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ARS Home » Southeast Area » Tifton, Georgia » Crop Genetics and Breeding Research » Research » Research Project #433375

Research Project: Use of Genome Wide Association Studies (GWAS) for the Elucidation of Genes Underlying Sorghum Resistance to the Sugarcane Aphid

Location: Crop Genetics and Breeding Research

Project Number: 6048-21220-018-08-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2017
End Date: Sep 1, 2021

Objective:
The sugarcane aphid (SCA: Melanaphis sacchari) poses a recent and severe pest challenge to grain sorghum growers and the entire related value chain. To address the SCA crisis, the current effort seeks to identify genetic and metabolic traits associated with SCA resistance or tolerance. Field-based assessments of 1) SCA resistance and 2) specialized defense-related metabolites will be analyzed in 2 large sorghum association panels, namely the Sorghum Association Panel (SAP) and the sorghum Bioenergy Association Panel (BAP) with seed stocks curated by the USDA Germplasm Resources Information Network (GRIN) and for which extensive genotype data are immediately available. All measured traits will be utilized for genome wide association studies (GWAS) using association mapping to identify quantitative trait loci (QTLs) and candidate genes associated with SCA resistance and sorghum defenses. Genetic and/or biochemical mechanisms uncovered can then be leveraged for targeted improvements in breeding for SCA resistance or tolerance in sorghum.

Approach:
Using multiple genotyped sorghum diversity panels, field collected ratings of sugarcane aphid (SCA) resistance or tolerance in sorghum will be analyzed using Genome wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with variation in scored SCA traits. Genes existing within the genetic interval spanned by statistically significant SNPs will be examined for candidate genes associated with aphid resistance, tolerance or specialized plant metabolism. Based the observed patterns, a select sorghum panel subset will be used for 3’-RNA-Seq-based transcriptomic analyses on SCA infested leaves to further delineate and narrow candidate gene(s) underlying altered SCA susceptibility. As complex biochemical traits that often mediate aphid resistance in plants, parallel metabolite-led GWAS will be conducted on sorghum biochemicals present during SCA attack that includes samples also experiencing interactions with adventitious fungi. Representative tissue samples from all sorghum lines will be analyzed by both gas chromatography mass spectrometry (GC/MS) and liquid chromatography mass spectrometry (LC/MS) collectively capturing nearly 2000 biochemical traits. Metabolite QTLs overlapping with significant SCA associated SNPs will be closely examined for candidate genes that could be responsible for the combined association and possible coupling of genetic and chemical mechanisms for further validation using established molecular and genetic approaches. Independent of the final mechanistic validation of genes responsible for SCA-related traits, the identification of genetic loci driving SCA resistance in sorghum can be utilized in targeted breeding improvements.