Friday, February 19, 2010

Getting really, really, close.....

We are getting really close to having a functional ionomics lab. Yesterday, the last major piece of equipment, the fan for the top of the exhaust system was installed on the roof. As you can see, it was quite a production....


Almost all the internal construction is finished and we are on schedule for the ICPs to be installed at the beginning of March.

In other news, the weighing robot is almost finished. This week I visited Paul Armstrong at the USDAs Engineering and Wind Erosion Research Unit in Manhattan Kansas. Paul has built a robot that can take single corn and soybean seeds from a 48 well plate, weigh them and then put them in a specified digestion tube. This turns out to be one of the bottleneck steps in our sample prep, so the robot will save us hours every day. Here is a photo of the robot with Paul in the background....

and here is a front view......

Before you know it, we will be cranking through samples.

Monday, February 1, 2010

Maize Grant Submitted

In collaboration with Owen Hoekenga (Boyce Thompson Institute/USDA-ARS/Cornell University), Mourad Ouzzani (Purdue University), Margaret Smith (Cornell University), and Paul Anderson (Danforth Center) I just submitted a grant to the NSF-Plant Genome Research Program entitled "Mineral Nutrient Gene Discovery and Gene X Environment Interactions Using the Nested Association Mapping Population in Maize".

Here is the abstract:

Maize is the most widely adapted and adopted crop on the planet. This is largely due to the amazing degree of genetic and phenotypic diversity that can be harnessed into adaptation to local conditions. While progress has been made in some aspects of adaptation, e.g. flowering time, little progress has been made with respect to adaptation to soil conditions at the molecular and genetic levels. This is ironic given the importance of plant-soil interactions as they relate to agricultural efficiency, sustainability and productivity. We will utilize the Nested Association Mapping (NAM) population, a unique and powerful genetic resource, to identify genes controlling the elemental composition (the ionome) of maize grain. We will measure the levels of 20 different elements: P, Ca, S, K, Mg, Sr, Rb (macronutrients or their chemical analogs); B, Cu, Fe, Zn, Mn, Co, Ni, Mo (micronutrients of significance to plant and human health); Na, Al, As, Se and Cd (minerals causing agricultural or environmental problems). We will leverage grain samples from the 5,000 recombinant inbred lines that constitute the NAM population, which have already been grown at four different locations with widely different soils. One expected outcome of our project is the identification, at single gene resolution, of loci and alleles that alter the accumulation of the mineral nutrients and toxic elements from different soil conditions. We will confirm these results and identify potential causative polymorphisms by association analysis. For 20 selected loci, we will create Heterogeneous Inbred Families (HIFs) that an extended team of collaborators will help us to evaluate in multiple soil environments, which we will select based upon screening soil samples provided by our extended team. The HIFs will confirm the predicted allelic affects and allow us investigate the interactions between genetic and environmental factors to determine grain quality. Additional outcomes for our project will be the identification of hundreds of genetic loci and dozens of nucleotide polymorphisms that determine the mineral nutritional content of maize grain. We will also gain a better understanding of how many of these genes interact with environmental factors.