Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition

• Published in: Journal of plant physiology 2016-04, Vol.170 (4), p.1989-1998
• Main Authors: Shakoor, Nadia, Ziegler, Greg, Dilkes, Brian P., Brenton, Zachary, Boyles, Richard, Connolly, Erin L., Kresovich, Stephen, Baxter, Ivan
• Format: Article
• Language: English
• Subjects: alleles; animal nutrition; BIOCHEMISTRY AND METABOLISM; biofuels; cadmium; calcium; chromosome mapping; elemental composition; Environment; genetic correlation; Genetic Variation; Genome-Wide Association Study; genotype-phenotype correlation; genotyping; grains; humans; Inheritance Patterns - genetics; ionome; loci; manganese; mineral content; Models, Biological; nickel; nutrient content; nutritive value; Phenotype; plant breeding; Polymorphism, Single Nucleotide - genetics; Quantitative Trait, Heritable; races; seedlings; seeds; Seeds - genetics; selection methods; sequence homology; single nucleotide polymorphism; Sorghum - genetics; Sorghum bicolor; statistical models; zinc
• ISSN: 0032-0889; 0176-1617; 1532-2548
• DOI: 10.1104/pp.15.01971

Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, 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 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, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement.