NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20431-6. doi: 10.1073/pnas.1310790110. Epub 2013 Dec 2.


Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.

Keywords: gene validation; marker-assisted breeding; pleiotropy; qTSN4.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles*
  • Gene Expression Regulation, Plant / physiology*
  • Organ Specificity / physiology
  • Oryza / genetics
  • Oryza / metabolism*
  • Plant Leaves / genetics
  • Plant Leaves / metabolism*
  • Plant Proteins / biosynthesis*
  • Plant Proteins / genetics
  • Plant Roots / genetics
  • Plant Roots / metabolism*


  • Plant Proteins