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Developing Salt- Tolerant Rice

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By Tanveer Ul Haq and Javaid Akhtar

Soil salinity (accumulation of salts in the crop root zone) is a major yield limiting factor in arid and semi arid climates. Of the 230 million hectares of irrigated land in the world, 19.5 per cent (45 million hectare) is salt-affected, much of which is in Asia where rice is the main cereal crop. Rice is also a staple food for more than half of the world population.

Soil salinity is a major constraint to the sustainability and expansion of rice cultivation in areas where rice production has not kept up with increasing demand from growing populations. In Pakistan, 6.67 million hectares of the irrigated land and one million hectares of the rice growing area are salt-affected and soil salinity accounts for reductions of about 40-70 per cent in crop yields on these soils.

To address the problem of soil salinity, the ability of rice to tolerate high concentration of salts has become a key research issue in the world. Salt tolerance (ability to grow under salinity) is a complex of different morpho-physiological processes which are controlled by many genes across the rice genome, and manipulation of any of these genes may result in an improved salt tolerance.

The ability of plants to regulate influx of salt, especially sodium (dominant lethal ion in salt affected soils) is one of the important factors determining rice salt tolerance. Under the salt stress, the above ground stems and leaves of a rice plant can accumulate a large number of sodium (Na+) ions, which will be forced to come back to the root in a tolerant variety. Investigations show that gene SKC1 functions in the recirculation of Na+ from shoots to roots, where it can be removed out of the root by other transporters. In this way, the toxicity caused by the Na+ ions may be neutralised and hence the rice is able to tolerate more salinity in the soil.

The traits which are controlled by more than one gene are called as quantitative traits. The regions within genomes which are associated with the quantitative traits and have more effect on the expression of a trait as compared to other regions are called quantitative trait loci (QTLs). The molecular markers are a powerful tool to understand the genetics of plants. There are two major groups of markers: morphological markers and molecular markers. Morphological markers are usually visually characterised phenotypic traits such as flower colour, seed shape and plant pigmentation; whereas the molecular or DNA markers reveal sites of variation in DNA between individual organisms or species.

The important genes may be tagged with nearby DNA markers in the genome. In molecular breeding, DNA markers are mainly used for the development of linkage maps which have been very helpful for the identification of genomic regions (QTLs) involved in the control of simple as well as quantitative traits. QTL mapping is the process of constructing linkage maps and performing QTL analysis for the detection of chromosomal regions associated with quantitative traits.

The selection of salt tolerant plants based on morphological markers was met with limited success and only 30 varieties of different species, which are claimed to be salt tolerant, have been released so far, for commercial use in the world. The conventional plant breeding techniques have been utilised in the best of their capacity for the selection of salt tolerant plants, but without significant outcome.

With advents in plant biotechnology as an aiding tool to conventional breeding, DNA markers technique has become a powerful tool to improve salt tolerance of rice by mapping and tagging of genes involved in the control of growth and yield under stressful environments. A selection based on DNA markers is more reliable as compared to morphological markers due to the reason that they are almost unlimited in number and also not affected by the environmental variables and developmental stage of the plant.

The researchers at the Centre of Advance Studies in Applied Genetics and Saline Agriculture (CAGSA), of the University of Agriculture, Fasialabad, have worked in collaboration with molecular biologists at Centre for Arid Zone Studies (CAZS), University of Wales, Bangor and the UK. They have made significant progress in mapping of QTLs for traits associated with sodium accumulation and potassium maintenance in the leaves after seven and 21 days salt stress in a mapping population of rice (Oryza sativa L.) cultivars.

After identification of tightly linked molecular markers, they can be used to select a large germplasm at the early growth stage through marker assisted selection. Marker assisted selection (MAS) can be used for monitoring the presence or absence of tolerant genes in breeding populations. It is more efficient, effective, reliable and cost effective as compared to conventional plant breeding methodologies. MAS can be used to combine important genes including tolerance genes, with the ultimate goal of producing varieties with more desirable characters. The conventional techniques of selection are laborious, time-consuming and comparatively less reliable; however, DNA marker technology, along with marker assisted selection, provides solutions for selecting and maintaining desirable genotypes. Thus MAS greatly facilitates breeders to conduct many rounds of selection in a limited time without depending on the development of artificial stress conditions.The DNA markers which have strong linkage with the traits associated with salt tolerance were located on rice chromosome-1 and include RM8094, K061, RM3412, RM10746, RM493 and RM10782. These DNA markers can be used as molecular tools for marker assisted selection of salt tolerant rice and will be very useful in breeding programmes at the regional rice research institutes to select and develop salt tolerant rice varieties with less yield reductions on salt affected lands.