Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity
Abstract
SUMMARY Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole‐genome sequencing (WGS) of 400 sorghum ( Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high‐density genomic marker set of 43 983 694 variants including single‐nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower‐density marker sets. WGS identified and scored variants in 5‐kb bins where available genotyping‐by‐sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergencemore »
- Authors:
-
[1];
[3];
- Department of Plant and Environmental Sciences Clemson University Clemson South Carolina 29634 USA, Advanced Plant Technology Clemson University Clemson South Carolina 29634 USA
- Advanced Plant Technology Clemson University Clemson South Carolina 29634 USA
- Center for Plant Science Innovation and Department of Agronomy and Horticulture University of Nebraska‐Lincoln Lincoln Nebraska 68588 USA
- Carolina Seed Systems Darlington South Carolina 29532 USA
- Department of Plant and Environmental Sciences Clemson University Clemson South Carolina 29634 USA, Pee Dee Research and Education Center Clemson University Florence South Carolina 29506 USA
- Department of Plant and Environmental Sciences Clemson University Clemson South Carolina 29634 USA, Advanced Plant Technology Clemson University Clemson South Carolina 29634 USA, Feed the Future Innovation Lab for Crop Improvement Cornell University Ithaca New York 14850 USA
- Publication Date:
- Research Org.:
- Clemson Univ., SC (United States); Univ. of Nebraska, Lincoln, NE (United States)
- Sponsoring Org.:
- USDOE Advanced Research Projects Agency - Energy (ARPA-E); USDOE Office of Science (SC)
- OSTI Identifier:
- 1878262
- Alternate Identifier(s):
- OSTI ID: 1878265; OSTI ID: 1904191
- Grant/Contract Number:
- DE‐AR0001134; DE‐SC0020355; AR0001134; SC0020355
- Resource Type:
- Published Article
- Journal Name:
- The Plant Journal
- Additional Journal Information:
- Journal Name: The Plant Journal Journal Volume: 111 Journal Issue: 3; Journal ID: ISSN 0960-7412
- Publisher:
- Wiley-Blackwell
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; sorghum bicolor; whole-genome sequencing; diversity panel, copy-number variants; genomic prediction; genome-wide association studies; selection signatures; pleiotropy; genotyping-by-sequencing; pan-genome
Citation Formats
Boatwright, J. Lucas, Sapkota, Sirjan, Jin, Hongyu, Schnable, James C., Brenton, Zachary, Boyles, Richard, and Kresovich, Stephen. Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity. United Kingdom: N. p., 2022.
Web. doi:10.1111/tpj.15853.
Boatwright, J. Lucas, Sapkota, Sirjan, Jin, Hongyu, Schnable, James C., Brenton, Zachary, Boyles, Richard, & Kresovich, Stephen. Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity. United Kingdom. https://doi.org/10.1111/tpj.15853
Boatwright, J. Lucas, Sapkota, Sirjan, Jin, Hongyu, Schnable, James C., Brenton, Zachary, Boyles, Richard, and Kresovich, Stephen. Tue .
"Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity". United Kingdom. https://doi.org/10.1111/tpj.15853.
@article{osti_1878262,
title = {Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity},
author = {Boatwright, J. Lucas and Sapkota, Sirjan and Jin, Hongyu and Schnable, James C. and Brenton, Zachary and Boyles, Richard and Kresovich, Stephen},
abstractNote = {SUMMARY Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole‐genome sequencing (WGS) of 400 sorghum ( Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25–72×), enabling the development of a high‐density genomic marker set of 43 983 694 variants including single‐nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower‐density marker sets. WGS identified and scored variants in 5‐kb bins where available genotyping‐by‐sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six F st peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.},
doi = {10.1111/tpj.15853},
journal = {The Plant Journal},
number = 3,
volume = 111,
place = {United Kingdom},
year = {Tue Jul 05 00:00:00 EDT 2022},
month = {Tue Jul 05 00:00:00 EDT 2022}
}
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