Major impacts of widespread structural variation on sorghum

SV contributes substantially to heritability. (A) Heritability estimates are improved by the addition of SVs. Narrow-sense heritability was estimated for 29 quantitative traits and one binary trait. The upper diagonal colored by melon is the area in which the heritability of SNP + SV is greater than the heritability of SNP only (h²_{SNP + SV} > h²_SNP). The lower diagonal colored by spring green is the area in which the heritability of SNP + SV is less than the heritability of SNP only (h²_{SNP + SV} < h²_SNP). The diagonal line illustrates where heritability estimates with and without SVs are the same (h²_{SNP + SV} = h²_SNP). Thirty traits were dotted by different colors in the plot. The embedded upper triangular dot plot shows the magnification of the shaded area. All of traits, except for 2015_ADF, were observed in the upper h²_{SNP + SV} > h²_SNP area, which indicates the predicted total heritability increase for most traits when taking both SNP and SVs into account compared with taking SNPs only into consideration. This was particularly marked for two traits: photoperiod sensitivity (pointed by blue arrow) and sorghum variety type (pointed by red arrow). (B) A bar plot for estimation of heritability contribution from SNP, copy number variations (CNVs), and REA-type variation. Narrow-sense heritability was estimated for 29 quantitative traits and one binary trait (Supplemental Table S7): (2014_ADF) acid detergent fiber content in 2014; (2014_Days_to_harvest) days to harvest in 2014; (2014_Dry_Weight) dry weight of biomass in 2014; (2014_Lignin) lignin content in 2014; (2014_NDF) neutral detergent fiber in 2014; (2014_NFC) nonfibrous carbohydrates content in 2014; (2014_WSC) water-soluble carbohydrates content in 2014; (2015_ADF) acid detergent fiber content in 2015; (2015_Days_to_harvest) days to harvest in 2015; (2015_Dry_Weight) dry weight of biomass in 2015; (2015_Lignin) lignin content in 2015; (2015_NDF) neutral detergent fiber in 2015; (2015_NFC) nonfibrous carbohydrates content in 2015; (2015_WSC) water-soluble carbohydrates content in 2015; (ADF) average acid detergent fiber content of 2014 and 2015; (Anthesis_date) date of anthesis; (Brix_maturity) brix content in maturity stage; (Brix_milk) brix content in milk stage; (Days_to_harvest) average days to harvest of 2014 and 2015; (Dry_tons_per_acre) dry tons per acre; (Dry_Weight) dry weight of biomass; (Lignin) lignin content; (NDF) average neutral detergent fiber content of 2014 and 2015; (NFC) average nonfibrous carbohydrates content of 2014 and 2015; (Pericarp_pigmentation) pericarp pigmentation; (Photoperiod_sensitivity) photoperiod sensitivity; (Sorghum_type) sorghum variety type (sweet, grain, and cellulosic); (Stalk_height) stalk height; (Total_fresh_weight) total fresh weight; and (WSC) average water-soluble carbohydrates content of 2014 and 2015. Blue bars, orange bars, and gray bars with green frame indicate the heritability contributions from SNPs, CNV-type variations, and REA-type variations, respectively. For most of the traits, CNV-type variations explained more variance than REA-type variations.