An assault on salt

An assault on salt

An assault on salt

Rising global concern. Filipino farmers living near the coastal areas in Quezon Province are devastated by saltwater intrusion. They are some of the farmers who will benefit the most from salt-tolerant rice varieties.

Summary points

  • Several million hectares of land suited to rice production in Asia are currently unexploited because of salinity and other related soil problems.
  • Salt-affected areas are predominantly inhabited by impoverished communities with fewer opportunities for food security and livelihood options.
  • Rice is suitable for rehabilitating these soils because of its ability to grow under flooding, and its high potential for genetic improvement.
  • Rice productivity in salt-affected areas is very low but can reasonably be raised to provide food for more than 10 million of the poorest people living off these lands.
  • The project aims to identify donors of superior tolerance mechanisms, and develop and use DNA markers to combine underlying QTLs/genes into varieties and breeding lines adapted to target areas.

Sea-level rise due to climate change brings about a frightening scenario of sea water intruding into the once-productive agricultural coastal areas, which will definitely add to the many million hectares of unproductive lands that are already affected by salinity in Pakistan, India, Bangladesh, and Vietnam, just to name a few countries.

In Bangladesh alone, salinity affects about 1 million hectares in coastal areas. Considered by some as a silent disaster, salinity has been making rice farmers poor and hungry because salinity-affected lands are unwilling to produce yields, especially of rice.

In 1997, IRRI’s rice breeding program for salinity tolerance, currently led by plant breeder Glenn Gregorio, was able to locate a major quantitative trait locus (QTL, or a genome region) that confers salt tolerance in rice on chromosome 1. It is known as Saltol (see Less salt, please on pages 24-25 inRice Today, Vol. 6, No. 2).

Since salinity is a complex abiotic stress, it entails a concerted effort of scientists with different expertise such as Abdelbagi Ismail, a plant physiologist; Mike Thomson, a molecular biologist; and R.K. Singh, a plant breeder, who is now based in Tanzania, Africa. Through molecular-assisted breeding, the IRRI salinity tolerance team and its partners in Bangladesh and at the Africa Rice Center were able to introgress Saltol into popular rice varieties in Asia such as BRRI dhan 28, BRRI dhan 29, IR64, BRRI dhan 11, Rassie, BG90-2, NERICA L19, and Sahel 108. Each of these varieties has helped translate some unproductive lands in South Asia and Africa into productive ones, making farmers more secure and unafraid to invest in saline-prone areas. For instance, BRRI dhan 47, which has Saltol, was released in Bangladesh in 2007 and has assured farmers of a harvest even during high tide when salinity intrusion is at its peak. In comparison, sensitive varieties yield almost nothing at all. BRRI dhan 28-Saltol is now being field-tested in Bangladesh. Moreover, salinity-tolerant BINA dhan 8 (IR66946-3R-149-1-1) is expected to be released in late 2010. This variety is suited for planting during boro andaman seasons.

Saltol contributes about 45% of the salinity tolerance in rice. But, even with this quantifiable success, the work of IRRI plant breeders does not stop here. Dr. Gregorio explained that, in the world of breeding, it is important to pinpoint the location of the gene on the chromosome in order to improve the performance of salinity-tolerant varieties and minimize trial and error in breeding. Thus, Dr. Gregorio and his team have embarked on fine-mapping and marker-assisted backcrossing for the Saltol gene.


They have been combing every recess of the 12 chromosomes of rice in order to locate other genes that can make the plant tolerant at both the seedling and booting stages.

In addition, the team was able to identify 33 simple sequence repeat markers and gene-based markers (easily detectable stretches of DNA) across the Saltol region. And, in collaboration with advanced research institutes, they were able to identify three putative candidate genes, SKC1SalT, and pectinesterase.

Fine-mapping using recombinant inbred lines and near-isogenic lines showed that some markers are closely linked to the salinity trait. These identified markers are being validated using a number of different breeding populations and the efficiency of the markers is being quantified.

Aside from Pokkali, the team used new sources of germplasm such as FL478, Cheriviruppu, Capsule, and Kalarata, among others, in mapping more QTLs for salinity tolerance and discovered major QTLs on chromosomes 1, 7, 8, and 10. “More efforts in research are geared toward identifying and combining more genes related to salinity for more stable tolerance,” Dr. Gregorio said.

Currently, more than 100 salinity-tolerant elite lines have been developed. Lines can be called elite if they exhibit a combination of superior traits such as high yield, good eating quality, resistance to pests and diseases, and tolerance of stresses. Generally, these lines can survive a high salinity of electrical conductivity of up to 12 deci-Siemens per meter, a degree of salt stress at which an ordinary variety simply can’t survive.

Moreover, these elite lines have been categorized according to their agronomic characteristics and they are now ready to cater to the specific needs of farmers in salinity-prone areas. In Bangladesh, for example, aside from better grain quality, farmers prefer varieties with less shattering because they transport newly harvested rice to their homes for threshing. Aside from planning the sowing time to avoid salt water intrusion during the critical stage of the plant, farmers prefer late-maturing varieties so that the plants will have more time to recover once affected by salinity. That is why, a trait such as days to maturity is also important.

With all these efforts, it is hoped that, in the future, rice farmers in saline-prone areas can sleep well and will be unafraid to invest in rice production because a combination of genes in the plant fights against salinity and assures farmers of a bountiful harvest whenever salinity strikes

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