Winter Reading - Page 5

ChrisK · February 25, 2013

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

ChrisK · February 25, 2013

Now in final published format.

Metabolic Engineering of Tomato Fruit Organic Acid Content Guided by Biochemical Analysis of an Introgression Line

ChrisK · April 2, 2013

Well, I know it's not winter anymore but everyone needs bedtime reading! This paper ran across my desk today at work. Thought some people might find it interesting since biodiversity and rhizosphere interactions come up occasionally.

ChrisK · May 8, 2013

Several new papers today:

Functional genomics of tomato in a post-genome-sequencing phase

K Aoki, Y Ogata, K Igarashi, K Yano, H Nagasaki… - Breeding science, 2013
Abstract Completion of tomato genome sequencing project has broad impacts on genetic
and genomic studies of tomato and Solanaceae plants. The reference genome sequence
derived from Solanum lycopersicum cv 'Heinz 1706'serves as the firm basis for ...

Current challenges and future potential of tomato breeding using omics approaches

M Kusano, A Fukushima - Breeding science, 2013
Abstract As tomatoes are one of the most important vegetables in the world, improvements in
the quality and yield of tomato are strongly required. For this purpose, omics approaches
such as metabolomics and transcriptomics are used not only for basic research to ...

Genes that influence yield in tomato

T Ariizumi, Y Shinozaki, H Ezura - Breeding science, 2013
Abstract Yield is the most important breeding trait of crops. For fruit-bearing plants such as
Solanum lycopersicum (tomato), fruit formation directly affects yield. The final fruit size
depends on the number and volume of cell layers in the pericarp of the fruit, which is ...

DNA marker applications to molecular genetics and genomics in tomato

K Shirasawa, H Hirakawa - Breeding science, 2013
Abstract Tomato is an important crop and regarded as an experimental model of the
Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and
advance the field of genetics, tomato has been subjected to DNA marker studies as one of ...

Dutch · May 10, 2013

Quote:

Originally Posted by ChrisK

Anybody still reading?

Yes, I am still reading. Thanks you Chris and Darrel!
Dutch

ChrisK · June 1, 2013

Tomato breeding in the genomics era: insights from a SNP array

Background

The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations.

Results

From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum 'Moneymaker' from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected grouping patterns, with S. pimpinellifolium as the most closely related to commercial tomatoesearlier results.

Conclusions

Our results show that a SNP search in only a few breeding lines already provides generally applicable markers in tomato and its wild relatives. It also shows that the Illumina bead array generated data are highly reproducible. Our SNPs can roughly be divided in two categories: SNPs of which both forms are present in the wild relatives and in domesticated tomatoes (originating from common ancestors) and SNPs unique for the domesticated tomato (originating from after the domestication event). The SNPs can be used for genotyping, identification of varieties, comparison of genetic and physical linkage maps and to confirm (phylogenetic) relations. In the SNPs used for the array there is hardly any overlap with the SolCAP array and it is strongly recommended to combine both SNP sets and to select a core collection of robust SNPs completely covering the entire tomato genome.

ddsack · June 1, 2013

Chris, keep posting as you find links, this is a valuable thread for research. Don't want to derail this thread, as the discussion is already elsewhere in the 2 cents - (New seed laws in the European Union thread), but after reading the above article in genetics, I became interested in who and where this research was being done. Turns out it is connected to Wageningen UR in the Netherlands. I went to their website and looked at some of the history of this university, and found they have had a division since 1976 DLO: Establishment of RIKILT, the National Quality Institute for Agricultural and Horticultural Products. The result of a merger of the National Agriculture Testing Station in Maastricht and the National Dairy Station in Leide. One thought jumped to another, and now I am wondering if politicians who enacted the restrictive seeds laws were pushed/advised to do so by legitimate university administration/researchers who are ultimately backed by money from large corporations. Looking at their financial figures, they get huge chunks of money from "contract research", especially in the Specialised Research Institutes section. I guess it should be a surprise to no one then, that EU government policy could be influenced by university scientists or at least the administrators of the programs, which would bump the visibility of their corporate sponsors down a bit. I have not done enough research (and don't have time to) to see if this is what happened or who the EU bad seed policy advisors were. Just wanted to comment that some of the links posted here continue to bring up interesting side topics and ruminations.

ChrisK · June 1, 2013

I've decided to stay out of those discussions and will continue to do so for various reasons. Too much hysteria and conspiracy theories with dis/mis-information, often by our most prodigious posters who quote and link to less than reliable sources (I'm being generous). I find the continual argumentum ad monsantium and Gish Gallops to be tiresome, trite and unproductive.

I am always happy to talk about the science of plants and agriculture with those that want to discuss, incl. explanations of any of the papers posted here. My interest is in good science not anecdote and poor "studies" by check-out line magazines.

Now, back on track. I will continue to post as I find interesting publications, glad you are finding them valuable and thought provoking!

Best.

Quote:

Originally Posted by ddsack

Chris, keep posting as you find links, this is a valuable thread for research. Don't want to derail this thread, as the discussion is already elsewhere in the 2 cents -

June 1, 2013

Quote:

Originally Posted by ChrisK

I've decided to stay out of those discussions and will continue to do so for various reasons. Too much hysteria and conspiracy theories with dis/mis-information, often by our most prodigious posters who quote and link to less than reliable sources (I'm being generous). I find the continual argumentum ad monsantium and Gish Gallops to be tiresome, trite and unproductive.

I am always happy to talk about the science of plants and agriculture with those that want to discuss, incl. explanations of any of the papers posted here. My interest is in good science not anecdote and poor "studies" by check-out line magazines.

Now, back on track. I will continue to post as I find interesting publications, glad you are finding them valuable and thought provoking!

Best.

Yep! and I am probably one of the prodigious posters.

I ask questions though for one very simple reason. Like corporal Klinger "I Know Nothing"

http://www.youtube.com/watch?v=UmzsWxPLIOo

It's all good information and has been good winter reading.

Ted

ChrisK · June 21, 2013

Anthocyanins Double the Shelf Life of Tomatoes by Delaying Overripening and Reducing Susceptibility to Gray Mold

Highlights

•Anthocyanin accumulation doubles the postharvest storage time of tomato fruit
•Anthocyanin enrichment reduces susceptibility of tomato fruit to Botrytis cinerea
•Longer shelf life is associated with high hydrophilic antioxidant capacity of fruit
•Anthocyanins perturb the dynamics of the ROS burst during infection by B. cinerea

ChrisK · July 1, 2013

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Abstract:

Although applied over extremely short timescales, artificial selection
has dramatically altered the form, physiology, and life history
of cultivated plants. We have used RNAseq to define both gene
sequence and expression divergence between cultivated tomato
and five related wild species. Based on sequence differences, we
detect footprints of positive selection in over 50 genes. We also
document thousands of shifts in gene-expression level, many of
which resulted from changes in selection pressure. These rapidly
evolving genes are commonly associated with environmental response
and stress tolerance. The importance of environmental
inputs during evolution of gene expression is further highlighted
by large-scale alteration of the light response coexpression network
between wild and cultivated accessions. Human manipulation
of the genome has heavily impacted the tomato transcriptome
through directed admixture and by indirectly favoring nonsynonymous
over synonymous substitutions. Taken together, our results
shed light on the pervasive effects artificial and natural selection
have had on the transcriptomes of tomato and its wild relatives

ChrisK · July 1, 2013

Genome Biology has a special plant issue with many open access original papers as well as reviews, one of which was about tomatoes and pathogen interactions.

ChrisK · July 15, 2013

Posting an older review since many are interested in breeding for various disease resistance. Thought it might be interesting to have an overview of what is happening at the molecular level, sometimes called the evolutionary dance between host and pathogen. Also sometimes called the arms race between the two!

The Dangl lab is highly regarded in this area and the review has been cited >2500 times to date.

The plant immune system

ChrisK · July 20, 2013

Stumbled on this one yesterday while looking for something else.

Adaptive evolution of threonine deaminase in plant defense against insect herbivores

In a nutshell, tomato expresses a gene in response to herbivore feeding. The ingested protein is cleaved in the lepidopteran gut where it becomes active and degrades threonine, an amino acid needed by the insect.

ChrisK · July 26, 2013

Pleiotropic Phenotypes of the sticky peel Mutant Provide New Insight into the Role of CUTIN DEFICIENT2 in Epidermal Cell Function in Tomato

Molecular and Genetic Characterization of a Novel Pleiotropic Tomato-Ripening Mutant

February 25, 2013	#61
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	*High-Density SNP Genotyping of Tomato (Solanum lycopersicum* L.) Reveals Patterns of Genetic Variation Due to Breeding** __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin

February 25, 2013	#62
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	Now in final published format. Metabolic Engineering of Tomato Fruit Organic Acid Content Guided by Biochemical Analysis of an Introgression Line __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin

May 8, 2013	#64
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	Anybody still reading? Several new papers today: Functional genomics of tomato in a post-genome-sequencing phase K Aoki, Y Ogata, K Igarashi, K Yano, H Nagasaki… - Breeding science, 2013 Abstract Completion of tomato genome sequencing project has broad impacts on genetic and genomic studies of tomato and Solanaceae plants. The reference genome sequence derived from Solanum lycopersicum cv 'Heinz 1706'serves as the firm basis for ... Current challenges and future potential of tomato breeding using omics approaches M Kusano, A Fukushima - Breeding science, 2013 Abstract As tomatoes are one of the most important vegetables in the world, improvements in the quality and yield of tomato are strongly required. For this purpose, omics approaches such as metabolomics and transcriptomics are used not only for basic research to ... Genes that influence yield in tomato T Ariizumi, Y Shinozaki, H Ezura - Breeding science, 2013 Abstract Yield is the most important breeding trait of crops. For fruit-bearing plants such as Solanum lycopersicum (tomato), fruit formation directly affects yield. The final fruit size depends on the number and volume of cell layers in the pericarp of the fruit, which is ... DNA marker applications to molecular genetics and genomics in tomato K Shirasawa, H Hirakawa - Breeding science, 2013 Abstract Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of ... __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin

June 1, 2013	#66
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	ok then. Tomato breeding in the genomics era: insights from a SNP array Background The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations. Results From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum 'Moneymaker' from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected grouping patterns, with S. pimpinellifolium as the most closely related to commercial tomatoesearlier results. Conclusions Our results show that a SNP search in only a few breeding lines already provides generally applicable markers in tomato and its wild relatives. It also shows that the Illumina bead array generated data are highly reproducible. Our SNPs can roughly be divided in two categories: SNPs of which both forms are present in the wild relatives and in domesticated tomatoes (originating from common ancestors) and SNPs unique for the domesticated tomato (originating from after the domestication event). The SNPs can be used for genotyping, identification of varieties, comparison of genetic and physical linkage maps and to confirm (phylogenetic) relations. In the SNPs used for the array there is hardly any overlap with the SolCAP array and it is strongly recommended to combine both SNP sets and to select a core collection of robust SNPs completely covering the entire tomato genome. __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin

June 1, 2013	#67
ddsack Tomatovillian™ Join Date: Jan 2006 Location: Northern Minnesota - zone 3 Posts: 3,220	Chris, keep posting as you find links, this is a valuable thread for research. Don't want to derail this thread, as the discussion is already elsewhere in the 2 cents - (New seed laws in the European Union thread), but after reading the above article in genetics, I became interested in who and where this research was being done. Turns out it is connected to Wageningen UR in the Netherlands. I went to their website and looked at some of the history of this university, and found they have had a division since 1976 DLO: Establishment of RIKILT, the National Quality Institute for Agricultural and Horticultural Products. The result of a merger of the National Agriculture Testing Station in Maastricht and the National Dairy Station in Leide. One thought jumped to another, and now I am wondering if politicians who enacted the restrictive seeds laws were pushed/advised to do so by legitimate university administration/researchers who are ultimately backed by money from large corporations. Looking at their financial figures, they get huge chunks of money from "contract research", especially in the Specialised Research Institutes section. I guess it should be a surprise to no one then, that EU government policy could be influenced by university scientists or at least the administrators of the programs, which would bump the visibility of their corporate sponsors down a bit. I have not done enough research (and don't have time to) to see if this is what happened or who the EU bad seed policy advisors were. Just wanted to comment that some of the links posted here continue to bring up interesting side topics and ruminations. __________________ Dee **************

June 21, 2013	#70
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	Anthocyanins Double the Shelf Life of Tomatoes by Delaying Overripening and Reducing Susceptibility to Gray Mold Highlights •Anthocyanin accumulation doubles the postharvest storage time of tomato fruit •Anthocyanin enrichment reduces susceptibility of tomato fruit to Botrytis cinerea •Longer shelf life is associated with high hydrophilic antioxidant capacity of fruit •Anthocyanins perturb the dynamics of the ROS burst during infection by B. cinerea __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin

July 1, 2013	#71
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato Abstract: Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin

July 15, 2013	#73
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	Posting an older review since many are interested in breeding for various disease resistance. Thought it might be interesting to have an overview of what is happening at the molecular level, sometimes called the evolutionary dance between host and pathogen. Also sometimes called the arms race between the two! The Dangl lab is highly regarded in this area and the review has been cited >2500 times to date. The plant immune system __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin

July 20, 2013	#74
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	Stumbled on this one yesterday while looking for something else. Adaptive evolution of threonine deaminase in plant defense against insect herbivores In a nutshell, tomato expresses a gene in response to herbivore feeding. The ingested protein is cleaved in the lepidopteran gut where it becomes active and degrades threonine, an amino acid needed by the insect. __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin

July 26, 2013	#75
ChrisK Tomatovillian™ Join Date: Mar 2011 Location: Raleigh, NC Posts: 1,448	*Pleiotropic Phenotypes of the sticky peel* Mutant Provide New Insight into the Role of CUTIN DEFICIENT2 in Epidermal Cell Function in Tomato Molecular and Genetic Characterization of a Novel Pleiotropic Tomato-Ripening Mutant** __________________ Blog: chriskafer.wordpress.com Ignorance more frequently begets knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science. --Charles Darwin