Abstract
Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.
Highlights
Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants
The genome size was estimated to be ~923 Mb based on a K-mer analysis (Supplementary Figure 2); this value is consistent with the reported c-value for this species[20]
We sequenced 132 individuals from an F6 population of recombinant inbred lines (RIL) at an average depth of ~10-fold and constructed a genetic map consisting of 18 linkage groups (LG) and 221,787 single nucleotide polymorphism (SNP) markers (Supplementary Figure 4)
Summary
Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Broomcorn millet has the highest water use efficiency (WUE, harvestable yield per water-use), probably because of its low respiration rate, short life cycle (60–90 days), and high harvest index[7,8]. It is mainly used for dryland farming where most other crops have failed, or as a summer rotation crop in temperate regions[6,9]. Panicum is traditionally classified as the typical NAD-ME subtype, while the closely related Setaria mainly use NADP-ME. Nomadic farmers adopted broomcorn millet as a crop 8000–10,000 years before the present (BP) on the
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