Tracking down the DNA for salt removal in a rice leaf sheath

A genome-wide association study (GWAS) of rice has found that genes for salt tolerance can be found in the indica variety of rice. The research, by a team of scientists in Japan and the Philippines, could lead to the development of rice strains capable of survival in less favourable environments.

Rice is currently both one of the most important cereals for millions of people and one of the least salt-tolerant. Salt stress damages rice by causing an accumulation of Na⁺ and Cl^– ions, causing premature leaf senescence, stunting and death of rice seedlings. In their article in the Annals of Botany Neang and colleagues write that rice has two methods of removing salt ions from the plant. The first is ‘salt removal by the root’ where the ions are removed from the xylem vessels into the parenchyma cells.The second, they add, is removal in the rice leaf sheath. In both cases different proteins sequester ions depending on whether they are Na⁺ or Cl^– ions.

In order to understand the molecules used in salt tolerance, Neang and colleagues used a GWAS to study the rice genome. By using a GWAS the scientists could compare different variations (alleles) of the same gene. Comparing which plants could remove salt from their leaf sheaths most effectively would identify the most promising plants for breeding more salt-tolerant varieties.

The team set up a study composed of six major sub-populations of rice: 70 indica, 49 aus, 61 temperate japonica, 61 tropical japonica, 11 aromatic and 44 highly admixed accessions, sourced from the the International Rice Gene Bank at the International Rice Research Institute (IRRI), in the Philippines. They also used two varieties as checks for salt-tolerance and salt-sensitivity.

“To our knowledge, this is the first report showing variation in the Na⁺ and Cl– removal ability in rice leaf sheath from diverse rice backgrounds consisting of all variety groups of O. sativa.” write Neang and colleagues. “The rice diversity panel consisting of 296 rice accessions showed a wide range of Na⁺ sheath:blade ratios, indicating a wide variation in the Na⁺ removal ability in leaf sheaths. In addition, correlation analysis results indicated that Na⁺ removal ability in leaf sheaths may contribute to lowering Na⁺ accumulation in leaf blades and salt tolerance at the whole-plant level. Therefore, it is suggested that Na⁺ removal in the leaf sheath is a crucial trait to make rice tolerant to salt stress by reducing Na⁺ concentrations in the leaf blade at the seedling stage.”

“Our GWAS data implied that rice accessions in the indica variety group are the major source of genes or alleles that mediate Na⁺ removal in leaf sheaths of rice. RNA-seq performance confirmed the expression level of candidate genes found in the GWAS study and revealed five upregulated and eight downregulated genes in the internal leaf sheath tissues in the presence of salt stress.”