Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition
Nadia Shakoor , Greg Ziegler , Brian P Dilkes , Zachary Brenton , Richard Boyles , Erin L Connolly , Stephen Kresovich , Ivan Baxter
Seedling establishment and seed nutritional quality require the sequestration of sufficient mineral nutrients. Identification of genes and alleles that modify element content in the grains of cereals, including Sorghum bicolor, is fundamental to developing breeding and selection methods aimed at increasing bioavailable mineral content and improving crop growth. We have developed a high throughput workflow for the simultaneous measurement of multiple elements in Sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel (SAP), representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome wide association was demonstrated by implementing rank transformation and a multilocus mixed model (MLMM) to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc (Zn) manganese (Mn), nickel (Ni), calcium (Ca) and cadmium (Cd) in sorghum seed. In addition to strong candidates for these four elements, we provide a list of candidate loci for several other elements. Our approach enabled identification of SNPs in strong LD with causative polymorphisms that can be used directly in plant breeding and improvement.