Structural Variation and the Rapid Diversification of Sorghum

Sorghum is the 5th most important cereal crop in the world, and present day varieties have been adapted for very diverse purposes as well as environmental locations, resulting in some strikingly distinct phenotypes. Typically, studies looking at the genetic basis of these traits have relied soley on Single Nucleotide Polymorphism (SNP) data, but the increased availability of long-read sequencing data for many plant species has made it clear that SNPs present an incomplete picture of genome variation. Structural Variations (SVs) can often have a larger impact on fitness and adaptive potential, making them an important evolutionary substrate and potentially novel targets for crop improvement. To better understand the landscape and role of SVs in sorghum, we are looking at:

  • The construction and utilization of sorghum pangenomes and their associated pantranscriptomes,
  • How structural variations affect gene expression differences,
  • Gene families with high levels of presence/absence variation in different sorghum varieties.

Downstrean Effects of Mutations in Sorghum-Specific Iron Transporters

In one potential example of a structural variant playing a key role in recent sorghum evolution, we found that a duplicated copy of a putative iron transporter unique to this species was highly correlated with differences in compositional traits, including stalk sugar production. You can read more about this study and our discovery of this gene in our 2021 G3 paper here. We are currently interested in questions related to how this new gene copy functions and how mutations impact downstream expression and phenotypes:

  • How do iron limiting or iron excess conditions affect the expression of different alleles of this gene, and how do early development changes in iron conditions impact mature phenotypes?
  • How are changes in expression in the iron-related pathways related to later changes in sugar production and sugar transport pathways?
  • What are the key regulators of these pathways that may represent the best targets for crop improvement?

Evolutionary Origins of Domesticated Sorghum

Many crop species have been suspected of having been domesticated more than once, but distinguishing between multiple origins versus a single origin followed by local adaptation and introgression is often difficult. We are using genome-wide SNP data and demographic modeling approaches to test the hypothesis of a second domestication even in western Africa, in order to better understand the origins of sorghum and the history of agriculture:

  • Scenario 1: Sorghum is domesticated once in central Africa (near present day Sudan), and then domesticated varieties are spread by humans to western Africa. After its introduction to west Africa, some domesticated sorghum varieties are backcrossed to local wild sorghum plants, making them genetically distinct and highly adapted to the region.
  • Scenario 2: Sorghum is domesticated twice, once in central Africa, but then again separately in western Africa. Because west African sorghums were derived from local wild sorghums, they have remained genetically distinct over the years.

Natural Diversity in Wild Sorghums Native to Africa

When species undergo domestication, there is typically a dramatic loss of genetic diversity and an increase in the accumulation of deleterious mutations. Sorghum is likely no exception to this, but presently we have limited knowledge of what genetic diversity looks like in the wild sorghum species that gave rise to the domesticated varieties we have now. We recently sequenced 15 wild sorghums that were collected near what is believed to be the origin of domestication in central Africa, and are exploring the following questions:

  • How genetically diverse is wild sorghum compared to domesticated sorghum, and are there putatively beneficial mutations that were lost in the domestication process?
  • What is the landscape of structural genomic variation, and what are the possible fitness consequences of these variants in both wild and domesticated sorghum?
  • How much of the present day variation in domesticated sorghum can be attributed to standing variation that already existed in the ancestral wild varieties?

Assembly and Annotation of the Wyeomyia smithii Genome

Wyeomyia smithii, commonly known as the Pitcher Plant Mosquito, is a unique species of mosquito that had adapted to complete its entire larval phase inside of the carnivorous purple pitcher plant. We are currently collaborating with researchers from the University of Oregon and Georgetown University to complete the first reference genome for the species in order to:

  • Identify changes in gene content or structure that might be responsible for Wyeomyia's unique adaptations
  • Find signals of positive selection that were important for the evolution of this species