Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition

Authors: SHAKOOR, NADIA - Danforth Plant Science Center; Ziegler, Gregory; DILKES, BRIAN - Purdue University; BRENTON, ZACHARY - Clemson University; BOYLES, RICHARD - Clemson University; CONNOLLY, ERIN - University Of South Carolina; KRESOVICH, STEPHEN - Clemson University; Baxter, Ivan

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/1/2016
Publication Date: 4/1/2016
Publication URL: http://handle.nal.usda.gov/10113/62907
Citation: Shakoor, N., Ziegler, G.R., Dilkes, B., Brenton, Z., Boyles, R., Connolly, E., Kresovich, S., Baxter, I.R. 2016. Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition. Plant Physiology. 170:1989-1998.

Interpretive Summary: Sorghum is a globally cultivated source of food, feed, sugar and fiber. Classified as a bioenergy feedstock, sorghum biomass also has unique advantages for sustainable biofuel production. Increasing the bioavailable elemental nutrient content in the edible portions of the crop has the potential to increase the value of sorghum for human and animal nutrition. Here we measured the elemental composition of a diverse panel of sorcghum accession grown in three differen locations. Using this data, we were able to identify which elements vary together, which will be useful for breeders trying to manipulate the levels of multiple mineral nutrients and anti-nutrients. We were also able to identify 255 genetic loci that were associated with the levels of the 20 elements we measured. Those loci will help to identify candidate genes for the improvement of sorghum and other crops such as Soybean.

Technical Abstract: Increasing the bioavailable elemental nutrient content in the edible portions of the crop has the potential to increase the value of sorghum for human and animal nutrition. Seedling establishment and seed nutritional quality are in part determined by 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 biofuel suitability. We have developed a high throughput workflow for the simultaneous measurement of multiple key elements in seeds. In combination with the genotyped Sorghum Association Panel (SAP), representing all major cultivated sorghum races from diverse geographic and climatic regions, we mapped alleles contributing to seed element variation across three environments. 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. The application of rank transformation and association mapping strategies towards compositional trait improvement enabled our identification of SNPs in strong LD with causative polymorphisms that can be used directly in plant breeding and improvement.