Data from: An SSR based approach incorporating a novel algorithm for identification of rare maize genotypes facilitates criteria for landrace conservation in Mexico

Hayano-Kanashiro C, Martìnez de la Vega O, Reyes-Valdés MH, Pons-Hernández J, Hernández-Godinez F, Alfaro-Laguna E, Herrera-Ayala JL, Vega-Sánchez MC, Carrera-Valtierra JA, Simpson J

Date Published: February 14, 2017

DOI: http://dx.doi.org/10.5061/dryad.c9086

 

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Title GenoMaiz Database
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Title DNA_plates
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Description 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
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Title Marker / Allele combinations.
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Description ## -- 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
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Title accessions
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Description ## -- 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
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Title bulks
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Description ## -- 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
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Title fingerprint (DNA profile for each bulk)
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Description ## -- 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. <Marker_allele> : 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]
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Title fingerprint_acc (DNA profile per accession)
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Description ## -- 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: <Marker_allele> : 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]
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Title lecturas (assignation of marker genotype per bulk)
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Description ## -- 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
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Title plates (where DNA samples are stored)
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Description ## -- 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
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Title rareness coefficients
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Description ## -- 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
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Title wells (within plate where DNA samples are stored)
Downloaded 11 times
Description ## -- 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
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When using this data, please cite the original publication:

Hayano-Kanashiro C, Martínez de la Vega O, Reyes-Valdés MH, Pons-Hernández J, Hernández-Godinez F, Alfaro-Laguna E, Herrera-Ayala JL, Vega-Sánchez MC, Carrera-Valtierra JA, Simpson J (2017) An SSR-based approach incorporating a novel algorithm for identification of rare maize genotypes facilitates criteria for landrace conservation in Mexico. Ecology and Evolution 7(6): 1680-1690. http://dx.doi.org/10.1002/ece3.2754

Additionally, please cite the Dryad data package:

Hayano-Kanashiro C, Martìnez de la Vega O, Reyes-Valdés MH, Pons-Hernández J, Hernández-Godinez F, Alfaro-Laguna E, Herrera-Ayala JL, Vega-Sánchez MC, Carrera-Valtierra JA, Simpson J (2017) Data from: An SSR based approach incorporating a novel algorithm for identification of rare maize genotypes facilitates criteria for landrace conservation in Mexico. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.c9086
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