Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

Jennifer E Spindel,Scott H Staggenborg,Joy Hollingsworth,Matthew Colgan,Julie Sievert,Robert Hutmacher,Christer Jansson,Jeffery Dahlberg,John P Vogel

doi:10.1186/s12864-018-5055-5

Abstract

BackgroundSorghum bicolor is the fifth most commonly grown cereal worldwide and is remarkable for its drought and abiotic stress tolerance. For these reasons and the large size of biomass varieties, it has been proposed as a bioenergy crop. However, little is known about the genes underlying sorghum’s abiotic stress tolerance and biomass yield.ResultsTo uncover the genetic basis of drought tolerance in sorghum at a genome-wide level, we undertook a high-density phenomics genome wide association study (GWAS) in which 648 diverse sorghum lines were phenotyped at two locations in California once per week by drone over the course of a growing season. Biomass, height, and leaf area were measured by drone for individual field plots, subjected to two drought treatments and a well-watered control. The resulting dataset of ~ 171,000 phenotypic data-points was analyzed along with 183,989 genotype by sequence markers to reveal 213 high-quality, replicated, and conserved GWAS associations.ConclusionsThe genomic intervals defined by the associations include many strong candidate genes, including those encoding heat shock proteins, antifreeze proteins, and other domains recognized as important to plant stress responses. The markers identified by our study can be used for marker assisted selection for drought tolerance and biomass. In addition, our results are a significant step toward identifying specific sorghum genes controlling drought tolerance and biomass yield.

Highlights

Sorghum bicolor is the fifth most commonly grown cereal worldwide and is remarkable for its drought and abiotic stress tolerance
Converted sorghum lines were selected to form the bulk of the panel based on the hypothesis that transition to flowering and the shift to reproductive growth stages have profound effects on genetic regulation of most, if not all traits, and that performing a genome wide association study (GWAS) in lines that did not flower would identify fewer polymorphisms linked to biomass and/or drought tolerance
A final set of 131,544 Single nucleotide polymorphism (SNP) with minor allele frequency (MAF) ≥ 0.01 were used for all GWAS analyses

Summary

Introduction

Sorghum bicolor is the fifth most commonly grown cereal worldwide and is remarkable for its drought and abiotic stress tolerance. For these reasons and the large size of biomass varieties, it has been proposed as a bioenergy crop. Sorghum is the fifth most commonly grown cereal crop worldwide, and over half a billion people rely on it as a daily food staple. While there have been many linkage mapping studies for drought tolerance quantitative trait loci (QTLs), there has been almost no validation of causal polymorphisms, which is a crucial step before results are of use to breeders, and the QTL regions identified in these linkage studies have been too large to identify meaningful candidate alleles [7,8,9,10,11,12,13]. Despite the many QTLs identified for drought tolerance in sorghum over the years, a well-designed GWAS for drought tolerance is needed to identify better candidates for causal polymorphisms underlying the remarkable drought tolerant characteristics of sorghum

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Results

Conclusion