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bioRxiv · 10.1101/019083

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
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Abstract

AbstractSeedling establishment and seed nutritional quality require the sequestration of sufficient element 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 element 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 evaluated in targeted selection strategies for plant breeding and improvement.\n\nOne sentence summaryHigh-throughput measurements of element accumulation and genome-wide association analysis across multiple environments identified novel alleles controlling seed element accumulation in Sorghum bicolor.\n\nThis project was partially funded by the iHUB Visiting Scientist Program (http://www.ionomicshub.org), Chromatin, Inc., NSF EAGER (1450341) to I.B. and BPD, NSF IOS 1126950 to IB, NSF IOS-0919739 to EC, and BMGF (OPP 1052924) to B.P.D.

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Nadia Shakoor, Greg Ziegler, Brian P Dilkes, Zachary Brenton, Richard Boyles, Erin L Connolly, Stephen Kresovich, Ivan Baxter. 2015-05-08. Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition. https://doi.org/10.1101/019083

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