A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism

Abstract

Background The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure to increase sugar accumulation in certain varieties of the cereal crop Sorghum bicolor is an excellent example of the latter; this has resulted in pronounced phenotypic divergence between sweet and grain-type sorghums, but the genetic mechanisms underlying these differences remain poorly understood. Results Here we present a new reference genome based on an archetypal sweet sorghum line and compare it to the current grain sorghum reference, revealing a high rate of nonsynonymous and potential loss of function mutations, but few changes in gene content or overall genome structure. We also use comparative transcriptomics to highlight changes in gene expression correlated with high stalk sugar content and show that changes in the activity and possibly localization of transporters, along with the timing of sugar metabolism play a critical role in the sweet phenotype. Conclusions The high level of genomic similarity between sweet and grain sorghum reflects their historical relatedness, rather than their current phenotypic differences, but we find key changes in signaling molecules and transcriptional regulators that represent new candidates for understanding and improving sugar metabolism in this important crop. Electronic supplementary material The online version of this article (10.1186/s12864-019-5734-x) contains supplementary material, which is available to authorized users.

Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

“…Grain sorghums usually contain less carbohydrate in the upper internodes at grain maturity compared with sweet sorghum varieties, due to mobilization of carbon from stems during grain filling. The divergence of stem related genes between the two types has previously been suggested from genetic variation analysis (Jiang et al , 2013; Cooper et al , 2019), and the present study suggests genomic divergence in stem-expressed genes based on their developmental transcriptomes and regulatory programs.…”

“…The analysis of temporal stem GRNs between grain and sweet sorghum varieties revealed striking differences in the regulatory landscape, which is not entirely surprising given the considerable phenotypic differences between grain and sweet sorghums. The sorghum BTx623 cultivar is an early maturing grain sorghum genotype with short stature, which is phenotypically distinct from the tall, late-maturing Della cultivar (sweet sorghum genotype), typically grown for stem sugars or high biomass yield (Jiang et al , 2013; Cooper et al , 2019). BTx623 encodes recessive alleles of the dwarfing gene Dw1 (Hilley et al , 2016) that encodes a protein involved in brassinosteroid signaling (Hirano et al , 2017) and Dw3 , a gene that encodes an ABCB1 auxin efflux transporter (Multani et al , 2003; Knöller et al , 2010), whereas Della is dominant for both dwarfing loci.…”

“…The difference in dwarfing genotype results in differences in internode lengths and the ratio of node/internode tissues in BTx623 and Della. Grain sorghums develop treachery elements during xylem formation earlier than sweet sorghums, and sweet sorghums accumulate more stem sugars compared to grain sorghum (Jiang et al , 2013; Cooper et al , 2019). Grain sorghums usually contain less carbohydrate in the upper internodes at grain maturity compared with sweet sorghum varieties, due to mobilization of carbon from stems during grain filling.…”

Comparative Analysis of In Vitro Responses and Regeneration between Diverse Bioenergy Sorghum Genotypes

“…Recent advances in genome editing offer significant potential for selective gene modification. The availability of sorghum whole genome sequences [9,23,24] means that breeders can begin to integrate these modifications into sorghum trait improvement programs, generating rapidly deployed enhancements in areas such as flowering time and plant height [22], as well as protein quality and digestibility [25]. However, genome editing still requires the initial transformation of the editing constructs into the genotype of interest, and the in vitro regeneration of these transformed cells into edited plants.…”

Profiling Alternative 3′ Untranslated Regions in Sorghum using RNA-seq Data

“…Grain sorghum ranks 5th in global cereal production (Boyles et al, 2019); grain sorghum and forage sorghum serve as significant sources for animal feed; sweet sorghum and energy sorghum are promising bioenergy crops for sugar-and lignocellulosic-based biofuels (Mullet et al, 2014;Mathur et al, 2017;Li et al, 2018;Yang et al, 2020). Sorghum has a relatively small diploid genome with several reference assemblies (Paterson et al, 2009;Deschamps et al, 2018;McCormick et al, 2018;Cooper et al, 2019).…”