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Transcriptome analysis of the Vernalization Response in Barley (Hordeum vulgare) Seedlings (Greenup et al. 2011)

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TLI vernalization chamber


VERNALIZATION

Vernalization is the response that a select number of species have that allows them to flower earlier after exposure to cold conditions for a 6-10 weekn period. It is economically important because people are able to harvest their grass crops earlier in vernalized plants as opposed to those you would need to plant in the spring and wait to flower until later in the summer. In the following sections I review a ladmark paper that identifies candidate genes from a transcritomic analysis of Barley seedlings.


INTRODUCTION

There are a number of genes that are responsible for cold tolerance and the vernalization response. Genes that are upregulated in short term cold are referred to as cold tolerance genes and get downregulated after the short term exposure to cold. This is in contract to genes that get up or downregulated in response to long term cold and remain up or downregulatd after the exposure. Among the vernalization reponse, keys regulators include VRN1, VRN2 and VRN3. The purpose of this study was to scan the trancriptome of the commonly studied Barley (Hordeum vulgare) to gain further insight into the other genes that are involved in this genetic network.
Journal.pone.0017900.g001


TRANSCRIPTOMICS

Transcriptomics is becoming an extremely large and important field of research because it allows researchers to look at the entire array of genes and their expressional differences in different environments and across different developmental time and in different environmental conditions.


METHODS

Seedlings were exposed to either prolonged cold or short term cold and total RNA was extracted from seedlings prior to either long or short term cold exposure and then again after transfer back to warm. RNA was extracted from both seedlings and from leaves to determine if there is an expressional difference in the seedlings versus the leaves before, during and after the vernaliztion response.


Journal.pone.0017900.g003

Gene expression changes as shown though venn diagrams

Journal.pone.0017900.g005

Gene expression changes in genes that were clustered by similar response to treatment


FIGURES


This figure shows the genes that are up and down regulated in the three categories examined: short term cold, long term cold and one day after long term cold (to evaluate if the genes that were upregulated/downregulated during long term cold remained so).


This figure shows the clusters of genes that were grouped based on their response to temperature transitions. Clusters 9 and 10 were identified as the vernalization clusters because they were down or up regulated only after prolonged exposure to cold and the expression level remained after transition back to the warm environemnt.


From this transcriptomic study a cluster of candidate vernalization genes were found that were previously not known to play a role in the vernalization response. Transcriptomics studies like these are important first steps to identify genes that were not previously known to play a role in spcific traits/responses/pathways.



GENOME WIDE ASSOCIATION STUDIES IN CROP PLANTS

There has been a recent surge in research on genome wide association and transcriptome studies on drought tolerant and vernalization dependednt crops. This research is using forward genetics to search the genome/transcriptome for genes that have sequential or expressional similarities to extrapolate about functional similarities. These studies look for syntenic regions among rice, barley, wheat and other cereals. Major regions of similarity have been identified that confer drought resistance among these plants.



EXTENSION STUDIES

Kadam et al. 2012 Genomic associations for drought tolerance on the short arm of wheat chromosome 4B.

This study picked up on the methods of the Greenup 2011 study and carried it a few steps farther by doing GWAS on the short arm of chromosome 4B in addition to transcriptome analysis.


Lai et al. 2012 Single nucleotide polymorphism discovery from wheat next-generation sequence data

This study used their sequenced transcriptome of wheat to identify SNPs from 3 different wheat varieties. This has been very difficult prior to next generation technology because of the sheer size of the wheat genome and number of homologs to try to seperate out.


LITERATURE CITED

A review on how Next Gen sequencing is crevolutionizing crop research here (American Journal of Botany)

Greenup, AG., Sasani A, Oliver SN, Walford SA, Millar AA et al. (2011) Transcriptome Analysis of the Vernalization Response in Barley (Hordeum vulgare) Seedlings. PLoS ONE 6(3): e17900. doi:10.1371/journal.pone.0017900

Kadam, S, Singh K, Shukla S, Goel S, Vikram P, Vasantrao P, Gaikwad K, Khanna-Chopra R, Singh N. (2012) Genomic associations for drought tolerance on the short arm of wheat chromosome 4B. Functional Intergrated Genomics 12:447-464.

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