Convergent Loss of Awn in Two Cultivated Rice SpeciesOryza sativaandOryza glaberrimaIs Caused by Mutations in Different Loci

Abstract

A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3, involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless.

Loss of function at RAE2 , a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice

“…3 C, i and ii and D, i and ii). These results support our previous report that a different gene(s), other than RAE2, is responsible for the awnless phenotype in O. glaberrima (15). The gene reported to cause awnlessness in African domesticated rice is RAE3.…”

“…Because other awn genes (e.g., RAE1/An-1 or LABA1) can mask RAE2's loss of function, this raises the possibility that RAE2 is conserved in the wild due to pleiotropic effects on other fitness phenotypes. On the other hand, although African rice maintained a functional RAE2 protein, we hypothesize that a mutation(s) in a different locus, designated RAE3, represses the awned phenotype in O. glaberrima (15). The story of RAE2 is part of a larger narrative about human selection.…”

“…Koshihikari (SI Appendix, Fig. S9A) (15). Phenotyping the two lines from these CSSL populations that harbored the RAE2 locus on chromosome 8 derived from O. nivara (WBSL18) or O. rufipogon (RSL23) demonstrated that line WBSL18 formed awns but RSL23 did not (SI Appendix, Fig.…”

“…1 B and C), two of the lines were observed to have long awns: Line GLSL13 carried an O. glaberrima introgression on chromosome 4 that included Regulator of Awn Elongation 1 (RAE1), which corresponds to An-1, and line GLSL25 carried an O. glaberrima introgression on chromosome 8 containing RAE2 (Fig. 1D) (15). RAE1 and RAE2 have been shown to have redundant roles based on the fact that a functional allele at one or both loci confers awns in O. sativa.…”

“…However, convergent evolution via different genes is another scenario by which shared phenotypes may arise from geographically independent domestication processes. Recently, we reported that the genetic regulation of awnlessness differs in the two species of cultivated rice (15). Awns are sharp spine-like structures extending from the lemmas of rice florets (Fig.…”