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

Abstract

Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice.awn | rice | signal peptide | parallel domestication | convergent evolution

Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

“…To determine the functional variation regulating awn formation on the basis of significant SNP/InDels, we classified the sequences of rice accessions into haplotypes An‐hap1, An‐hap2, An‐hap3 and An‐hap4. Comparing the numbers of cysteines (C) in GLA (Bessho‐Uehara et al ., ) it became evident that An‐hap1 and An‐hap2 were 6C type, whereas An‐hap3 and An‐hap4 were 7C and 4C types respectively. The rare SNP1 variant in An‐hap1 occurred only in japonica .…”

“…Amino acid sequence analysis indicated that the InDel3 deletion caused a premature stop codon and truncated protein (Figure S4). LOC_Os08 g37890 is the same locus as Hap.A/B/C (Yano et al ., ), GAD1 (Jin et al ., ) and RAE2 (Bessho‐Uehara et al ., ; Jin et al ., ; Yano et al ., ) that belong to the epidermal patterning factor‐like protein (EPFL) family and regulate awn development. Thus, LOC_Os08 g37890 was postulated to be the most likely candidate gene for GLA .…”

“…The precursor peptide of RAE2 / GAD1 must be ruptured under the action of lyase to form a mature polypeptide. RAE2 / GAD1 regulates awn development, as well as grain number per panicle and grain length (Bessho‐Uehara et al ., ; Jin et al ., ). The above reports demonstrated that genes controlling awn phenotype have pleiotropic effects on yield‐related traits.…”

Grass flowers: An untapped resource for floral evo‐devo

“…Asian and African rice were domesticated independently (Vaughan et al, ), and awn loss is likely due to changes at separate loci. QTL analyses show that awn loss in African rice is under the control of an independent locus to An‐1 , as African rice has functional copies of both An‐1 and RAE2/GAD1 (Furuta et al, ; Bessho‐Uehara et al, ). There is also evidence for independent loci controlling the development of barbed rice awns.…”

“…This result indicates that the critical mutation may have arisen independently in China and in the Himalayas (Yuo et al, ). Similarly, RAE2/GAD1 has likely been repeatedly inactivated in Asian rice cultivars (Bessho‐Uehara et al, ). These results demonstrate that awn development and evolution can have a complex history, even within a single genus.…”