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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 #386828

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

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

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