Alternative oxidases (AOX) belong to a protein family (AOX1, 2) found ubiquitously in plants that act as alternative terminal oxidases in the mitochondrial electron transport chain (mETC). AOX1A is known to be stress responsive and acts to mitigate oxidative stress by preventing the overreduction of mETC components and in turn the production of reactive oxygen species. As AOX bypasses complexes III and IV of the mETC, it is energy wasteful and could potentially sacrifice yield in crop plants. To date, significant expression of AOX under non-stress conditions has only been observed in legumes, where AOX2 isoforms are constitutively expressed, although variation between chickpea cultivars has been observed. The constitutive expression of AOX2 in legumes in not understood, but impaired growth and reproduction seen in soybean as a result of the simultaneous antisense knockout of all isoforms suggests an intrinsic role of the AOX family in legume development. This study looks at the role of the AOX family in the development of legumes and how they can be utilised to optimise yield and stress tolerance of pulse crops. The model legume, Lotus japonicus, possesses a naturally occurring long terminal repeat transposon, Lotus retrotransposon 1 (LORE1) which can be utilised to study plants with singular AOX knockouts.