DOI: 10.5061/dryad.c9086
title: Data from: An SSR based approach incorporating a novel algorithm for identification of rare maize genotypes facilitates criteria for landrace conservation in Mexico

description: 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.
description: GenoMaiz
 DatabaseGenoMaiz27-12-2016.sqlDNA_platesInformation 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 NULLMarker / 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 NULLMAL.txtaccessions## -- 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 NULLaccession.txtbulks## -- 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 NULLfingerprint (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.txtfingerprint_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.txtlecturas (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 NULLlecturas.txtplates (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 NULLplates.txtrareness 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 NULLrareness.txtwells (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 NULLwells.txt