Cottongen

GWAS data on fiber quality and yield traits at AD1-NBI added (3/25)

New GWAS data on fiber quality and yield traits at G.hirsutum AD1-NBI genome data published by CRI-CAAS are available (Ref. Liu, et al.)

The data can be accessed via CottonGen's Search QTL/GWAS and this video shows you How to GWAS Search and Viewing in MapViewer

The data is downloadable at CottonGen's 'Data Download' (https://www.cottongen.org/data/download), too.

Human-Readable Name	-- G. hirsutum (AD1) 'TM-1' T2T JZU v1.0 proteins (79,642)
Database Path	/mainlab/web/temp/db/cottongen/AD1_TM1_T2T_ZJU_v1.protein.blast.fasta
Database Type	protein
FASTA Header Format	default
External Database	CottonGen Database
RegEx	/^(\S+).*/
Link-out Type	link

Human-Readable Name	-- G. hirsutum (AD1) 'TM-1' T2T JZU v1.0 CDs (79,642)
Database Path	/mainlab/web/temp/db/cottongen/AD1_TM1_T2T_ZJU_v1.CDS.blast.fasta
Database Type	nucleotide
FASTA Header Format	default
External Database	CottonGen Database
RegEx	/^(\S+).*/
Link-out Type	link

Human-Readable Name	G. hirsutum (AD1) 'TM-1' T2T JZU v1.0 Genome (26 chrom. 88 scaffolds)
Database Path	/mainlab/web/temp/db/cottongen/AD1_TM1_T2T_ZJU_v1.genomic.blast.fa
Database Type	nucleotide
FASTA Header Format	default
External Database	JBrowse for AD1_TM1_T2T_ZJU_v1
RegEx	/^(\S+).*/
Link-out Type	jbrowse

GWAS and QTL of 117 Indian cotton germplasm for six yield-related traits available (Joshi B, et al. 2023}

Human-Readable Name	-- G. barbadense (AD2) '3-79' HAU v3.0 proteins (136,847)
Database Path	/mainlab/web/temp/db/cottongen/AD2_3-79_HAU_v3.0.protein.blast.fasta
Database Type	protein
FASTA Header Format	default
External Database	CottonGen Database
RegEx	/^(\S+).*/
Link-out Type	link

Human-Readable Name	-- G. barbadense (AD2) '3-79' HAU v3.0 CDs (136,847)
Database Path	/mainlab/web/temp/db/cottongen/AD2_3-79_HAU_v3.0.CDS.blast.fasta
Database Type	nucleotide
FASTA Header Format	default
External Database	CottonGen Database
RegEx	/^(\S+).*/
Link-out Type	link

Human-Readable Name	G. barbadense (AD2) '3-79' HAU v3.0 Genome (26 chrom. 1,662 scaffolds)
Database Path	/mainlab/web/temp/db/cottongen/AD2_3-79_HAU_v3.0.genomic.blast.fa
Database Type	nucleotide
FASTA Header Format	default
External Database	JBrowse for AD2_379_HAU_v3
RegEx	/^(\S+).*/
Link-out Type	jbrowse