Kumar Ayushi, Rajasekaran Ravikesavan, Krishnamoorthy Iyanar, Alagarswamy Senthil, Chandrakumar K, Pulapet Sowmya, Markkandan Kesavan, Kanagarajan Selvaraju, Narayanan Manikanda Boopathi
Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
Department of Plant Physiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
BMC Plant Biol. 2025 Aug 4;25(1):1023. doi: 10.1186/s12870-025-06999-5.
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.
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.
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.
黍（Panicum miliaceum L.）是最古老的驯化作物之一，仍是一种未得到充分利用的资源，在营养和产量方面具有巨大潜力。随着育种观念的不断发展，基因组知识对于培育新作物品种变得越来越重要。然而，关于本土黍的基因组信息有限，这阻碍了其充分利用。本研究通过汇编本地品种ATL1及其突变衍生物TNPmPEM 001的叶绿体基因组（cp.基因组）数据来填补这一空白，旨在促进新品种的培育。
黍品种ATL1和TNPmPEM 001的叶绿体基因组均呈现出典型的四分体结构。虽然它们的总长度（139837 bp）、小单拷贝（SSC：12795 bp）、大单拷贝（LSC：84522 bp）和反向重复（IR：20560 bp）区域相同，但这些指标与参考基因组不同，参考基因组的总长度为139826 bp，具有不同的SSC（12574 bp）、LSC（81682 bp）和IR（22785 bp）区域。虽然大豆、棉花、向日葵和豌豆构成了外类群，但系统发育分析表明ATL1、TNPmPEM 001与参考cp.基因组以及与小米之间存在紧密联系。在两个被研究的cp.基因组中鉴定出调节光合作用成分（光系统I和II、NADH脱氢酶、细胞色素复合体、rubisco以及核糖体/tRNA/rRNA基因）的蛋白质编码基因，这为未充分利用的C作物如黍的光合作用效率的基因组基础提供了关键见解，黍是提高适应胁迫的可持续农业的关键性状。此外，在突变衍生物中专门鉴定出的11个独特的简单序列重复（SSR）标记，为旨在提高农艺性状的标记辅助育种计划提供了新工具。
这些发现填补了黍基因组学中的关键空白，特别是印度地方品种分子资源有限的问题。突变衍生的SSR和结构变异为在可变光周期下提高产量稳定性提供了可操作的目标，这是边际农业生态系统中适应气候变化的黍育种的优先事项。
