Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy

Jian Sun,Hualong Liu,Yan Jia,Mingfang Feng,Jingguo Wang,Dongwei Xie,Minghui Zhang,Hongwei Zhao,Luomiao Yang,Hongliang Zheng,Detang Zou

doi:10.1186/s12284-018-0218-1

Abstract

BackgroundCold stress can cause serious abiotic damage that limits the growth, development and yield of rice. Cold tolerance during the booting stage of rice is a key factor that can guarantee a high and stable yield under cold stress. The cold tolerance of rice is controlled by quantitative trait loci (QTLs). Based on the complex genetic basis of cold tolerance in rice, additional efforts are needed to detect reliable QTLs and identify candidate genes. In this study, recombinant inbred lines (RILs) derived from a cross between a cold sensitive variety, Dongnong422, and strongly cold-tolerant variety, Kongyu131, were used to screen for cold-tolerant loci at the booting stage of rice.ResultsA novel major QTL, qPSST6, controlling the percent seed set under cold water treatment (PSST) under the field conditions of 17 °C cold water irrigation was located on the 28.4 cM interval on chromosome 6. Using the combination of bulked-segregant analysis (BSA) and next-generation sequencing (NGS) technology (Seq-BSA), a 1.81 Mb region that contains 269 predicted genes on chromosome 6 was identified as the candidate region of qPSST6. Two genes, LOC_Os06g39740 and LOC_Os06g39750, were annotated as “response to cold” by gene ontology (GO) analysis. qRT-PCR analysis revealed that LOC_Os06g39750 was strongly induced by cold stress. Haplotype analysis also demonstrate a key role of LOC_Os06g39750 in regulating the PSST of rice, suggesting that it was the candidate gene of qPSST6.ConclusionsThe information obtained in this study is useful for gene cloning of qPSST6 and for breeding cold-tolerant varieties of rice using marker assisted selection (MAS).

Highlights

Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice
The information obtained in this study is useful for gene cloning of qPSST6 and for breeding cold-tolerant varieties of rice using marker assisted selection (MAS)
The percent seed set under cold water treatment (PSST) values of the cold-tolerant parent KY131 were extremely significant higher than those of the coldsensitive DN422 in all 3 years (Fig. 1, Table 1), indicating the stronger cold tolerance of KY131 compared to DN422

Summary

Introduction

Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice. A cold-water irrigation system has been developed as a reliable identified method of determining cold tolerance at the booting stage of rice. Rice plants are maintained in a cold deep-water irrigated pool during the entire booting stage, and the spikelet fertility was used to examine the cold tolerance of rice varieties (Shirasawa et al 2012). This method exposes rice plants in field growth conditions, and its accurate evaluation results are still widely used for selecting cold-tolerant lines and developing coldtolerant rice varieties (Matsunaga 2005; Jia et al 2015)

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Discussion

Conclusion