Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice

Yongzhen Wu,Lubin Tan,Hongwei Cai,Chuanqing Sun,Shuangshuang Zhao,Jie Zhao,Xin Ma,Yanyan Tang,Xianran Li,Bosen Zhang,Liyun Jiang

doi:10.1038/s41467-018-06509-2

Abstract

Improving the yield by modifying plant architecture was a key step during crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 in Asian cultivated rice (Oryza sativa), which is closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene, harbors a tandem repeat of seven zinc-finger genes. Three of these genes regulate the plant architecture, suggesting that the deletion also promoted the critical transition from the prostrate growth and low yield of wild rice (O. rufipogon) to the erect growth and high yield of Asian cultivated rice. We refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Further, a similar but independent 113-kb deletion is detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, eliminating a tandem repeat of zinc-finger genes, may have been involved in the parallel domestication of plant architecture in Asian and African rice.

Highlights

Improving the yield by modifying plant architecture was a key step during crop domestication
Previous report revealed that the identical mutations of prostrate growth 1 were selected to achieve better plant architecture in Asian cultivated rice[18]
To isolate genes associated with this transition in plant architecture during rice domestication, we identified an introgression line (DIL29) that displayed the semi-prostrate phenotype

Summary

Introduction

Improving the yield by modifying plant architecture was a key step during crop domestication. We show that a 110-kb deletion on the short arm of chromosome 7 in Asian cultivated rice (Oryza sativa), which is closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene, harbors a tandem repeat of seven zinc-finger genes. Three of these genes regulate the plant architecture, suggesting that the deletion promoted the critical transition from the prostrate growth and low yield of wild rice (O. rufipogon) to the erect growth and high yield of Asian cultivated rice. A similar but independent 113-kb deletion is detected at the RPAD locus in African cultivated rice, indicating that a common mechanism might be shared in the parallel domestication of plant architecture in both Asian and African cultivated rice

Methods

Results

Conclusion