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.
Proso millet (Panicum miliaceum) has high water use efficiency (WUE), a short growing-season, and is highly adapted to a semi-arid climate. Genomic resources for proso millet are very limited. Large numbers of DNA markers and other genomic tools in proso millet can readily be developed by using genomic resources in related grasses. The objectives of the present report were to 1) test and characterize switchgrass SSR markers for use in proso millet, and 2) elucidate repeat-motifs in proso millet based on new SSR marker analysis. A total of 548 SSR markers were tested on 8 proso millet genotypes. Out of these, 339 amplified SSR markers in proso millet. This showed that 62% of the switchgrass SSR markers were transferable to proso millet. Of these 339 markers, 254 were highly polymorphic among the 8 proso genotypes. The resolving power of these 254 polymorphic SSR markers ranged from 0.25 -14.75 with an average of 2.71. The 254 polymorphic SSR markers amplified 984 alleles in the ranges of 50 bp to 1300 bp. The majority of the SSR markers (221 of 254) amplified dinucleotide repeats. Based on SSR marker analysis, AG/GA was the most abundant repeat-motifs in proso millet. Switchgrass genomic information seems to be the most useful for developing DNA markers in proso millet. Markers developed in this study will be helpful for linkage map construction, mapping agronomic traits and future molecular breeding efforts in proso millet.
Proso millet (Panicum miliaceum L.) is the best rotational crop in most dryland production areas in the semiarid US High Plains because of the highest water use efficiency among all cereal crops and short growing season. In the United States, it is used for birdseed, but it is used mostly for human consumption in Asia and Europe. Genomic resources and genetic research of this crop are limited. There is no report of molecular marker‐based genetic diversity analysis of the US germplasm, which is important for its genetic improvement. The objective of this study was to evaluate genetic diversity of US proso millet germplasm based on DNA markers. A set of 90 proso millet genotypes (landraces and cultivars) and 100 simple‐sequence repeat (SSR) markers were used. Cluster analysis was based on unweighed pair‐group method with arithmetic average (UPGMA) and principal component analysis (PCA) using NTSYSpc software. A total of 1287 alleles with size range from 40 to 1500 bp were amplified by the 100 SSR markers. The US proso millet germplasm used in this report is highly genetically diverse. The genotypes formed one major and two minor groups, which correspond to their geographic origin, pedigree, and morphoagronomic traits with few exceptions. All the cultivars developed in the United States remained together in a subcluster within Group 2. Many of these SSR markers with high resolving power were very informative and could be useful for further genetic diversity studies of proso millet. This study would have significant implications for future proso millet genetic improvement.
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