Setaria

About: Setaria is a research topic. Over the lifetime, 1538 publications have been published within this topic receiving 26282 citations. The topic is also known as: Setaria plant.

Reference genome sequence of the model plant Setaria

Abstract: We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago.

Abstract: 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.

Genome sequence of foxtail millet ( Setaria italica ) provides insights into grass evolution and biofuel potential

Abstract: Completion of genome sequences for the diploid Setaria italica reveals features of C4 photosynthesis that could enable improvement of the polyploid biofuel crop switchgrass (Panicum virgatum). The genetic basis of biotechnologically relevant traits, including drought tolerance, photosynthetic efficiency and flowering control, is also highlighted. Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C4 biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C4 photosynthesis pathway were also identified.

Differential response of antioxidant compounds to salinity stress in salt‐tolerant and salt‐sensitive seedlings of foxtail millet (Setaria italica)

Abstract: The modulation of antioxidant components was comparatively analysed in a salt-tolerant (cv. Prasad) and salt-sensitive (cv. Lepakshi) cultivar of foxtail millet (Setaria italica L.) under different NaCl concentrations. Under conditions of salt stress, the salt-tolerant cultivar exhibited increased total superoxide dismutase (SOD) and ascorbate peroxidase (APX) activity, whereas both enzyme activities decreased in acutely salt-stressed seedlings of the sensitive cultivar. At 200 mM NaCI, the tolerant foxtail millet cultivar responded with induction of cytosolic Cu/Zn-SOD and the Mn-SOD isoform at the protein level. The induced accumulation of the cytosolic Cu/Zn-SOD protein/activity is positively correlated with an elevated level of the cytosolic APX gene activity. The elevated cytosolic Cu/Zn-SOD and cytosolic APX activity correlates with an induced accumulation of their transcripts. Tolerant 5-day-old seedlings grown during high salinity treatment (200 mM NaCI) contained a lower amount of Na + ions and showed a lower electrolyte leakage than sensitive seedlings. In conclusion, our comparative studies indicate that salt-induced oxidative tolerance is conferred by an enhanced compartment-specific activity of the antioxidant enzymes in response to compartment-specific signals.

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

Abstract: Foxtail millet (Setaria italica) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a haplotype map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.