README.collection.yml

---
# identifier: required - name of the directory holding the collection - NOT quoted since any LIS identifier need not be quoted
identifier: Sanzi_x_Vita7.gen.Pottorff_Ehlers_2012

# provenance: information on the source of the data
provenance: Close Lab, UC-Riverside

# source: URL pointing to the data source
source: "http://viggs.dna.affrc.go.jp/"

# synopsis: required - short description of the collection
synopsis: "A segregating population of 122 RILs, advanced from Sanzi x Vita 7, reveals a QTL, a candidate gene, and a SNP marker for hastate leaf shape."

# related_to: (comma-separated) identifier(s) of related collection(s) in the LIS datastore
related_to: Sanzi.gnm1.YNCM,Sanzi.gnm1.ann1.HFH8

# scientific name: Genus species
scientific_name: Vigna unguiculata

# taxid: NCBI taxonomy id
taxid: 3917

# scientific_name_abbrev: LIS datastore gensp abbreviation: lower case first three letters of genus plus first two letters of species
scientific_name_abbrev: vigun

# genotype: list of genotypes, one for a single genotype, A x B for a biparental map, or a longer list of genotypes used
genotype:
  - Sanzi x Vita 7

# description: required - long description of this collection
description: "In this study, we analyzed the genetics of leaf morphology in a segregating cowpea RIL population, Sanzi (sub-globose) x Vita 7 (hastate). A QTL was identified for the “hastate leaf shape” locus, Hls, which was positioned on the cowpea consensus genetic map and cowpea physical map. A candidate gene was identified using syntenic relationships between cowpea, soybean and Medicago. In addition, a SNP marker was found which co-segregated with the leaf morphology genotypes and phenotype, which could be used as a molecular marker for breeding purposes."

# chromosome_prefix: required for genome collections - comma-separated prefix(es) identifying chromosome entries in genome_main.fasta
chromosome_prefix: Chr

# supercontig_prefix: required for genome collections - comma-separated prefix(es) identifying scaffolds/contigs/supercontigs
supercontig_prefix: Scaffold

# bioproject: NCBI BioProject accession
bioproject: PRJNA243847

# sraproject: the NCBI SRA project accession
sraproject: SRP046307

# dataset_doi: DOI pointing to the dataset (e.g. an SRA URL)
dataset_doi: 10.1111/tpj.13404

# genbank_accession: NCBI Genbank accesssion ID
genbank_accession: GCA_000741045.2

# original_file_creation_date: date when the data were created at the source (YYYY-MM-DD)
original_file_creation_date: "2014-11-21"

# local_file_creation_date: date when the data were placed on the LIS datastore (YYYY-MM-DD)
local_file_creation_date: "2018-08-01"

# dataset_release_date: the date when this collection was released to the public (YYYY-MM-DD)
dataset_release_date: "2018-08-03"

# publication_doi: required - DOI pointing to the publication associated with this collection
publication_doi: 10.1186/1471-2164-13-234

# publication_title: title of the publication associated with this collection
publication_title: "Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species"

# contributors: semicolon-separated list of contributors in last, first format, typically the publication authors
contributors: "Pottorff, Marti; Ehlers, Jeffrey D; Fatokun, Christian; Roberts, Philip A; Close, Timothy J"

# citations: single long-form bibliographical citation of the publication
citation: "Pottorff, M., Ehlers, J. D., Fatokun, C., Roberts, P. A. & Close, T. J. Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species. BMC Genomics 13, 234 (2012)"

# data_curators: comma-separated list of curators that put this collection together
data_curators: Pooja Umale, Steven Cannon, Wei Huang, Andrew Farmer

# public_access_level: describes level of public access
public_access_level: public

# license: data usage license
license: Open

# keywords: comma-separated list of keywords associated with this collection
keywords: cowpea,leaf morphology

#########################################
## collection type-specific attributes ##
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# genotyping_platform: platform used in a genotyping experiment
genotyping_platform: Cowpea1MSelectedSNPs

# genotyping_method: description of the genotyping method used in a genotyping experiment
genotyping_method: "The Sanzi x Vita 7 population was genotyped at the F8 generation using bi-allelic SNP markers from the 1536-marker Illumina GoldenGate Assay."

# expression_unit: the data unit used in an RNA-seq expression experiment
expression_unit: TPM

# geoseries: the NCBI Geoseries accession
geoseries: GSE42679