Identification and Pleiotropic Effect Analysis of GSE5 on Rice Chalkiness and Grain Shape.

Liangrong Jiang,Furong Liao,Hui Zhong,Yaqin Deng,Qingqing Liu,Yi Tao,Rongyu Huang,Jingsheng Zheng,Jiaoping Zhang,Yumin Huang,Xianbin Jiang,Houcong Wang

doi:10.3389/fpls.2021.814928

Abstract

Chalkiness is one of several major restricting factors for the improvement of rice quality. Although many chalkiness-related quantitative trait loci have been mapped, only a small number of genes have been cloned to date. In this study, the candidate gene GSE5 of a major quantitative trait locus (QTL) for rice chalkiness, qDEC5, was identified by map-based cloning. Phenotyping and haplotype analysis of proActin:GSE5 transgenic line, gse5-cr mutant, and 69 rice varieties further confirmed that GSE5 had the pleiotropic effects and regulated both chalkiness and grain shape. Genetic analysis showed GSE5 was a dominant gene for grain length and a semi-dominant gene for grain width and chalkiness. The DNA interval closely linked to GSE5 was introgressed to Zhenshan 97B (ZB) based on molecular marker-assisted selection, and the improved ZB showed lower chalkiness and longer but smaller grains, which showed that GSE5 played an important role in breeding rice varieties with high yield and good quality. Transcriptomics, proteomics, and qRT-PCR analyses showed that thirty-nine genes associated with carbon and protein metabolism are regulated by GSE5 to affect the formation of chalkiness, including some newly discovered genes, such as OsCESA9, OsHSP70, OsTPS8, OsPFK04, OsSTA1, OsERdj3A, etc. The low-chalkiness lines showed higher amino sugar and nucleotide sugar metabolism at 10 days after pollination (DAP), lower carbohydrate metabolism at 15 DAP, and lower protein metabolism at 10 and 15 DAP. With heat shock at 34/30°C, rice chalkiness increased significantly; OsDjC10 and OsSUS3 were upregulated at 6 and 12 DAP, respectively, and OsGSTL2 was downregulated at 12 DAP. Our results identified the function and pleiotropic effects of qDEC5 dissected its genetic characteristics and the expression profiles of the genes affecting the chalkiness formation, and provided a theoretical basis and application value to harmoniously pursue high yield and good quality in rice production.

Highlights

Rice is a staple food for more than half of the global population
The results showed that the percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC) of the three lines at 34/30◦C all significantly or extremely significantly increased, and the grain length (GL) of proActin:GSE5 and gse5-cr at 34◦C significantly decreased, while the GL of Zhonghua 11 (ZH11) and the grain width (GW) of the three lines showed no difference at the two temperatures (Figure 11A)
The results showed the expression of GSE5 increased markedly at 6 and 12 days after pollination (DAP) in proActin:GSE5 and decreased markedly at 12 DAP in gse5-cr at 28/26◦C compared with ZH11 (Figures 11B,C)

Summary

Introduction

Rice is a staple food for more than half of the global population. Previous studies showed that the current rice quality was generally inadequate and that the main factor that restricted improvement of rice quality was the chalkiness trait (Qi, 2011; Xu et al, 2011; Meng et al, 2012). Rice chalkiness is strongly influenced by environmental conditions, especially the temperature at the grain filling stage (Kentaro et al, 2016; Chen et al, 2017; Kabir et al, 2017; Cheng et al, 2019). Great variations exist in the chalkiness trait among rice varieties. The percentage of grains with chalkiness (PGWC) and the degree of endosperm chalkiness (DEC) of an elite rice variety, Jiafuzhan, is close to zero under various environmental conditions (Wang et al, 2007). The chalkiness trait is mainly controlled by genetic factors, and some rice germplasms can maintain a low level of chalkiness regardless of different ecological regions (Cheng et al, 2019; Zhou et al, 2019). The primary task in decreasing rice chalkiness is to improve the chalkiness-related genetic characteristics. The major genes related to chalkiness must be identified and cloned to perform functional analyses and facilitate comprehensive dissection of the genetic network for the chalkiness trait

Methods

Results

Conclusion