Traditional varieties are key to modern rice farming

Analysing root growth and yield of rice plants.

Highlighted article: Rico Gamuyao, Joong Hyoun Chin, Juan Pariasca-Tanaka, Paolo Pesaresi, Sheryl Catausan, Cheryl Dalid, Inez Slamet-Loedin, Evelyn Mae Tecson-Mendoza, Matthias Wissuwa & Sigrid Heuer (2012). The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488, 535–539 doi:10.1038/nature11346

Over centuries, many local rice varieties have been bred into a few modern varieties which are extensively farmed throughout much of Asia. In regions where soil is poor such as western India and Thailand, rice crops are dependent on rainfall, frequently suffering from floods and draughts, and importantly also require phosphorus fertilizer. Phosphorus is an essential plant nutrient, and as phosphorus fertilizer is made from a finite store of phosphorus rock the current situation in the parts of Asia with poor soil is not sustainable.

A solution to this problem was found in a traditional rice variety, Kasalath. Another traditional rice variety has already supplied modern rice breeders with submergence tolerant gene SUB1, which enables rice plants to survive up to two weeks of flooding. A decade ago, a major quantitative trait locus was identified in Kasalath that conferred tolerance to phosphorus deficient soil. This locus was labelled Pup1, and last year the Heuer group at the International Rice Research Institute defined a core set of Pup1 markers and used them to backcross Pup1 into modern rice varieties, which were grown in their natural environments and all produced significantly more rice in P-deficient conditions than their wildtype counterpart. These Pup1 introgression lines also showed improved root growth under stress.

The next stage of the Pup1 research was to sequence the locus and identify the gene. Gamuyao et al. found a locus which included a 90 kb transposon-rich insertion-deletion absent from modern varieties of rice that cannot tolerate P-deficiency. A gene within that region was identified as the gene conferring tolerance to P-deficiency, and was named PHOSPHOUS-STARVATION TOLERANCE 1 (PSTOL1).

Gamuyao et al. then classified the Pstol1 protein as a receptor-like cytoplasmic kinase, and demonstrated it has serine/threonine protein kinase activity. They generated transgenic plants with over-expression and low-expression of Pstol1, using modern rice varieties indica and japonica as backgrounds. PSTOL1 over-expression in P-deficient conditions improved grain yield by more than 60%. In the same P-deficient soil, plants with low-transgene expression behaved comparably to the wildtype lines.

In introgression lines containing the Pup1 locus, Pstol1 is expressed in P-deficient conditions but otherwise has low expression. However, phosphorus content of the soil had no effect on root growth – expression of Pstol1 caused increased root dry weight, total root length and total root surface area in indica. Pup1 introgression lines showed the same root phenotype. These experiments were complimented by others in which PSTOL1 was down-regulated in Kasalath, causing a reduction in root mass.

To investigate the role of Pstol1 in root growth, Gamuyao et al. expressed β-glucuronidase (GUS) under the Pstol1 promotor in IR64 plants. GUS staining was detected in the stem nodes, which are the formation sites of the crown roots that will develop into the main root system. The team concluded Pstol1 indirectly regulates early crown root development and, and are currently investigating whether transcription factors directly involved in gene regulation that may be downstream of Pstol1 are phosphorylated by Pstol1.

Teaching resources

There are two teaching resources in plant nutrients from SAPS:

– a practical experiment for 14-16 year olds entitied ‘The effects of different levels of minerals on plant growth.’

– Activities for 11-16 year olds on ‘What do plants need to grow?

The National STEM centre also has a page on understanding plant nutrition, with advice and teaching resources for 11-16 year olds.


Sigrid Heuer and the team involved with the PSTOL1 discovery. “We have now hit the jackpot and found PSTOL1, the major gene responsible for improved phosphorus uptake and understand how it works,” said Heuer.

Image credits: all IRRI, via Flickr: Preparing root samples, performance screening of breeding lines at IRRI_Philipines, and PSTOL1, phosphorus uptake research team members.

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