Branched-chain amino acids ( BCAA s) are three of the nine essential amino acids in human and animal diets and are important for numerous processes in development and growth. However, seed BCAA levels in major crops are insufficient to meet dietary requirements, making genetic improvement for increased and balanced seed BCAA s an important nutritional target. Addressing this issue requires a better understanding of the genetics underlying seed BCAA content and composition. Here, a genome-wide association study and haplotype analysis for seed BCAA traits in Arabidopsis thaliana revealed a strong association with a chromosomal interval containing two BRANCHED-CHAIN AMINO ACID TRANSFERASES , BCAT1 and BCAT2 . Linkage analysis, reverse genetic approaches, and molecular complementation analysis demonstrated that allelic variation at BCAT2 is responsible for the natural variation of seed BCAA s in this interval. Complementation analysis of a bcat2 null mutant with two significantly different alleles from accessions Bayreuth-0 and Shahdara is consistent with BCAT2 contributing to natural variation in BCAA levels, glutamate recycling, and free amino acid homeostasis in seeds in an allele-dependent manner. The seed-specific phenotype of bcat2 null alleles, its strong transcription induction during late seed development, and its subcellular localization to the mitochondria are consistent with a unique, catabolic role for BCAT2 in BCAA metabolism in seeds. Glossary BCAA branched-chain amino acid IVD isovaleryl-coenzyme A dehydrogenase BCAT branched-chain amino acid aminotransferase QTL quantitative trait locus GWAS genome-wide association study LC-MS/MS liquid chromatography–tandem mass spectrometry FAA free amino acid SNP single nucleotide polymorphism FDR false discovery rate MLMM multiple-locus mixed model LD linkage disequilibrium Bay Bayreuth-0 Sha Shahdara Col-0 Columbia DAF days after flowering YFP yellow fluorescent protein CFP cyan fluorescent protein BLUP best linear unbiased predictor MAF minor allele frequency
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