Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings

Bing Han,Leiyue Geng,Longzhi Han,Di Cui,Guilan Cao,Hui Zhang,Yanjie Wang,Xiaoding Ma

doi:10.1186/s12284-019-0363-1

Abstract

In this study, the cold-tolerance capacity of 133 varieties of weedy rice was evaluated based on the comprehensive evaluation index D, with Kongyu 131 used as a cold-tolerant control. A total of 39.8% of the 133 varieties were considered ‘strong’, indicating that weedy rice populations indeed have relatively strong cold-tolerance capacity as a whole, and the robust cold-tolerant varieties WR29 and WR157 were identified. Regression analysis showed that the metrics including the nitrogen recovery index, superoxide dismutase (SOD) content and malondialdehyde (MDA) content correlated significantly (P < 0.05) with cold tolerance and could be used as indicators of cold tolerance. On the basis of a transcriptome analysis of WR157, a robust cold-tolerant variety identified in this study, a total of 4645 putative DEGs were identified in treated groups compared to the control groups, with 2123 upregulated DEGs and 2522 downregulated DEGs. All upregulated DEGs were enriched on 1388 terms, all downregulated DEGs were enriched on 1566 terms; 911 of the 2123 upregulated DEGs fell into 98 KEGG categories and 1103 of the 2522 downregulated DEGs were in 115 categories. Further analysis showed that GO:0019740 and GO:0006808 are involved in nitrogen utilization; GO:0009269 and GO:0009414 are related to the stress response; and GO:0016491 and GO:0016614 are related to oxidoreductase activity.BackgroundWeedy rice (Oryza) is a related pest species of cultivated rice (Oryza sativa L.) that has strong abiotic stress resistance; however, the comprehensive mechanism governing its cold tolerance is poorly understood.ConclusionOur comprehensive evaluation based on five morphological indices and nine physiological indicators revealed outstanding levels of cold-tolerance capacity among weedy rice varieties from different regions and revealed some terms related to cold tolerance via transcriptome analysis. Our results underscored the reliable evaluation methods for additional cold tolerance studies and revealed several genes related to cold tolerance, which will help researchers breed cultivated rice varieties to increase their cold-tolerance capacity. These traits have the ability to increase seedling survival rate and growth, as well as future yields.

Highlights

Weedy rice (Oryza) is a related pest species of cultivated rice (Oryza sativa L.) that has strong abiotic stress resistance; the comprehensive mechanism governing its cold tolerance is poorly understood
Our comprehensive evaluation based on five morphological indices and nine physiological indicators revealed outstanding levels of cold-tolerance capacity among weedy rice varieties from different regions and revealed some terms related to cold tolerance via transcriptome analysis
Our results underscored the reliable evaluation methods for additional cold tolerance studies and revealed several genes related to cold tolerance, which will help researchers breed cultivated rice varieties to increase their cold-tolerance capacity

Summary

Introduction

Weedy rice (Oryza) is a related pest species of cultivated rice (Oryza sativa L.) that has strong abiotic stress resistance; the comprehensive mechanism governing its cold tolerance is poorly understood. Weedy rice is a type of rice that produces fewer grains and occurs as a pest species within fields of cultivated rice. Weedy rice has strong resistance to stress (cold, drought and salt), while cold damage severely influences the growth and yield of cultivated rice. Cold stress has demonstrated negative impacts on rice yields in 25 countries worldwide (Cruz et al 2013), and the Studies of cold tolerance use evaluation indices to identify the cold-tolerance capacity of rice crops (Kuroki et al 2007, Ma et al 2015, Li et al 2018). Xiao et al (2014) identified cold-tolerance capacities at the bud stage via the Cold stress has demonstrated negative impacts on rice yields in 25 countries worldwide (Cruz et al 2013), and the Studies of cold tolerance use evaluation indices to identify the cold-tolerance capacity of rice crops (Kuroki et al 2007, Ma et al 2015, Li et al 2018). Yang et al (2010) used the cold response index (CRI) and seed setting rate (SSR) to evaluate cold tolerance. Xiao et al (2014) identified cold-tolerance capacities at the bud stage via the

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Conclusion