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Trait Diversity and Potential for Selection Indices Based on Variation Among Regionally Adapted Processing Tomato Germplasm

Trait Diversity and Potential for Selection Indices Based on Variation Among Regionally Adapted Processing Tomato Germplasm | Plant Breeding and Genomics News | Scoop.it

"For many horticultural crops, selection is based on quality as well as yield. To investigate the distribution of trait variation and identify those attributes appropriate for developing selection indices, we collected and organized information related to fruit size, shape, color, soluble solids, acid, and yield traits for 143 processing tomato (Solanum lycopersicum L.) lines from North America. Evaluation of the germplasm panel was conducted in a multiyear, multilocation trial. Data were stored in a flat-file format and in a trait ontology database, providing a public archive. We estimated variance components and proportion of variance resulting from genetics for each trait. Genetic variance was low to moderate (range, 0.03–0.51) for most traits, indicating high environmental influence on trait expression and/or complex genetic architecture. Phenotypic values for each line were estimated across environments as best linear unbiased predictors (BLUPs). Principal components (PC) analysis using the trait BLUPs provided a means to assess which traits explained variation in the germplasm. The first two PCs explained 28.0% and 16.2% of the variance and were heavily weighted by measures of fruit shape and size. The third PC explained 12.9% of the phenotypic variance and was determined by fruit color and yield components. Trait BLUPs and the first three PCs were also used to explore the relationship between phenotypes and the origin of the accessions. We were able to differentiate germplasm for fruit size, fruit shape, yield, soluble solids, and color based on origin, indicating regional breeding programs provide a source of trait variation. These analyses suggest that multitrait selection indices could be established that encompass quality traits in addition to yield. However, such indices will need to balance trait correlations and be consistent with market valuation."

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Special Webinar Series of NAPB in partnership with PBCC and PBG starts April 29th

Special Webinar Series of NAPB in partnership with PBCC and PBG starts April 29th | Plant Breeding and Genomics News | Scoop.it
Register for upcoming webinars and view past recordings. The Plant Breeding and Genomics Webinar Series describes and demonstrates widely...
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Click on the webinar title to follow the link to the registration page. Advanced registration for the live webinars is required. After registering you will receive a confirmation email containing information about joining the webinar.

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ainslime mount's comment, June 14, 12:50 AM
Its fabulous
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2014 Synapsis Symposium | Department of Plant Breeding and Genetics on April 25th

2014 Synapsis Symposium | Department of Plant Breeding and Genetics on April 25th | Plant Breeding and Genomics News | Scoop.it
3rd Annual Cornell University Graduate Student Plant Breeding Symposium
April 25, 2014
8:00 AM - 5:00 PM EST (One more online Plant Breeding Symposium coming up. This one is April 25 sponsored by Cornell Univ and DuPont...
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Application of Genomics to Strawberry Breeding Webinar - eXtension

Application of Genomics to Strawberry Breeding Webinar - eXtension | Plant Breeding and Genomics News | Scoop.it
Register now to attend Start day/time: Thursday, May 1, 2014 at 1:00 pm Eastern Time (-05:00 GMT) Add to calendar Register now at...
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Vance M. Whitaker from the University of Florida Gulf Coast Research and Education Center will present a webinar on the application of genomics to strawberry breeding.

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SNP Discovery for mapping alien introgressions in wheat

Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L).
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Plant Breeding Summer Workshops at Ohio State University OARDC, Wooster, OH

Plant Breeding Summer Workshops at Ohio State University OARDC, Wooster, OH | Plant Breeding and Genomics News | Scoop.it
Plant Breeding and Genomics News's insight:

Session 1:  Field Design and Analysis June 23-27

Session 2:  Marker Assisted Selection July 7-11

Session 3:  Genome Wide Analysis July 21-25

 

 

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Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses

Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and strawberry. Early studies on lactone biosynthesis suggest that several enzymatic pathways could be responsible for the diversity of lactones, but detailed information on them remained elusive. In this study, we have integrated genetic mapping and genome-wide transcriptome analysis to investigate the molecular basis of natural variation in γ-decalactone content in strawberry fruit.
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TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline | Plant Breeding and Genomics News | Scoop.it

Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Herein we describe a bioinformatics pipeline, tassel-gbs, designed for the efficient processing of raw GBS sequence data into SNP genotypes. The tassel-gbs pipeline successfully fulfills the following key design criteria: (1) Ability to run on the modest computing resources that are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8–16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished “pseudo-reference” consisting of numerous contigs. We describe the tassel-gbs pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the tassel-gbs pipeline provide robust tools for studying genomic diversity.


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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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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, 4:24 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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Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation

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The largest genus in the conifer family Pinaceae is Pinus, with over 100 species. The size and complexity of their genomes (∼20–40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence. In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence. The MAKER-P annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence. Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers. Among the conifer gene families, 159 are composed exclusively of loblolly pine members. The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%.

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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, 6:06 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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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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High density SNP and SSR-based genetic maps of two independent oil palm hybrids

“ Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.”
Via Biswapriya Biswavas Misra
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Biswapriya Biswavas Misra's curator insight, April 29, 10:30 AM
Abstract (provisional)Background

Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.

Results

A 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 (LGs) linkage groups were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed.

Conclusions

The high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm.

sledderwool's comment, June 13, 1:27 AM
Its very good
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2014 - 4th Annual National Association of Plant Breeders Meeting

2014 - 4th Annual National Association of Plant Breeders Meeting | Plant Breeding and Genomics News | Scoop.it
Plant Breeding and Genomics News's insight:
“Breeding for Water Stress”
Minneapolis, MN August 5-8, 2014Registration opens in AprilEarly Bird Discount ends May 30, 2014Draft agenda posted


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Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches

Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches | 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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Genome-wide Two-marker linkage disequilibrium mapping of quantitative trait loci

In a natural population, the alleles of multiple tightly linked loci on the same chromosome co-segregate and are passed non-randomly from generation to generation. Capitalizing on this phenomenon, a group of mapping methods, commonly referred to as the linkage disequilibrium-based mapping (LD mapping), have been developed recently for detecting genetic associations. However, most current LD mapping methods mainly employed single-marker analysis, overlooking the rich information contained within adjacent linked loci.
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Identification of a strawberry flavor gene candidate using an integrated genetic-genomic-analytical chemistry approach

There is interest in improving the flavor of commercial strawberry (Fragaria × ananassa) varieties. Fruit flavor is shaped by combinations of sugars, acids and volatile compounds. Many efforts seek to use genomics-based strategies to identify genes controlling flavor, and then designing durable molecular markers to follow these genes in breeding populations. In this report, fruit from two cultivars, varying for presence-absence of volatile compounds, along with segregating progeny, were analyzed using GC/MS and RNAseq. Expression data were bulked in silico according to presence/absence of a given volatile compound, in this case γ-decalactone, a compound conferring a peach flavor note to fruits.
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Trait by trait, plant scientists swiftly weed out bad seeds through marker ... - Washington Post

Trait by trait, plant scientists swiftly weed out bad seeds through marker ... - Washington Post | Plant Breeding and Genomics News | Scoop.it
Trait by trait, plant scientists swiftly weed out bad seeds through marker ...
Washington Post
The rest he will discard. Krivanek, 42, is part of a new generation of plant breeders who are transforming the 10,000-year history of plant selection.
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Plant Breeders Release First 'Open Source Seeds'

Plant Breeders Release First 'Open Source Seeds' | Plant Breeding and Genomics News | Scoop.it
Scientists and food activists are launching a campaign to promote seeds that can be freely shared, rather than protected through patents and licenses. They call it the Open Source Seed Initiative.

Via Valerio Hoyos-Villegas
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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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Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.
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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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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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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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