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Efforts to sequence the rice genome

  • Efforts to sequence the rice genome

    Asim Munawar1*, Aqsa Arshad1, Muhammad Ishaque Mastoi2, Shehbaz Sharif1 and Muhammad Ali3

    1Department of Entomology, University of Agriculture Faisalabad.

    2Department of Plant and Environmental Protection, NARC, Park Road Islamabad.

    3 Department of Clinical Medicine and Surgery, University of Agriculture Faisalabad.


    *Corresponding author:

    Asim Munawar

    A rapidly growing supply of DNA from ancient skeletons is changing evolutionary history. The agricultural revolution was one of the most profound events in human history, leading to the rise of modern civilization. Now, in the first study of its kind, an international team of scientists has found that after agriculture arrived in Europe 8,500 years ago, people’s DNA underwent widespread changes, altering their height, digestion, immune system and skin color. Researchers had found indirect clues of some of these alterations by studying the genomes of living Europeans. But the new study, they said, makes it possible to see the changes as they occurred over thousands of years. Before the rise of agriculture, Europe was home to a population of hunter-gatherers. Then a wave of people arrived whose DNA resembles that of people in the Near East. It’s likely that they brought agriculture with them. Disease-resistant crops have the potential to reduce crop losses. This Review discusses how advances in genetic and genomic technologies are contributing to efforts by plant breeders to generate durable, broad-spectrum disease resistance in crop plants.

    • Rice genome:

    A generalized Picture of sequencing genome 

    Rice (Oryza sativa) has the smallest genome of all of the major cereal crops, making it an excellent candidate to serve as a model system for cereal genomics. Together the cereals (maize, wheat, barley, and rice) constitute 60% of the agricultural production in the world. More than 500 million tons of maize, wheat, and rice are produced each year. Comparisons of the genetic and physical maps of the cereal crops have revealed that they are largely syntenic, conserving both gene order and orientation on the chromosomes. This synteny is a reflection of their recent evolution from a common ancestor approximately 50–70 million years ago. The high level of synteny means that once the precise gene order is known for one species, it can be used for positional cloning of genes for all the other cereals. Wheat has a considerably larger genome than maize and is on the outside. The locations of genes that control traits such as height or seed shattering are indicated on the chromosomes of the different species. In addition to its small genome size, rice has a high-density genetic map with over 3,300 markers on it that has been linked to a physical map with over 3,000 markers. Other genomic resources include an extensive EST collection of over 100,000 entries; researchers’ current goal is to obtain 1 million ESTs. Among other useful attributes of rice is that recombinant DNA can be introduced into the genome (a process known as transformation) far more efficiently than in maize or most of the other cereals. This factor allows rice researchers to manipulate genes with relative ease to determine their function in the plant under a range of environmental conditions.

    • Efforts to sequence the rice genome:

    Reminiscent of how the human genome was sequenced, sequencing of the rice genome was performed by both public and private entities. An international consortium, the International Rice Genome Sequencing Project (IRGSP), set out to sequence the rice genome via a clone-by-clone approach. Another publicly funded effort by the Beijing Genomics Institute used the whole-genome shotgun approach to produce a draft sequence, as did two companies, Monsanto and Syngenta. Two different subspecies of rice were sequenced. The Chinese group sequenced the Indica subspecies, which is the most widely cultivated species in China. The other three groups sequenced the Japonica (Nipponbare), subspecies which is the principal cultivar (crop subspecies) grown in Japan, as well as in the United States. The groups had different goals: The IRGSP intended to produce a high-quality sequence at coverage that would serve as the gold standard for 10x comparisons to other cereal genomes. For Syngenta, the primary goal was to have sufficient coverage to be able to map certain phenotypic traits such as plant size and fertility. It also used the rice sequences to produce a microarray that could be used with the RNA from other cereals such as maize.

    • Facts about the rice genome:

    From the different sequencing efforts, the following has emerged as a picture of the rice genome: Its size is approximately 430 Mbp, which is about 3.3 times bigger than the Arabidopsis genome and about one seventh the size of the human genome. The number of genes was originally estimated from the draft sequences as being between 35,000 and 50,000. However, the completed sequence indicated it was higher—probably around 60,000 genes. This is approximately twice the number of genes in Arabidopsis and significantly more than the number of genes thought to be in the human genome. Nested retroposons are found primarily in intergenic regions in the rice genome. This location is in contrast to that of the human genome, where retroposons are also found in intron. There is evidence that alternative splicing is very important in animals for generating protein diversity. However, this does not appear to be the case for plants, which appear to prefer to use gene duplications instead. It is hypothesized that in animals, the presence of retroposons in intron may be linked to the signals that allow for differential splicing.

    • Rice and Arabidopsis genomes:

    No large regions of synteny were observed between rice and Arabidopsis. However, when the predicted genes from Arabidopsis were compared with those from rice, it was found that over 80% had strong homology, suggesting that they are likely orthodox. The reverse, however, was not true: Only 50% of the predicted rice genes have homologues in Arabidopsis. Because the divergence between monocots (rice) and dicots (Arabidopsis) is only 150–200 million years, it is surprising to see the lack of homology for 50% of rice genes. It is thought that this lack of homology may be due to a series of duplication events that took place in the rice genome. There also appears to have been a shift in amino acid usage in rice that may make it difficult to recognize the duplicated genes as homolog’s.

    Genome of Rice (1) and Arabidopsis (2) (Plate#2)


    Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. The need remains to plot a rice landscape in other jurisdictions; particularly in countries that are the primary producers or consumers of rice.

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