Ten new high quality genome assemblies for diverse bioenergy sorghum genotypes

Authors: VOELKER, WILLIAM - University Of North Carolina; KRISHNAN, KRITTIKA - University Of North Carolina; CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory; ALEXANDER, LOUIE - University Of North Carolina; LU, ZHENYUAN - Cold Spring Harbor Laboratory; OLSON, ANDREW - Cold Spring Harbor Laboratory; Ware, Doreen; SONGSOMBOON, KITTIKUN - University Of North Carolina; PONCE, CRISTIAN - University Of North Carolina; BRENTON, ZACHARY - Clemson University; BOATWRIGHT, LUCA - Clemson University; COOPER, ELIZABETH - University Of North Carolina

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/9/2022
Publication Date: 1/4/2023
Citation: Voelker, W.G., Krishnan, K., Chougule, K., Alexander, L.C., Lu, Z., Olson, A., Ware, D., Songsomboon, K., Ponce, C., Brenton, Z.W., Boatwright, L., Cooper, E.A. 2023. Ten new high quality genome assemblies for diverse bioenergy sorghum genotypes. Frontiers in Plant Science. 13:1040909. https://doi.org/10.3389/fpls.2022.1040909.
DOI: https://doi.org/10.3389/fpls.2022.1040909

Interpretive Summary: Genetic diversity is important for stable production of crops, including sorghum, which is valued for its efficiency and drought tolerance. The researchers sequenced 10 high value sorghum genomes from the recently published Carbon-Partitioning Nested Association Mapping (CP-NAM) population and searched for genetic diversity to help create new varieties of sorghum that are sustainable and could be essential for optimizing sorghum as a bioenergy feedstock. One way to discover new sources of genetic diversity is to look at the other forms of a gene (alleles) at a given location (locus). These changes in the genetic code can include insertions, deletions, inversions, and transpositions. These structural genomic mutations are an important source of variation in crop species. The researchers identified over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs). Well over half (~65%) of these variants were unique to a single genome. 1.6% of the SNPs and 10% of the SV overlapped the genes and affected function. Over a third of protein coding genes and over 75% of noncoding genes annotated in this study were not previously found in other assembled sorghum genomes indicating untapped genetic diversity in the Sorghum population. As the researchers further explored these structural genomic mutations, they gain new insights into the genetic architectures of complex and agronomically important traits.

Technical Abstract: Sorghum (Sorghum bicolor (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity and its tolerance to drought. In order to capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations. Expanding on a recently developed mapping population, we generated de novo genome assemblies for 10 parental genotypes from this population and identified a comprehensive set of over 24 thousand large structural variants (SVs) and over 10.5 million single nucleotide polymorphisms (SNPs) that can be integrated into both ongoing and future mapping studies for bioenergy sorghum. We show that SVs and nonsynonymous SNPs are enriched in different gene categories, emphasizing the need for long read sequencing in crop species to identify novel variation. Furthermore, we highlight SVs and SNPs occurring in genes and pathways with known associations to critical bioenergy-related phenotypes and characterize the landscape of genetic differences between sweet and cellulosic genotypes