Genetic characterization of aSorghum bicolormultiparent mapping population emphasizing carbon-partitioning dynamics

Abstract

Sorghum bicolor, a photosynthetically efficient C4 grass, represents an important source of grain, forage, fermentable sugars, and cellulosic fibers that can be utilized in myriad applications ranging from bioenergy to bioindustrial feedstocks. Sorghum’s efficient fixation of carbon per unit time per unit area per unit input has led to its classification as a preferred biomass crop highlighted by its designation as an advanced biofuel by the U.S. Department of Energy. Due to its extensive genetic diversity and worldwide colonization, sorghum has considerable diversity for a range of phenotypes influencing productivity, composition, and sink/source dynamics. To dissect the genetic basis of these key traits, we present a sorghum carbon-partitioning nested association mapping population generated by crossing 11 diverse founder lines with Grassl as the single recurrent female. By exploiting existing variation among cellulosic, forage, sweet and grain sorghum carbon partitioning regimes, the sorghum carbon-partitioning nested association mapping population will allow the identification of important biomass-associated traits, elucidate the genetic architecture underlying carbon partitioning and improve our understanding of the genetic determinants affecting unique phenotypes within Poaceae. We contrast this nested association mapping population with an existing grain population generated using Tx430 as the recurrent female. Genotypic data are assessed for quality by examining variant density, nucleotide diversity, linkage decay, and is validated using pericarp and testa phenotypes to map known genes affecting these phenotypes. We release the 11-family nested association mapping population along with corresponding genomic data for use in genetic, genomic, and agronomic studies with a focus on carbon-partitioning regimes.

Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum using Multiscale Phenotypes

“…The sorghum Carbon-Partitioning nested association mapping (CP-NAM) panel [29] contains 11 subpopulations generated using diverse parental accessions from the sorghum Bioenergy Association Panel (BAP) [33] and the recurrent parent, Grassl -an accession capable of accumulating significant biomass and fermentable carbohydrates per unit time and area [44]. NAM populations contain sets of RIL families generated from the diverse founders, and as such, benefit from recombination of the founder genotypes, high allele richness, higher statistical power, and are less sensitive to genetic heterogeneity [29,45]. As the CP-NAM covers the diversity of sorghum types and carbon-partitioning regimes, it represents an excellent source of genotypic and phenotypic diversity to elucidate the genetic architecture underlying carbon fixation, translocation, and utilization so that source/sink dynamics and compositional traits may be understood holistically while simultaneously meeting the demands dictated by a 2/26 changing environment [29].…”

“…NAM populations contain sets of RIL families generated from the diverse founders, and as such, benefit from recombination of the founder genotypes, high allele richness, higher statistical power, and are less sensitive to genetic heterogeneity [29,45]. As the CP-NAM covers the diversity of sorghum types and carbon-partitioning regimes, it represents an excellent source of genotypic and phenotypic diversity to elucidate the genetic architecture underlying carbon fixation, translocation, and utilization so that source/sink dynamics and compositional traits may be understood holistically while simultaneously meeting the demands dictated by a 2/26 changing environment [29]. Here, we employ quantitative trait locus (QTL) mapping, univariate linear-mixed models (LMMs), and multivariate-response linear-mixed models (MV-LMMs) to identify loci associated with the primary carbon sinks represented by structural and non-structural carbohydrate content in sorghum.…”

Genome-wide association studies of mineral and phytic acid concentrations in pea (Pisum sativum L.) to evaluate biofortification potential

“…Accessions with unavailable species information were annotated as P. sativum in this study for both admixture analysis and principal components analysis (PCA). The Q matrix was then sorted by the ancestry coefficients for each subpopulation, assigning individuals with coefficients >50% to the corresponding subpopulation ( Boatwright et al 2021 ). Principal components (PCs) were calculated during analysis with GAPIT ( Wang and Zhang 2020 ); the first two PCs were graphed using R and assigned a color based on available species information.…”

Sorghum Association Panel Whole-Genome Sequencing Establishes Pivotal Resource for Dissecting Genomic Diversity

“…The accessions in the SAP were selected to maximize the genetic and phenotypic diversity of the panel as well as capture accessions that are important for understanding the demographic history and historical breeding importance based on known resistances or tolerances to abiotic and biotic stresses [4]. Sorghum’s broad geographic distribution [12, 4] and carbon-partitioning regimes [13] have resulted in two classification systems that distinguish accessions based on variation by race and carbon partitioning, with race representing the predominant classification system in the SAP. Sorghum is classified into five botanical races: bicolor, caudatum, durra, guinea, and kafir, which are thought to have formed through multiple domestication and adaptation events across different clines [14, 5].…”