Title: Quantile-quantile (Q-Q) Plot of six fiber traits generated from GWAS analysis following mixed linear model (MLM) using GAPIT software. A) Fiber elongation (ELO), B) Micronaire (MIC), C) Short fiber content (SFC), D) Fiber strength (STR), E) Upper half mean fiber length (UHM), and F) Uniformity index (UI). Description of data: Q-Q plots of six fiber traits generated from GWAS analysis following MLM are included in this figure. The X and Y axis have the expected and observed negative logarithm 10 of p value, respectively generated during GWAS analysis. (DOCX 207Â kb

Christopher D. Delhom

David D. Fang

Dewayne D. Deng

Don C. Jones

Doug J. Hinchliffe

Gregory N. Thyssen

Jack C. McCarty

Johnie N. Jenkins

Linghe Zeng

Md Sariful Islam

BMC Genomics

Md Islam (257385)

Gregory Thyssen (531000)

Johnie Jenkins (3407099)

Linghe Zeng (3407102)

Christopher Delhom (3407096)

Jack McCarty (3407090)

Dewayne Deng (3407105)

Doug Hinchliffe (3407108)

Don Jones (3407093)

David Fang (3399707)

The Francis Crick Institute

Additional file 10: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: A heat map showing the relationships between RILs. Marker data were used to measure the relationships among 547 RILs of the MAGIC population. The red diagonal represents perfect relationship of each RIL and the symmetric off-diagonal elements represent relationship measured [in this case identity by descent (IBD)] for pairs of lines. No cluster of related lines was found as no block of diagonal warmer color appeared. The dendrogram on the right shows the results of a cluster analysis on the IBD matrix. Description of data: The relationship between the RILs of MAGIC population derived from JMPGenomics 6.0 is included in this figure. (DOCX 111Â kb

Additional file 3: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Springer - Publisher Connector

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: MAGIC population RILs pedigree and their corresponding family information. Description of data: Five hundred fifty RIL names, their pedigree and family information were included in this table. (XLSX 78Â kb

Additional file 2: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: Annotated genes within 71 M bp and 76 M bp region of chromosome A07 and their RNA-seq data. Description of data: This table contains gene name and associated annotation near the detected loci on chromosome A07. The RNA-seq data from our previous studies for the gene are also included in this table. First column have the gene name followed by physical location, Arabidopsis ortholog gene, gene description and RPKM value of RNA-seq data for the different RNA libraries. (XLSX 75 kb

Additional file 15: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: Linkage disequilibrium (LD) contour plot by chromosome generated from JMP genomics 6.0. Description of data: The LD contour plots for all the 26 Upland cotton chromosomes are included in this figure. The LD contour plot were generated from the square of correlation coefficients (r2) between markers located on each chromosome at different physical distances (bp) using JMP genomics 6.0 software. The X and Y axis have the physical distance of two markers. The square of correlation coefficients (r2) presents as color code (blue to red â 1.000 to 0.000). (DOCX 1734Â kb

Additional file 8: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: Alignment of Acala Ultima (AU) and TM-1 (Ref) alleles of Gh_A07G2049. Primer locations for CFBid0004 are highlighted yellow. Description of data: This file contains alignment of parental line AU (row number 1) and TM-1 (row number 2) alleles of gene Gh_A07G2049. The 18 bp deletion in the coding sequence in AU at 17,875 to 17,893 bp on gene has also been presented. The forward and reverse primer sequences for indel marker CFBid0004 has been highlighted as yellow at either side of the 18 bp deletion. (PDF 4439 kb

Additional file 18: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: SNP and SSR markers and their physical location on TM-1 draft genome. Description of data: This figure contains 6039 GBS based SNP and 223 SSR markers name, associated allele and physical location on allotetraploid cotton TM-1 draft genome. (XLSX 343Â kb

Additional file 6: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: RT-qPCR gene expression analyses of selected genes related to cell wall activity during fiber development between Acala Ultima (AU) and Tamcot Pyramid (TP). A) CONSTANS-like 9 (Gh_A07G1753); B) RAB GTPase homolog A5E (Gh_A07G1758); C) Unknown protein family, DUF538 (Gh_A07G1784); D) Auxin-responsive protein (Gh_A07G1795); E) Oxidoreductase, zinc-binding dehydrogenase family protein (Gh_A07G1803); F) O-Glycosyl hydrolases family protein (Gh_A07G1802). Description of data: This file contains the results of RT-qPCR analysis data performed on six genes that were used to compare relative expression levels between superior line AU and inferior line TP. Four (8, 14, 28 and 22 DPA) developing fiber samples were used for RT-qPCR analysis. RT-qPCR values were corrected to 18S gene for each sample. For each treatment group two qPCR measurements were taken for each of three biological replicates and then averaged. (DOCX 161Â kb

Additional file 16: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

Title: LD contour plot in the Upland cotton genomic region of 71 to 77 Mb on chromosome A07. LD contour was created from genotypic data of 547 RILs of Upland cotton MAGIC population using JMP genomics 6.0 software. X axis is physical distance in Mb and r2 (CorrCoeff2) between marker pair is shown in different color block as per legend. Description of data: LD contour plot of genomic region of 71 to 77 Mb on chromosome A07 is included in this figure. Red color represents the higher r2 value between two markers due to LD block. The square of correlation coefficients (r2) presents as color code (red to blue – 1.000 to 0.000). (DOCX 69 kb

Additional file 14: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

https://figshare.com/articles/Additional_file_12_of_A_MAGIC_population-based_genome-wide_association_study_reveals_functional_association_of_GhRBB1_A07_gene_with_superior_fiber_quality_in_cotton/4322912

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

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Springer - Publisher Connector

The Francis Crick Institute

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