Genetic Maize

Volker Brendel, professor of bioinformatics at Iowa State, spoke at the Maize Genetics Conference about the need for a better system of community annotation of the maize genome. The genome of the popular maize inbred line B73 is sequenced, but we don’t actually know what a lot of the code stands for. It’s going to take a lot of collaborative effort to discover and annotate (explain) the function of each gene and to put all of that information in one place so it will be useful.
Volker reminds us that the Arabidopsis 2010 funding is running out, so we need to assess the plant genetics situation. How many genes do we know the function of? There is still much to learn.
Maize is uniquely positioned to replace Arabidopis as a focus for basic plant research due to the many resources that are already established, the most important of which is the extensive maize genetics community (he didn’t say it, but there is another reason why maize is a better choice than Arabidopsis right now – all of our major grains are very closely related, so work on maize applies to rice, wheat, sorghum, and more). The community needs to work together in the annotation process, assigning functions to the genes that have been sequenced, putting the data from a variety of sources together to make a bigger picture. Each researchers has a favorite gene (pathway, organelle, etc) – how can each of the researchers contribute to the annotation process?
PlantGDB is a comparative genomics site funded by NSF has information on 14 species, including maize, which is very useful. However, no matter how clever the computer programs are, the human touch is still needed. Filling in information on any of these species helps us to better understand all of them. On the site, community members can flag genes for which the models don’t seem to fit, and can contribute alternative explanations. The final goal is to have every gene model approved by the relevant community member(s). When a person annotates a gene, the PlantGDB committee reviews it, approves it, and the information is shortly available on the site. Annotating the genes you are working on is your civil duty, something you owe due to public funding you receive.
After Volker’s talk, the attendees discussed what is the public’s role in the attenuation process should be. There are a lot of cases where the the gene model can be checked without any lab work, simply by looking at the sequences. Some members of the community think we should harness the brainpower of thousands of biology undergraduate students by assigning annotations for class. I like the idea of getting students involved, and hope they follow through.Diversity of people to represent the maize genetics community.
A panel discussion followed, where a lot of great new ideas for annotation were brought up (unfortunately I don’t have the names of some of the people that spoke).
One panel member said we need “Zeazomics” – a collection of information including genomics, metabolimics, proteomics, and whatever else we can come up with – to fill in gaps in our knowledge. being able to link all of this information together will lead to stronger explanations of the phenotypes we see. He said this process will not be definitive, it will create a series of hypothesis that will lead to more hypotheses. The hypothesis testing will lead to functional biolgoy, from physiology to biochemistry to cell biology and more. Additional genome sequencing is necessary to capture the entire diversity of maize. Maize is the model for grasses, for crops, for future applications like biofuels. Now is the time to push maize research to a much higher level.
To accomplish all this, we’ll need to take care of a few things, as the other panel members and members of the community brought up:

• Need to have reciprocal links from genes from MaizeGDB to NCBI Entrez Gene. Currently, about 20,000 NCBI Entrez Genes need links back to MaizeGDB.
• To help with annotation, Lisa Harper, curator of MaizeGDB, will do a movie that shows the common problems of using the databases, including how the genome changes over time as the contigs are reordered, etc. This is needed because people are often working off of older copies of the information for a given gene, as it might not be updated frequently enough.
• There is also a need to integrate microarray data into the databases. Particularly complicated are those microarrays that are specific to a particular tissue and/or developmental stage. Volker says that this problem is common and new technologies with new ways to visualize data are necessary.
• MaizeGDB needs a forum such that people working on the same genes can coordinate their work.
• iPlant is organizing a workshop in St. Louis in June to help coordinate the various genome annotation groups.

• There is a plan to create outreach information that any member of the maize community will be able to download and use to communicate the needs and accomplishments to the public and to government officials.

Pam Johnson, Chair of the Research and Business Development Action Team of the National Corn Growers Association, presented a briefing at the Maize Genetics Conference. She has words of frustration, words of hope, and words of encouragement for the maize genetics community.
Pam, a 5th generation farmer from Iowa, is the voice of 300,000 corn growers. She works as an advocate for public research and for public and private partnerships. The official mission of the NCGA is “to create and increase opportunities for corn growers”, but the goals are expanding in recognition of increasing global population and increasing needs for food and energy. A world where people have their needs met will be a more stable world, and corn can help make that possible.
The title of Pam’s talk is “Research and the Recession: How Obama and the Stimulus Package Impact the Future of Agricultural Research”. She had intended to speak about funding going towards the new National Institute of Food and Agriculture, but those decisions have been delayed by congress, so she instead focuses on the future of corn.
NCGA is the voice on Capital Hill for science and funding. The NGCA can’t lobby, but can educate on behalf of their members. She must show results to get funding, and must be able to show how research will benefit the constituents of the elected officials she speaks with.  The NCGA worked closely with the Obama transition team, encouraging the appointment of science friendly appointees. The stimulus package holds additional funds for the USDA and some programs. Corn is a national treasure and we haven’t yet used it to it’s full potential.
In her role as advocate, Pam works to keep funding focused on research, particularly corn research, including big items like the National Plant Genome Initiative funded by the National Science Foundation. The NPGI has created opportunities for collaborations through the Interagency Working Group. The research conducted by the NPGI is bigger than any one company or any one agency, so the strength is really in collaborative research.
In 2020, the NCGA anticipates producing about 17,000 bushels of corn per year in the US, with the additional grain going toward ethanol. Pam says that the food vs fuel issue is a myth, as we are able to produce enough for both. There have been significant reductions of greenhouse gas emissions due to the use of biofuels. There are 180 biorefineries in the US right now. We should stop throwing stones at each other and work together.
There are more transgenic field trial release permits from the USDA for corn than for any other crop. Corn growers are supportive of getting more technology in the fields, and NCGA acknowledges everyone’s contribution to the pipeline that starts with basic research and ends with the consumer.
Pam closes her talk with some inspiration from Travis Smiley: “These times will separate the truth tellers from the power grabbers. The responsibility to restore hope lies with each of us.” and from Thomas Friedman: “Scientists are afraid of being advocates but advocates are not afraid of being scientists.” Pam asks us to “show up, speak up, form personal relationships with legislators, separate myth from the truth… let’s go to work!“

The 51st Maize Genetics Conference is just as overwhelming as I remembered from the the 49th (50 was in Washington DC and was too expensive for me to go). We have 480+ maize geneticists all in one resort in St. Charles, IL, presenting 244 posters, 4 plenary talks, 35 short talks, and innumerable conversations about maize. The topics range from perfecting the corn genome sequence to writing and using software to help us navigate it to the intricate details of transposons and centromeres… and a little bit of applied work as well. There’s no way one person could convey all of the information presented here, but I hope I can share some of the tidbits that were particularly interesting to me in my next few posts. You can find the entire 201 page program on the MaizeGDB website, which includes abstracts of all of the posters and talks. Many people will upload their talks and posters to the website, I’ll let you know when they go up.

The NCCC-167 meeting is over, and I’m very glad to have had the opportunity to attend. The acronym stands for North Central Communications Committee, and 167 is the USDA-ARS project number. It turns out that there are hundreds of projects, some of which are designated for conferences and communications, such as this one. Apparently this particular conference used to be NCR-2 (North Central Region) but the rumor is that a Kansas corn breeder forgot to renew the project in time, so the group had to reapply and got a much higher number. That happened so long ago that 167 is a well recognized number in the corn breeding community.
The most important idea I took from the meeting, besides the reminder that there’s a lot more to scientists than you’d think from just reading their papers (as I described in NCCC-167), is that groups really need to stay organized. The Maize Genetics Community is well structured and very large, as can be seen from the huge number of attendees at the Maize Genetics Conference (more on that in another post, it’s where I am at this very moment). There are just as many if not more maize breeders as there are maize geneticists, but they don’t have as cohesive of a community. I’m not sure why this is, but it certainly seems to be a problem. Without strong lines of communication across the community, the group has a decreased ability to apply for collective grants, less ability to share information and techniques, etc. The importance of breeding will only grow as climate change brings diseases and pests to areas where they did not exist before and as population growth demands higher yields. My major professor and  a few others in the community seem dedicated to bringing stability and continuity to the group. I look forward to watching it grow back to its former glory.
I took extensive notes on the wonderful talks at NCCC-167, and hope to post more about them in the coming days. Most importantly, I’m anticipating additional information about breeding high methionine maize for organic chicken feed from Walter Goldstein of the Michael Fields Agricultural Institute. We may not see eye to eye on every topic, but I certainly agree that we could use nutritionally enhanced corn, and that’s one heck of an important place to start a conversation!
For now, I must turn my attention to the Maize Genetics Conference – let’s hope I can keep up!

Shawn Kaeppler is a researcher at the Great Lakes Bioenergy Center, a DOE Bioenergy Research Center, and the University of Wisconsin Department of Agronomy. Specific to this center is a lot of work on sustainability, including work on energy balance. You may be surprised, then, to hear that Shawn’s group is working on corn stover, but they have a strong rationale for doing so. Corn is closely related to the potential biofuel perennials miscanthus and switchgrass. They work in corn because of the resources available like a sequenced genome and large germplasm sources, and will then use the knowledge they acquire to improve the grasses.
Groups within the Great Lakes Bioenergy Center and the Agronomy Department of the University of Wisconsin are working on determining how much stover can be removed from the field. Some must remain to prevent erosion and to contribute to soil carbon. There is no easy answer, as the amount you can remove depends on soil quality, slope of the field, farming practices, and more. Some areas will need to retain more stover than others.
Core to biofuel research (as with most other breeding efforts) is screening diverse germplasm for candidate genes that correlate with traits like biomass yield and ethanol potential. Shawn’s group uses three main methods: microarrays in specific tissues, QTL analysis, and searching for candidate genes directly.
Specific traits under analysis fall under biomass quality and biomass quantity. Quality traits include using ruminant digestibility parameters because these qualities seem to be quite related to biofuel production, and provide an overall picture rather than focusing on one biochemical pathway. Quantity traits include stalk diameter and internode length.
One trait that might be related to quality is vegetative phase change, which refers to the time when juvenile tissues transition to adult tissues. Phase change timing is a trait susceptible to selection. This research addresses how timing differentials are inherited and whether having more juvenile tissue positively effects biomass quantity and quality. They found no relationship between the time of phase change and digestibility of the whole plant (without grain), however there is a relationship (although not significant) between the proportion of leaves that are still juvenile and digestibility. Overall, it seems that increasing juvenile tissue does not increase digestibility and also reduces yield because the tissue is more susceptible to disease and insects, and may senesce before harvest. This is good to know, because researchers can move on to traits that do affect digestibility / biomass quality.
Candice Hansey is a student of Shawn Kaeppler at the University of Wisconsin studying biomass quality. Her work answers the question: how can we measure ethanol potential? Simultaneous saccharification and fermentation is a great method, but very low throughput (takes a whole day to do 15 samples). Instead, they use established methods to measure forage quality (digestibility). The samples are put into a packet of filter paper, weighed, then subjected to a succession of different solvents that dissolve different fractions of the samples which then leave the filter packet. For example, the last solvent is 72% sulfuric acid which dissolves everything except acid-insoluable lignin. With this method, they can determine what percentage of each sample is lignin, carbohydrate, etc. Candy has screened different plant parts at different levels of maturity to see which might best predict the digestibility of the total adult plant. Unfortunately, the most predictive tissue was the stalk at developmental phase R6, but dissecting adult plants is a hassle. She determined that whole plant analysis is the best way to screen for digestibility.
These projects are great example of how negative results can be just as useful in moving science forward as positive results. Thanks to Shawn and Candy, we now know some areas of research that can be “checked off”, so to speak, allowing resources to be used in other areas.
Note: this post consists of my notes of Shawn and Candy’s talks at NCCC-167 2009, and was posted with their agreement.