Optical Mapping of Rice DNA

Michael Bechner

Three Main Questions

1) Why rice? What is the importance from a societal point of view? Scientific point of view?

2) What is optical mapping? How is an Optical Map of Rice made?

3) Where can we go from here? What use is all of this information?

Why Rice? It’s important to Society.

• Approx. 600 million tons of rice produced in 1999.

• 21% of the world’s daily caloric intake comes from rice.

• Asia accounts for 90% of rice production and consumption.

• Rice is a human consumption crop that is not generally used for livestock (e.g. corn).

Importance of Rice in the Four Largest Countries

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20000

40000

60000

80000

100000

120000

140000

160000

180000

Rice Consumed (1000 tons)

China

India

U.S.

Indonesia

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Population(millions)

China

India

U.S.

Indonesia

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Pounds/person/year

China

India

U.S.

Indonesia

Source: IRRI World Rice Statistics

Daily Calories from Rice

China

31%

69%Rice

Other

India

32%

68%Rice

Other

U.S.3%

97%

Rice

Other

Indonesia

52%48%

Rice

Other

Source: IRRI World Rice Statistics

Why we need to study rice

• To meet rising population needs, especially in Asia, rice production needs to increase by 70% in the next 30 years.

• Since available farming land is becoming more scarce, farmers will need to be able to increase the yield of each plant.

• In addition, we also want to find ways of protecting crops from environmental stress, parasites, disease, and competition from weeds.

• The rice genome will help us identify ways of solving these problems.

Why start with rice?

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Genome Size (M b)

Rice

Maize (Corn)

Barley

Wheat

Oat

• Small Genome Size• A lot of data already

available about rice DNA through major sequencing projects.

• The larger crop genomes have much of the same DNA only repeated many times

Microscopic channels

Used to stretch out DNA molecules so they are parallel to each other.

Microscopic Image of Rice DNA

An idea about scale

20 microns

100 nanometers

6.7 nm60 base pairs

300 base pairs (or 30 helix turns)

1 micron=.00004 inches

Width of humanhair: 50-70 microns

Bacteria: 2 microns

What will an optical map of rice do?

• A map would give us an overview of the structure of the rice genome.

• Sequence often has gaps. We can compare our map with the sequence, find the overlap, and help fill the gaps.

What do we do with this?

• We use this map first to assist in the finishing of the sequence.

• The sequence can be used to quickly identify and study regions involved in growth, disease resistance, drought resistance, and grain quality.

• Increased understanding of rice traits by studying the sequence will allow breeders to obtain better hybrids in a much shorter time.

The Rice Team

• Laboratory of Molecular and Computational Genomics– Dr. David C. Schwartz

• Project leaders:– Osmat Azzam-Jefferson; Ana Garic-Stankovic

• Lab technicians, grad students, and computer personnel:

– Michael Bechner; Aaron Andersen; Jessica Severin; Natalie Kaech; Rod Runnheim; Dan Forrest; Eileen Dimalanta; Shiguo Zhou; Erika Kvikstad; Andrew Kile; Alex Lim; Chris Churas