Comparative chloroplast genomics of wild-type Panicum miliaceum cv. ATL1 and its M mutant line: insights for molecular breeding applications.

Background: Proso millet (Panicum miliaceum L.), one of the oldest domesticated crop, remains an underexploited resource with significant potential for nutrition and yield. With evolving breeding perspectives, genomic knowledge is increasingly vital for developing new crop varieties. However, the limited genomic information on indigenous proso millet hinders its full utilization. This study addresses this gap by compiling chloroplast genome (cp. genome) data for the native variety ATL1 and its mutant derivative TNPmPEM 001, aiming to facilitate the development of new varieties.

Results: Both Panicum miliaceum cv. ATL1 and TNPmPEM 001 chloroplast genomes exhibited the characteristic quadripartite structure. While they shared identical total lengths (139 837 bp), small single-copy (SSC: 12 795 bp), large single-copy (LSC: 84 522 bp), and inverted repeat (IR: 20 560 bp) regions, these metrics diverged from the reference genome, which displayed a total length of 139 826 bp, with distinct SSC (12 574 bp), LSC (81 682 bp), and IR (22 785 bp) regions. While soybean, cotton, sunflower, and pea constituted outgroups, the phylogenetic analysis showed a tight link between ATL1, TNPmPEM 001 and reference cp. genome as well as with little millet. The identification of protein-coding genes regulating photosynthesis components (photosystems I and II, NADH dehydrogenase, cytochrome complexes, rubisco, and ribosomal/tRNA/rRNA genes) in both investigated cp. genomes provides critical insights into the genomic basis of photosynthesis efficiency in underutilized C crops like proso millet, a key trait for improving stress-resilient sustainable agriculture. Additionally, 11 unique simple sequence repeat (SSR) markers, exclusively identified in the mutant derivative, offer novel tools for marker-assisted breeding programs targeting agronomic trait enhancement.

Conclusions: These findings address critical gaps in proso millet genomics, particularly the limited molecular resources for Indian landraces. The mutant-derived SSRs and structural variants offer actionable targets for enhancing yield stability under variable photoperiods, a priority for climate-resilient proso millet breeding in marginal agroecosystems.