Genetic characterization of a Sorghum bicolor multiparent 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 (NAM) 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 NAM 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 NAM 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 are validated using pericarp and testa phenotypes to map known genes affecting these phenotypes. We release the 11-family NAM population along with corresponding genomic data for use in genetic, genomic, and agronomic studies with a focus on carbon-partitioning regimes.

Keywords: MPP; carbon-partitioning; genome-wide association study; genotype-by-sequencing; multiparental populations; nested association mapping; pericarp color.

Figure 1

Linkage decay (Pearson’s correlation coefficient squared) plotted against the distance in kilobases across the genome.

Figure 2

Principal component analysis plot using the whole CP-NAM population. Parents are labeled with the common name. The individual samples of the recurrent parent, Grassl, are additionally labeled with “x.” Each RIL family is represented by the male parent PI.

Figure 3

Genome-wide, population admixture of the CP-NAM. Individuals (x-axis) are shown as vertical bars colored in proportion to their estimated ancestry within each cluster (y-axis) based upon 15 ancestral populations (K = 15) where each genetically distinct ancestral population is given a unique color.

Figure 4

CP-NAM PCA with admixture coloration. Individuals were classified as Q1–Q15 as determined by the proportion of ancestral admixture. Cells 1–11 represent individual RIL families represented by the paternal identifier while the 12th cell contains the entire CP-NAM population.

Figure 5

Univariate GWAS for pericarp pigmentation. The −log10 P-values (y-axis) are plotted against the position on each chromosome (x-axis). Each circle represents a SNP, and the red dashed line represents the Bonferroni-corrected threshold.

Figure 6

Univariate GWAS for binary encoding of yellow pericarp pigmentation. The −log10 P-values (y-axis) are plotted against the position on each chromosome (x-axis). Each circle represents a SNP, and the red dashed line represents the Bonferroni-corrected threshold.

Figure 7

Multivariate GWAS for pericarp color and testa pigmentation. The −log10 P-values (y-axis) are plotted against the position on each chromosome (x-axis). Each circle represents a SNP, and the red dashed line represents a Bonferroni-corrected threshold.