Genetic variation and expression diversity between grain and sweet sorghum lines

Abstract

BackgroundBiological scientists have long sought after understanding how genes and their structural/functional changes contribute to morphological diversity. Though both grain (BT×623) and sweet (Keller) sorghum lines originated from the same species Sorghum bicolor L., they exhibit obvious phenotypic variations. However, the genome re-sequencing data revealed that they exhibited limited functional diversity in their encoding genes in a genome-wide level. The result raises the question how the obvious morphological variations between grain and sweet sorghum occurred in a relatively short evolutionary or domesticated period.ResultsWe implemented an integrative approach by using computational and experimental analyses to provide a detail insight into phenotypic, genetic variation and expression diversity between BT×623 and Keller lines. We have investigated genome-wide expression divergence between BT×623 and Keller under normal and sucrose treatment. Through the data analysis, we detected more than 3,000 differentially expressed genes between these two varieties. Such expression divergence was partially contributed by differential cis-regulatory elements or DNA methylation, which was genetically determined by functionally divergent genes between these two varieties. Both tandem and segmental duplication played important roles in the genome evolution and expression divergence.ConclusionSubstantial differences in gene expression patterns between these two varieties have been observed. Such an expression divergence is genetically determined by the divergence in genome level.

A Sorghum bicolorexpression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums

“…Differential expression between sweet and grain sorghum has recently been shown [21,40], and our results further validate this observation, with the majority of sugar-related genes showing differential expression among tissues and genotypes. For example, sweet and high biomass varieties showed consistently higher expression of SPS2 and SPS5, sugar phosphate enzymes thought to play significant roles in sucrose biosynthesis, compared to grain varieties (Figure 7).…”

DNA Markers in Diversity Analysis

“…Similar SNP variations across 8 accessions have been reported through short-read genome sequencing of 8 diverse accessions of sorghum (Nelson et al 2011). Recently, Jiang et al (2013) adapted an integrative approach by using computational and experimental analyses to study the expression diversity between grain and sweet sorghum lines. It was observed that the genome sequences of grain and sweet sorghum exhibited considerable differences, but only limited divergence was observed in their functional genes, though more than 3,000 differentially expressed genes were detected between the grain and sweet sorghum varieties.…”

Sorghum Molecular Breeding

“…A total of 13 groups of variable size was recorded Billot et al (2013) number of alleles (29.7 %). Recently, Jiang et al (2013) adapted an integrative approach by using computational and experimental analyses to study the expression diversity between grain and sweet sorghum lines. African genotypes contributed 88.6 % of alleles, whereas those from the remaining parts of the world contributed 85.0 % of alleles.…”

“…SNPs may be present within coding or non-coding sequences of genes or in the intergenic regions between genes at different frequencies in different chromosome regions (Jiang 2013). SNP is the ultimate marker representing a single nucleotide difference between two individuals.…”