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 MaizeGDB Homepage

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