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Series GSE89126 Query DataSets for GSE89126
Status Public on Mar 30, 2017
Title Mutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max
Organism Glycine max
Experiment type Expression profiling by high throughput sequencing
Summary The soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation and the recessive k1 mutation can epistatically overcome the dominant I and i-i alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the i-i and i-k alleles of the I locus, which restrict pigment to the hilum or saddle region of the seed coat, respectively. To identify the K1 locus, we compared RNA-Seq data from dissected regions of two Clark isolines having similar saddle phenotypes mediated by CHS siRNAs but different genotypes (homozygous i-k K1 versus homozygous i-i k1). By examining differentially expressed genes, mapping information, and genome resequencing, we identified a 129-bp deletion in Glyma.11G190900 encoding Argonaute5 (AGO5), a member of the Argonaute family. Amplicon sequencing of several independent saddle pattern mutants from different genetic backgrounds revealed independent lesions affecting AGO5, thus establishing Glyma.11G190900 as the K1 locus. Non-functional AGO5 from k1 alleles leads to altered distributions of CHS siRNAs, thus explaining how the k1 mutation reverses the phenotype of the seed coat regions from yellow to pigmented, even in the presence of the normally dominant I or i-i alleles.
Overall design Immature seed coats of 100-200 mg with chimeric pigmented phenotypes of Clark 8 (i-k, K1) or Clark 18a (i-i, k1) were separated into the regions destined to become either the black saddle region or the yellow sections. Extracted mRNAs were subjected to high throughput sequencing and analyzed for expression analyses to determine the genetic differences conferred by the K1 locus or the differences in expression in different dissected regions of the seed coat.
Contributor(s) Cho YB, Vodkin LO
Citation(s) 28351993
Submission date Oct 24, 2016
Last update date May 15, 2019
Contact name Lila O. Vodkin
Phone 217-244-6147
Organization name University of Illinois
Department Crop Sciences
Lab Lila Vodkin
Street address 1201 W. Gregory Dr.
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
Platforms (1)
GPL15008 Illumina HiSeq 2000 (Glycine max)
Samples (12)
GSM2359176 Clark8_K1_blacksaddle_BR1
GSM2359177 Clark8_K1_yellowsectors_BR1
GSM2359178 Clark8_K1_blacksaddle_BR2
BioProject PRJNA350330
SRA SRP092002

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
GSE89126_RPKMs_for_12_RNA-Seq_libraries_of_K1_versus_k1_seed_coats.txt.gz 5.8 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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