Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

  title={Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance},
  author={Kevin J. Tsai and Mei-Yeh Jade Lu and Kai-Jung Yang and Meng-yun Li and Yu-Chuan Teng and Shihmay Chen and Maurice S. B. Ku and Wen-Hsiung Li},
  journal={Scientific Reports},
The diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular… 

De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

A new improved high-quality reference genome sequence of Setaria italica was assembled and inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11, which had the highest genomic continuity.

A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system.

The development of xiaomi, a rapid-cycling mini foxtail millet mutant as a C4 model system and an ideal model system for functional studies of C4 plants is reported.

Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory

It is found that Trihelix family members in foxtail millet and other grasses mostly preserved their ancestral chromosomal locations during millions of years’ evolution.

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.

An investigation into the beneficial effects and molecular mechanisms of humic acid on foxtail millet under drought conditions

HA (100 mg L-1) was found to promote the growth of foxtail millet under drought conditions and SETIT_016654mg may play a role in the effect of HA on foxtailed millet via control of the metabolic pathway.

Detection of genomic loci associated with chromosomal recombination using high-density linkage mapping in Setaria

The result of this study suggest that QTLs analysis of Type II traits using RILs might provide an opportunity to further understand meiotic recombination using high throughput genome sequencing and genotyping technologies.



Reference genome sequence of the model plant Setaria

A high-quality reference genome sequence for foxtail millet (Setaria italica) is generated and regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion are identified.

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

A draft genome anchored onto nine chromosomes and annotated 38,801 genes was produced and key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum.

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species

For the first time, large-scale eSSR markers are generated in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.

FmMDb: A Versatile Database of Foxtail Millet Markers for Millets and Bioenergy Grasses Research

The Foxtail millet Marker Database is the first database which provides complete marker information to the plant science community attempting to produce elite cultivars of millet and bioenergy grass species, thus addressing global food insecurity.

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.]

A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria, and represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.

Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses.

The cross-compatibility of S. italica and S. viridis suggests that gene flow is likely between wild and domesticated accessions, and these grasses provide novel opportunities to study abiotic stress tolerance and as models for bioenergy feedstocks.

Mapping of Quantitative Trait Locus (QTLs) that Contribute to Germination and Early Seedling Drought Tolerance in the Interspecific Cross Setaria italica×Setaria viridis

Both the wild green foxtail genotype and the foxtails millet cultivar contributed the favorite alleles for traits detected in this trial, indicating that wild Setaria viridis populations may serve as a reservoir for novel stress tolerance alleles which could be employed in foxtailed millet breeding.

Maize and millet transcription factors annotated using comparative genomic and transcriptomic data

A comprehensive genome-wide annotation of TFs and TCs in maize B73 and in two strains of foxtail millet is conducted and many new TF and TC families are identified, which may facilitate the study of regulation of gene expression, tissue morphogenesis, and C4 photosynthesis in maize and millet.

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

Both methods applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS) and selected genes will facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.

Population Genetics and Structure of a Global Foxtail Millet Germplasm Collection

Genetic structure analyses revealed that foxtail millet germplasm accessions are structured along both on the basis of races and geographic origin, and the maximum proportion of variation was due to among individuals within populations.