Pan-genome analysis in sorghum highlights the extent of genomic variation and sugarcane aphid resistance genes

Authors: WANG, BO - Cold Spring Harbor Laboratory; JIAO, YINPING - Cold Spring Harbor Laboratory; CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory; OLSON, ANDREW - Cold Spring Harbor Laboratory; HUANG, JIAN - Oklahoma State University; LLACA, VICTOR - Corteva Agriscience; FENGLER, KEVIN - Corteva Agriscience; WEI, XUEHONG - Cold Spring Harbor Laboratory; WANG, LIYA - Cold Spring Harbor Laboratory; WANG, XIAOFEI - Cold Spring Harbor Laboratory; REGULSKI, MICHAEL - Cold Spring Harbor Laboratory; DRENKOW, JORG - Cold Spring Harbor Laboratory; GINGERAS, THOMAS - Cold Spring Harbor Laboratory; Hayes, Chad; Armstrong, John; Huang, Yinghua; Xin, Zhanguo; Ware, Doreen

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 1/4/2021
Publication Date: 1/4/2021
Citation: Wang, B., Jiao, Y., Chougule, K., Olson, A., Huang, J., Llaca, V., Fengler, K., Wei, X., Wang, L., Wang, X., Regulski, M., Drenkow, J., Gingeras, T., Hayes, C.M., Armstrong, J.S., Huang, Y., Xin, Z., Ware, D. 2021. Pan-genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes. bioRxiv. https://doi.org/10.1101/2021.01.03.424980.
DOI: https://doi.org/10.1101/2021.01.03.424980

Interpretive Summary: We assembled two high quality sorghum genomes TX2783 and TX436 using PacBio and BioNano long-read sequencing technologies. Together with other public sorghum genomes BTX623, TX430 and Rio, we identified extensive large and small structural variations (SVs) using TX2783 as a reference. We reported a region that contributes to sugarcane aphid resistance, and also identified SVs that segregate with sugarcane aphid resistance using nanopore sequencing.

Technical Abstract: Sorghum bicolor, one of the most important grass crops worldwide, has been known to harbor high genetic diversity. We constructed chromosome-level genome assembly for two important sorghum inbred lines: TX2783 and TX436. The final high quality reference assemblies consists of 19, 18 scaffolds with a contig N50 25.6 of 20.3Mb respectively. Together with other public sorghum genomes BTX623, TX430 and Rio, we identified extensive large and small structural variations (SVs) using TX2783 as a reference. Genome-wide scan of disease resistance genes (R gene) showed high-levels of diversity in these five sorghum accessions . To characterize the genes related to sugarcane aphid (SCA) resistance in TX2783, we mapped the resistance region on chromosome 6 using a RIL population. We also identified SVs segregating for SCA resistance using Nanopore sequencing. In summary, this study provided the first overview of the extent of genomic structural variations, and R genes in the sorghum population, and potential targets for disease resistance breeding.