RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice

Fuan Niu; Mingyu Liu; Shiqing Dong; Xianxin Dong; Ying Wang; Can Cheng; Huangwei Chu; Zejun Hu; Fuying Ma; Peiwen Yan; Dengyong Lan; Jianming Zhang; Jihua Zhou; Bin Sun; Anpeng Zhang; Jian Hu; Xinwei Zhang; Shicong He; Jinhao Cui; Xinyu Yuan; Jinshui Yang; Liming Cao; Xiaojin Luo

doi:10.3390/ijms241210303

RNA-Seq Transcriptome Analysis and Evolution of OsEBS, a Gene Involved in Enhanced Spikelet Number per Panicle in Rice

Int J Mol Sci. 2023 Jun 18;24(12):10303. doi: 10.3390/ijms241210303.

Authors

Fuan Niu^{1

2}, Mingyu Liu¹, Shiqing Dong¹, Xianxin Dong¹, Ying Wang¹, Can Cheng², Huangwei Chu², Zejun Hu², Fuying Ma¹, Peiwen Yan¹, Dengyong Lan¹, Jianming Zhang², Jihua Zhou², Bin Sun², Anpeng Zhang², Jian Hu¹, Xinwei Zhang¹, Shicong He¹, Jinhao Cui¹, Xinyu Yuan¹, Jinshui Yang¹, Liming Cao², Xiaojin Luo¹

Affiliations

¹ State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China.
² Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.

Abstract

Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding.

Keywords: evolution; haplotype; rice; spikelet number per panicle; transcriptome.

MeSH terms

Gene Expression Profiling
Oryza* / genetics
Phylogeny
Plant Breeding
RNA-Seq
Transcriptome

Grants and funding

31971918; 21N11900100/National Natural Science Foundation of China; the Shanghai Science and Technology Innovation Action Plan Project