Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species

Kanako Bessho-Uehara,Takashi Makino,Yoshiyuki Yamagata,Hideshi Yasui,Atsushi Yoshimura,Motoyuki Ashikari,Tomonori Takashi

doi:10.3390/plants10040725

Kanako Bessho-Uehara, Takashi Makino + Show 5 more

Open Access

https://doi.org/10.3390/plants10040725

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Journal: Plants	Publication Date: Apr 8, 2021
Citations: 7	License type: CC BY 4.0

Affiliation: Tohoku University, Kyushu University, Nagoya University

Abstract

Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.

Highlights

Rice is a major staple food that provides the caloric requirements for nearly one-fourth of the world’s population [1]
Several genes have been identified for awn development in rice, including An-1/REGULATOR OF AWN ELONGATION 1 (RAE1) [11,13], LABA1/An-2 [12,14], RAE2/GAD1/GLA [16,17,18], TOB1 [19], and GLA1 [20]; among these, An-1/RAE1, LABA1/An-2, and RAE2/GAD1/GLA appear to have been selected through Asian rice domestication [11,12,16]
To explore the novel loci for regulating awn development and to clarify the conservation of RAE1 and RAE2 gene function among the AA genome rice group, we examined 11 sets of chromosome segment substitution lines (CSSL) by comparing genotypes and awn phenotypes

Summary

Introduction

Rice is a major staple food that provides the caloric requirements for nearly one-fourth of the world’s population [1]. Compared with the wild progenitors, the cultivated rice species share a common set of morphological characteristics, including non-shattering seeds, white pericarp color, erect tiller growth, and short-awned or awnless seed [4,5,6,7]. These domesticated traits contributed to increasing rice yield, grain quality, and cultivation efficiency. Wild rice species develop an awn, which is a long extension of the lemma tip. Identifying the genes conditioning awn will provide insight into the domestication process in rice and may lead to increased rice grain production by breeding.

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