Project List: Published research projects with GitHub repositories:
Genomic Patterns of Structural Variation in Sorghum
In this study, we identified genome-wide Structural Variations (SVs) in a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. We show that most SVs appear to be evolving neutrally, but a handful of population-specific SVs are found in genes related to biotic and abiotic stress responses, supporting the possibility that they may contribute to local adaptation.
View on GitHub G3 Paper
Sweet Sorghum Reference Genome
We generated a new high-quality reference genome for sweet sorghum and compared it to the publicly available grain sorghum genome. We also performed comparative transcriptomics and found 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.
View on GitHub BMC Genomics Paper
Grain Sorghum QTL Studies
In two separate papers, we use coordinated association and linkage mapping to reveal QTLs that are prime targets to improve both grain quality and grain yield in sorghum. A more robust knowledge of the genetics underlying these complex traits could provide insights into molecular breeding strategies that aim to increase genetic gain.
View on GitHub TAG Paper CropSci Paper
Genetic Divergence in Monarcha Flycatchers of the Solomon Islands
In this study, we used Illumina-sequenced ddRAD tags to identify genomewide patterns of differentiation in three recently diverged island populations of the Monarcha castaneiventris flycatcher of the Solomon Islands. We found that a phylogenetic analysis based on these SNPs produced a taxonomy wherein the two melanic populations appear to have evolved convergently, rather than from a single common ancestor, in contrast to their original classification as a single subspecies.
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Genomic Variation in Darwin's Finches
We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome, (ii) SNPs linked to the candidate genes are dispersed throughout the genome, and (iii) micro- and macro-evolutionary variation involve some shared and some unique genomic regions.
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Bioenergy Sorghum Association Panel
To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in grasses, we have established and characterized an association panel of diverse Sorghum bicolor accessions.
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Convergent Plumage Color Alleles
Using a combination of candidate gene and reduced representation genomic sequencing approaches,we explore the genetic basis of and the evolutionary processes that mediate similar plumage colour shared by isolated populations of the Monarcha flycatcher of the Solomon Islands.
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Genome-Wide Association Studies of Grain Yield
Characterization of grain yield per primary panicle (YPP), grain number per primary panicle (GNP), and 1000-grain weight (TGW) in sorghum [ (L.) Moench], a hardy C cereal with a genome size of ∼730 Mb, was implemented in a diversity panel containing 390 accessions.
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