Anaerobic germination in direct-seeded rice
Channel: International Rice Research Institute
Date: 2011-08-01

Also see: http://irri.org/about-irri/annual-reports/annual-report-2010/a-spark-of-life-without-oxygen 

For centuries, rice seedlings have traditionally been grown in standing water and then transplanted into the field. Transplanting is backbreaking work that requires 250--350 person-hours per hectare or 25% of the total labor requirement of rice production.

In recent years, direct seeding of rice has gained popularity in many regions, mainly because it is significantly less labor intensive. And, because it may require less water, direct seeding, which was traditionally used only on relatively small areas of upland and lowland rice production, is becoming more important in irrigated fields given the growing scarcity of water.

The International Rice Research Institute (IRRI; http://irri.org ) is developing DSR varieties that can germinate, elongate, and stay alive even while completely submerged in water in the presence of little or no oxygen (anaerobic germination).

Having identified varieties capable of anaerobic germination, Dr. Ismail, along with plant breeders David Mackill and Endang Septiningsih (featured in this video clip), began exploring the genetic mechanisms of this trait by mapping the quantitative trait loci (QTLs) in a population derived from Khao Hlan On. QTLs are stretches of DNA that are closely linked to the genes responsible for useful traits such as anaerobic germination and QTL analysis has become a fast and powerful method for discovering highly desirable genes.

Dr. Septiningsih proceeded to develop near-isogenic lines (NILs), a set of plants that are genetically identical but with one or a few variations found in specific locations of a gene or DNA sequence on a chromosome.

She and her team started to fine-map one of the major QTLs identified from Khao Hlan On and to identify candidate genes that may control the desired but missing trait in DSR. By working together with molecular biotechnologist Dr. Inez Slamet-Loedin, they are also trying to validate several candidate genes underlying the QTL.

Dr. Septiningsih and her team have also mapped QTLs from a population derived from Mazhan Red. A major QTL on chromosome 7 has been targeted for fine mapping and marker-assisted selection. Furthermore, they have also identified more varieties capable  tolerance of anaerobic conditions during germination and these have become potential sources of  QTLs that could increase the ability of DSR varieties to germinate under water. Additionally, they have begun to develop NILs carrying different QTLs in the background of several elite cultivars.

To complement the molecular work, a conventional breeding program has begun to develop improved breeding lines that are better suited to direct-seeded systems.

"Once the genes and alleles that confer the trait are identified and better understood, these can be combined through QTL pyramiding to develop rice varieties that can survive field flooding immediately after direct seeding," said Dr. Septiningsih. "This can be achieved through molecular marker-assisted breeding that is integrated with a conventional breeding program."