Sorghum Association Panel Whole-Genome Sequencing Establishes Pivotal 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 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.

Genomic prediction of hybrid performance for agronomic traits in sorghum

“…Genome-wide markers for the inbred parents were generated from whole genome resequencing using Illumina NovaSeq 6000. The sequenced reads were aligned to version 3.1.1 of sorghum reference genome BTx623 ( McCormick et al 2018 ), single nucleotide polymorphism variants were called using joint calling in GATK pipeline and imputed using Beagle at 99% accuracy [for details see Boatwright et al (2021) ]. The phased genotypic data were filtered using vcftools ( Danecek et al 2011 ) to only allow 1% missingness and 2% minor allele frequency resulting in 7,804,754 total SNPs, which was further thinned using vcftools to only include one SNP marker every 100 bp to a total SNP count of 2,687,342 for computational efficiency.…”

Complex Trait Analysis of Human Gut Microbiome-Active Traits in Sorghum bicolor: a new category of human health traits in food crops

“…MATs and the genetic architecture driving them in sorghum are likely to be far more complex than the ten QTL identified in our study because genetic diversity of the BTx623 and IS3620C parents represents only a fraction of the total genetic diversity of the Sorghum bicolor species (40,41). Indeed, genetic analysis of MATs in populations such as the Sorghum Association Panel (41)(42)(43), which captures genetic diversity of sorghum from all four of the major subpopulations that appear to represent two independent domestication events, will help provide a more comprehensive picture of MATs in sorghum and the underlying genetics.…”

Harnessing the strigolactone biosynthesis mutant lgs1 to combat food insecurity in Africa

“…The SAP is also extensively sequenced providing vital data for downstream resistance breeding. Based on our analysis and previous work (Boatwright et al 2022), the SAP comprises all major botanical races of sorghum (caudatum, kafir, guinea, and durra) and a mixed population believed to have originated from bicolor -one of the earliest races to undergo domestication (Harlan & Stemler, 1976). We adopted a simple methodology for discovery of Strigaresistance alleles in sorghum based on PCR screening using two sets of primers -making it applicable in basic laboratories without the need for sophisticated equipment and resources for advanced molecular screening.…”

“…For this study, we selected a large collection of sorghum accessions, the Sorghum Accession Panel (SAP), maintained by the United States Department of Agriculture Agricultural Research Service (USDA-ARS) (https://www.ars-grin.gov/). High quality genotypic data is available for the SAP including genotyping by sequencing, single nucleotide polymorphism (SNP) markers (Morris et al 2013) and whole genome sequencing (WGS) (Boatwright et al 2022) making the SAP suitable for subsequent molecular breeding studies. The SAP provides a further advantage because it comprises converted tropical lines (Kleinet al 2008) of diverse genotypes and geographic origin as well as breeding lines that are photoperiod-insensitive, elite inbred, improved cultivars, and landraces selected to capture maximum genetic and phenotypic diversity (Casa et al 2008).…”