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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #411371
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: Long-read sequencing broadens access to genetic and transcript diversity for high-value traits in sorghum

Author
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item Scheffler, Brian
item Simpson, Sheron
item Ware, Doreen

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/12/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: In the pursuit of enhancing our understanding of sorghum genetics, we present a study utilizing long-read sequencing to unravel genetic and transcript diversity, particularly focusing on high-value traits. Leveraging the PacBio Revio, we produced 14 Sorghum assemblies, resulting in a notable improvement with a greater N50 (>50 Mb) and BUSCO metrics (>98%) and remarkably fewer gaps compared to prior sorghum assemblies without the need for HiC positional information. These assemblies have been strategically prioritized for traits encompassing quality attributes and disease resistance, a class of rapidly evolving adaptive genes.The new Kinnex kit has provided unprecedented access to long transcripts. Remarkably, a 10-day-old sequencing sample captures more than 60% of the reference gene locus and ~2K novel intergenic loci having a median gene length ~2.3Kb, offering a rapid and efficient means of exploring genetic landscapes. Our analysis has revealed for known reference annotation ~11K novel isoforms with previously uncharacterized exons, enriching our understanding of the sorghum transcriptome. Furthermore, over ~47% of the multi-gene reference loci exhibit intron retention, adding a layer of complexity.. Beyond transcript discovery, the Mas Iso-seq approach has empowered the refinement of gene structures. This study not only expands our understanding of genetic and transcript diversity in sorghum but also highlights the potential applications of long-read sequencing in unraveling the intricacies of high-value traits in crop genetics.