PT  - JOURNAL ARTICLE
AU  - J. Lucas Boatwright
AU  - Sirjan Sapkota
AU  - Hongyu Jin
AU  - James C. Schnable
AU  - Zachary Brenton
AU  - Richard Boyles
AU  - Stephen Kresovich
TI  - Sorghum Association Panel Whole-Genome Sequencing Establishes Pivotal Resource for Dissecting Genomic Diversity
AID  - 10.1101/2021.12.22.473950
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.12.22.473950
4099  - http://biorxiv.org/content/early/2021/12/24/2021.12.22.473950.short
4100  - http://biorxiv.org/content/early/2021/12/24/2021.12.22.473950.full
AB  - 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 with distinct histories of evolutionary divergence and local adaptation. 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 38X (25X-72X), enabling the development of a high-density genomic-marker set of 43,983,694 variants including SNPs (~ 38 million), indels (~ 5 million), and CNVs (170,000). We observe slightly more deletions among indels and a much higher prevalence of deletions among copy number variants compared to insertions. This new marker set enabled the identification of several putatively novel 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 Fst 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 been and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.Competing Interest StatementJCS has equity interests in Data2Bio LLC, a company that provides genotyping services using sequencing technology. The authors declare no other conflicts of interest.