The genome of broomcorn millet

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.

Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia

“…Unlike the genomes of most polyploid grasses, the teff subgenomes are relatively small (∼300 Mb), with high gene density and low transposable element content. The subgenomes are highly syntenic along their length with no evidence of major inversions or structural rearrangements, contrasting patterns observed in other similarly aged allopolyploids such as wheat 37 , canola ( Brassica napus ) 38 , strawberry ( Fragaria ananassa ) 39 , cotton 40 , and proso millet 41 . The general stability of the teff subgenomes may be attributed to low rates of homoeologous exchange.…”

Genome-wide analysis of the NAC transcription factor family in broomcorn millet (Panicum miliaceum L.) and expression analysis under drought stress

“…To better understand the function of PmNAC genes in broomcorn millet, the transcription levels of PmNAC genes in different tissues, i.e., seedlings at one week of age, shoots at three weeks of age, leaf blades, leaf sheaths, stems, inflorescences, and roots at the eight weeks of age, and mature seeds at 12 weeks of age, were investigated using publicly available transcriptome datasets [58]. The Fragments Per Kilobase per Million mapped reads (FPKM) values of the PmNAC genes are listed in Additional file 1: Table S4, and a hierarchical clustering analysis and heatmap were generated to display the expression patterns of the PmNAC genes (Fig.…”

“…The transcriptome data available online were used to explore the expression patterns of PmNAC genes in various tissues and different growth stages of broomcorn millet [58]. Seedlings at one week of age, shoots at three weeks of age, leaf blades, leaf sheaths, stems, inflorescences, and roots at eight weeks of age, and mature seeds at 12 weeks of age were sampled to investigate the expression patterns of PmNAC genes.…”

“…The genome of broomcorn millet was recently published, providing an important resource for further molecular research in this species [57]. In addition, large RNA sequencing (RNA-seq) expression data from different tissues are also available [58]. Based on these data, NAC gene family members in broomcorn millet were identified in the present study.…”

Thinking Outside of the Cereal Box: Breeding Underutilized (Pseudo)Cereals for Improved Human Nutrition

“…Yes (Appels et al, 2018) Yes (Schnable et al, 2009) Yes (Yu et al, 2002) Yes (Zou et al, 2019) No Yes (Vanburen et al, 2019) Yes (Clouse et al, 2016) Yes (Zhang et al, 2017) No Yes (Jarvis et al, 2017) While language barriers do not exist in excess for broomcorn millet and canary seed, the diffusion of information about their cultivation is inhibited by their niche in the market. As broomcorn millet is used as birdseed outside of East Asia, and canary seed almost ubiquitously so, their cultivation has been restricted to growers with connections to distributers in the birdseed market-a market already possessing a limited demand.…”