Fig. 1: Natural variations in GC1 are highly associated with glume coverage in sorghum.
From: Natural variation in Glume Coverage 1 causes naked grains in sorghum
a Five defined glume coverage degrees in diverse sorghum accessions. The corresponding thin line near each spikelet means quantitative glume length. Bar = 2 mm. VHGC very high glume coverage, HGC high glume coverage, MGC moderate glume coverage, LGC low glume coverage, VLGC very low glume coverage. b Manhattan plot from GWAS analysis of glume coverage in the natural SAP sorghum population. The gray horizontal line indicates the Bonferroni-adjusted significance threshold (P = 1E−06). c Map-based cloning of GC1 locus through the 1678 offspring plants of RHLs (see “Methods” section). The violin plot represents threshing rate. The dotted line in the middle is the median. The thin rectangles mean genomic region. The thick arrows depict five annotated genes. The red color represents the candidate gene. Relative expression of the five annotated genes at S1 (primordia), S2 (young panicle), and S3 (mature panicle) stages in two parental lines. Data are mean ± s.e.m. n = 3 biological replicates. Association analysis between the genetic variations and glume coverage in 58 sorghum inbred lines. The red dot shows the leading association signal on the fifth exon of the third candidate gene. d Nucleotide polymorphisms within the GC1 coding region of 482 sorghum accessions. Four detected malfunctional variations (highlight in red) in the fifth exon of GC1: a “GTGGC” insertion (gc1-a), a “G” deletion (gc1-b), a “C-A” substitution (gc1-c) and a 165 bp fragment insertion (gc1-d). Hap. haplotype. e GC1-based association mapping between the seven variations and four spikelet related traits in 188 sorghum accessions. LD analysis between the seven causal sites in the coding region indicates the linkage association signals. P-values were determined by two-tailed unpaired t-test. The three leading variant sites (+4151, +4158, and +4285) show highly association signals with strong LD which are highlighted by black lines. Source data are provided as a Source Data file.
