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A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation., (© 2022. The Author(s).)

Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using Compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize ( Zea mays ) and sorghum ( Sorghum bicolor ), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe-quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa., (© 2020 American Society of Plant Biologists. All Rights Reserved.)