Since maize was domesticated in Mexico around 9000 years ago, local farmers have selected and maintained seed stocks with particular traits and adapted to local conditions. In the present day many of these landraces are still cultivated, however increased urbanization and migration from rural areas implies a risk that this invaluable maize germplasm may be lost. In order to implement an efficient mechanism of conservation in situ, the diversity of these landrace populations must be estimated. Development of a method to select the minimum number of samples that would include the maximum number of alleles and identify germplasm harboring rare combinations of particular alleles will also safeguard the efficient ex-situ conservation of this germplasm. To reach this goal a strategy based on SSR analysis and a novel algorithm to define a minimum collection and rare genotypes using landrace populations from Puebla State, Mexico was developed as a “proof of concept” for methodology that could be extended to all maize landrace populations in Mexico and eventually to other native crops. The SSR based strategy using bulked DNA samples allows rapid processing of large numbers of samples and can be set up in most laboratories equipped for basic molecular biology. Therefore, continuous monitoring of landrace populations locally could easily be carried out. This methodology can now be applied to support incentives for small farmers for the in situ conservation of these traditional cultivars.
GenoMaiz Database
GenoMaiz27-12-2016.sql
DNA_plates
Information about the plate that contains the DNA sample.
DNAplate_id: Numerical identifier (unique per row)
ESTADO: State (of Mexico) where the accession was originally collected.
DNA_plate: Plate where the DNA is stored in our facilities.
DNA_well: Well within plate where the DNA is stored in our facilities.
accesion: Unique key for accession.
** - Technical description of columns - **
Field Type Null Key Default Extra
DNAplate_id int(5) NO PRI NULL auto_increment
ESTADO varchar(20) NO NULL
DNA_plate int(2) NO NULL
DNA_well varchar(3) NO NULL
accesion varchar(10) YES NULL
Marker / Allele combinations.
## -- Table MAL -- ##
Information about the Marker / Allele combination
(all reported Marker / Allele combinations are in this table)
unid: Numerical identifier (unique per row)
marcador: SSR marker.
id_estado: State identifier.
lim_inf: Lower limit of the lecture.
lim_sup: Upper limit of the lecture.
alelo: Allele number.
** - Technical description of columns - **
Field Type Null Key Default Extra
unid int(5) NO PRI NULL auto_increment
marcador varchar(20) NO MUL NULL
id_estado varchar(2) NO NULL
lim_inf float NO NULL
lim_sup float NO NULL
alelo int(2) NO MUL NULL
MAL.txt
accessions
## -- Table accession -- ##
Information about each one of the maize accessions reported.
id: Numerical identifier (unique per row)
acc_id: Identifier of accession.
acc_id_ori: Original accession identifier (external to our collection).
localidad: Locality (place) where the accession was collected.
tipo0: Type 0 (secondary type of maize, can correspond with maize race)
tipo: Primary type of maize accession as reported by collector.
tipo2: Type 2 (tertiary type of maize, reported by collector),
color0: Secondary kernel color (if reported by collector).
color: Primary kernel color (checked by our curators).
lat_gra: Latitude of collection; degrees.
lat_min: Latitude of collection; minutes.
lat_seg: Latitude of collection; seconds.
lon_gra: Longitude of collection; degrees.
lon_min: Longitude of collection; minutes.
lon_seg: Longitude of collection; seconds.
asnm: Height above sea level of collection; meters.
UTM_X: UTM X coordinate of collection.
UTM_Y: UTM Y coordinate of collection.
** - Technical description of columns - **
Field Type Null Key Default Extra
id int(3) NO NULL
acc_id varchar(5) NO MUL NULL
acc_id_ori varchar(20) YES NULL
localidad varchar(100) YES NULL
tipo0 varchar(50) YES MUL NULL
tipo varchar(50) YES NULL
tipo2 varchar(50) YES NULL
color0 varchar(50) YES MUL NULL
color varchar(50) YES NULL
lat_gra float YES NULL
lat_min float YES NULL
lat_seg float YES NULL
lon_gra float YES NULL
lon_min float YES NULL
lon_seg float YES NULL
asnm int(4) YES NULL
UTM_X float YES NULL
UTM_Y float YES NULL
accession.txt
bulks
## -- Table bulks -- ##
Information about `bulks' (mixtures) of DNA from individual samples.
row_id: Numerical identifier (unique per row)
updated: Date / Time of last update for the information.
bulk: Bulk identifier.
well_in_bulk: Well of plate where the sample is stored.
bulk_accesion: Identifier of accession / bulk.
indiv: Number of individual DNA sample.
indiv_well: Well of individual DNA sample.
indiv_mic_lit: Quantity stored.
** - Technical description of columns - **
Field Type Null Key Default Extra
row_id int(5) NO PRI NULL auto_increment
updated timestamp NO CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP
bulk varchar(5) YES NULL
well_in_bulk varchar(3) YES NULL
bulk_accesion varchar(7) YES NULL
indiv int(2) YES NULL
indiv_well varchar(3) YES NULL
indiv_mic_lit int(3) YES NULL
fingerprint (DNA profile for each bulk)
## -- Table fingerprint -- ##
Information about all marker types of each bulk within accession.
NOTE: Each one of the marker types is a numerical variable, with 0 if the sample
was negative for that marker type and 1 otherwise.
acc: Accession identifier.
batch: Bulk (batch) identifier.
: Combination marker / allele (contents 0 or 1; see above)
...
[There are 328 posible marker / allele columns]
** - Technical description of columns - **
Field Type Null Key Default Extra
acc varchar(5) NO MUL NULL
batch int(1) NO MUL NULL
PHI015_0 int(1) YES 0
PHI015_63 int(1) YES 0
...
[There are 328 marker / allele columns]
fingerprint.txt
fingerprint_acc (DNA profile per accession)
## -- Table fingerprint_acc -- ##
Information about about all marker types (fingerprint) in a given accession.
NOTE: Each one of the marker types is a numerical variable, with the number of bulks
(batches) that were positive for each particular marker type, thus the variables
can take values 0, 1, 2 or 3.
acc: Accession identifier.
PHI015_0: value for allele 0 of marker PHI015; can be 0, 1, 2 or 3.
In general:
: Combination marker / allele (contents 0 or 1; see above)
...
[There are 328 marker / allele columns]
** - Technical description of columns - **
Field Type Null Key Default Extra
acc varchar(5) NO MUL NULL
PHI015_0 int(1) YES 0
...
[There are 328 posible marker / allele columns]
fingerprint_acc.txt
lecturas (assignation of marker genotype per bulk)
## -- Table lecturas -- ##
Information about the readings for each batch (bulk)
lec_id: Numerical identifier (unique per row)
accesion: Full accession identifier = state_id acces_id
state_id: State identifier (two characters).
acces_id: Accession identifier within state (three digits)
id_group: Batch (bulk) identifier.
marker: SSR Marker.
alelo_bp: Allele identified.
reading_bp: Raw lecture.
** - Technical description of columns - **
Field Type Null Key Default Extra
lec_id int(5) NO PRI NULL auto_increment
accesion varchar(5) YES MUL NULL
state_id varchar(2) YES NULL
acces_id varchar(3) YES NULL
id_group int(1) YES MUL NULL
marker varchar(15) YES MUL NULL
alelo_bp float YES NULL
reading_bp float YES NULL
lecturas.txt
plates (where DNA samples are stored)
## -- Table plates -- ##
Information about plates where the DNA samples are stored.
plate_id: Numerical identifier (unique per row)
updated: Last time information was updated.
plate: Plate identifier.
** - Technical description of columns - **
Field Type Null Key Default Extra
plate_id int(5) NO PRI NULL auto_increment
updated timestamp NO CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP
plate varchar(100) YES NULL
plates.txt
rareness coefficients
## -- Table rareness -- ##
Information about the rareness coefficient (see text).
accesion: Unique accession identifier.
r_whole: Rareness coefficient taking the whole collection.
r_state: Rareness coefficient taking only the state collection.
r_maiz: Rareness coefficient taking the maize (but not teosinte) collection.
r_TE: Rareness coefficient taking only teosinte collection.
r_PL: Rareness coefficient taking only Puebla collection.
r_TB: Rareness coefficient taking only Tabasco collection.
r_TL: Rareness coefficient taking only Tlaxcala collection.
r_GT: Rareness coefficient taking only Guanajuato collection.
** - Technical description of columns - **
Field Type Null Key Default Extra
accesion varchar(5) YES MUL NULL
r_whole double YES NULL
r_state double YES NULL
r_maiz double YES NULL
r_TE double YES NULL
r_PL double YES NULL
r_TB double YES NULL
r_TL double YES NULL
r_GT double YES NULL
rareness.txt
wells (within plate where DNA samples are stored)
## -- Table wells -- ##
Information about the wells (within plate) where the DNA sample is stored.
well_id: Numerical identifier (unique per row)
updated: Last time the information was updated.
plate_id: Numerical identifier of plate.
plate: Identifier of plate.
well: Identifier of well (within plate).
** - Technical description of columns - **
Field Type Null Key Default Extra
well_id int(5) NO PRI NULL auto_increment
updated timestamp NO CURRENT_TIMESTAMP on update CURRENT_TIMESTAMP
plate_id int(5) YES NULL
plate varchar(100) YES NULL
well varchar(100) YES NULL
wells.txt