Characteration and comparative analysis of the whole chloroplast genomes of five common millet (Panicum miliaceum).
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ABSTRACT:
SUBMITTER: Cao X
PROVIDER: S-EPMC7954509 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Drought stress is a major abiotic stress that causes huge losses in agricultural production. Proso millet (Panicum miliaceum L.) can efficiently adapt to drought stress and provides important information and gene resources to improve drought tolerance. However, its complex drought-responsive mechanisms remain unclear. RESULTS:Among 37 core Chinese proso millet cultivars, Jinshu 6 (JS6) was selected as the drought-sensitive test material, whereas Neimi 5 (NM5) was selected as the drought-tolerant test material under PEG-induced water stress. After sequencing, 1695 differentially expressed genes (DEGs) were observed in JS6 and NM5 without PEG-induced water stress (JS6CK and NM5CK). A total of 833 and 2166 DEGs were found in the two cultivars under simulated drought by using 20% PEG-6000 for 6 (JS6T6 and NM5T6) and 24?h (JS6T24 and NM5T24), respectively. The DEGs in JS6T6 and JS6T24 treatments were approximately 0.298- and 0.754-fold higher than those in NM5T6 and NM5T24, respectively. Compared with the respective controls, more DEGs were found in T6 treatments than in T24 treatments. A delay in the transcriptional responses of the ROS scavenging system to simulated drought treatment and relatively easy recovery of the expression of photosynthesis-associated genes were observed in NM5. Compared with JS6, different regulation strategies were observed in the jasmonic acid (JA) signal transduction pathway of NM5. CONCLUSION:Under PEG-induced water stress, NM5 maintained highly stable gene expression levels. Compared with drought-sensitive cultivars, the different regulation strategies in the JA signal transduction pathway in drought-tolerant cultivars may be one of the driving forces underlying drought stress tolerance.
| S-EPMC6737659 | biostudies-literature
Project description:The origin of millet from Neolithic China has generally been accepted, but it remains unknown whether common millet (Panicum miliaceum) or foxtail millet (Setaria italica) was the first species domesticated. Nor do we know the timing of their domestication and their routes of dispersal. Here, we report the discovery of husk phytoliths and biomolecular components identifiable solely as common millet from newly excavated storage pits at the Neolithic Cishan site, China, dated to between ca. 10,300 and ca. 8,700 calibrated years before present (cal yr BP). After ca. 8,700 cal yr BP, the grain crops began to contain a small quantity of foxtail millet. Our research reveals that the common millet was the earliest dry farming crop in East Asia, which is probably attributed to its excellent resistance to drought.
| S-EPMC2678631 | biostudies-literature
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:PREMISE OF THE STUDY:Proso millet (Panicum miliaceum; Poaceae) is a minor crop with good nutritional qualities and strong tolerance to drought stress and soil infertility. However, studies on genetic diversity have been limited due to a lack of efficient genetic markers. METHODS:Illumina sequencing technology was used to generate short read sequences of proso millet, and de novo transcriptome assemblies were used to develop a de novo assembly of proso millet. Genic simple sequence repeat (SSR) markers were identified and used to detect polymorphism among 56 accessions. Population structure and genetic similarity coefficient were estimated. RESULTS:In total, 25,341 unique gene sequences and 4724 SSR loci were obtained from the transcriptome, of which 229 pairs of SSR primers were validated, which resulted in 14 polymorphic genic SSR primers exhibiting 43 total alleles. According to the ratio of polymorphic markers (6.1%, 14/229), there are potentially 288 polymorphic genic SSR markers available for genetic assay development in the future. Bayesian population analyses showed that the 56 accessions comprised two distinct groups. DISCUSSION:A genetic structure and cluster assay indicated that the accessions from the Loess Plateau of China shared a high genetic similarity coefficient with those from other regions and that there was no correlation between genetic diversity and geographic origin. The transcriptome sequencing data and millet-specific SSR markers developed in this study establish an excellent resource for gene discovery and may improve the development of breeding programs in proso millet in the future.
| S-EPMC5546162 | biostudies-literature
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: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:Current agricultural production depends on very limited species grown as monocultures that are highly vulnerable to climate change, presenting a threat to the sustainability of agri-food systems. However, many hundreds of neglected crop species have the potential to cater to the challenges of climate change by means of resilience to adverse climate conditions. Proso millet (Panicum miliaceum L.), one of the underutilised minor millets grown as a rainfed subsistence crop, was selected in this study as an exemplary climate-resilient crop. Using a previously calibrated version of the Agricultural Production Systems Simulator (APSIM), the sensitivity of the crop to changes in temperature and precipitation was studied using the protocol of the Coordinated Climate Crop Modelling Project (C3MP). The future (2040-2069) production was simulated using bias-corrected climate data from 20 general circulation models of the Coupled Model Intercomparison Project (CMIP5) under RCP4.5 and 8.5 scenarios. According to the C3MP analysis, we found a 1°C increment of temperature decreased the yield by 5-10% at zero rainfall change. However, Proso millet yields increased by 5% within a restricted climate change space of up to 2°C of warming with increased rainfall. Simulated future climate yields were lower than the simulated yields under the baseline climate of the 1980-2009 period (mean 1707 kg ha-1) under both RCP4.5 (-7.3%) and RCP8.5 (-16.6%) though these changes were not significantly (p > 0.05) different from the baseline yields. Proso millet is currently cultivated in limited areas of Sri Lanka, but our yield mapping shows the potential for expansion of the crop to new areas under both current and future climates. The results of the study, indicating minor impacts from projected climate change, reveal that Proso millet is an excellent candidate for low-input farming systems under changing climate. More generally, through this study, a framework that can be used to assess the climate sensitivity of underutilized crops was also developed.
| S-EPMC10035905 | 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: Not available
| S-EPMC11335613 | 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