Abstract
BackgroundThe 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.ResultsHere 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.ConclusionsThe 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.
Highlights
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
Present-day sorghum genotypes continue to form genetic clusters according to their race and historical geography [3,4,5,6], these clusters do not reflect the extent of diversity among modern sorghums, which include morphologically distinct types optimized for different end uses [1], even among closely related individuals of the same race
There were 54 genes that appeared to be unique to Rio, which is slightly lower similar to previous observations based on short read sequencing [10]
Summary
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. Sorghum bicolor (L.) Moench is a widely grown cereal crop that has been adapted to a range of habitats and bred for diverse purposes, resulting in drastic phenotypic differences among certain types. Both genetic and phenotypic diversity in sorghum have been driven by its spread throughout the African continent as well as the Middle East, India, and parts of Asia [1], which has resulted in distinct botanical races largely defined by their floral architecture and seed characteristics [2, 3]. The current reference genome for sorghum is the inbred ‘BTx623,’ a short-stature, early maturing genotype used primarily for production of grain sorghum hybrids This genotype is phenotypically very distinct from the tall, late maturing sorghums typically grown for stem sugars or high biomass yield [1]. While previous studies have found that changes in transport activity, rather than in sugar synthesis, appear to drive differences in sugar accumulation; the genetic mechanisms underlying these changes have remained elusive using currently available resources [7, 8]
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