Corn Maze from Getty Images
I just want to start this off by saying that I was NOT the woman who called the police yesterday, because her family was lost in a corn maze coincidently nearby New England Biolabs. It could have easily been me – but I swear it wasn’t! View the amusing story here.
Ah autumn. It’s harvest time in New England. It’s usually a lot of fun. Going to the farm…picking apples, getting lost in corn mazes, riding tractor hay rides. Who doesn’t love this season?
The epigenetics contribution to genetically food and crop science has been on my mind as a topic for a while now. Everyone lauds a good cook. But we all seldom appreciate the work done by the farmer, never mind the work of scientists improving food quality and production!
Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in Maize. Plant Physiology Preview. (October 6, 2011) Yang et al. is the first study to produce a biomarker panel to quantitatively measure an agronomic trait, across environmental conditions among a broad range of hybrids. It’s an important trait too. Nitrogen efficiency is the rate limiting step for crop yield. Overall farming productivity and sustainability are both strongly linked to nitrogenous fertilizer use.
Here are some of the most interesting parts of the study. Transcriptome microarrays were used initially on greenhouse maize samples growing long term in sufficient or limiting nitrogen. Samples were taken at varied times of day, and seasons of the year, among two maize hybrids. As controls, plants subjected to drought and nutrient depletion stress were also tested. No difference was noted in the nitrogen status biomarkers of control stressed plant samples. 112 probe sets were validated as long term growth, nitrogen status biomarker genes.
The researchers then further demonstrated the useful range of this biomarker set to quantify in planta nitrogen status using qPCR gene expression assays. Samples from plants which were starved for 28 days and then temporarily exposed to sufficient nitrogen for 2 hours, were distinguishable from plants which were starved for only 2 hours by their gene expression in the biomarker set. Pretty impressive! The signatures were present across multiple plant tissue types, (roots, leaves etc) in 27 different field grown hybrids. Sixteen different field sites with varied rainfall, and soil types, were tested. The transcriptome profiles correlated across the board with ultimate grain yield.
Meta-analysis showed 3707 genes, (or about 7% of the maize transcriptome), are nitrogen responsive. Half of the genes are involved in known functional pathways, nitrogen metabolism, carbohydrate, amino acid, lipid secondary metabolites, transport, signal transduction, co-factor metabolism, hormone-responsive pathways and transcriptional regulation. Ultimately, they reduced the final biomarker panel to 8 genes through statistical analysis…beyond the limits of my expertise, so no comment here!
Using epigenomics, these authors from the Monsanto Company, met their goal of accessing crop responses to varying nitrogen conditions. Their transcriptome biomarkers are a promising tool which quantifies in planta nitrogen status – measuring the plant’s physiological status, independently from geneotype or phenotype.
There is further work to be done to define the molecular processes correlating crop yield and nitrogen efficiency. More hybrids will be tested. It may be that some of the genes from this biomarker set will become useful targets for plant breeding in the future. Although the authors make clear that individual genes chosen as biomarkers, may not necessarily aid nitrogen efficiency. Speaking of new hybrids and genetics…maybe somebody needs to breed some produce worthy GFP corn, so that we American, New Englanders don’t get so frightened at night in a maze of maize!
Yang S, Wu J, Ziegler T, Yang X, Zayed A, Rajani MS, Zhou D, Basra A, Schachtman D, Peng M, Armstrong C, Caldo R, Morrell J, Lacy M, & Staub J (2011). Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in Maize. Plant physiology PMID: 21980173
