Genome Sequencing Studies in Rice

What is Genome Sequencing ?

Figure 1. Crop and plant genomes and their application.

• The basis of all biological life is the genetic code. Thus, access to the primary DNA sequence, i.e. the genome, and how genes are encoded within the genome, has become a fundamental resource in biology. Genome sequencing (also known as full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.
  
  

• The study of plant biology in the 21st century is, vastly different from that in the 20th century. One driver for this has been the use of Genome Sequencing to reveal the genetic blueprints for not one but dozens of plant species, as well as resolving genome differences in thousands of individuals at the population level. Genomics technology has advanced substantially since publication of the first plant genome sequence, that of Arabidopsis thaliana, in 2000. Plant genomics researchers have readily embraced new algorithms, technologies and approaches to generate genome, transcriptome and epigenome datasets for model and crop species that have permitted deep inferences into plant biology.

Rice Genome Sequencing

• Rice (Oryza sativa) has been cultivated for more than 9000 years and is a major food staple for over 50% of the human population. Using the approach taken by the Arabidopsis Genome Initiative, the genome of rice (Oryza sativa) was finally completely by the International Rice Genome Sequencing Project with a BAC-by-BAC method, yielding the only other plant genome sequence after Arabidopsis that is of 'finished quality' (International Rice Genome Sequencing Project 2005).
  
  
• As the first crop genome sequenced, rice provides an excellent opportunity to illustrate the impact on plant biology and breeding of having access to a finished genome sequence for a species of major socio-economic importance. Using existing genetic and genomic resources and tools (mutants, genetic populations and transformation techniques [52,53]), rice researchers were rapidly able to integrate and apply genome sequence information to understand rice genome structure and evolution as well as to discover and mine genes, including those underlying complex traits of agricultural importance. Members of large gene families [such as transcription factors, peptide transporters, kinases, nucleotide binding leucine-rich repeats (NB-LRRs), microRNAs and germins] have been discovered through genome-wide surveys, enabling their cellular functions to be dissected and their roles in plant growth and development to be elucidated (e.g. 151 members of the rice NAC transcription family).
  
  
• In another example, genome sequence enabled identification and positional cloning of genes responsible for traits selected during domestication, including the seed-shattering trait, led to the identification of molecular changes selected during domestication. This enabled, for the first time, the integration of major effect genes into a single map, thereby providing a foundation for breeders to link these easily recognizable landmarks to QTL studies and improve breeding programs.
  
  

Crop and plant genomes and their application

• The Figure 1 gives the approximate timeline of when crop genomes were sequenced along with the underlying techniques and sequencing strategy used. Hybrid strategies which use BAC by BAC and WGS are indicated by the placement of a genome twice. Also note that the distinction between pure NGS and Hybrid sequencing is sometimes arbitrary as many genome projects rely on previously generated Sanger sequences. In addition, some major applications are marked by symbols: Grains for an improvement in grain quality, a flower for flowering time and a tomato for a tomato ripening trait.
  

Projects List

Project Title	Species	Published years	Academic Journal	RiceWiki Project ID
A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. indica )	Oryza sativa L. ssp. indica	2002	Science	IC4R001-Genome-2002-11935017
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp.japonica)	Oryza sativa L. ssp. Japnoica	2002	Science	IC4R002-Genome-2002-11935018
The map-based sequence of the rice genome	Oryza sativa L. ssp. Japnoica	2005	Nature	IC4R003-Genome-2005-16100779
Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution	Oryza brachyantha	2013	Nature Communications	IC4R004-Genome-2013-23481403
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data	Oryza sativa L. ssp. Japnoica	2013	Rice	IC4R005-Genome-2013-24280374
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication	Oryza glaberrima	2014	Nature Genetics	IC4R006-Genome-2014-25064006
Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility	Oryza longistaminata	2015	Molecular Plant	IC4R007-Genome-2015-26358679
Indica rice genome assembly, annotation and mining of blast disease resistance genes	Oryza sativa L. ssp. indica	2016	BMC Genomics	IC4R008-Genome-2016-26984283
Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice	Oryza sativa L. ssp. indica	2014	DNA Research	IC4R009-Genome-2014-24578372