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Abiotic Stress Signaling and Responses in Plants

Abiotic Stress Signaling and Responses in Plants | CropScJV | Scoop.it
As sessile organisms, plants must cope with abiotic stress such as soil salinity, drought, and extreme temperatures. Core stress-signaling pathways involve protein kinases related to the yeast SNF1 and mammalian AMPK, suggesting that stress signaling in plants evolved from energy sensing. Stress signaling regulates proteins critical for ion and water transport and for metabolic and gene-expression reprogramming to bring about ionic and water homeostasis and cellular stability under stress conditions. Understanding stress signaling and responses will increase our ability to improve stress resistance in crops to achieve agricultural sustainability and food security for a growing world population.

Via Andres Zurita
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Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato

Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato | CropScJV | Scoop.it

Ethylene is the main regulator of climacteric fruit ripening, by contrast the putative role of other phytohormones in this process remains poorly understood. The present study brings auxin signaling components into the mechanism regulating tomato fruit ripening through the functional characterization of Auxin Response Factor2 (SlARF2) which encodes a downstream component of auxin signaling. Two paralogs, SlARF2A and SlARF2B, are found in the tomato genome, both displaying a marked ripening-associated expression but distinct responsiveness to ethylene and auxin. Down-regulation of either SlARF2A or SlARF2B resulted in ripening defects while simultaneous silencing of both genes led to severe ripening inhibition suggesting a functional redundancy among the two ARFs. Tomato fruits under-expressing SlARF2produced less climacteric ethylene and exhibited a dramatic down-regulation of the key ripening regulators RIN, CNR, NOR and TAGL1. Ethylene treatment failed to reverse the non-ripening phenotype and the expression of ethylene signaling and biosynthesis genes was strongly altered in SlARF2 down-regulated fruits. Although both SlARF proteins are transcriptional repressors the data indicate they work as positive regulators of tomato fruit ripening. Altogether, the study defines SlARF2 as a new component of the regulatory network controlling the ripening process in tomato.


Via Pierre-Marc Delaux
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Nature Genetics: A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat (2015)

Nature Genetics: A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat (2015) | CropScJV | Scoop.it

As there are numerous pathogen species that cause disease and limit yields of crops, such as wheat (Triticum aestivum), single genes that provide resistance to multiple pathogens are valuable in crop improvement1, 2. The mechanistic basis of multi-pathogen resistance is largely unknown. Here we use comparative genomics, mutagenesis and transformation to isolate the wheat Lr67 gene, which confers partial resistance to all three wheat rust pathogen species and powdery mildew. The Lr67 resistance gene encodes a predicted hexose transporter (LR67res) that differs from the susceptible form of the same protein (LR67sus) by two amino acids that are conserved in orthologous hexose transporters. Sugar uptake assays show that LR67sus, and related proteins encoded by homeoalleles, function as high-affinity glucose transporters. LR67res exerts a dominant-negative effect through heterodimerization with these functional transporters to reduce glucose uptake. Alterations in hexose transport in infected leaves may explain its ability to reduce the growth of multiple biotrophic pathogen species.

News & Views at http://www.nature.com/ng/journal/v47/n12/full/ng.3456.html


Via Kamoun Lab @ TSL
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MYB-FL controls gain and loss of floral UV absorbance, a key trait affecting pollinator preference and reproductive isolation

Adaptations to new pollinators involve multiple floral traits, each requiring coordinated changes in multiple genes. Despite this genetic complexity, shifts in pollination syndromes have happened frequently during angiosperm evolution. Here we study the genetic basis of floral UV absorbance, a key trait for attracting nocturnal pollinators. In Petunia, mutations in a single gene, MYB-FL, explain two transitions in UV absorbance. A gain of UV absorbance in the transition from bee to moth pollination was determined by a cis-regulatory mutation, whereas a frameshift mutation caused subsequent loss of UV absorbance during the transition from moth to hummingbird pollination. The functional differences in MYB-FL provide insight into the process of speciation and clarify phylogenetic relationships between nascent species.


Via Pierre-Marc Delaux
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such a nice work! 

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Visualising Global Scientific Collaboration - Digital Science

Visualising Global Scientific Collaboration - Digital Science | CropScJV | Scoop.it
Visualising Global Scientific Collaboration

Via Nader Ale Ebrahim
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Front. Plant Sci.: MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility (2015)

Front. Plant Sci.: MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility (2015) | CropScJV | Scoop.it

Many plant-pathogenic xanthomonads rely on Transcription Activator-Like (TAL) effectors to colonize their host. This particular family of type III effectors functions as specific plant transcription factors via a novel programmable DNA-binding domain. Upon binding to the promoters of plant disease susceptibility genes in a sequence-specific manner, the expression of these host genes is induced. However, plants have evolved specific strategies to counter the action of TAL effectors and confer resistance. One mechanism is to avoid the binding of TAL effectors by mutations of their DNA binding sites, resulting in resistance by loss-of-susceptibility. This article reviews our current knowledge of the susceptibility hubs targeted by Xanthomonas TAL effectors, possible evolutionary scenarios for plants to combat the pathogen with loss-of-function alleles, and how this knowledge can be used overall to develop new pathogen-informed breeding strategies and improve crop resistance.

 

Hutin M, Pérez-Quintero AL, Lopez C and Szurek B


Via Nicolas Denancé, Roland Kölliker
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Baker Lab: MicroRNA regulation of plant innate immune receptors (2012)

Baker Lab: MicroRNA regulation of plant innate immune receptors (2012) | CropScJV | Scoop.it

Plant innate immunity depends on recognition of pathogen effectors and triggering of host defenses. Major classes of innate immune receptors, the nucleotide binding-leucine rich repeat receptors (NLRs) and leucine rich repeat (LRR) receptors are encoded by large families of resistance (R)-genes. NLR and LRRs are activated by recognition of specific pathogen effectors and once activated they trigger the hypersensitive cell-death response. While multiple NLRs and LRRs protect plants from diverse pathogens their inherent cell death activity and the large number of encoding R-genes in plant genomes require strict regulation.

 

Plant microRNAs (miRNAs) and small interfering RNAs (siRNAs) guide sequence-specific silencing of genes, repetitive DNA and viruses through Watson-Crick base pairing and play essential regulatory roles in development, genome function and host defines. We discovered novel miRNA families whose members silence R-gene encoding NLRs and LRRs including those that confer resistance to the major pathogens of Solanaceae crops. Many of these novel miRNAs belong to a structurally and functionally unique class of 22-nt miRNAs and amplify silencing by triggering the production of secondary trans-acting siRNAs (tasiRNAs) from cleaved transcripts. The lab further showed that miRNA overexpression leads to attenuated R-gene mediated pathogen resistance. We propose that the R-gene miRNAs and tasiRNAs form a regulatory silencing network to fine tune pathogen defense responses and facilitate expansion and evolution of new NLRs.

 

Li F, Pignatta D, Bendix C, Brunkard J, Cohn M, Tung J, Sun H, Kumar P, and B Baker. 2012. MiRNA regulation of plant innate immune receptors. Proc. Natl. Acad. Sci. USA 109, 5:1790-1795.


Via Kamoun Lab @ TSL
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Root anatomical phenes predict root penetration ability and biomechanical properties in maize (Zea Mays)

Root anatomical phenes predict root penetration ability and biomechanical properties in maize (Zea Mays) | CropScJV | Scoop.it

Via Andres Zurita
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Andres Zurita's curator insight, May 31, 2015 5:16 PM

The ability of roots to penetrate hard soil is important for crop productivity but specific root phenes contributing to this ability are poorly understood. Root penetrability and biomechanical properties are likely to vary in the root system dependent on anatomical structure. No information is available to date on the influence of root anatomical phenes on root penetrability and biomechanics. Root penetration ability was evaluated using a wax layer system. Root tensile and bending strength were evaluated in plant roots grown in the greenhouse and in the field. Root anatomical phenes were found to be better predictors of root penetrability than root diameter per se and associated with smaller distal cortical region cell size. Smaller outer cortical region cells play an important role in stabilizing the root against ovalization and reducing the risk of local buckling and collapse during penetration, thereby increasing root penetration of hard layers. The use of stele diameter was found to be a better predictor of root tensile strength than root diameter. Cortical thickness, cortical cell count, cortical cell wall area and distal cortical cell size were stronger predictors of root bend strength than root diameter. Our results indicate that root anatomical phenes are important predictors for root penetrability of high-strength layers and root biomechanical properties.

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Milestones of Plant Evolution

Milestones of Plant Evolution | CropScJV | Scoop.it
Nearly all life and our human culture depend on plants. We consume plants and plant-derived material every day in large amounts as food, raw material for clothes, construction etc. However, most of us might not be aware of that plants (defined in a broad sense as oxygen-producing photosynthesizing organisms, as in this book) did so much more for us over the past 3.8 billion years. Without the great oxygenation event no complex animal life (as we know it) would have been possible on earth. Plants produced the fossil energy resources which enabled the industrial revolution and which we still depend on.

Via Jean-Michel Ané
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Truffle hunting in Provence

Truffle hunting in Provence | CropScJV | Scoop.it
Nelly Pellegrin is always accompanied by Flair when she goes truffle-hunting. The Brittany dog may be only three years old, but he is already expert at finding "black diamonds".

The dog's pointer-like behaviour directs his mistress to these underground sac fungi in her truffle garden near Cabrieres-d'Aigues in south-eastern France's Vaucluse department.

A brief and slippery ascent leads to a stand of holm oaks where the roots of the trees have been inoculated with the slow-growing truffle mycorrhiza - truffle cultivation reaches back to the early 19th century.

"Cherche les truffes," Pellegrin commands, and Flair immediately begins sniffing for the scent he has been trained to find.

Via Jean-Michel Ané
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Best of Plants 2014: Plant-based antibodies used to treat Ebola Virus Disease

Best of Plants 2014: Plant-based antibodies used to treat Ebola Virus Disease | CropScJV | Scoop.it

 

One of the biggest stories of 2014 was the spread of Ebola Virus Disease, and antibodies produced in plants are one of the few therapies shown to be effective. Plant-derived antibodies produced by MAPP pharmaceuticals in tobacco had previously been tested successfully on monkeys (http://www.pnas.org/content/109/44/18030), but this summer were used to save the lives of two American missionaries (http://edition.cnn.com/2014/10/03/health/ebola-tobacco-plant/). Plant-production of phamaceuticals (aka molecular pharming) can be cheaper than production in animals or cell lines, and this year has demonstrated this technology to be fast, versatile and effective.


Via Mary Williams
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nice!!!!

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Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida | CropScJV | Scoop.it

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.


Via Pierre-Marc Delaux
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Frontiers | Microbiomes: unifying animal and plant systems through the lens of community ecology theory | Microbial Symbioses

Frontiers | Microbiomes: unifying animal and plant systems through the lens of community ecology theory | Microbial Symbioses | CropScJV | Scoop.it
field of microbiome research is arguably one of the fastest growing in biology. Bacteria feature prominently in studies on animal health, but fungi appear to be the more prominent functional symbionts for plants. Despite the similarities in the ecological organization and evolutionary importance of animal-bacterial and plant–fungal microbiomes, there is a general failure across disciplines to integrate the advances made in each system. Researchers studying bacterial symbionts in animals benefit from greater access to efficient sequencing pipelines and taxonomic reference databases, perhaps due to high medical and veterinary interest. However, researchers studying plant–fungal symbionts benefit from the relative tractability of fungi under laboratory conditions and ease of cultivation. Thus each system has strengths to offer, but both suffer from the lack of a common conceptual framework. We argue that community ecology best illuminates complex species interactions across space and time. In this synthesis we compare and contrast the animal-bacterial and plant–fungal microbiomes using six core theories in community ecology (i.e., succession, community assembly, metacommunities, multi-trophic interactions, disturbance, restoration). The examples and questions raised are meant to spark discussion amongst biologists and lead to the integration of these two systems, as well as more informative, manipulatory experiments on microbiomes research.

Via Christophe Jacquet
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EffectorP: predicting fungal effector proteins from secretomes using machine learning

EffectorP: predicting fungal effector proteins from secretomes using machine learning | CropScJV | Scoop.it

Effector prediction is tricky and essential. This should be a great resource for mycologists!


Via Bradford Condon, Elsa Ballini
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Swedish Board of Agriculture: a CRISPR-Cas9 mutant is not a GMO - Umeå Univ (2015)

Swedish Board of Agriculture: a CRISPR-Cas9 mutant is not a GMO - Umeå Univ (2015) | CropScJV | Scoop.it

The Swedish Board of Agriculture has... confirmed the interpretation that some plants in which the genome has been edited using the CRISPR-Cas9 technology do not fall under the European GMO definition. This is important for the wide use of such plants to contribute to solving some of the escalating challenges of mankind.

CRISPR-Cas9 is a technique... allowing scientists to make small edits in the genetic material of an organism, edits that can also occur naturally. Instead of hoping that such edits occur by natural recombination, they can now be deliberately introduced in a targeted and precise manner. CRISPR-Cas9 can thus be used in many ways in plant science and breeding.

 

Plants that fall within the scope of EU GMO legislation are subject to a very strict regulatory regime (in reality making it impossible to grow them in the field in most EU countries). Plants that fall outside the scope can be grown without restriction. Since “inside or outside of the GMO definition” will decide whether or not plant scientists will be able to use the technique for practical applications, plant scientists and breeders have been waiting for the authorities’ decision concerning CRISPR-Cas9... 

 

Countries such as Argentina have announced that similarly edited plants fall outside their GMO legislation, but no decision has been taken yet inside the EU. A complicating factor is that the technique can be used in several different ways with the consequence that some of the resulting plants may fall outside while others may fall inside the GMO legislation. Now, for the first time, concrete examples have been evaluated by a competent authority, and the Swedish Board of Agriculture announced... that some Arabidopsis plants that have been modified using CRISPR-Cas9 fall within the scope of the legislation while others do not... 

 

“What we now have done pinpoints the problem; using CRISPR-Cas9 we can create a plant that in ALL aspects is identical to one that is not considered to be a GMO. Common sense and scientific logic says that it is impossible to have two identical plants where growth of one is, in reality, forbidden while the other can be grown with no restrictions; how would a court be able to decide if the cultivation was a crime or not? But regulatory logic is not necessarily the same as scientific logic, and it is therefore important that the Swedish Board of Agriculture has interpreted the definition in this way”...  

 

This interpretation opens up the possibility that this technique can be used to address some of the biggest challenges for mankind, expressed in the sustainable development goals recently suggested by the United Nations... “We hope that this clear and logical interpretation will also be applied to other similar cases.

 

The EU commission announced some time ago that it would present its interpretation of the legislation, but has not yet been able to come to an agreement. All ‘GMO issues’ divide the EU and this has led to paralysis for more than a decade. We think that the opinion by the Swedish Board of Agriculture will get a lot of international attention”...  

 

http://www.umu.se/english/about-umu/news-events/news/newsdetailpage/green-light-in-the-tunnel-opinion-of-the-swedish-board-of-agriculture--a-crispr-cas9-mutant-but-not-a-gmo.cid259265

 


Via Alexander J. Stein
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Breeding to Optimize Agriculture in a Changing World - Wang &al (2015) - Crop J

The world is changing! The population continues to grow rapidly, and societal behavior (including consumption habits) is experiencing rapid evolution, particularly in developing countries. Demand for and pressure on resources (mainly land and water) continues to increase... Climate changes pose further and less-predictable challenges... An increase of more than 70% food is needed by 2050 to meet the demands of the increasing population...

 

Crop management and breeding are the pillars of efforts to tackle the present and future challenges of food production. China and the European Union (EU) face common challenges in the changing world. Both are dedicating great R&D efforts to agriculture, food security, and food safety, to increase food production and improve product quality in an environmentally sustainable manner. In view of the common challenges, a three-year EU-China project called “Breeding to Optimize Chinese Agriculture (OPTICHINA)” was launched in June of 2011 as a new strategy that may serve as a model to reinforce systematic cooperation on agricultural research... 

 

In recent decades, breeding has contributed a greater than 50% increase of the world’s food crop production. However, in a changing world, an urgent issue is to accelerate plant breeding for increased yield potential and better adaptation to drought, heat, and other abiotic stresses together with the surge of new biotic challenges, so as to meet the future demand for agricultural production. The only viable way to solve the issue is to raise the productivity of existing farmland, but it is a great challenge to increase food production and improve product quality in an environmentally sustainable manner. To reach this goal, plant breeding requires intensive and integrated application of a wide range of sciences and technologies.

 

To meet the challenge, we must develop more productive, stable, and nutritious varieties of agricultural crops, which incorporate both high intrinsic yield potential and resilience to climatic and biotic constraints, while improving the efficiency of resource use. To ensure the success of future plant breeding, we must adopt a multidisciplinary approach combining the field expertise of breeders with advanced phenotyping based on a physiological understanding of the crop, molecular tools and approaches (such as MAS, transgenic, TILLING, omics, and genomewide selection) provided by biotechnology, and the support of advanced data analysis and management.

 

http://dx.doi.org/10.1016/j.cj.2015.05.001

 


Via Alexander J. Stein
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Developmental Cell: Chloroplast Stromules Function during Innate Immunity (2015)

Developmental Cell: Chloroplast Stromules Function during Innate Immunity (2015) | CropScJV | Scoop.it
Chloroplast stromules are induced during plant immune responsesPro-PCD signals such as SA and H2O2 induce stromulesStromules form dynamic connections with nucleus during immune responsesConstitutively induced stromules enhance PCD during plant immune responses


Inter-organellar communication is vital for successful innate immune responses that confer defense against pathogens. However, little is known about how chloroplasts, which are a major production site of pro-defense molecules, communicate and coordinate with other organelles during defense. Here we show that chloroplasts send out dynamic tubular extensions called stromules during innate immunity or exogenous application of the pro-defense signals, hydrogen peroxide (H2O2) and salicylic acid. Interestingly, numerous stromules surround nuclei during defense response, and these connections correlate with an accumulation of chloroplast-localized NRIP1 defense protein and H2O2 in the nucleus. Furthermore, silencing and knockout of chloroplast unusual positioning 1 (CHUP1) that encodes a chloroplast outer envelope protein constitutively induces stromules in the absence of pathogen infection and enhances programmed cell death. These results support a model in which stromules aid in the amplification and/or transport of pro-defense signals into the nucleus and other subcellular compartments during immunity.


Via Kamoun Lab @ TSL
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mmatshepo sibuyi's curator insight, July 31, 2015 4:49 AM

chloroplast consist of green pigments called chlorophyll that plants use in the process of photosynthesis

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Domestication: Sweet! A naturally transgenic crop

Domestication: Sweet! A naturally transgenic crop | CropScJV | Scoop.it
Nature Plants, Published online: 2 June 2015; | doi:10.1038/nplants.2015.77

Via Roland Kölliker
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so, what now  about "GMO are not natural"? One more time the problem isn't the science behind is the use we do of it! 

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Roland Kölliker's curator insight, June 3, 2015 1:58 AM

quote: "Essentially, the bacteria have sex with the plant"

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New PPH publication "Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis thaliana" in Plant Cell

New PPH publication "Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis thaliana" in Plant Cell | CropScJV | Scoop.it

By, Rik Kooke, Frank Johannes, René Wardenaar, Frank Becker, Mathilde Etcheverry, Vincent Colot, Dick Vreugdenhil and Joost J.B. Keurentjes


Via Wilco Ligterink
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Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost.

Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, May 13, 2015 12:44 AM
AbstractBackground

Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost.

Results

Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada. Four imputation algorithms were compared (mean value (MI), singular value decomposition (SVD), expectation maximization (EM), and a newly derived, family-based k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and wood attributes. Single- and multi-site GS prediction models were developed using the Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different assumption about trait architecture. Finally, using PCA, multi-trait GS prediction models were developed. The EM and kNN-Fam imputation methods were superior for 30 and 60% missing data, respectively. The RR-BLUP GS prediction model produced better accuracies than the GRR indicating that the genetic architecture for these traits is complex. GS prediction accuracies for multi-site were high and better than those of single-sites while multi-site predictability produced the lowest accuracies reflecting type-b genetic correlations and deemed unreliable. The incorporation of genomic information in quantitative genetics analyses produced more realistic heritability estimates as half-sib pedigree tended to inflate the additive genetic variance and subsequently both heritability and gain estimates. Principle component scores as representatives of multi-trait GS prediction models produced surprising results where negatively correlated traits could be concurrently selected for using PCA2 and PCA3.

Conclusions

The application of GS to open-pollinated family testing, the simplest form of tree improvement evaluation methods, was proven to be effective. Prediction accuracies obtained for all traits greatly support the integration of GS in tree breeding. While the within-site GS prediction accuracies were high, the results clearly indicate that single-site GS models ability to predict other sites are unreliable supporting the utilization of multi-site approach. Principle component scores provided an opportunity for the concurrent selection of traits with different phenotypic optima.

 
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Scientists agree: Coffee naps are better than coffee or naps alone

Caffeinate immediately before napping and sleep for 20 minutes or less. You won't regret it.
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