified have produced a special video tribute to the late Dr. Norman Borlaug,...

Via Mary Williams, Alberto Boldt
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Royse Murphy reflects on history of plant breeding at Cornell

Royse Peak Murphy discusses his recollections of the plant breeding department at Cornell with fellow plant breeder Donald R. Viands. Murphy, who joined the ...
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USDA NIFA has announced the FY 2014 Agricultural and Food Research Initiative (AFRI) Competitive Grants Program

USDA NIFA has announced the FY 2014 Agricultural and Food Research Initiative (AFRI) Competitive Grants Program | Plant Breeding and Genomics News | Scoop.it

AFRI Details: Project types supported by AFRI within this RFA include single-function Research Projects, multi-function Integrated Projects, and Food and Agricultural Science Enhancement (FASE) Grants. Grants shall be awarded to address priorities in United States agriculture in the areas listed below.  NIFA offers two new programs areas (CARE and Exploratory).  

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A Quantitative Framework for Flower Phenotyping in Cultivated Carnation (Dianthus caryophyllus L.)

A Quantitative Framework for Flower Phenotyping in Cultivated Carnation (Dianthus caryophyllus L.) | Plant Breeding and Genomics News | Scoop.it

Most important breeding goals in ornamental crops are plant appearance and flower characteristics where selection is visually performed on direct offspring of crossings. We developed an image analysis toolbox for the acquisition of flower and petal images from cultivated carnation (Dianthus caryophyllus L.) that was validated by a detailed analysis of flower and petal size and shape in 78 commercial cultivars of D. caryophyllus, including 55 standard, 22 spray and 1 pot carnation cultivars.

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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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Luther Burbank Dug Deep To Rise As Top Plant Breeder - Investor's Business Daily

Luther Burbank Dug Deep To Rise As Top Plant Breeder - Investor's Business Daily | Plant Breeding and Genomics News | Scoop.it
Luther Burbank Dug Deep To Rise As Top Plant Breeder
Investor's Business Daily
By 32, Luther Burbank was already called a wizard of plant breeding.
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creditrepairaid's comment, April 3, 12:29 AM
This is so great!
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Plant breeders seek hardiness, disease resistance - TwinCities.com

Plant breeders seek hardiness, disease resistance - TwinCities.com | Plant Breeding and Genomics News | Scoop.it
Home Blundering Gardener. The University of Minnesota's Landscape Arboretum continues to impress. A breakthrough many consider the ornamental plant breeders' most stunning achievement is Zone 4 hardy Northern ...
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Genomics in the Journals - GenomeWeb

Genomics in the Journals GenomeWeb In the first paper, researchers hailing from Translational Genomics Research Institute, the University of British Columbia, and elsewhere described performing whole-genome and -exome sequencing of 12 cases,...
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Pine tree yields longest genome ever sequenced - CBS News

Pine tree yields longest genome ever sequenced - CBS News | Plant Breeding and Genomics News | Scoop.it
Pine tree yields longest genome ever sequenced CBS News Understanding the loblolly pine's genetic code could lead to improved breeding of the tree, which is used to make paper and lumber and is being investigated as a potential biofuel, the...

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From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism

Tomato (Solanum lycopersicum) establishes a beneficial symbiosis with arbuscular mycorrhizal (AM) fungi. The formation of the mycorrhizal association in the roots leads to plant-wide modulation of gene expression. To understand the systemic effect of the fungal symbiosis on the tomato fruit, we used RNA-Seq to perform global transcriptome profiling on Moneymaker tomato fruits at the turning ripening stage.

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, March 23, 3:06 PM

Abstract (provisional)Background

Tomato (Solanum lycopersicum) establishes a beneficial symbiosis with arbuscular mycorrhizal (AM) fungi. The formation of the mycorrhizal association in the roots leads to plant-wide modulation of gene expression. To understand the systemic effect of the fungal symbiosis on the tomato fruit, we used RNA-Seq to perform global transcriptome profiling on Moneymaker tomato fruits at the turning ripening stage.

Results

Fruits were collected at 55 days after flowering, from plants colonized with Funneliformis mosseae and from control plants, which were fertilized to avoid responses related to nutrient deficiency. Transcriptome analysis identified 712 genes that are differentially expressed in fruits from mycorrhizal and control plants. Gene Ontology (GO) enrichment analysis of these genes showed 81 overrepresented functional GO classes. Up-regulated GO classes include photosynthesis, stress response, transport, amino acid synthesis and carbohydrate metabolism functions, suggesting a general impact of fungal symbiosis on primary metabolisms and, particularly, on mineral nutrition. Down-regulated GO classes include cell wall, metabolism and ethylene response pathways. Quantitative RT-PCR validated the RNA-Seq results for 12 genes out of 14 when tested at three fruit ripening stages, mature green, breaker and turning. Quantification of fruit nutraceutical and mineral contents produced values consistent with the expression changes observed by RNA-Seq analysis.

Conclusions

This RNA-Seq profiling produced a novel data set that explores the intersection of mycorrhization and fruit development. We found that the fruits of mycorrhizal plants show two transcriptomic "signatures": genes characteristic of a climacteric fleshy fruit, and genes characteristic of mycorrhizal status, like phosphate and sulphate transporters. Moreover, mycorrhizal plants under low nutrient conditions produce fruits with a nutrient content similar to those from non-mycorrhizal plants under high nutrient conditions, indicating that AM fungi can help replace exogenous fertilizer for fruit crops.

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Plant breeding by Pete Perry

In his 100th video, PETE PERRY passes on his knowledge of plant breeding with primulas and narcissus. Pete has been breeding plants since the 1960s. and has ...
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Breeding Plants for the Future: The Second in the More Crop per Plot Series - Horticulture Week

Breeding Plants for the Future: The Second in the More Crop per Plot Series - Horticulture Week | Plant Breeding and Genomics News | Scoop.it
Breeding Plants for the Future: The Second in the More Crop per Plot Series
Horticulture Week
Numerous innovations are dramatically changing plant breeding and the potential performance of crop varieties.
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skimpynodes's comment, March 10, 2:14 AM
nice
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Plant Breeding Academy Opens In Nairobi That Will Boost Africa’s Food Supply With Improved Indigenous Crops

Plant Breeding Academy Opens In Nairobi That Will Boost Africa’s Food Supply With Improved Indigenous Crops | Plant Breeding and Genomics News | Scoop.it
The African Orphan Crops Consortium (AOCC) today opened the African Pl...
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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

Plant Breeding and Genomics News's insight:

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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