Major impacts of widespread structural variation on sorghum

Zhang, Zhihai; Gomes Viana, Joao Paulo; Zhang, Bosen; Walden, Kimberly K. O.; Paul, Hans Müller; Moose, Stephen P.; Morris, Geoffrey P.; Daum, Chris; Barry, Kerrie W.; Shakoor, Nadia; Hudson, Matthew E.

doi:10.1101/gr.278396.123

Major impacts of widespread structural variation on sorghum

Journal Article · Wed Mar 13 00:00:00 EDT 2024 · Genome Research

DOI:https://doi.org/10.1101/gr.278396.123· OSTI ID:2426602

^[1]; Gomes Viana, Joao Paulo ^[2]; Zhang, Bosen ^[2]; Walden, Kimberly K. O. ^[2]; Paul, Hans Müller ^[2]; Moose, Stephen P. ^[2]; ^[3]; Daum, Chris ^[4]; Barry, Kerrie W. ^[4]; Shakoor, Nadia ^[5]; ^[2]

University of Illinois at Urbana-Champaign, IL (United States); University of Illinois Urbana-Champaign
University of Illinois at Urbana-Champaign, IL (United States)
Colorado State University, Fort Collins, CO (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Donald Danforth Plant Science Center, St. Louis, MO (United States)

Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype–phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.

View Accepted Manuscript (DOE)

Research Organization:: Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; SC0018420

OSTI ID:: 2426602

Journal Information:: Genome Research, Journal Name: Genome Research Journal Issue: 2 Vol. 34; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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Major impacts of widespread structural variation on sorghum

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