scholarly journals The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene

2019 ◽  
Author(s):  
Sujan Mamidi ◽  
Adam Healey ◽  
Pu Huang ◽  
Jane Grimwood ◽  
Jerry Jenkins ◽  
...  
Keyword(s):  
Genetic Basis ◽  
De Novo ◽  
Foxtail Millet ◽  
Complex Trait ◽  
Leaf Angle ◽  
Setaria Viridis ◽  
Model Species ◽  
Seed Shattering ◽  
Major Predictor ◽  
Wild Accessions

AbstractDiverse wild and weedy crop relatives hold genetic variants underlying key evolutionary innovations of crops under domestication. Here, we provide genome resources and probe the genetic basis of domestication traits in green millet (Setaria viridis), a close wild relative of foxtail millet (S. italica). Specifically, we develop and exploit a platinum-quality genome assembly and de novo assemblies for 598 wild accessions to identify loci underlying a) response to climate, b) a key ‘loss of shattering’ trait that permits mechanical harvest, and c) leaf angle, a major predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validated Less Shattering1 (SvLES1) as a novel gene for seed shattering, which is rendered non-functional via a retrotransposon insertion in SiLes1, the domesticated loss-of-shattering allele of S. italica. Together these results and resources project S. viridis as a key model species for complex trait dissection and biotechnological improvement of panicoid crops.

scholarly journals A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

2020 ◽  
Vol 38 (10) ◽  
pp. 1203-1210 ◽  
Author(s):  
Sujan Mamidi ◽  
Adam Healey ◽  
Pu Huang ◽  
Jane Grimwood ◽  
Jerry Jenkins ◽  
...  
Keyword(s):  
Complex Traits ◽  
De Novo ◽  
Foxtail Millet ◽  
Wild Plant ◽  
Leaf Angle ◽  
Setaria Viridis ◽  
Model Species ◽  
Seed Shattering ◽  
A Genome ◽  
Wild Accessions

Abstract Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria viridis), a model species for studies of C4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a ‘loss of shattering’ trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR–Cas9 genome editing, we validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.

scholarly journals High Differentiation among Populations of Green Foxtail, Setaria viridis, in Taiwan and Adjacent Islands Revealed by Microsatellite Markers

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 159
Author(s):  
Wei-Hsun Hsieh ◽  
Yen-Chiun Chen ◽  
Hsien-Chun Liao ◽  
Yann-Rong Lin ◽  
Chih-Hui Chen
Keyword(s):  
Gene Flow ◽  
Foxtail Millet ◽  
Agricultural System ◽  
Mountain Range ◽  
Setaria Viridis ◽  
Wild Populations ◽  
Model Species ◽  
Genetic Characteristics ◽  
Green Foxtail ◽  
Low Diversity

Setaria viridis (L.) Beauv., or green foxtail, is native to Eurasia and is the putative ancestor of foxtail millet. Due to the advantageous genetic characteristics of S. viridis, it is a model species for C4 plants. However, S. viridis has seriously spread to the agricultural system around the world because of its wide adaptability. This study is aimed to understand the distribution of S. viridis in Taiwan, and also to investigate the genetic diversity and relationships among different wild populations. A total of 141 S. viridis collected at 10 sites with sampling sizes ranging from 8 to 24 plants in Taiwan were analyzed by 13 highly polymorphic SSR markers, and 6.1 alleles per locus were detected in our study. The relationships of collected S. viridis mostly corresponded to its distribution in different parts of Taiwan revealed by PCoA and phylogenetic tree. Similarly, the results for population structure showed the significance of collecting site or geographical factors. Finally, the extent of gene flow was studied with the genetic differentiation (FST) and Nm values, and two S. viridis populations were found to significantly contain the existence of gene-flow events. In conclusion, S. viridis showed a pattern of low diversity and heterozygosity within a population, but high differentiation among populations because of its selfing attribute and the barriers of sea and mountain range for gene flow. In addition, the founder effect may be the other reason for this pattern of population genetic structure.

scholarly journals Study of Flowering Pattern in Setaria viridis, a Proposed Model Species for C4 Photosynthesis Research

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Govinda Rizal ◽  
Kelvin Acebron ◽  
Reychelle Mogul ◽  
Shanta Karki ◽  
Nikki Larazo ◽  
...  
Keyword(s):  
C4 Photosynthesis ◽  
Foxtail Millet ◽  
Time Lapse ◽  
Setaria Viridis ◽  
Model Species ◽  
Flowering Pattern ◽  
Bioenergy Grasses ◽  
Green Foxtail ◽  
Proposed Model ◽  
Simple Growth

Green foxtail millet (Setaria viridis) has NADP-ME type of C4 photosynthesis. Because of its short life cycle, small genome size of ~515 Mb, small plant stature, high number of seed set, simple growth requirements, and wide adaptability, this diploid (2n=18) weed is proposed to be a model species for the study of C4 photosynthesis. It is also a representative of bioenergy grasses and a model for genetic study of invasive weeds. Despite having all traits of a model species, it is difficult to cross-pollinate because its flowering behavior is not well studied. We used time lapse digital recording to study the flowering time and pattern along a single panicle. We found that flowering in Setaria was triggered by the darkness of the night and when the temperature was lower than 35°C. The anthesis of all the spikelets in a panicle took up-to three nights flowering from 9:30 pm to 10:00 am in the morning. Each spikelet has three phases of anthesis during which pollination occurs. A spikelet remains open for less than three hours. The pollination time for each spikelet is less than 60 minutes. Information from this study will facilitate the geneticists and plant breeders to plan for efficient crossing of Setaria.

scholarly journals Special Issue: Genetic Basis of Phenotypic Variation in Drosophila and Other Insects

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1212
Author(s):  
J. Spencer Johnston ◽  
Carl E. Hjelmen
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Basis ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Complete Genomic Sequence ◽  
Special Issue ◽  
Model Species ◽  
Road Map ◽  
Generation Sequencing ◽  
Complete Genomic

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map [...]

scholarly journals Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chunyan Li ◽  
Melisa Olave ◽  
Yali Hou ◽  
Geng Qin ◽  
Ralf F. Schneider ◽  
...  
Keyword(s):  
Coastal Waters ◽  
Genetic Basis ◽  
De Novo ◽  
Ocean Currents ◽  
Rapid Adaptation ◽  
Developmental Gene ◽  
De Novo Genome Assembly ◽  
Biogeographic Patterns ◽  
Hippocampus Erectus ◽  
New Habitats

AbstractSeahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses’ worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring “bony spines” adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.

scholarly journals De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis

DNA Research ◽  
2019 ◽  
Vol 26 (3) ◽  
pp. 195-203 ◽  
Author(s):  
Hideki Hirakawa ◽  
Katsuhiko Sumitomo ◽  
Tamotsu Hisamatsu ◽  
Soichiro Nagano ◽  
Kenta Shirasawa ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Discovery ◽  
Whole Genome ◽  
Model Species

scholarly journals Phytolith Analysis for Differentiating between Foxtail Millet (Setaria italica) and Green Foxtail (Setaria viridis)

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
pp. e19726 ◽  
Author(s):  
Jianping Zhang ◽  
Houyuan Lu ◽  
Naiqin Wu ◽  
Xiaoyan Yang ◽  
Xianmin Diao
Keyword(s):  
Foxtail Millet ◽  
Setaria Italica ◽  
Setaria Viridis ◽  
Phytolith Analysis ◽  
Green Foxtail

scholarly journals Unexpected Geographic Variability of the Free Running Period in the Linden Bug Pyrrhocoris apterus

2016 ◽  
Vol 31 (6) ◽  
pp. 568-576 ◽  
Author(s):  
Lenka Pivarciova ◽  
Hanka Vaneckova ◽  
Jan Provaznik ◽  
Bulah Chia-hsiang Wu ◽  
Martin Pivarci ◽  
...  
Keyword(s):  
Technological Progress ◽  
Genetic Basis ◽  
Model Organisms ◽  
Geographic Variability ◽  
Model Species ◽  
Pyrrhocoris Apterus ◽  
Free Running ◽  
Field Lines ◽  
Free Running Period ◽  
Remarkable Progress

Circadian clocks keep organisms in synchrony with external day-night cycles. The free running period (FRP) of the clock, however, is usually only close to—not exactly—24 h. Here, we explored the geographical variation in the FRP of the linden bug, Pyrrhocoris apterus, in 59 field-lines originating from a wide variety of localities representing geographically different environments. We have identified a remarkable range in the FRPs between field-lines, with the fastest clock at ~21 h and the slowest close to 28 h, a range comparable to the collections of clock mutants in model organisms. Similarly, field-lines differed in the percentage of rhythmic individuals, with a minimum of 13.8% and a maximum of 86.8%. Although the FRP correlates with the latitude and perhaps with the altitude of the locality, the actual function of this FRP diversity is currently unclear. With the recent technological progress of massive parallel sequencing and genome editing, we can expect remarkable progress in elucidating the genetic basis of similar geographic variants in P. apterus or in similar emerging model species of chronobiology.

scholarly journals An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals

2018 ◽  
Vol 5 (2) ◽  
pp. 171589 ◽  
Author(s):  
Yu-Long Li ◽  
Dong-Xiu Xue ◽  
Bai-Dong Zhang ◽  
Jin-Xian Liu
Keyword(s):  
Data Reduction ◽  
De Novo Assembly ◽  
Genetic Variance ◽  
Restriction Site ◽  
De Novo ◽  
Optimal Number ◽  
Rad Sequencing ◽  
Conservation Genomics ◽  
Model Species

Restriction site-associated DNA (RAD) sequencing is revolutionizing studies in ecological, evolutionary and conservation genomics. However, the assembly of paired-end RAD reads with random-sheared ends is still challenging, especially for non-model species with high genetic variance. Here, we present an efficient optimized approach with a pipeline software, RADassembler, which makes full use of paired-end RAD reads with random-sheared ends from multiple individuals to assemble RAD contigs. RADassembler integrates the algorithms for choosing the optimal number of mismatches within and across individuals at the clustering stage, and then uses a two-step assembly approach at the assembly stage. RADassembler also uses data reduction and parallelization strategies to promote efficiency. Compared to other tools, both the assembly results based on simulation and real RAD datasets demonstrated that RADassembler could always assemble the appropriate number of contigs with high qualities, and more read pairs were properly mapped to the assembled contigs. This approach provides an optimal tool for dealing with the complexity in the assembly of paired-end RAD reads with random-sheared ends for non-model species in ecological, evolutionary and conservation studies. RADassembler is available at https://github.com/lyl8086/RADscripts.

Mining, characterization and application of transcriptome-based SSR markers in Chinese jiaotou

2018 ◽  
Vol 16 (4) ◽  
pp. 306-314
Author(s):  
Chan Liu ◽  
Qing Tang ◽  
Chaohua Cheng ◽  
Ying Xu ◽  
Zemao Yang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Large Scale ◽  
Trinucleotide Repeat ◽  
De Novo ◽  
Local Varieties ◽  
Genetic Studies ◽  
Oxidation Reduction ◽  
Ssr Loci ◽  
Wild Accessions ◽  
Expressed Sequence

AbstractChinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembledde novoby a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

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