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Setaria genome sequencing: an overview

  • Charu Lata
  • Manoj PrasadEmail author
Commentary

Abstract

The genus Setaria includes two important C4 Panicoid grass species, namely S. italica (cultivated) and S. viridis (weed; wild ancestor), which together represent an appropriate model system for architectural, physiological, evolutionary, and genomic studies in related grasses. It is a diploid, inbreeder, self-fertile annual cereal grass having short life cycle and minimal growth requirements. There close relatedness to biofuel crops like switch grass and napier grass further signifies their importance. Further, foxtail millet is an important food and fodder grain crop grown in arid and semi-arid regions in many parts of the world. Therefore, an increasing interest in these species has led to a gradual accumulation and development of genomic data and genetic resources. Setaria genome sequencing is an outcome of such endeavors. These sequencing efforts uncovered several distinctive attributes of Setaria genome that may help in understanding its physiology, evolution and adaptation. This will not only aid in comparative genomics studies of Setaria and related crops including bioenergy grasses but also help in rapid advancements of genomics information for developing varieties with superior traits either through marker-assisted selection (MAS) or using transgenic approaches in these crops.

Keywords

Biofuel Crop improvement Millets Marker-aided breeding Setaria Single nucleotide polymorphism 

Abbreviations

BGI

Beijing Genome Initiative

USDOE-JGI

United States Department of Energy-Joint Genome Initiative

SNP

Single Nucleotide Polymorphism

TEs

Transposable elements

miRNAs

microRNAs

ESTs

Expressed-sequence tags

LTRs

Long terminal repeats

LINES

Long Interspersed Nuclear Elements

Notes

Acknowledgments

This study was supported by the core grant from National Institute of Plant Genome Research and Department of Science & Technology (DST), Govt. of India. Charu Lata acknowledges DST, Govt. of India, New Delhi for the INSPIRE Faculty Award (Grant No.IFA-11LSPA-01).

References

  1. Bennetzen JL, Schmutz J, Wang H et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30:555–561PubMedCrossRefGoogle Scholar
  2. Chan C, Qi X, Li M-W, Wong F-L, Lam H-M (2012) Recent developments of genomic research in Soybean. J Genet Genomics 39:317–324PubMedCrossRefGoogle Scholar
  3. Gupta S, Kumari K, Das J, Lata C, Puranik S, Prasad M (2011) Development and utilization of novel intron length polymorphic markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Genome 54:586–602PubMedCrossRefGoogle Scholar
  4. Gupta S, Kumari K, Sahu PP, Vidapu S, Prasad M (2012) Sequence based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Cell Rep 31:323–337PubMedCrossRefGoogle Scholar
  5. Lata C, Sahu PP, Prasad M (2010) Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochem Biophys Res Commun 393:720–727PubMedCrossRefGoogle Scholar
  6. Lata C, Gupta S, Prasad M (2012) Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses. Crit Rev Biotechnol. doi: 10.3109/07388551.2012.716809 PubMedGoogle Scholar
  7. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D, Prasad M (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res. doi: 10.1093/dnares/dst002 Google Scholar
  8. Zhang J, Liu T, Fu J et al (2007) Construction and application of EST library from Setaria italica in response to dehydration stress. Genomics 90:121–131PubMedCrossRefGoogle Scholar
  9. Zhang G, Liu X, Quan Z et al (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol 30:549–554PubMedCrossRefGoogle Scholar

Copyright information

© Society for Plant Biochemistry and Biotechnology 2013

Authors and Affiliations

  1. 1.National Institute of Plant Genome Research (NIPGR)New DelhiIndia
  2. 2.National Research Centre on Plant BiotechnologyNew DelhiIndia

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