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Series GSE268725 Query DataSets for GSE268725
Status Public on Jun 04, 2024
Title A systems genomics and genetics approach to identify the genetic regulatory network for lignin content in Brassica napus seeds
Organism Brassica napus
Experiment type Expression profiling by array
Summary Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eighty-three subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality.
 
Overall design cRNAs were amplified from total RNA samples (2 µg) and labeled with either cy3 or cy5 using the Quick Amp labeling kit, Two Color (Agilent, Catalogue: 5190-0444) according to the manufacturer’s instructions, followed by purification with the Qiagen RNeasy Mini Kit (Qiagen, Catalogue 74104) and quantification with a NanoDrop ND-1000. Purified cRNAs (2 µg) were fragmented and hybridized to the Agilent 4x44K Brassica arrays (Parkin et al., 2010) for 17 h at 65°C with a rotation of 10 rpm according to the manufacturer’s protocol. Arrays were washed with the Agilent Gene Expression Washing buffers according to the manufacturer’s protocol and scanned with GenePix 4000B as described by Parkin et al. (2010). Four and two biological replications were performed for the parental lines and the SG lines, respectively, with dye-swaps applied to the biological replicates to minimize dye effects from the two colour systems (Lee et al., 2004).
 
Contributor(s) Zhang W, Higgins E, Robinson S, Wayne C, Boyle K, Sharpe AG, Fobert PR, Parkin IP
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date May 30, 2024
Last update date Jun 04, 2024
Contact name wentao zhang
E-mail(s) wentao.zhang@nrc-cnrc.gc.ca
Organization name NRC-Canada
Street address 110 Gymnasium Pl
City Saskatoom
State/province SK
ZIP/Postal code S7N 0W9
Country Canada
 
Platforms (1)
GPL15739 Agilent-022520 Brassica napus 4x44K (Probe Name version)
Samples (200)
GSM8297569 DH-Rep1
GSM8297570 DH-Rep2
GSM8297571 PSA-Rep1
Relations
BioProject PRJNA1118325

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE268725_DH-cy3_vs_PSA-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_DH-cy3_vs_PSA-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_PSA-cy3_vs_DH-cy5_3_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_PSA-cy3_vs_DH-cy5_4_.gpr.gz 4.9 Mb (ftp)(http) GPR
GSE268725_SG-10-cy3_vs_SG-201-cy5_1_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-100-_cy3_vs_SG-22-_cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-103-cy3_vs_SG-276-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-107-cy3_vs_SG-306-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-108-cy3_vs_SG-278-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-115-cy3_vs_SG-75-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-118-cy3_vs_SG-159-cy5_1_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-120-cy3_vs_SG-204_cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-121-cy3_vs_SG-303-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-122-cy3_vs_SG-285-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-130-cy3_vs_SG-25_cy5_1_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-132-cy3_vs_SG-178-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-135-cy3_vs_SG-146-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-137-cy3_vs_SG-54-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-146-cy3_vs_SG-135-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-150-cy3_vs_SG-208-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-159-cy3_vs_SG-118-cy5_2_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-163-cy3_vs_SG-242-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-165-cy3_vs_SG-175-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-166-cy3_vs_SG-262-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-168-cy3_vs_SG-221-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-171-cy3_vs_SG-206-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-172-cy3_vs_SG-29-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-175-cy3_vs_SG-165-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-178-cy3_vs_SG-132-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-18-cy3_VS_SZG-232-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-19-cy3_vs_SG-214-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-201-cy3_vs_SG-10-cy5_2_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-204-cy3_vs_SG-120-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-206-cy3_vs_SG-171-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-208-cy3_vs_SG-150-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-209-cy3_vs_SG-80-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-214-cy3_vs_SG-19-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-216-cy3_vs_SG-243-cy5_1_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-22-cy3_vs_SG-100-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-221-cy3_vs_SG-168-cy5_1_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-224-cy3_vs_SG-229-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-229-cy3_vs_SG-224-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-230-cy3_vs_SG-295_cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-231-cy3_vs_SG-330-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-232-cy3_vs_SG-18-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-233-cy3_vs_SG-90_cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-24-cy3_vs_SG-225-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-240-cy3_vs_SG-30-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-241-cy3_vs_SG-258-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-242-cy3_vs_SG-163-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-243-cy3_vs_SG-216-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-246-cy3_vs_SG-265-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-247-cy3_vs_SG-269-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-249-cy3_vs_SG-281-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-25-cy3_vs_SG-130-cy5_2_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-253-cy3_vs_SG-273-cy5_2_.gpr.gz 5.3 Mb (ftp)(http) GPR
GSE268725_SG-254-cy3_vs_SG-318-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-258-cy3_vs_SG-241-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-259-cy3_vs_SG-321-cy5_1_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-261_cy3_vs_SG-324_cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-262-cy3_vs_SG-166-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-265-cy3_vs_SG-246-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-266-cy3_vs_SG-270-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-267-cy3_vs_SG-294-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-269-cy3_vs_SG-247-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-270-cy3_vs_SG-266-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-271-cy3_vs_SG-284_cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-273-cy3_vs_SG-253-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-276-cy3_vs_sg-103-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-278-cy3_vs_SG-108-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-281-cy3_vs_SG-249-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-284-cy3_vs_SG-271_cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-285-cy3_vs_SG-122-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-29-cy3_vs_SG-172-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-294-cy3_vs_SG-267-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-295-cy3_vs_SG-230-cy5_3_.gpr.gz 5.0 Mb (ftp)(http) GPR
GSE268725_SG-30-cy3_vs_SG-240-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-300-cy3_vs_SG-64-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-303-cy3_vs_SG-121-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-306-cy3_vs_SG-107-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-309-cy3_vs_SG-85-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-317-cy3_vs_SG-9-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-318-cy3_vs_SG-254-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-321-cy3_vs_SG-259-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-324-cy3_vs_SG-261-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-33-cy3_vs_SG-65_cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-330-cy3_vs_SG-231-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-333-cy3_vs_SG-67-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-351-_cy3_vs_SG-5-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-5-cy3_vs_SG-351-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-54-cy3_vs_SG-137-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-64-cy3_vs_SG-300-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-65_cy3_vs_SG-33_cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-67-cy3_vs_SG-333-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-75-cy3_vs_SG-115-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-80-cy3_vs_SG-209_cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_SG-85-cy3_vs_SG-309-cy5_1_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-9-cy3_vs_SG-317-cy5_2_.gpr.gz 5.1 Mb (ftp)(http) GPR
GSE268725_SG-90-cy3_vs_Sg-233-cy5_2_.gpr.gz 5.2 Mb (ftp)(http) GPR
GSE268725_Sg-225-cy3_vs_SG-24-cy5_1_.gpr.gz 5.2 Mb (ftp)(http) GPR

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