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New Version of the Integrated Breeding Platform's Breeding Management System 2.0 Available

New Version of the Integrated Breeding Platform's Breeding Management System 2.0 Available | Homunculi | Scoop.it

The Breeding Management System (BMS) is free software for plant breeding, offering database management of pedigrees, genotypes, nurseries, trials, and seed inventory.  The BMS includes crop databases for nine species loaded with curated data from public breeding programs. Use the BMS to perform statistical analysis of phenotypic trials and facilitate marker-assisted decision making.  The new version includes a data import tool to assist the transfer of established breeding data to the BMS database

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BMC Plant Biology | Abstract | Genes responding to water deficit in apple (Malus x domestica Borkh.) roots

Individual plants adapt to their immediate environment using a combination of biochemical, morphological and life cycle strategies. Because woody plants are long-lived perennials, they cannot rely on annual life cycle strategies alone to survive abiotic stresses. In this study we used suppression subtractive hybridization to identify genes both up- and down-regulated in roots during water deficit treatment and recovery. In addition we followed the expression of select genes in the roots, leaves, bark and xylem of 'Royal Gala' apple subjected to a simulated drought and subsequent recovery.
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BMC Genomics | Abstract | Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource.
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The Nexus of Food, Energy, and Water - Journal of Agricultural and Food Chemistry (ACS Publications)

The Earth’s population is expected to exceed 9 billion by 2050, posing significant challenges in meeting human needs while minimally affecting the environment. To support this population, we will need secure and safe sources of food, energy, and water. The nexus of food, energy, and water is one of the most complex, yet critical, issues that face society. There is no more land to exploit, and the supply of fresh water in some areas of the world limits the use of land for food. All solutions must also deal with the overlay of global climate change. Meeting current and future populations needs will require security in food, energy, and water supplies. A nexus approach is needed to improve food, energy, and water security integrating the management of the limited resources while transitioning to a more “green” economy, which provides adequate food, energy, and water for the expanding human population.

 
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BMC Bioinformatics | Full text | inPHAP: Interactive visualization of genotype and phased haplotype data

To understand individual genomes it is necessary to look at the variations that lead to changes in phenotype and possibly to disease. However, genotype information alone is often not sufficient and additional knowledge regarding the phase of the variation is needed to make correct interpretations. Interactive visualizations, that allow the user to explore the data in various ways, can be of great assistance in the process of making well informed decisions. But, currently there is a lack for visualizations that are able to deal with phased haplotype data.
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Optimizing Resource Allocation for Multistage Selection in Plant Breeding with R Package Selectiongain

Optimizing Resource Allocation for Multistage Selection in Plant Breeding with R Package Selectiongain | Homunculi | Scoop.it

Most plant-breeding programs involve multistage selection, but hitherto no flexible and computationally efficient software has been freely available for calculating the selection gain and optimizing the allocation of resources under these conditions. Here we describe the use of the newly-developed R package selectiongain that enables (i) calculation of the selection gain for up to 20 selection stages and (ii) a grid search of the optimum allocation of resources (number of candidates, locations, and testers) for given costs and correlations among the selection criteria in each stage. The capabilities of our software are demonstrated with an example taken from the literature on selecting doubled haploid lines in maize across three stages.

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The Effects of GM Technology on Maize Yield

In the United States, maize (Zea mays L.) farmers have adopted genetic-modification technology rapidly since its first commercialization in 1996. By 2012, 88% of U.S. maize is planted with genetically modified (GM) hybrids. Our objective in the paper is to present an empirical analysis of the determinants of U.S. maize yield using experimental maize production data, with a focus on the interaction effects of GM technology, management, and risk. Genetic-modification technology had a stronger impact on the lower end of maize yield distribution within a trial thereby reducing exposure to downside risk. A strong interaction exists between GM technology and crop rotations: GM reduces the adverse effects of maize–maize rotation on yield. As such, GM technology is found to be a substitute for crop rotation. Genetic-modification technology increases the yield gains associated with higher planting density. This indicates that GM technology offers good prospects for future improvements in maize productivity.

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BMC Genomics | Abstract | Variation block-based genomics method for crop plants

In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits.
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Wild rice key to global food security - ABC Online

Wild rice key to global food security - ABC Online | Homunculi | Scoop.it
“Wild rice key to global food security ABC Online Professor Henry, from the Queensland Alliance for Agriculture and Food Innovation (QAAFI), is convinced these remote wetlands could hold the key to global food security.”
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Crop yield components – photoassimilate supply- or utilisation limited-organ development


Yield potential is the genome-encoded capacity of a crop species to generate yield in an optimal growth environment. Ninety per cent of plant biomass is derived from the photosynthetic reduction of carbon dioxide to organic carbon (photoassimilates – primarily sucrose). Thus, development of yield components (organ numbers and individual organ masses) can be limited by photoassimilate supply (photosynthesis arranged in series with phloem transport) or by their inherent capacity to utilise imported photoassimilates for growth or storage. To this end, photoassimilate supply/utilisation of crop yield has been quantitatively re-evaluated using published responses of yield components to elevated carbon dioxide concentrations across a selection of key crop species including cereal and pulse grains, fleshy fruits, tubers and sugar storing stems and tap roots. The analysis demonstrates that development of harvested organ numbers is strongly limited by photoassimilate supply. Vegetative branching and, to a lesser extent, flower/pod/fleshy fruit abortion, are the major yield components contributing to sensitivity of organ numbers to photoassimilate supply. In contrast, harvested organ size is partially dependent (eudicots), or completely independent (cereals), of photoassimilate supply. Processes limiting photoassimilate utilisation by harvested organs include membrane transport of soluble sugars and their allocation into polymeric storage products.

 
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Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding

Harvesting the Promising Fruits of Genomics: Applying Genome Sequencing Technologies to Crop Breeding | Homunculi | Scoop.it
Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.
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The next Green Revolution may rely on microbes — NOVA Next | PBS

The next Green Revolution may rely on microbes — NOVA Next | PBS | Homunculi | Scoop.it
To feed a planet of 9 billion, scientists are breeding mycorrhizal fungi that promise to boost crop yields by unlocking more nutrients in the soil.
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Plant Methods | Abstract | GrainScan: a low cost, fast method for grain size and colour measurements

Measuring grain characteristics is an integral component of cereal breeding and research into genetic control of seed development. Measures such as thousand grain weight are fast, but do not give an indication of variation within a sample. Other methods exist for detailed analysis of grain size, but are generally costly and very low throughput. Grain colour analysis is generally difficult to perform with accuracy, and existing methods are expensive and involved.
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Challenges to develop nitrogen-fixing cereals by direct nif-gene transfer

Challenges to develop nitrogen-fixing cereals by direct nif-gene transfer | Homunculi | Scoop.it
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Some regions of the developing world suffer low cereal production yields due to low fertilizer inputs, among other factors. Biological N2 fixation, catalyzed by the prokaryotic enzyme nitrogenase, is an alternative to the use of synthetic N fertilizers. The molybdenum nitrogenase is an O2-labile metalloenzyme composed of the NifDK and NifH proteins, which biosyntheses require a number of nif gene products. A challenging strategy to increase cereal crop productivity in a scenario of low N fertilization is the direct transfer of nifgenes into cereals. The sensitivity of nitrogenase to O2 and the apparent complexity of nitrogenase biosynthesis are the main barriers identified so far. Expression of active NifH requires the products of nifM, nifH, and possibly nifU and nifS, whereas active NifDK requires the products of nifH, nifD, nifK, nifB, nifE,nifN, and possibly nifU, nifS, nifQ, nifV, nafY, nifW and nifZ. Plastids and mitochondria are potential subcellular locations for nitrogenase. Both could provide the ATP and electrons required for nitrogenase to function but they differ in their internal O2 levels and their ability to incorporate ammonium into amino acids.

  
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Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus

Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus | Homunculi | Scoop.it

Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola,Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napusgermplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napusis limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified.

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Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed ofS. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifoliumto map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits.

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Effects of Crop Canopies on Rain Splash Detachment

Effects of Crop Canopies on Rain Splash Detachment | Homunculi | Scoop.it

Crops are one of the main factors affecting soil erosion in sloping fields. To determine the characteristics of splash erosion under crop canopies, corn, soybean, millet, and winter wheat were collected, and the relationship among splash erosion, rainfall intensity, and throughfall intensity under different crop canopies was analyzed through artificial rainfall experiments. The results showed that, the mean splash detachment rate on the ground surface was 390.12 g/m2·h, which was lower by 67.81% than that on bare land. The inhibiting effects of crops on splash erosion increased as the crops grew, and the ability of the four crops to inhibit splash erosion was in the order of winter wheat>corn>soybeans>millet. An increase in rainfall intensity could significantly enhance the occurrence of splash erosion, but the ability of crops to inhibit splash erosion was 13% greater in cases of higher rainfall intensity. The throughfall intensity under crop canopies was positively related to the splash detachment rate, and this relationship was more significant when the rainfall intensity was 40 mm/h. Splash erosion tended to occur intensively in the central row of croplands as the crop grew, and the non-uniformity of splash erosion was substantial, with splash erosion occurring mainly between the rows and in the region directly under the leaf margin. This study has provided a theoretical basis for describing the erosion mechanisms of cropland and for assisting soil erosion prediction as well as irrigation and fertilizer management in cultivated fields.

 
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Genetic Mapping Using Genotyping-by-Sequencing in the Clonally Propagated Cassava

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Cassava (Manihot esculenta L.) is one of the most important food crops in the tropics, but yields are far below their potential. The gene pool of cassava contains natural genetic diversity relevant to many important breeding goals, but breeding progress has been slow, partly because of insufficient genomic resources. As a first step toward implementing genomewide genetic studies that will facilitate rapid genetic gain through breeding, we genotyped-by-sequencing a set of 182 full-sibs population of cassava that segregated in several traits: resistance to the cassava mosaic disease (CMD) and yield under CMD pressure; increased carotenoid content in storage roots; color of stem exterior and anthocyanin pigmentation in the petioles, inner root skin, and apical leaves. Employing a rare-cutting restriction enzyme, PstI, in a genotyping-by-sequencing (GBS) library preparation, we obtained 2478 segregating single nucleotide polymorphisms (SNPs), of which 1257 passed standard filtering for missing genotypes and deviation from expected genotypic frequencies. We mapped 772 SNPs across 19 linkage groups and anchored 313 unique scaffolds from the version 4.1 of the cassava genome assembly. Most of the studied morphological traits as well as resistance to CMD and root carotenoid content showed qualitative inheritance. As expected, quantitative trait loci analysis for these traits revealed single loci surrounded by small confidence intervals. Yield under CMD was associated with the CMD resistance locus. We show that GBS is a powerful genotyping tool that provides a sufficient number of markers for unraveling the genetic architecture of Mendelian traits in cassava in addition to the development of a robust genetic map that can help anchor unassembled genomic scaffolds.

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Selection for Verticillium Wilt Resistance in Cotton

Verticillium wilt (VW), caused by the soil-borne fungus Verticillium dahliae Kleb., is one of the most destructive diseases in Upland cotton (Gossypium hirsutum L.) production in the U.S. and worldwide. Development of VW-resistant cultivars remains the only economic option for controlling the disease. The objective of this review was to summarize the progress in screening methods, resistance sources, and genetics, quantitative trait locus (QTL) mapping, marker-assisted selection (MAS) and breeding for VW resistance in cotton. Even though Gossypium barbadense L. carries high levels of resistance, its resistance has not been transferred into commercial Upland cultivars. Many Acala cotton cultivars developed in New Mexico and California between the 1940s and the 1990s, and some commercial transgenic cultivars are tolerant or moderately resistant to VW. However, due to difficulties in achieving consistent and uniform inoculation and infection with V. dahliae, both qualitative and quantitative inheritance of VW resistance have been reported in numerous studies for resistant G. barbadense and Upland genotypes. Several QTL analyses have shown the existence of VW resistance QTLs on almost all the tetraploid cotton chromosomes; however, QTLs have most frequently been detected on c5, c7, c8, c11, c16, c17, c19, c21, c23, c24, and c26. This has led to MAS for progeny with favorable QTL alleles for VW resistance in several experiments. Phenotypic selection for VW resistance has been inefficient, while the effectiveness and efficiency of MAS remain to be validated. There is an urgent need for the development of better plant inoculation and screening methods, and for more molecular mapping studies to discern the genetic basis of VW resistance in cotton.

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Variability of Root Traits in Spring Wheat Germplasm

Variability of Root Traits in Spring Wheat Germplasm | Homunculi | Scoop.it

Root traits influence the amount of water and nutrient absorption, and are important for maintaining crop yield under drought conditions. The objectives of this research were to characterize variability of root traits among spring wheat genotypes and determine whether root traits are related to shoot traits (plant height, tiller number per plant, shoot dry weight, and coleoptile length), regions of origin, and market classes. Plants were grown in 150-cm columns for 61 days in a greenhouse under optimal growth conditions. Rooting depth, root dry weight, root: shoot ratio, and shoot traits were determined for 297 genotypes of the germplasm, Cultivated Wheat Collection (CWC). The remaining root traits such as total root length and surface area were measured for a subset of 30 genotypes selected based on rooting depth. Significant genetic variability was observed for root traits among spring wheat genotypes in CWC germplasm or its subset. Genotypes Sonora and Currawa were ranked high, and genotype Vandal was ranked low for most root traits. A positive relationship (R2≥0.35) was found between root and shoot dry weights within the CWC germplasm and between total root surface area and tiller number; total root surface area and shoot dry weight; and total root length and coleoptile length within the subset. No correlations were found between plant height and most root traits within the CWC germplasm or its subset. Region of origin had significant impact on rooting depth in the CWC germplasm. Wheat genotypes collected from Australia, Mediterranean, and west Asia had greater rooting depth than those from south Asia, Latin America, Mexico, and Canada. Soft wheat had greater rooting depth than hard wheat in the CWC germplasm. The genetic variability identified in this research for root traits can be exploited to improve drought tolerance and/or resource capture in wheat.

 
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'Borne by the rest of the world': deforestation has global impact, reduces food security

'Borne by the rest of the world': deforestation has global impact, reduces food security | Homunculi | Scoop.it
“Research indicates that areas with more forest cover tend to have superior food resilience compared to areas with less. In addition, the loss of forest cover to deforestation has long-term impacts not only locally, but also globally.”
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BMC Plant Biology | Abstract | A genomic perspective on the important genetic mechanisms of upland adaptation of rice

Cultivated rice consists of two important ecotypes, upland and irrigated, that have respectively adapted to either dry land or irrigated cultivation. Upland rice, widely adopted in rainfed upland areas in virtue of its little water requirement, contains abundant untapped genetic resources, such as genes for drought adaptation. With water shortage exacerbated and population expanding, the need for breeding crop varieties with drought adaptation becomes more and more urgent. However, a previous oversight in upland rice research reveals little information regarding its genetic mechanisms for upland adaption, greatly hindering progress in harnessing its genetic resources for breeding and cultivation.
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Genome Elimination: Translating Basic Research into a Future Tool for Plant Breeding

Genome Elimination: Translating Basic Research into a Future Tool for Plant Breeding | Homunculi | Scoop.it
During the course of our history, humankind has been through different periods of agricultural improvement aimed at enhancing our food supply and the performance of food crops. In recent years, it has become apparent that future crop improvement efforts will require new approaches to address the local challenges of farmers while empowering discovery across industry and academia. New plant breeding approaches are needed to meet this challenge to help feed a growing world population. Here I discuss how a basic research discovery is being translated into a potential future tool for plant breeding, and share the story of researcher Simon Chan, who recognized the potential application of this new approach—genome elimination—for the breeding of staple food crops in Africa and South America.
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Bangor University plant breeding scheme benefits millions

Bangor University plant breeding scheme benefits millions | Homunculi | Scoop.it

Participatory varietal selection (PVS) has led to new varieties being grown on at least 500,000 hectares and has provided a 15-40% improvement in yield over traditionally grown varieties.

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