Trait associations in the pangenome of pigeon pea ( Cajanus cajan )JZhaoauthorP EBayerauthorPRuperaoauthorR KSaxenaauthorA WKhanauthorA AGoliczauthorH TNguyenauthorJBatleyauthorDEdwardsauthorR KVarshneyauthorPigeon pea (Cajanus cajan) is an important orphan crop mainly grown by smallholder farmers inIndia and Africa. Here, we present the first pigeon pea pangenome based on 89 accessionsmainly from India and the Philippines, showing that there is significant genetic diversity inPhilippine individuals that is not present in Indian individuals. Annotation of variable genessuggests that they are associated with self-fertilization and response to disease. We identified225 SNPs associated with nine agronomically important traits over three locations and twodifferent time points, with SNPs associated with genes for transcription factors and kinases.These results will lead the way to an improved pigeon pea breeding programme.PigeonpeaGenetics and GenomicsFood and Nutrition2020-01Wiley Open AccessArticle