Comprehensive Transcriptome Analysis of GS3 Near-Isogenic Lines During Panicle Development in Rice (Oryza sativa L.).

Wenhua Liang,Yadong Zhang,Fengqin Hu,Tao Chen,Chunfang Zhao,Weicong Qi,Yuanda Lv,Cailin Wang

doi:10.3389/fgene.2022.857143

Wenhua Liang, Yadong Zhang + Show 6 more

Open Access

https://doi.org/10.3389/fgene.2022.857143

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Abstract

Panicle architecture is an important agronomic trait in rice that affects rice yields and quality. The GRAIN SIZE 3 (GS3) locus has been identified as a major quantitative trait locus (QTL) affecting grain length and weight. The current understanding of the function of the GS3 gene, especially concerning the regulatory mechanism of panicle development, is still in its infancy. In this study, we generated GS3 near-isogenic lines (NILs) by successive crossing and backcrossing of TD70 (large grain) with Kasalath (small grain), using Kasalath as the recurrent parent. To identify potential transcription dynamic changes in rice panicle formation and grain shape, we deeply analyzed transcriptional profiles for the NILs (NIL-GS3 and NIL-gs3) at three different panicle developmental stages (S, M, and L). A total of 887, 1,768, and 1,478 differentially expressed genes (DEGs) were identified at stages S, M, and L, respectively. We also found 542 differential expressed long non-coding RNAs (lncRNAs). Co-expression analysis further revealed significant clusters associated with different development periods in NIL-gs3 lines. Gene Ontology and KEGG enrichment analysis revealed G-protein signaling and hormones pathway were successively activated at the M and L stages of NIL-gs3, which indicated activation of the G-protein signaling pathway might trigger the down-streaming hormone signaling transduction. we found that other hormones such ABA, Auxin, CK were significantly enriched in the L stage in the NIL-gs3. We highlighted the synergistic interplay of G-protein and multiple hormones signaling pathways and their essential roles in regulating rice panicle formation and the grain shape. Our study provides an invaluable resource for further molecular mechanistic studies that affect rice grain size and provide new insight for directed selection by marker-assisted backcross breeding.

Highlights

Rice is one of the most important food crops globally, feeding more than half of the world’s population
Previous studies have confirmed that GRAIN SIZE 3 (GS3) is the major quantitative trait locus (QTL) that controls grain length and weight in rice, with an SNP (C→A) mutation in the second exon leading to early termination of translation and a subsequent long-grain phenotype (Fan et al, 2006; Fan et al, 2009; Mao et al, 2010)
The grain width of near-isogenic lines (NILs)-gs3 increased by 9.17%, but we did not note any significant difference in grain thickness

Summary

Introduction

Rice is one of the most important food crops globally, feeding more than half of the world’s population. It is important to improve grain size in rice breeding, as it is closely related to yield, and quality. Investigating the gene expression regulation associated with grain development can potentially provide an avenue for improving crop yield and quality. The GS3 gene is located in the pericentromeric region of rice chromosome 3 and encodes a predicted membrane protein that regulates grain size by controlling cell proliferation. This QTL has been shown to control grain size and play a role as a negative regulator concerning grain and organ size (Fan et al, 2006; Mao et al, 2010)

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