Panicum miliaceum subsp. miliaceum
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ABSTRACT:
PROVIDER: PRJNA916977 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A Platinum Grade Genome of Broomcorn Millet Reveals Subgenome Evolution and Organization in Panicum Crops
| PRJNA1058154 | ENA
Project description:Proso millet Genome sequencing and assembly
| PRJNA429322 | ENA
Project description:Panicum miliaceum is the most important and ancient domesticated crops in the world. The complete chloroplast genome of P. miliaceum was sequenced using the Illumina Hiseq platform (Illumina Inc., San Diego, CA). The chloroplast genome of P. miliaceum was 139,929 bp in length, with 38.60% GC content. It contains a pair of inverted repeats (IRs) (22,723 bp) which were separated by a large single copy (LSC) (81,918 bp) and a small single copy region (SSC) (12,565 bp). A total of 132 genes were annotated, which included 84 protein coding genes, 40 tRNA genes and eight rRNA genes. The neighbour-joining (NJ) phylogenetic analysis with the reported chloroplast genomes showed that P. miliaceum chloroplasts are most closely related to those of the Gramineae family.
| S-EPMC7799612 | biostudies-literature
Project description:Panicum miliaceum subsp. miliaceum Raw sequence reads
| PRJNA917474 | ENA
Project description:Proso millet (Panicum miliaceum L.) or broomcorn millet is among the most important food crops to be domesticated by humans; it is widely distributed in America, Europe, and Asia. In this study, we genotyped 578 accessions of P. miliaceum using 37 single-sequence repeat (SSR) markers, to study the genetic diversity and population structure of each accession. We also investigated total phenolic content (TPC) and superoxide dismutase (SOD) activity and performed association analysis using SSR markers. The results showed that genetic diversity and genetic distance were related to geographic location and the fixation index (Fst). Population structure analysis divided the population into three subpopulations. Based on 3 subpopulations, the population is divided into six clusters in consideration of geographical distribution characteristics and agronomic traits. Based on the genetic diversity, population structure, pairwise Fst, and gene flow analyses, we described the topological structure of the six proso millet subpopulations, and the geographic distribution and migration of each cluster. Comparison of the published cluster (cluster 1) with unique germplasms in Japan and South Korea suggested Turkey as a possible secondary center of origin and domestication (cluster 3) for the cluster. We also discovered a cluster domesticated in Nepal (cluster 6) that is adapted to high-latitude and high-altitude cultivation conditions. Differences in phenotypic characteristics, such as TPC, were observed between the clusters. The association analysis showed that TPC was associated with SSR-31, which explained 7.1% of the total variance, respectively. The development of markers associated with TPC and SOD will provide breeders with new tools to improve the quality of proso millet through marker-assisted selection.
| S-EPMC8537217 | biostudies-literature
Project description:Broomcorn millet (Panicum miliaceum L.) is one of the world's oldest cultivated cereals, with several lines of recent evidence indicating that it was grown in northern China from at least 10,000 cal bp. Additionally, a cluster of archaeobotanical records of P. miliaceum dated to at least 7000 cal bp exists in eastern Europe. These two centres of early records could either represent independent domestications or cross-continental movement of this cereal that would predate that of any other crop by some 2 millennia. Here, we analysed genetic diversity among 98 landrace accessions from across Eurasia using 16 microsatellite loci, to explore phylogeographic structure in the Old World range of this historically important crop. The major genetic split in the data divided the accessions into an eastern and a western grouping with an approximate boundary in northwestern China. A substantial number of accessions belonging to the 'western' genetic group were also found in northeastern China. Further resolution subdivided the western and eastern genepools into 2 and 4 clusters respectively, each showing clear geographic patterning. The genetic data are consistent with both the single and multiple domestication centre hypotheses and add specific detail to what these hypotheses would entail regarding the spread of broomcorn millet. Discrepancies exist between the predictions from the genetic data and the current archaeobotanical record, highlighting priorities for investigation into early farming in Central Asia.
| S-EPMC3258423 | biostudies-literature
Project description:Panicum miliaceum (broomcorn millet) is a tetraploid cereal, which was among the first domesticated crops, but is now a minor crop despite its high water use efficiency. The ancestors of this species have not been determined; we aimed to identify likely candidates within the genus, where phylogenies are poorly resolved. Nuclear and chloroplast DNA sequences from P. miliaceum and a range of diploid and tetraploid relatives were used to develop phylogenies of the diploid and tetraploid species. Chromosomal in situ hybridization with genomic DNA as a probe was used to characterize the genomes in the tetraploid P. miliaceum and a tetraploid accession of P. repens. In situ hybridization showed that half the chromosomes of P. miliaceum hybridized more strongly with labelled genomic DNA from P. capillare, and half with labelled DNA from P. repens. Genomic DNA probes differentiated two sets of 18 chromosomes in the tetraploid P. repens. Our phylogenetic data support the allotetraploid origin of P. miliaceum, with the maternal ancestor being P. capillare (or a close relative) and the other genome being shared with P. repens. Our P. repens accession was also an allotetraploid with two dissimilar but closely related genomes, the maternal genome being similar to P. sumatrense. Further collection of Panicum species, particularly from the Old World, is required. It is important to identify why the water-efficient P. miliaceum is now of minimal importance in agriculture, and it may be valuable to exploit the diversity in this species and its ancestors.
| S-EPMC4071833 | biostudies-literature
Project description:To elucidate the mechanisms underlying photoperiodic responses, we investigated the genomic and metabolomic responses of two broomcorn millet (Panicum miliaceum L.) genotypes. For this purpose, light-insensitive (D32) and light-sensitive (M51) genotypes were exposed to a 16 h photoperiod (long-day (LD) conditions) and an 8 h photoperiod (short-day (SD) conditions), and various transcriptomic and metabolomic changes were investigated. A total of 1664, 2564, 13,017, and 15548 DEGs were identified in the SD-D, LD-D, LD-M, and SD-M groups, respectively. Furthermore, 112 common DEGs were identified as well. Interestingly, most DEGs in the different groups were associated with photosynthesis and phenylpropanoid and carotenoid biosynthesis. In addition, 822 metabolites were identified under different treatments. The main metabolites, including L-malic and fumaric acids, were identified in the negative mode, whereas brucine and loperamide were identified in the positive mode. KEGG analysis revealed that the metabolites in the different groups were enriched in the same metabolic pathway of the TCA cycle. Furthermore, in negative mode, the metabolites of M51 were mainly D-glucose, whereas those of D32 were mainly L-malic and fumaric acids. One photoperiod candidate gene (C2845_PM11G01290), annotated as ATP6B, significantly increased the levels of L-malic and fumaric acids. In conclusion, our study provides a theoretical basis for understanding the molecular mechanisms of photoperiodic response regulation and can be used as a reference for marker development and resource identification in Panicum miliaceum L..
| S-EPMC11408615 | biostudies-literature
Project description:Broomcorn millet (Panicum miliaceum) is a key domesticated cereal that has been associated with the north China centre of agricultural origins. Early archaeobotanical evidence for this crop has generated two major debates. First, its contested presence in pre-7000 cal. BP sites in eastern Europe has admitted the possibility of a western origin. Second, its occurrence in the 7th and 8th millennia cal. BP in diverse regions of northern China is consistent with several possible origin foci, associated with different Neolithic cultures. We used microsatellite and granule-bound starch synthase I (GBSSI) genotype data from 341 landrace samples across Eurasia, including 195 newly genotyped samples from China, to address these questions. A spatially explicit discriminative modelling approach favours an eastern Eurasian origin for the expansion of broomcorn millet. This is consistent with recent archaeobotanical and chronological re-evaluations, and stable isotopic data. The same approach, together with the distribution of GBSSI alleles, is also suggestive that the origin of broomcorn millet expansion was in western China. This second unexpected finding stimulates new questions regarding the ecology of wild millet and vegetation dynamics in China prior to the mid-Holocene domestication of millet. The chronological relationship between population expansion and domestication is unclear, but our analyses are consistent with the western Loess Plateau being at least one region of primary domestication of broomcorn millet. Patterns of genetic variation indicate that this region was the source of populations to the west in Eurasia, which broomcorn probably reached via the Inner Asia Mountain Corridor from the 3rd millennium BC. A secondary westward expansion along the steppe may have taken place from the 2nd millennium BC.
| S-EPMC6236650 | biostudies-literature