Multiomics approach unravels fertility transition in a pigeonpea line for a two‐line hybrid systemL TPazhamalaauthorPChaturvediauthorPBajajauthorSSrikanthauthorAGhatakauthorAChitikineniauthorABellaireauthorAHinganeauthorC V SKumarauthorK BSaxenaauthorWWeckwerthauthorR KSaxenaauthorR KVarshneyauthorPigeonpea [Cajanus cajan (L.) Millsp.] is a pulse crop cultivated in the semi-arid regions of Asia and Africa. It is a rich source of protein and capable of alleviating malnutrition, improving soil health and the livelihoods of small-holder farmers. Hybrid breeding has provided remarkable improvements for pigeonpea productivity, but owing to a tedious and costly seed production system, an alternative two-line hybrid technology is being explored. In this regard, an environmentsensitive male sterile line has been characterized as a thermosensitive male sterile line in pigeonpea precisely responding to day temperature. The male sterile and fertile anthers from five developmental stages were studied by integrating transcriptomics, proteomics and metabolomics supported by precise phenotyping and scanning electron microscopic study. Spatio-temporal analysis of anther transcriptome and proteome revealed 17 repressed DEGs/DEPs in sterile anthers that play a critical role in normal cell wall morphogenesis and tapetal cell development. The male fertility to sterility transitionwasmainly due to a perturbation in auxin homeostasis, leading to impaired cellwallmodification and sugar transport. Limited nutrient utilization thus leads to microspore starvation in response to moderately elevated day temperature which could be restored with auxin-treatment in the male sterile line. Our findings outline a molecular mechanism that underpins fertility transition responses thereby providing a process-oriented two-line hybrid breeding framework for pigeonpea.Plant BreedingPigeonpeaGenetics and GenomicsFood and Nutrition2020-06Crop Science Society of AmericaArticle