JOHNSTON, IOWA

Pioneer Hi-Bred International, Inc.

Use of maize EST databases to identify and isolate homologs for genes with putative function identified from other species and genera --Helentjaris, TG With the advent of large collections of ESTs (expressed sequence tags) for maize, it is now possible to "mine" these databases for corn homologs to genes characterized first in other species where some level of functional understanding has been established. While cloning methods based upon hybridization are sometimes successful, they are often frustrated by low degrees of nucleotide similarity, depending upon the availability of a gene sequence from a species of close similarity. "in silico" cloning via computer analyses of EST collections on the other hand can be comparatively straightforward when these collections are available and comprehensive in their gene coverage. Instead of dedicating several person-months to isolate a maize homolog starting from an Arabidopsis or other dicot sequence, this search can take minutes on the computer. Starting with sequences from more distantly-related organisms, such as yeast or mammals, where many of our current gene sequences and understanding are currently archived, isolation by hybridization can be nearly impossible but is again greatly facilitated by analyses of computer-translated EST sequences. Consequently it is no longer a daunting task to isolate homologs for individual genes first characterized in other species and where known, whole pathways can now be identified and isolated in corn for study.

For the last couple of years I have been mining the original Pioneer/HGS EST database, and more recently the Dupont corn EST database, for maize homologs for specific biochemical, hormonal, and gene regulation pathways. My purpose was to acquire corn homologs representing pathways of interest to our team's research in yield stability. This list of putative corn homologs runs into the several hundreds of ESTs and many of these have been characterized by our group at some level, i.e. full length insert sequencing, mapping, expression, in some cases even TUSC-based searches for insertional inactivations. While they have proven invaluable for our purposes, we are still limited by a more detailed understanding of their function in corn and are unable to dedicate enough time to fully explore them. Consequently we would like to make a number of these clones available to interested researchers who wish to characterize them further in corn, emphasizing the placement of groups of clones by pathway with individual investigators. At this point it is relatively straightforward for us to arrange a materials transfer agreement to supply public researchers not only with the clones but also any other associated information and biomaterials we have to facilitate their own studies. Our hope is that as knowledge about these genes grows, it will of course add to our understanding the role of these genes within the context of our own research efforts. I urge researchers who might be interested in any of the genes or pathways in the appended table to contact me directly and discuss their interest. An even larger set of clones with somewhat less characterization is also available from pathways including carbohydrate metabolism and starch biosynthesis, cell cycle genes, and other hormone pathways.

The appended table contains a list of individual maize ESTs/clones which have each been characterized to represent different genes, the first column containing a clone identifier. The next column contains a descriptive name for its closest homolog. Next is a column indicating whether the clone is full length or not. The fourth column indicates a chromosomal bin where the clone has been mapped in the maize genome. The last column indicates those genes where a TUSC search for Mu insertions has been initiated.
 
EST candidate gene pathway size map location TUSC?
001 ABA insensitive 1/2 mutant ABA  no   no
002 ABA insensitive 1/2 mutant ABA  no   no
003 ABA insensitive 1/2 mutant ABA  no   no
004 ABA insensitive 1/2 mutant ABA  no 3.09-10 no
005 ABA insensitive 1/2 mutant ABA  no 6.07-08 no
006 ABA insensitive 1/2 mutant ABA  no   no
007 ABA insensitive 4/sun06 mutant ABA  FL   no
008 ABA-induced protein kinase ABA  FL 9.04 no
009 ABA-induced protein kinase ABA  no 7.04 no
010 farnesyl tranferase a-subunit ABA  FL 2.08 no
011 farnesyl tranferase b-subunit ABA  FL 3.06 yes
012 ADP-G PPase/bt2-like carbohydrate metab FL 2.06 yes
013 ADP-G PPase/sh2-like carbohydrate metab FL 6.08 no
014 GRR1 carbohydrate metab no   no
015 hexose/sugar transporter carbohydrate metab no   no
016 hexose/sugar transporter carbohydrate metab FL   no
017 hexose/sugar transporter carbohydrate metab FL   no
018 hexose/sugar transporter carbohydrate metab no 5.04 no
019 hexose/sugar transporter carbohydrate metab FL   no
020 hexose/sugar transporter carbohydrate metab FL   no
021 SPF1 transcription factor carbohydrate metab no 7.04 no
022 sucrose symporter carbohydrate metab no   no
023 sucrose symporter carbohydrate metab FL   no
024 G-binding protein a-subunit cytokinin response FL 1.02 no
025 G-binding protein b-subunit cytokinin response FL 1.09 no
026 G-coupled receptor cytokinin response FL 6.04 yes
027 HP homolog cytokinin response FL   no
028 HP homolog cytokinin response FL   no
029 HP homolog cytokinin response FL   no
030 AP2-containing/DREB2 gene regulation FL 8.02 yes
031 AP2-contaning/Tiny-like gene regulation no 8.03 no
032 AP2-contaning/Tiny-like gene regulation FL 9.04 no
033 N2-regulated protein kinase gene regulation no   no
034 N2-regulated protein kinase gene regulation FL   no
035 protein phosphatase/GLC7-like gene regulation FL   no
036 MAP kinase signalling FL 9.06 no
037 MAP kinase signalling FL 2.08 no
038 MAP kinase signalling FL 4.1 no
039 MAP kinase signalling FL   no
040 MAP kinase <aux signalling no 5.03 no
041 MAP kinase <aux signalling FL 5.04 yes
042 MAP kinase <ga signalling FL 9.05 yes
043 MAP kinase <sa signalling no 6.01 no
044 MAP kinase <sa signalling FL 6.01 no
045 MAP kinase kinase signalling FL 9.03 no
046 MAP kinase kinase signalling no 5.08 no
047 MAP kinase kinase signalling FL 3.07 no
048 MAP kinase kinase signalling no 5.05-06 no
049 MAP kinase kinase kinase signalling Fl 3.07/8.06 no
050 MAP kinase kinase kinase signalling no   no
051 MAP kinase kinase kinase signalling FL 1.1 no
052 MAP kinase kinase kinase signalling no 9.00-01 no
053 MAP kinase kinase kinase signalling no 10.04 no
054 MAP kinase kinase kinase CTR1-like signalling no 5.06 no
055 MAP kinase kinase kinase epsilon signalling FL   no
056 MAP kinase phosphatase signalling no 1.08 no
057 MAP kinase phosphatase signalling FL 5.07 yes
058 "Os-1p, At histidine kinase" signalling no 8.06 no
059 "protein phosphatase, MP2C >STE11" signalling no 6.00-01 no
060 MCAF1/POP sugar sensing no 7s no
061 Prl1 sugar sensing FL 1.09 yes
062 SNF1 sugar sensing no 2.05 no
063 SNF1 sugar sensing FL   yes
064 SNF1 sugar sensing no   no
065 SNF1 sugar sensing no 1.03 yes
066 SNF1 sugar sensing FL   no
067 SNF1 sugar sensing no   no
068 SNF1/WPK4 sugar sensing FL 3.06 no
069 SNF4 sugar sensing no 1.08-11 no
070 "spindly-like, TPR-containing" sugar sensing no   no

 


Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

Return to the MNL 74 On-Line Index
Return to the Maize Newsletter Index
Return to the Maize Genome Database Page