Genome-wide Association Mapping of Cold Tolerance Genes at the Seedling Stage in Rice.

Yong Liu,Deyong Zhang,Xinqiu Tan,Houxiang Kang,Jinling Liu,Guo-Liang Wang,Minghao Liu,Yufei Deng,Yinghui Xiao,Dan Wang,Zhilong Wang,Chengang Li,Yue Wang

doi:10.1186/s12284-016-0133-2

Abstract

BackgroundRice is a temperature-sensitive crop and its production is severely affected by low temperature in temperate and sub-tropical regions. To understand the genetic basis of cold tolerance in rice, we evaluated the cold tolerance at the seedling stage (CTS) of 295 rice cultivars in the rice diversity panel 1 (RDP1), these cultivars were collected from 82 countries.ResultsThe evaluations revealed that both temperate and tropical japonica rice cultivars are more tolerant to cold stress than indica and AUS cultivars. Using the cold tolerance phenotypes and 44 K SNP chip dataset of RDP1, we performed genome-wide association mapping of quantitative trait loci (QTLs) for CTS. The analysis identified 67 QTLs for CTS that are located on 11 chromosomes. Fifty-six of these QTLs are located in regions without known cold tolerance-related QTLs.ConclusionOur study has provided new information on the genetic architecture of rice cold tolerance and has also identified highly cold tolerant cultivars and CTS-associated SNP markers that will be useful rice improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0133-2) contains supplementary material, which is available to authorized users.

Highlights

Rice is a temperature-sensitive crop and its production is severely affected by low temperature in temperate and sub-tropical regions
The rice diversity panel 1 (RDP1) collection consists of 6 subpopulations including 64 tropical japonica (TRJ), 58 temperate japonica (TEJ), 45 ADMIX, 11 AROMATIC, 52 AUS and 65 indica (IND) cultivars (Fig. 1b)
High cold tolerance was exhibited by 57 cultivars in the TRJ group and by 51 in the TEJ group, whereas low cold tolerance was exhibited by 51 cultivars in the IND group and by 45 in the AUS group (Fig. 1c). These results suggested that both temperate and tropical japonica rice cultivars are tolerant of cold stress and that the indica and AUS cultivars are sensitive to cold stress

Summary

Introduction

Rice is a temperature-sensitive crop and its production is severely affected by low temperature in temperate and sub-tropical regions. Traditional QTL mapping using bi-parental or multiple cross populations identified more than 250 QTLs on all 12 chromosomes for rice cold tolerance at different growth and development stages (Yang et al 2015; Xiao et al 2015; Mao et al 2015; Zhu et al 2015). Among these QTLs, several genes have been fine mapped, including Ctb (Saito et al 2004), qCT8 (Kuroki et al 2007), qCTB7 (Zhou et al 2010), qCTB3 (Shirasawa et al 2012), and qCT-3-2 (Zhu et al 2015) for cold tolerance at the booting stage, qCTS12 (Andaya and Tai, 2006), qCTS4 (Andaya and Tai, 2007), qCtss (Koseki et al 2010), qSCT1 and qSCT11 (Kim et al 2014), qLOP2 and qPSR2-1 (Xiao et al 2015) for CTS, qLTG3-1 for germination cold tolerance

Methods

Results

Discussion

Conclusion