Sorghum Association Panel whole‐genome sequencing establishes cornerstone resource for dissecting genomic diversity

Abstract

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.

Comparative GWAS identifies a role for Mendel’s green pea gene in the nonphotochemical quenching kinetics of sorghum, maize, and arabidopsis

“…In this study, we quantified various parameters related to NPQ kinetics for 339 sorghum genotypes grown under both low-nitrogen and high-nitrogen conditions in 2020 and 2021 and performed GWAS using high-density genetic markers from resequencing data (Boatwright et al . 2022).…”

“…A published set of 43 million segregating single nucleotide polymorphisms (SNPs), structural variants, and insertion/deletions (InDels) derived from whole–genome resequencing of the sorghum association panel (Boatwright et al . 2022) was filtered using VCFtools v.0.1 (Danecek et al .…”

“…2008; Mural et al . 2021; Boatwright et al . 2022), a drought-tolerant and nitrogen-use-efficient relative of maize that is widely grown as a staple crop in Subsaharan Africa and South Asia.…”

Genetic control of morphological traits useful for improving sorghum

“…Rapid innovations in next-generation sequencing techniques, such as restriction site-associated DNA sequences ( Baird et al 2008 ), have made genome-wide high-density DNA marker information readily and inexpensively available, allowing for higher-resolution QTL analysis and GWAS to further advance sorghum gene hunting. Furthermore, whole-genome re-sequencing data for 400 sorghum accessions have recently been reported ( Boatwright et al 2022 ), and GWAS using this ultra-high-density marker information is expected to accelerate sorghum genomic research. In addition to the above re-sequencing data, with the availability of the sorghum gene expression atlas ( Makita et al 2015 , Shakoor et al 2014 ), the recent completion of sorghum pan-genomes ( Tao et al 2021 ), and the development of SorghumBase online ( Gladman et al 2022 ), we are entering an exciting new era of sorghum genomic research.…”

Characterization of adaptation mechanisms in sorghum using a multi-reference back-cross nested association mapping design and envirotyping

“…This analysis was based on 137'003 SNPs common to the SAP (Boatwright et al 2022) and SGT (https://www.globalsorghuminitiative.org/) panels. From a merge of these 2 studies, we excluded all wild accessions and kept SNP with less than 20% of missing data and with a Minor Allele Frequency (MAF) higher than 5%.…”